GENERAL BOTANY

BOTANY. The study of the biology of plants. Plantae. The Greeny Things.

Why should we care about the study of PLANTS?

 Without plants, most of life on earth as we know it would not exist.

 Plants comprise about 98% of the earth's biomass!
 Plants are primarily responsible for creating our oxygen-rich atmosphere via the light reactions of photosynthesis.
 Plants are the earth's main autotrophs and fixers of carbon and nitrogen.
 Plants provide the habitat and food upon which almost all other living things ultimately depend.
 Plants are responsible for most of the products on which you rely to survive (vegetable and animal matter), have a good quality of life (fabric for clothing, medicines), as well as
the more frivolous ones (spices, perfumes, dyes, dissolvable sutures, food stabilizers, emulsifiers, Starbuck's, etc.).
 And don't forget the potential of biofuels (ethanol produced from food crops)
 Almost every living (terrestrial, and many aquatic) thing interacts with plants in csome way. Plants are involved in every type of symbiotic community interaction known.

Recall: A community is an assemblage of populations in a particular area or habitat. It is the living portion of the ecosystem.
The number of different species found in an ecosystem comprise that system's species diversity. Diversity varies greatly among ecosystems, and hence, so do the interactions
among populations in those ecosystems.

 Individualistic Hypothesis (H.A. Gleason)

A chance assemblage of species found in the same area because they happen to have similar biological requirements.

 Interactive Hypothesis (F.E. Clements)

An assemblage of closely linked species, locked into mandatory association and biological interactions. The community functions as an integrated unit.

Although Gleason's hypothesis for community organization has received the most support from field-based studies, species interactions are important components of community
dynamics.

When it comes to the plant community, the Interactive Hypothesis is more strongly supported. It is the plant community--determined by climate and soil conditions--that
determines what else can live in any particular ecosystem or biome.

SYMBIOSIS - This term (from the Greek sym, meaning "together" and bios, meaning "life") refers to the members of two different species (i.e., two populations) having some sort
of ecological interaction that affects both populations. Here are some of the theoretical types of interactions that can evolve over many generations. When two species coevolve.

"+" means that the population benefits from the interaction

"-" means that the population is harmed by the interaction

"0" means that the population is not affected by the interaction

Let's see what we can come up with for various types of plants...
type of interaction pop'n A pop'n B nature of effect
obligate mutualism + + both populations benefit and cannot survive
without one another
EXAMPLE: Bucket Orchid and Euglossine Bee
type of interaction pop'n A pop'n B nature of effect
protocooperation + + both populations benefit but can survive without
one another
 EXAMPLE: Think: Agriculture
type of interaction pop'n A pop'n B nature of effect
competition - - populations inhibit one another
EXAMPLES: Dense Forest; Allelopathic Plants
type of interaction pop'n A pop'n B nature of effect
predation + - one population kills and feeds on the other
EXAMPLES: You Might Know Some of These Guys...
type of interaction pop'n A pop'n B nature of effect
parasitism + - one population (parasite) feeds on, but does not
kill outright members of the other population
(host)
EXAMPLE: Yes, there are Parasitic Plants, some of them beloved.
type of interaction pop'n A pop'n B nature of effect
commensalism + 0 one population (the commensal) benefits from
the other, which is not affected
EXAMPLE: Epiphytes of many kinds.

Plants are studied at various levels in biology...

 Plant Anatomy - The study of the internal and external structure of plants.
Early plant anatomists included Italian anatomist and all-around Science GuyMarcello Malpighi, who discovered
plant tissues in stems and roots, and English botanist Nehemiah Grew, who more accurately described the
structure of wood than anyone had ever done before.
 Plant Physiology
This field was first established by Johann Baptista van Helmont, Belgian physician and chemist, who is sometimes
credited with being the earliest Father of Western Medicine. He was the first to establish that plants do not have
the same nutritional needs as animals. (His most famous botanical experiment was that of planting a willow twig
 in a tub of soil, and meticulously monitoring its growth. At the end of his experiment, he noted that the willow had
gained 164 pounds, and attributed it to water it had absorbed. We know now that most of the biomass gained was
due to photosynthesis...but you have to give him credit for early plant physiology experimentation.)
 Plant Taxonomy
The earliest plant taxonomist was Carl Linne himself. All his described species still bear his stamp:
Raphanus sativus L.
More modern study of plants has evolved from these early disciplines:
 Plant Genetics and Biotechnology
 Plant Biochemistry
 Biomedical Botany (Ethnobotany)
 Plant Biogeography
 Ecology
o Biomes are defined by the climate and the flora

o Forests affect the quantity and quality of available fresh water)

o Plant diversity affects animal diversity: The greater the botanical diversity, the greater the animal diversity.

(duh) Amazingly, probably a third of organisms that should be considered "plants" have yet to be described
and named...

The study plants is a vital, active field in almost every area of biology. In 1938, 11,000 papers on botanical subjects
were published, and the number has grown every year since then.
Perhaps no area is so pressing as the Ecological Connection.
To set the tone for our tour through the Mighty Kingdom Plantae, I present an Academy Award Winner for Best
Animated Film (1987). Though it is fiction, it accurately depicts what can happen when plants are destroyed in a large
area of land...and what can happen when they come back.
The Man Who Planted Trees

a film by Frederic Back from a story by Jean Giono

The Molecules that Make Plant Cells...Different

By now, you should be very familiar with the four basic types of biological macromolecules, their subunits, and their functions. Recall...

 nucleic acids, polymers of nucleotides (A, T, C, G, U)

 proteins, polymers of amino acids (22 flavors!)
 carbohydrates, polymers of sugars (monosaccharides or disaccharides)
 lipids, polymers of fatty acids
NUCLEIC ACIDS Everyone here has had first year biology, and so should have a basic understanding of how DNA and RNA work. But in case you've
forgotten, here is a very brief and extremely simple baby overview of genetics.

The basic structure and function of DNA is conservative across taxa, and is one of the most unifying characters of life on earth. There is nothing significantly
different about plant DNA, compared to that of other taxa, other than the instructions encoded in plant DNA.

As in animals, ATP (and GTP)--components of nucleic acids, when in polymer form--are the "energy currency" of the cell. Their high-energy phosphate bonds
yield 7.3kcal/mole, upon hydrolysis.

PROTEINS In most organisms, protein comprises more than 50% of the biomass of the individual. In plants, however, cellulose makes up the bulk of the
organism, with protein coming in a distant second.

Like other organisms, plants use about 20 different kinds of amino acids to construct their unique proteins, but there is nothing significantly different about
plant proteins compared with those of other organisms. They are constructed the same way, with different proteins having characteristic...

 primary structure (order of the amino acids)

 secondary structure (pleating and helix formation)
 tertiary structure (folding of pleated sheets and helices into 3-D structures)
 quaternary structure (multiple polypeptides combined to form a functional unit)

As in other organisms, proteins in plants may be structural (helix or pleated sheets), or functional (enzymes, usually with complex tertiary or quaternary
structure).

(What is an "essential" amino acid? What are the essential amino acids for Homo sapiens? (lys, trp, thr, met, his, phe, leu, val, ileu) And where do we get
them?)

CARBOHYDRATES In animals, carbohydrates are used primarily for short-term energy storage.
In plants, however, carbohydrates are not only used for energy storage, but also make up the main structure of the organism itself.
Simple Carbohydrates (Sugars)
The three most abundant simple sugars synthesized by plants are
 glucose - the primary sugar used for energy in cellular respiration. (In animals and many other organisms, it's also the primary transport sugar moved around via the blood
stream or other transport systems in the body--but not in plants!)
 sucrose - the a major transport sugar in plants, is intimately involved with water movement through phloem (as we'll see later).
 fructose - another storage sugar, primarily sequestered in aqueous solution as polysaccharides called fructans
Complex Carbohydrates
Starch is one of the defining biological macromolecules of Plantae and its closest relatives. Starch, a polymer of glucose, comes in two forms:

 amylose (unbranched chain of glucose)

 amylopectin (branched glucose chains) (similar to glycogen, but not as branched)

...and is used for long-term energy storage, sequestered as starch granules inside plant cells. Starch granules may play other roles as well, as we'll see.
Fructans are another storage polysaccharide, but these are composed of primarily of fructose. After starch and sucrose, fructans are probably the most abundant storage
carbohydrates in plants. Synthesized from fructose and sucrose in the plant vacuoles, fructans may be linear or branched, with a basic trisaccharide structure known as
a kestose(fructose and sucrose polymer):

Because fructans are water soluble, they can be stored in much higher concentrations than starches, which are stored as relatively voluminous granules.

Our friend CELLULOSE is the most abundant organic molecule on the planet.
Cellulose is found in the form of microfibrils that make up the main structural molecules of the plant cell wall.
Like starch, cellulose is a polymer of glucose. But a subtle shift in chemical structure changes it from highly digestible nutrient into The Perfect Structural Material for plants.

You may recall from other courses that glucose can exist in two structural forms, alpha (on the left) and beta (on the right):
In aqueous solution in the plant cell, these two forms flip back and forth, and stay in equilibrium, about 50:50. But when the glucose molecules join to form polymers, there can be
more of one form or the other.

 Starch (and glycogen, "animal starch") are composed entirely of alpha-glucose.

 Cellulose is composed entirely of beta-glucose.

The digestive enzymes capable of breaking down chains of alpha glucose--found in the vast majority of heterotrophs--do not recognize nor bind to beta-glucose chains. Only a few
types of organisms can produce enzymes capable of digesting the beta-glucose chain that is cellulose. (Can you name some of them?)

Think of the evolutionary implications of the tiny shift that occurred when an enzyme appeared that linked beta-glucoses together, instead of alpha-glucoses. And then think of
how rare the mutation that allowed any organisms to break that mighty chain!

LIPIDS (a.k.a., triglycerides) These are molecules such as fats and waxes, composed of single or branched fatty acid chains. They are nonpolar and hydrophobic, meaning that
they are neither soluble nor miscible with water.

Fats serve structural roles in cell membranes (modified fats known as phospholipids), of course. But let's talk more about their metabolic role. Lipids may be...

 fats (solid at room temperature) or

 oils (liquid at room temperature)
 saturated (no double bonds between the carbons in the chain)
 unsaturated (one to many double bonds (and hence, fewer hydrogens) between the C's)
 used for high-energy, long-term storage (fat yields 9.1kcal/g when oxidized, as opposed to 3.8kcal/g of carbohydrate or 3.1kcal/g of protein!)
 important in the architecture of plant cells and bodies, making plants resistant to desiccation, and facilitating water transport.

Two important lipids unique to plants: cutin and suberin.

These are major structural components of cell walls in higher, terrestrial plants. Cutin and suberin form matrices around plant cells in which waxes are embedded, and the complex
fatty barrier effectively prevents water from travelling anywhere such a barrier exists.

The cuticle of plant cells exposed to the outside world is (1) secreted by the epidermal cells of stems and leaves and (2) composed of cutin impregnated with wax (cuticular wax).
The cuticle prevents water loss through the epidermal cells, but also necessitates the existence of stomates, gas-exchange pores, in terrestrial plants with a thick cuticle.
The cork (outermost layer of the bark of woody plants is the main location you'll find suberin. It's arranged in layers alternating with waxes to prevent water loss from woody
stems that no longer have an epidermal layer.
We'll also find that suberin plays a very important role in the transport of water through the root cortex, preventing interstitial entry of water into the root, and hence, creating a
selectively-permeable membrane into the root in a layer called the endodermis.
Stay tuned for more thrills!

Various species of plants manufacture waxes unique to their taxa, and many are of commercial importance. Your text mentions carnauba wax, used as a polish for everything
from cars to floors. It's extracted from the leaves of the Carnauba Wax Palm (Copernicia cerifera) of the Amazon. (So long, car polish...)

Steroids are lipids whose basic structure is that of four connected hydrocarbon rings. Functional groups attached to this basic steroid backbone determine the function of the many
different steroids found in living organisms.

A hydroxyl group in the carbon-3 position makes the steroid a sterol (an alcohol; remember?). These function to stabilize plasma membranes. Sitosterol is the main form found in
plants and their closest relatives, green algae:
Cholesterol, the main plasma-membrane stabilizing sterol in animal cells is quite rare in plants:

Steroids also may function as hormones, or be hormone precursors. The discovery of estrogen- and progesterone-like compounds in plants has spawned a new area of biomedical
research, not only in cancer treatment, but also in the treatment of symptoms associated with menopause.
Secondary Metabolites: Plant Defense Plants are literally rooted to the spot. They can't flee predators/herbivores. But that certainly doesn't mean they are defenseless. Plants are the
greatest generals on the battlefield of chemical warfare.

Metabolites are just what the name implies: compounds made via metabolic reactions. Primary metabolites are those found in all cells, and are necessary for normal cellular
function and energy transduction. They include the biolgical macromolecules and simple sugars.

Secondary metabolites are complex chemical compounds that are NOT found in every cell, and not found in every species of plant. Once thought to be waste products of
metabolism, they are now know to be vital for many plant functions, including

 analog to animal neurotransmitters (albeit a lot slower)

 natural antibiotics (meant to benefit the plant!)
 herbivore deterrents
 allelopathic compounds
 pollinator attractants
 seed-disperser attractants
 protection from harmful UV radiation

Like animal hormones, plant secondary metabolites are usually produced in a specific location of the plant, and then transported for storage (usually in vacuoles) to another part of
the plant.

The compounds often follow a Circadian rhythm, with concentration varying in a diurnal cycle, or seasonally, or even with environmental influence, depending on the plant
producing it and the specific compound being produced.

Three major types of secondary metabolites:

 alkaloids
 terpenoids
 phenolics

Alkaloids
These are produced by plants primarily as a means to deter herbivores, and, as one might expect from such a compound, they mimic some of the naturally occurring compounds in
animals and compete for the same receptors in animal cells.
The first alkaloid formally described from a plant was morphine from the opium poppy. Though it was described in 1806, it had been used by people as a painkiller and as a
recreational drug for centuries before Western scientists figured out what it was. Many synthetic opioids are now in production by pharmaceutical companies that have taken the
basic formula of morphine and changed it to mitigate some of its more harmful effects.

Cocaine is another well-known alkaloid with pharmaceutical use. It, too, has been modified and now synthetic derivatives serve as local anesthetics (lidocaine, marcaine, etc.).

Caffeine is produced by several different types of plants, primarily in the family Rubiaceae (coffee, tea, Cacao). In nature, it inhibits the growth of nearby seedlings, preventing
competition for soil resources. This effect is known as allelopathy.

Theophyllines are similar stimulants produced by tea plants, and are even more powerful stimulants that caffeine. But because they are generally found in lower concentration in
leaves than caffeine, most people are not aware of their effects. (But when you drink a cup of tea...)

Nicotine is another stimulant meant to deter herbivores. What's with us humans, anyway?

Atropine is found in a number of different plants. One local source is the Angel's Trumpet, which also produces some other very deadly alkaloids.

If you've ever been to the ophthalmologist and had your pupils dilated, you've had the joy of atropine. Though it's now used medicinally, it was once used as a...beauty aid! (See
what you missed if you didn't come to class?) (Our friend Atropa belladona...)

Terpenoids/Terpenes
The most common secondary metabolites in plants, there are more than 22,000 described!

Terpenes may serve as photosynthetic accessory pigments (carotenoids), hormones (giberellins, abscisic acid), plasma membrane components (sterols), or electron transport
molecules (ubiquinone, plastoquinone), which we'll discuss as they come up.

The basic subunit of terpenes is isoprene (C5H8), and other terpenoids are classified by the number of isoprene subunits they contain. Isoprene itself is produced in vast quantities
by plants, especially on hot days. The Smoky Mountains were "smoggy" long before the cars arrived: isoprene is a major component of smog in forested areas, where plants
produce it to stabilize plasma membranes in photosynthetic cells and thylakoids when it's very hot.

Common terpenes include:

 monoterpenoids (two isoprene subunits plus functional groups)

 sesquiterpenoids (three isoprene subunits plus functional groups)
 diterpenoids (four isoprene subunits plus functional groups)

Essential oils are usually mono- or sesquiterpenoids that create the aroma that plants use to attract pollinators, deter herbivores, kill fungi or bacteria, or inhibit the growth of
competing plants.
What are some examples?
Are all essential oils NICE?

Taxol has gotten considerable press as a potential anti-cancer agent. It was first discovered in the rare Pacific Yew Tree (Taxus brevifolia), but similar compounds have now been
isolated from other, less endangered yew species. Synthetic versions have since been made in the lab, giving hope for cancer patients as well as for the conservation of the yew
trees.

Rubber is a HUGE terpene, consisting of hundreds or thousands of isoprene units. It starts out as milky latex and is processed into the flexible, bouncy substance with so many
commercial uses and applications.

Cardiac glycosides induce heart attack in large concentrations (as in when eaten by an unsuspecting herbivore noshing on Foxglove or other cardiac glycoside-producing plants).
But modified and taken in small quantities, these compounds can actually slow and strengthen the heartbeat. Many of the most toxic plant families (e.g., Asclepiaceae (milkweeds),
Apocynaceae (dogbane)) produce cardiac glycosides. Cardiac glcosides taste NASTY, and are important in the aposematic protection of butterflies that feed on milkweeds as
larvae.

A Tale of an Unfortunate Bluejay

Phenolic Compounds
If you've taken organic chemistry, then you know that a phenol is simply an aromatic carbon ring with a hydroxyl group attached. But plants do know how to use a phenol! If only
we could figure out what they're doing with them.

Phenolics are found in almost all plant cells, and the function of many is not well understood. Many are pigments, such as flavonoids, the most recently famous of which
is resveratrol, found in red grapes (and red wine). This compound not only is reported to lower serum cholesterol levels (mechanims not known), but also is an estrogen mimic
that may be helpful in treating breast cancer.

Anthocyanins are phenolic pigments ranging in color from dark red to purple. Flavones and flavonols are pale ivory-colored pigments that may convert to sugar when
temperatures are very cold.

Different flavonoids are used by plants to attract micorhizzal fungi, or bacterial symbionts to set up a mutualistic relationship.

Tannins are bitter-tasting phenolic compounds employed by flowering woody plants as defense against herbivores. These are found in high concentrations in wood, as well as the
outer layers of unripe fruit (why?).
And as their name implies, these compounds can be used to denature protein and "tan" animal hides.

Salycilate is our friend. First discovered in willow bark (Salix sp.for which the compound is named), this is the active ingredient in aspirin. But did the willow tree kindly make
aspirin for US?
Salycilate is vital to the plant for SAR: Systemic Acquired Resistance, a sort of plant immune response seen in many flowering plants (Anthophyta). When the plant is injured by
bacteria or fungi in one area of the plant, salycilates are involved in a complex chemical cascade that allows the neighboring tissues of the plant and the rest of its body to later
resist attack by the same and similar pathogens!

The activation of the SAR response requires accumulation of endogenous salicylic acid, which is triggered by the presence of a pathogen. In the best-studied model system of the
SAR response is known from Wall Cress (Arabidopsis thaliana). In this plant, the high concentration of salicylic acid activates a molecular signal transduction pathway that is
identified by a gene called nim1 (also known as npr1 or sai1). The pathway results in heightened immunity to all pathogens in uninfected parts of the plant.

Lignin is the second most abundant of all organic molecules, and it is localized in plant cell walls. Lignin forms a polymer comprised of three large alcohol subunits (coumaryl
(primarily in flowering plants), coniferyl (primarily in gymnosperms), and sinapyl (primarily in grasses)), and the structure of lignins varies widely with species.

Lignin provides compressional strength to the cell wall, unlike the flexible strength conferred by cellulose. Without lignin, terrestrial plants probably could not have reached the
sizes they do today, as cellulose does not provide enough resistance to gravity itself.

Waterproof, lignin is also useful in directing water flow through the xylem, as the cellular subunits of xylem are rich in lignin.

Lignin, Cellulose, Fungi, and Wood Rot

Lignin is nearly indestructible. There are almost no organisms on earth (with the exception of a few types of fungi) that can break down lignins. Its natural color is reddish-brown.
By looking at the color of a rotting log, you can tell which type of fungal (i.e., Wood Rot Decay Fungi) decomposer has been at work.

Fungi categorized as Brown Rot Fungi feed mainly upon celluloses, and cannot fully break down lignin. Wood broken down by these fungi tends to look reddish-brown in color
because of the liginin residues, and falls apart in relatively large chunks as the network of cellulose is destroyed.
These fungi are more common in cool, wet climates, such as the rainforests of the Pacific northwest.

By contrast, fungi categorized as White Rot Fungi can fully break down and utilize lignin (as well as cellulose and hemicellulose polymers), so wood being broken down by these
fungi appears greyish white (due to the cellulose residues lating longer). Wood affected with "white rot" will more gradually lose its strength, and become spongy, rather than fall
apart in blocks/cubes.
Lignin's first role in plants may have been as a natural microbe inhibitor, and only later was it sequestered for other uses.

Unfortunately, it's not a nice compound when extracted during the manfacture of wood pulp, as it breaks down into toxic aromatic compounds that are dumped into nearby water.
A paper mill is not a good neighbor.

The Plant Cell is Special

Do cells give rise to organisms (The Cell Model), or do organisms give rise to cells (The Organism Model)?

And does it matter?

Plants, like any multicellular organisms, are a conglomeration of cells that show a complex division of labor. Plants have different types of cells, as we'll see
later. And they have tissues and even organs. But the basic unit of plant life, the cell, has properties and structures that make it different from those of other life
forms.

Let's have a look at those specialities...

Everyone here should know the difference between prokaryotic and eukaryotic cells. Plants, of course, are composed of the latter.

The plant cell is surrounded by the cell wall, just external to the plasma membrane forming the boundary of the protoplast. The protoplast consists of the
cytoplasm (the cytosol, and all the membrane-bounded organelles, as well as the non-organelle structural and functional components that help the cell function)
and the nucleus (nucleoplasm and internal nuclear components, such as chromatin).
Many intracellular structures (with which you should already be familiar) are not significantly different across eukaryotes. These include

 endoplasmic reticulum
 Golgi (dictyosome)
 flagella and cilia
 cytoskeletal components
 mitochondria
 nucleus (and contents)

But what's different about the PLANT CELL?

Vacuoles

 membrane-bound cavities within the cytoplasm of a cell

 usually filled with liquid
 used for
o nutrient (sugar, protein) storage
o mineral salts storage (e.g., calcium oxalate crystals or evil needles)
o pigment storage (anthocyanins)
o waste disposal
o sequester/provide permanent housing for toxic secondary metabolites
o provide structural support via turgor
o in seed cells, vacuoles store proteins needed for early germination and growth
 The large, central vacuole in a mature plant cell takes up about 80 - 90% of the cell volume, and displaces organelles towards the plasma membrane
(why might this be useful?) As the plant cell matures, the central vacuole forms via fusion of smaller vacuoles derived from the Golgi.
 The membrane surrounding the vacuole is known as the tonoplast, and is an important transport pathway inside the plant cell.
 The liquid inside the vacuole is known as cell sap, and its chemical composition usually is markedly different from that of the surrounding cytosol, as
various substances are actively transported inside it.
 The content of the vacuoles varies with cell type as well as with plant species.

Plastids
There are several different types of plastids, organelles unique to plants. Three main types are:
  chloroplast - site of photosynthesis
 chromoplasts - contain colored pigments
 leucoplasts - multi-purpose, unpigmented plastids

Mature plastids develop from small, green protoplastids in growing, embryonic plant cells.
If a developing plastid is deprived of light, it goes into a sort of arrested development, becoming an etioplast containing a characteristic,
crystalline prolamellar body that will develop into grana, once it's again exposed to light.

Chloroplasts
No one here should be a stranger to the chloroplast and its components.

It is believed that these are the descendants of ancient bacterial symbionts that were probably similar to some living cyanobacteria, such as this one:
You may recall the Autogenous and Endosymbiont Models of Eukaryotic Cell Evolution:
How are chloroplasts like bacteria?

 DNA in nucleoids (no histones); circular

 ribosomes

...and not like them?

 chloroplast construction requires input from nuclear DNA

 contain chlorophyll a, chlorophyll b and carotenoids embedded in thylakoids
Chloroplasts synthesize sugars, amino acids and fatty acids--they're the organelle that feeds the world.

Chromoplasts

 As their name implies, these contain color, mostly due to carotenoid (yellow, orange, red) and xanthophyll (yellow) pigments stored in their vacuoles and oil droplets.
 Highly concentrated in the petals of animal-pollinated flowers and the skins of animal-dispersed fruit, they function in providing color necessary to attract pollinators and seed
dispersers.
 They usually develop from chloroplasts that lose their chlorophyll, replacing it with carotenoids or other pigments.
 When leaves change color in autumn, it is due to the loss of chlorophyll from the chloroplasts, which retain their existing carotenoids (which once functioned as accessory
pigments in photosynthesis). These chloroplasts have become chromoplasts.

Leukoplasts

 Although the name means "white," these plastids are colorless.

 They lack the internal membrane system seen in chloroplasts and chromoplasts.
 Some synthesize and store nutrients, and are named for their storage product:

 amyloplasts store starches

 proteinoplasts store proteins
 elaioplasts store lipids

 Leukoplasts vary in shape, from ovoid to amoeboid.

 Some leukoplasts are biosynthetically active, taking part in the manufacture of fatty acids, amino acids and other organic components needed by the cell.
 A chloroplast that loses its chlorophyll due to light deprivation technically becomes a leukoplast, but once it's exposed to light it reverts to its former chloroplast glory.

Overview of plastid relationships:

Stromules
Plastids inside plant cells are often interconnected by a network of microscopic tubules known as stromules. These are filled with stroma, the same thick fluid that bathes the
thylakoids, and where carbohydrate synthesis takes place during the light-independent reactions of photosynthesis.
Stromules connect every type of plastid, where they facilitate protein transfer between plastids. They range in diameter from about 0.35 - 0.85 μm, though their precise morphology
and distribution in any given cell varies among plant tissues, and may change as the plant passes through various stages of development. Highly dynamic, stromules can change
shape very quickly via the action of cytoskeletal components such as actin.

Peroxisomes
These ubiquitous organelles are found in all eukaryotes. They are responsible for metabolizing fatty acids and proteins, and some contain enzymes (peroxidases) that break down
hydrogen peroxide, a toxic waste product of metabolism (remember the animal equivalent of peroxidase? Hint: Remember your enzyme lab in BIL 151!)
Like lysosomes, peroxisomes paricipate in the secretory pathway of a cell, but--unlike lysosomes (which are derived from the Golgi, and not found in plants--can replicate by
enlarging and then dividing. (They still proteins and enzymes encoded by the nuclear DNA to do this; hence, they are not as "independent" as mitochondria or chloroplasts.)

The Cell Wall

The cell wall is one of the most defining characters of the plant cell.
Not just a "box" around the protoplast, it is a dynamic, metabolic participant in cell metabolism, growth, and structure.

Recall the structure of cellulose:

Growing cells form the primary cell wall, composed primarily of cellulose in its matrix and sandwiching a middle lamella made of pectin between adjacent cells. Older cells may
form a secondary cell wallinside the original one, as we'll see. The secondary cell wall is primarily made for structural strength, though it is metabolically active. (Your specially
directed reading assignment: "Growth of the Cell Wall Involveds Interactions among Plasma Membrane, Secretory Vescicles, and Microtubules" on page 56-57. Sometimes I just
like to make you do stuff.)

Cellulose forms the bulk of the plant cell wall, and the microfibrils themselves are embedded in a matrix/sheath composed of or containing

 hemicelluloses
 pectins
 glycoproteins
 various enzymes
 lignins (in some cell walls--not all)
  cutins, suberins, waxes (in cells on the outside of the plant body)

Hemicelluloses

 Highly variable across cell types and plant species, hemicellulose is a branching macromolecule contstructed of 5- and 6-carbon sugars. They are generally insoluble in pH 7
water, but more soluble in basic solutions. (What happens to your kitchen sponge when you use bleach on it? Why?)
 Hemicelluloses limit the stretchiness of the cell wall by linking adjacent microfibrils and preventing them from sliding against each other for unlimited distances. As you might
guess from this, hemicelluloses are involved in controlling cell enlargement. Hemicelluloses are classified on the basis of their component sugars. Xylose, mannose, and galactose
form the hemicellulose backbone; arabinose, glucuronic acid, and galactose form the side chains. The latter confer different chemical characteristics on the hemicellulose.
 For example, hemicelluloses that contain acids in their side chains are slightly charged and water-soluble. Other hemicelluloses are insoluble.

Digestibility/fermentability of the hemicelluloses (by intestinal microflora) is also influenced by the particular sugars and their positions. For example, hexose and uronic acid are
more readily recognized by bacterial enzymes than the other hemicellulose sugars, so hemicelluloses containing them are more easily broken down by bacteria.

 Most are not, though. Which explains why hemicellulose-rich foods such as wheat bran and whole grains do what they do.
Pectins

 These are water-soluble, highly hydrophilic polysaccharides that form gels in solution. Because pectins attract so much water, they are responsible for the spongy, flexible nature
of growing plant cells (the walls of which may be more than 65% water!)
 The pectin backbone is usually an unbranched chain of D-galacturonic acid units. Other carbohydrates (mostly simple sugars) may be linked to the backbone, and affect the
pectin's particular properties.
 Pectins form part of the primary cell wall of plants and most of the middle lamella between adjacent cells. They're sort of a gooey cellular glue.

Glycoproteins

 These sugar-protein compounds are the structural protein components of plant cell walls. The best known are the extensins, a term that turns out to be a misnomer. Extensins
actually may prevent cell wall extension, instead conferring rigid strength to the wall by anchoring its other components.

The Secondary Cell Wall

A growing cell produces the typical, external primary cell wall, separated from other plant cells by the pectin layer known as the middle lamella. Actively dividing cells and
those that are metabolically very active (photosynthetic cells, secretory cells, etc.) typically have only that primary cell wall.

Some cells--particularly those in which compressional strength is paramount, such as in the components of wood--lay down additional layers inside the primary wall to form
the secondary wall.
The distinct layers, highly lignified and each with cellulose fibers laid down in different planes, are termed S1, S2, and S3, from outer to inner layer. What do you suppose is the
advantage to this type of lamination?

Intracellular Communication: Pits and Plasmodesmata

With all this layering, how do the cells "talk" to one another?
 Primary cell walls have thinner areas known as primary pit fields.
 Pit fields contain small openings in the wall through which cytoplasmic extensions known as plasmodesmata (singular, plasmodesma) extend between cells.
 The plasmodesmata are bounded by plasma membrane along their length, and a single tube of endoplasmic reticulum, the desmotubule extends through each plasmodesma.
 When the cell constructs a secondary cell wall, it doesn't lay down secondary wall over the primary wall's pit fields.
 This creates perforations in the secondary wall called pits. (Sometimes a pit is formed even if there's no pit field.)
 Pits of adjacent cells are usually appressed to each other so that the two primary cell wall and middle lamella form a selectively permeable pit membrane.
pit---primary wall---middle lamella---primary wall--pit

...comprises the pit pair through which the cells can transmit water, nutrients, hormones, etc.

Cell Cycle Specialities of the Plant Cell

You should all be familiar with the stages of mitosis and meiosis. In general, these are not different between animals and plants, with a few notable exceptions.

 plants lack centrioles (but of course still have microtubules)

 plants undergo mitosis all their lives, in special ever-embryonic/totipotent areas kown as meristems. These are located primarily at the tips of shoots and the tips of roots, though
they may be temporarily found in other locations, such as the margins of growing leaves.
 Unique Interphase Events:

 Before active mitosis starts, the nucleus migrates to the center of the cell and is anchored there by strands of cytoplasm.
 These strands gradually merge to form a sheet of cytoplasm, the phragmosome that bisects the cell at the plane of division.
 A ring of microtubules (the preprophase band) forms just under the plasma membrane and extends to form a plane (also encircling the nucleus) where the mitotic spindle
will eventually form.
 Once the mitotic spindle forms, the preprophase band disintegrates.
 Although the new cell wall doesn't form until telophase, it starts forming in the middle of the cell and expands outwards, occupying exactly the place once occupied by the
preprophase plate. (Why? We don't know.)
 The phragmoplast is composed of overlapping microtubules and actin filaments, which apparently orient the components of the new cell wall (hemicelluloses, pectins,
enzymes, etc. delivered in Golgi-derived vescicles) in their proper positions.
 phragmoplast tubules trap dictyosome vesicles at the midpoint between the two new nuclei.
 The vesicles begin to fuse, from the center of the cell --> outward, joining to form a single, large vesicle.
 Endoplasmic reticulum "trapped" between fusing vescicles become the desmotubules of the future plasmodesmata, and remain connected across the new daughter cells.
 Inside the large vesicle, the middle lamella and the two primary walls on either side of it form.
 The vesicles continue to fuse outwards until they meet the existing cell wall.
 When the vesicle membrane meets the cell wall, it fuses with the plasma membrane apressed to that cell wall and becomes the plasma membrane separating the two
daughter cells.
 The new cell wall that was once inside the vesicle now fuses to the existing cell wall via the deposition of hemicellulose and pectin molecules.
(also see figure 4-18 in your text.)

And we have new cells.

From Seed to Sprout: Plant Embryogenesis

Fact #1. The plants with which we are all most familiar make seeds.
Fact #2. Therefore, we tend to assume that all plants make seeds.
Fact #3. Not all plants make seeds.
Only the most derived taxa of plants, those commonly called gymnosperms ("naked seed" plants, such as pines, firs, and other "evergreens")
and angiosperms (flowering plants) package their embryos in the complex little food packet/travel module called a SEED.

We'll be dealing only with angiosperms today.

Angiosperms are classified in Phylum Anthophyta, and they are not only the largest, most diverse group of plants, but also the most complex. Unique to the
anthophyta are flowers, clusters of specialized leaves that participate in reproduction.

And when it comes to reproduction, plants do it very differently from any other type of organism. Only plants (and a few of their more primitive algal relatives)
undergo

Alternation of Generations

In this type of life cycle, a diploid plant gives "birth" to a haploid plant generation, and that haploid generation reproduces to create another diploid generation.
The generations alternate this way, with each generation having a different ploidy than its predecessor. We'll cover this in more detail later, but a few
definitions now will help:
  sporophyte - a diploid plant; produces spores via meiosis. May be male, female or bisexual.
 gametophyte - a haploid plant; produces sperm and/or ova via mitosis. May be male, female, or bisexual.
 spore - haploid cell that will grow via mitosis into a gametophyte
o microspore - spore that grows into a male gametophyte
o megaspore - spore that grows into a female gametophyte
 sporangium - structure that houses developing spores
o microsporangium - sporangium that grows microspores (male)
o megasporangium - sporangium that grows megaspores (female)
 sporophyll - a leaf that bears sporangia
o microsporophyll - bears spores that grow into male gametophytes
o megasporophyll - bears spores that grow into female gametophytes
 gamete - as in animals, these are sperm or ova
 zygote - as in animals, this is the fused sperm + ovum (fertilized ovum)
 seed - structure, found only in gymnosperms and angiosperms, that houses the spore as it grows into a gametophyte

A few other definitions you might recall...

 dicot - a plant that has two embryonic leaves (cotyledons)

 monocot - a plant that has only one embryonic leaf

(These designations are largely artificial, and not taxonomically very helpful. But since dicots and monocots are economically important for different reasons,
we still like to know the differences between them. We'll review those later in the semester.)

The Flower: Where it All Begins

In flowering plants, the specialized, spore-bearing leaves called microsporophylls (male) and megasporophylls (female) are arranged in a FLOWER, a
collection of highly specialized leaves.

Ready? On your mark. Get set...

Let's look at the flower from the bottom UP.
The stalk attaching the flower to the stem is known as the PEDUNCLE, and the slightly inflated "platform" on which the flower itself rests is called
the RECEPTACLE. The outermost leaves of a dicot flower are usually small and greenish, and are known as the SEPALS. Collectively, they comprise
the CALYX.

Internal to the sepals are the PETALS, collectively comprising the COROLLA. The calyx and corolla together make up the PERIANTH.
The Male
The male sporophylls (microsporophylls), located just inside the petals, are the STAMENS. Each stamen consists of a thin, stalklike FILAMENT and the
boxlike ANTHER.

Inside the anther, special diploid cells known as microspore mother cells are dividing via meiosis to give rise to microspores. Each microspore will
grow and differentiate via mitosis to become the male gametophyte, POLLEN. Each pollen grain is an individual, genetically unique plant that
contains two sperm.
The Female
The female sporophylls (megasporophylls), located just inside the stamens, are the CARPELS. Each carpel consists of a terminal, sticky pad called
the STIGMA (where pollen will land and germinate), a stalklike STYLE, and a rounded, ovule-containing base known as the OVULARY.
Inside the ovulary diploid megasporangia contain megaspore mother cells which undergoing meiosis to give rise to megaspores. Each megaspore will
undergo a specialized series of mitotic nuclear divisions without cytokinesis, resulting in coenocytic organism, the female gametophyte. Though she's
little more than a mass of cytoplasm containing 8 nuclei, she is an individual, genetically unique plant living in side her mother, the sporophyte--though
she hardly looks like a plant!
A closer look at the female gametophyte:

The mature gametophyte inside the megasporangium, which will eventually become the seed, is known as the ovule. An ovule is, essentially, a seed waiting to
happen.
The Fates of the Nuclei

 ovum - fuses with one sperm to become the zygote

 polar nuclei - both fuse with one sperm to become 3n, nutritive endosperm
 synergids - disintegrate, after fertilization (help guide the pollen tube and sperm to the ovum)
 antipodals - disintegrate after fertilization (function unclear)

Let's have a look at plant fertilization and ovule development.

The result is the seed:

And that's where we'll go from here.

The Embryo

 Inside the seed, the zygote undergoes an initial, asymmetric, transverse division. This establishes the polarity of the embryo: which end will be the root, and which will be the
shoot.
 The smaller (upper) end of this two-cell stage is the chalazal pole, and the lower end is the micropylar pole.
 The small apical cell at the chalazal pole will become most of the plant embryo.
 The larger basal cell at the micropylar pole will become the suspensor, which anchors the embryo to the inside wall of the seed.
 The apical cell divides and grows into a spherical embryo proper (EP in the diagram below) connected by a long suspensor to the seed wall.

The first leaves of the plant are known as the cotyledons. These arise via divisions along the margins of the globular embryo to form the heart shaped embryo. The cotyledons
and shoot elongate to form the torpedo shaped embryo, the walking stick embryo, and finally the mature embryo.

A more detailed view of just the embryo:

 The three precursors to all the tissues to come, the PRIMARY MERISTEMS, are now developed:

 protoderm - gives rise to epidermis and its derivatives

 ground meristem - gives rise to all ground tissues (next lecture!)
 procambium - gives rise to the vascular tissues, xylem and phloem

You can see their relative positions above, as well as here:

The protoderm arises via periclinal (i.e., parallel to the embryo surface) divisions. The ground meristem and procambium arise via vertical divisions inside the protoderm. The
resulting "topography":

The Suspensor
In flowering plants, the suspensor is metabolically active. Not only does it anchor the embryo to the inside of the seed wall, it also provides nutrients, growth regulators, and
hormones.

By the torpedo stage, the suspensor is undergoing massive apoptosis (programmed cell death), as its job is done.

Suspensor cells removed from the presence of the embryo proper are able to grow into an embryo. Study of mutants in which inhibitory signals from the EP are lacking, the
suspensor is seen to grow into a twin embryo inside the seed, though the embryo is often not correctly formed.

The Mature Embryo and Seed

Remember: until the seed is fully mature, it is still attached to its parent sporophyte, and as the embryo grows inside the seed, nutrients from the parent plant continuously flow into
the seed. The endosperm becomes very large, forming a nutrient reserve for the embryo when it germinates, and before it can photosynthesize.

At maturity, the stalk (the funiculus or placenta) connecting the ovule to the wall of the ovule (fruit!) dehisces from the ovule/seed, and the seed is on its own.

The seed loses moisture as it further develops, and the outer wall (seed coat) becomes very hard, and impermeable to water. It's now ready for travel, a self-contained system
complete with embryo and food source.

Getting Away from the Parents

Seeds are dispersed in many different ways...

By wind, water, animal transport (internal or external), and even by tiny explosions.

Germination
Some seeds will not germinate until they have undergone a process known as after-ripening, which triggers a series of biochemical events, allowing the embryo to become
competent to germinate. For example, some temperate species will not germinate until after they have been exposed to very cold temperatures. This prevents premature
germination before winter is over.
Other seeds must pass through an animal's digestive tract and become scarified before they can imbibe water and become metabolically active.

Still others must pass through fire. This is common in biomes where annual fires are part of the normal climate. (Of what use could this be, evolutionarily?)

Oxygen, light, and temperature all may play a role in breaking dormancy of seeds, and the after-ripening stimulus that works depends on the species of plant and the evolutionary
history of its forbears.

One thing all share, though, is the need to imbibe water. Most mature seeds have very low water content (5-20% water), so they must drink before the new plant can grow.

 water washes away the hormone embedded in the seed coat (abscisic acid) that inhibits germination
 water activates metabolism, starting the enzymatic work that frees nutrients in the endosperm for the growing embryo to use in breaking free.
The bean shows epigeous germination, in which the cotyledons emerge from the soil, following the arch of the hypocotyl.

The pea shows hypogeous germination, in which the cotyledons stay underground because it is the epicotyl that arches out, protecting the delicate meristem--leaving the
cotyledons behind.

The corn plant, a monocot, does not arch out of the soil to protect the apical meristem. Instead, a tough sheath covers the young root (coleorhiza) and young shoot (coleoptile) and
emerges first, followed shortly by the radicle (embryonic root) and the first shoot of the young plant.

From that point on, it's all up to the Mighty Meristem, whom we'll meet next time.
Plant Cells and Tissues Plants became truly land-dwelling with the advent of:

1. spores with durable, protective walls

2. thickened waxy cuticle over the epidermis

3. stomates that open and close

4. our old pal, lignin:

5. progression of alternation of generations so that the gametophyte is a small, ephemeral stage, and the sporophyte a large, persistent stage. (More on this later)

Once plants invaded terrestrial habitats, natural selection took over, and individuals with adaptive mutations radiated and changed to pioneer an entirely new
world available to them. And that meant changing from unicellular, relatively undifferentiated ancestral algae into complex organisms with specialized cell
types as well as simple and complex tissues and organs.

PLANT ORGANS There are only three:

 root
 stem
 leaf

Plant organs are generally defined by the presence of more than one type of tissue. So before we embark on our study of plant organs, let's have a look at their
components.

PLANT CELLS One picture is worth a lot of words.

PLANT TISSUES A tissue is defined as an aggregation of cells coordinated to perform a particular function or set of functions.

Tissues may be

 meristematic (embryonic and totipotent)

 simple (composed of only one type of cell), such as
o parenchyma
o collenchyma
o sclerenchyma
 complex (composed of more than one type of cell), such as
o dermal (protective covering)
o vascular (conducting tissue)
 xylem (conducts water and dissolved minerals)
 phloem (conducts water and dissolved organics)
o ground (bulk of the body; primarily parenchyma, collenchyma & sclerenchyma)
MERISTEMS: Source of all other tissues

Meristems are regions of undifferentiated, embryonic cells. Initially, the cells are totipotent and can differentiate/mature into any other type of cell.

Recall the terminology for sequentially less versatile undifferentiated cells:

 totipotent cells have the capacity to develop into any type of cell.
 pluripotent cells can develop into many, but not all different types of cells.
 multipotent cells can develop into multiple types of cells, but not as many types as pluripotent cells.

Meristems are present throughout the life of the plant, and are the source of seasonal new growth in both height (primary meristems) and girth (secondary
meristems).
Meristematic cells are also found at the margins of such structures as growing leaves or flower petals. As they divide, they differentiate and lose their
totipotency until the structure is fully grown and mature.

Height and Girth: Primary and Secondary Meristems

 Primary meristems: located at the tips of roots and shoots. Responsible for increase in plant length. Apical meristems are located in two different areas of the stems and roots:

 apical buds (at the tips roots and shoots)

 axillary buds (located in the leaf axils)

 Secondary (a.k.a. lateral) meristems: located in the margins of the stem and root (vascular and cork cambium). Responsible for increase in girth.

 vascular cambium - gives rise to secondary xylem and phloem

 cork cambium - give rise to the periderm, which replaces the epidermis in woody plants.

Note: Only plants with a vascular cambium can produce true, botanical WOOD, which is composed of concentric rings of xylem.

Here are where you'll find the meristems...

 Primary growth and primary structures arise from the apical/primary meristems.
 Secondary growth and secondary structures arise from the lateral meristems.

CELLS OF THE GROUND TISSUES

 parenchyma - the generalized, box-shaped cell with uniformly thick cell walls
 (when parenchyma cells have a high density of chloroplasts, they are sometimes referred to as "chlorenchyma" cells)

 collenchyma - corners of the cell wall are thickened with cellulose

 sclerenchyma - highly lignified and cellulose-rich cell walls, these are dead and hollow at maturity.
o fibers - long, slender, tapered cells
o sclerids - small, granular clusters

CELLS OF THE VASCULAR TISSUES

 XYLEM

Xylem conducts water and inorganic substances from the roots to the aboveground parts of the plant, and out the stomates. A complex tissue, it consists of several
different types of cells.

o conducting cells (tracheids and/or vessel elements)

 tracheids - long, tapering cells covered with multiple pits
 vessel elements - tubelike and of greater diameter than tracheids, these are stacked end-to-end to form long, strawlike structures called vessels.
 At maturity, tracheids and vessel elements are dead and hollow, lacking a living protoplast.

Vessel elements, though they conduct water more rapidly, are more "risky" for the plant. Unlike tracheids, in which water must pass through the pit membranes, vessel
elements have large pores. This means that air bubbles formed (e.g., during freezing and thawing of xylem sap in the spring) will be trapped inside an individual tracheid,
and cannot block water flow.

A vessel element can accumulate bubbles, and one good-sized bubble can break the water column in an entire vessel, making it useless. (Think of your cut roses!)

The growing conditions under which tracheids and vessel elements form determines whether they will be either flexible or rigid at maturity. Once the conducting cell has
reached its final size and shape, apoptosis (programmed cell death) takes place, and the protoplast disintegrates, leaving a hollow conducting element.

 ground cells (parenchyma, collenchyma, sclerenchyma)

These form the structural support around the conducting cells.

 parenchyma - provide nutrient storage and storage of other substances, such as aromatic and other protective secondary metabolites. These are present in vertical strands in
primary xylem, and also in radially arranged rays in secondary xylem. Sclerenchyma fibers form a large part of wood biomass.

 PHLOEM

 sieve cells - pores small, uniform; dovetail end to end

 sieve tube members (= elements) - pores on some walls are larger than sieve cell pores, and are clustered to form SIEVE PLATES. These are most commonly found on the
end walls, and are areas of contact between adjacent sieve tube members. These are more derived than sieve cells.

At maturity, the conducting cells of phloem contain a protoplast (unlike xylem, which is dead and hollow at maturity): but it has NO MAJOR ORGANELLES.

 albuminous cells (gymnosperms & more primitive taxa)

 companion cells (angiosperms)
 transfer cells (high surface area for chemical transfers)
 ground cells (parenchyma, sclerenchyma, collenchyma)

More about companion cells and albuminous cells...

 In angiosperms
each sieve tube member is associated with a COMPANION CELL, which is a fully equipped parenchyma cell that performs all necessary metabolic functions for both
cells.

 The two are joined by numerous plasmodesmata, creating a large surface area for transport between the two cell membranes.
  The two are derived from the same progenitor (mother) cell.

 In gymnosperms
each sieve cell is associated with an albuminous cell.

 This performs the same function as the companion cell in angiosperms, but it is NOT derived from the same progenitor cell as the sieve cell it serves.

DERMAL TISSUES These are the "skin" of the plant. Epidermis is found in herbaceous plants, and in those that become woody, it is replaced by the periderm, which originates
from the cork cambium.
 EPIDERMIS
This very complex tissue consists largely of flattened cells that lack chloroplasts. Specialized cells found in the epidermis include

 guard cells (bordering the stomates)

 trichomes (cell with a long, hairlike extension)

The botanical terms...

 glabrous: hairless
 pubescent: fuzzy
 hirsute: hairy

...all refer to the presence or absence of foliar trichomes.

e.g. - root hairs, surface hairs on leaves & stems, special absorbing trichomes in epiphyte foliage, salt-secreting cells

 gland cells - produce and/or store a wide variety of compounds, from nectar to poisons (often associated with trichomes) to...just about anything.

 PERIDERM
This is a secondary epidermis, produced by the cork cambium. It consists of

 phellum (cork) which is heavily impregnated with waxy suberin.

 cork cambium

Directly beneath the periderm lies the phloem. The periderm and the phloem together comprise the BARK of a woody plant.

The overall arrangement of tissues in a generalized stem cross-section can be seen here:
And the progression of their development:
The Leaf: Site of Photosynthesis & Transpiration The leaf is arguably the most diverse and specialized plant organ across taxa. It was the most recent plant
organ to evolve, and is not found in the most primitive plants. The leaf is the main site of photosynthesis and gas exchange in most plants. External Anatomy
of the Leaf:

 leaves lacking a petiole, and attached directly to the stem at the base are said to be sessile
 In most monocots, the leaf base is expanded to surround the point of stem attachment, forming a sheath. Monocot leaves lack a petiole, yet another characteristic that links this
monophyletic group.

Phyllotaxy Phyllotaxy is arrangement of leaves along the length of the stem at the nodes.

 helical - one leaf per node, with each one slightly offset from the previous so that the leaves form a spiral along the stem. (What do you suppose is the advantage to this
arrangement?)
 distichous or alternate - one leaf per node, offset in opposite directions, alternating. Typical of grasses.
 opposite - two leaves per node, set in opposite directions

 opposite and dicussate - two leaves per node, set in opposite directions, with successive leaves at each nodes arranged at right angles from each other. Typical of members
of the mint family, like this basil...

 whorled - multiple leaves per node, set in a spiral.

Individual Leaf Morphology

 simple leaf - a single blade, not divided into sections. These can come in several shapes, for example...

 simple, pinnate - feather-shaped

 simple, palmate - palm-shaped
 simple, cordate - heart-shaped
 simple, orbicular - round
 simple, reniform - kidney-shaped
 ...and many MORE.

 lobed leaf - the margin of the leaf is indented, but not all the way to the midrib. For example...

 pinnately lobed - feather-shaped

 palmately lobed - palm-shaped

 compound leaf - leaf blade is divided into leaflets, all the way down to the midrib (which is called the rachis in a compound leaf). These can be...

 pinnately compound - feather-shaped leaf composed of leaflets

o even - even number of leaflets
o odd - odd number of leaflets
o doubly pinnate - leaflets are divided into leaflets (can be even or odd)
 palmately compound - palm-shaped leaf composed of leaflets
 Other diagnostic characters of leaves include

 leaf margin morphology

 leaf venation pattern

Internal anatomy of the leaf:

From top surface downward, note the...

 cuticle - a noncellular, waxy sheet of cutin secreted by the epidermis

 epidermis - this one-cell thick layer of "skin" tissue lacks chloroplasts.
 palisade mesophyll - layer of photosynthetic parenchyma (chlorenchyma) of a tall, columnar shape.
 spongy mesophyll - second layer of photosynthetic parenchyma (chlorenchyma), this one with copious air spaces to facilitate transpiration.
 vein system (xylem on top; phloem on bottom)
 lower epidermis - contains most of the stomates
 lower cuticle - usually a thinner layer than the upper layer

Here's what an actual cross section micrograph looks like...

The Epidermis Metabolically active and often composed of diverse cell types, this is the plant's first line of defense against environmental insult.

 generalized epidermal cells

 trichomes
 guard cells

The typical epidermal cell is flattened and elongate, though the ratio of length to width may vary across species. Note the lack of chloroplasts in the cells!

The epidermal cells secrete and are covered by a waxy cuticle, shown here from above, and in cross-section:

Because of its tight structure and the waxy cuticle, the epidermis provides strength and form to the leaf.

Stomates
Gas exchange pores, stomates are located primarily on the underside of leaves in most plant species, but may also occur on the top. In some species, stomates occur only on the
upper surface. (What type of plant would you expect to have stomates on the tops of leaves only?)
Opening and closing of stomates occurs in response to light conditions, environmental humidity, and water content of the plant body in general. (More on this when we talk about
water movement through plants.)

 hydrophyte - plant evolved to thrive in very wet conditions

 xerophyte/xeriphyte - plant evolved to thrive in very dry conditions
 mesophyte - plant evolved to thrive in moderate conditions (with respect to water)

Would you expect a xerophyte to have relatively few, or relatively many stomates, compared to a mesophyte?

VOTE.
DISCUSS.

What water-saving epidermal features do xerophytes have?

 numerous trichomes (some with secreted resins)

 thick waxy cuticle
 few upper surface stomates
 stomates recessed into grooves on the leaf surface

The Mesophyll

Mesophyll is the leaf's ground tissue, composed primarily of parenchyma containing a great density of chloroplasts (hence, this is chlorenchyma).

 Pallisade Parenchyma - vertical, columnar cells closest to the upper epidermis. These have more chloroplasts than the rest of the mesophyll, and most photosynthesis seems to
take place in the pallisade parenchyma.
 Spongy Parenchyma - these are typical, box-shaped cells, with much more air/fluid space between them than the pallisade cells. Fewer chloroplasts, but photosynthesis still
takes place here. This is the site of water and gas exchange, with the air spaces in the spongy mesophyll connected directly to the stomates.
The Vascular System The vascular system is distributed throughout the mesophyll, and is visible on the surface of the leaf as the venation pattern.

A cross section of the petiole reveals that the phloem is on the bottom of each vein, and the xylem is on top (picture it as peeling away from the stem as it grows outward from the
stem). Both are primary, and do not develop from the vascular cambium.
 major veins - readily visible, associated with the "ribs" (protruding ridges on the undersides of the leaf)
 minor veins - netted throughout the mesophyll, these are responsible for most of the collection of photosynthate directly from the photosynthetic parenchyma, and join the major
veins at various junctions.

Major veins are not in contact with photosynthetic cells or to the intercellular spaces of the mesophyll, as they are surrounded by dense parenchyma.

Minor veins are surrounded by small cylinders of dense parenchyma that form a bundle sheath around each vein. Bundle sheaths complete enclose each minor vein, all the way to
the tip, and act much the way the endodermis of the root does: all photosynthates and other materials must pass through the sheath in order to get to the vein for transport, so the
sheath cells act as a selectively permeable barrier, controlling the substances that the vascular system transports from the leaf.

In some plants bundle sheath extensions travel from the tips of the veins to the epidermis, and may permit the transport of water from the xylem to the leaf epidermis.

Where Do Baby Leaves Come From? Leaf primordia are initiated by masses of cells at the edges of the apical meristems, and includes all three primary meristems. These cells are
called the founder cells of the leaf, and they give rise to the budding leaf primordia, as shown below.
Leaf Modifications and Specializations Leaves show the greatest diversity of modification of all the plant organs. An overview of some of these follows, but you will encounter
leaves that will amaze and astound you beyond what you see here.

 sporophylls - specialized for reproduction

 leaves modified for high rainfall - drip tips

 leaves modified for very dry environments

 leaves modified for extreme environments (wind; cold)
 leaves modified for carnivory

Leaf structure and shape is intimately related to the environmental conditions under whch the plant evolved, but also in which it has developed. The genetic plasticity of plant
organs is clearly reflected in such things as variable shapes, pigmentation and sizes of leaves and stems on the same plant that grow in sun versus shade, or other variable
environments.
The Stem This organ is responsible for the aboveground structure of the plant, and is involved in both structural support and vascular transport.Recall the
general external anatomy of a stem:
Recall the locations of the apical and lateral meristems.

 APICAL meristems (located at the tips of roots and shoots) give rise to three PRIMARY MERISTEMS (protoderm, ground meristem, and procambium).

And also recall:

 ground meristem - develops into ground tissues

 procambium - develops into vascular tissues and the vascular cambium
 protoderm - develops into the dermal system

A cross section of a generalized, herbaceous dicot stem appears on the left:

Note that young, herbaceous stems may have stomates for gas exchange, though the leaf is the main site of gas exchange, with many more stomates than the stem.

Secondary Growth in Stems LATERAL MERSTEMS are cylindrical, secondary meristems in both stem and root that give rise to either vascular tissue or secondary dermal
tissues. They are the

 vascular cambium - located between xylem and phloem

 cork cambium - located between phloem and bark

Recall the progression of secondary growth in the two lateral meristems.

 determinate growth: growth that occurs during a finite juvenile phase, and then stops.
 indeterminate growth: growth that occurs throughout the life of the organism.
 annual plant: lives for about a year, flowers and dies
 perennial plant: lives for more than one year
Annual plants lack secondary growth, and remain herbaceous throughout their short lives. Many perennials do not develop true wood, though they may become somewhat
"woody" as their older tissues lignify and become more structurally supported with cellulose, resins, and other substances.

Still others may undergo extensive tissue growth via the vascular cambium. Only these plants produce what is known as true, botanical WOOD.

Stems and Wood All plants begin their development as HERBACEOUS (i.e., non-woody) organisms. True WOODY plants eventually develop WOODY stems.

Shown diagramatically, the tissue layers are arranged like so:

 heartwood: dead center of the woody stem in which conducting elements of xylem are clogged with tannins and resin, and no longer function to conduct fluids.
 sapwood: external ring of xylem still conducting fluids
 springwood: large-lumen xylem formed in spring
 summerwood: small-lumen xylem formed in summer/late autumn, just before dormancy
The wood of many species may contain species-specific aromatic compounds. Consider:

 Why put those in the wood, of all places?

 What side effects might this have on humans who use wood?

 wood turning
 wood shavings used for litters
 aromatic wood insect repellants

Monocot Stems No tour of stems would be complete without a brief mention of the highly derived stems of monocot anthophytes. A cross section is shown on the right of the
diagram we saw above:
Note the absence of concentric rings of vascular tissue. Instead, xylem and phloem are both distributed throughout the pith of the stem in discrete vascular bundles.

Monocots (with the exception of the most primitive species, the Joshua Tree (Yucca brevifolia Engelm. var. brevifolia; Family Liliaceae) ) lack a vascular cambium or cork
cambium. Therefore, these monocots do not produce true, botanical wood (concentric rings of xylem), although they may be very "woody" in some cases (e.g., palms, large
bamboos).

Stem Gas Exchange How does an enormous tree get enough oxygen for its needs, if all its skin is woody?
In some species, gas exchange pores called lenticels. These are "spongy" regions found on the bark of stems (and sometimes aerial roots) of woody vascular plants. These areas,
which form around what used to be groups of stomates, allow gas exchange between internal tissues and atmosphere across the periderm, which is otherwise impermeable to gases.

The cork cells of the lenticel, unlike those forming the rest of the cork, have minute air spaces between them that allow oxygen and other gases to enter and leave the plant tissues.

You've probably seen lenticels, but didn't realize you were seeing them.

Even a few fruits have lenticels; these are often accessory fruits (i.e., fruits developed from more than just an ovulary). In the case of the apple or pear, the skin is what used to be
the flower receptacle: a modified stem.
Stem Specializations Stems may be highly derived in form and function.

 rhizome - underground stem. Typical of ferns and some other plants

 tuber - underground storage stem is a modified rhizome.
 tendril - typical of climbing vines, these respond to touch and grow around supporting items.
 stolon - above-ground propagative root (e.g. strawberry; spider plant) that produces new plantlets asexually. (A form of cloning) These are often called "runners". (Other
examples: strawberries, many grasses)
 bulb - an underground stem consisting of a dense basal plate (a shortened stem axis), and growing point or shoot primordium, enclosed by thick, fleshy modified leaves.
 corm - a solid modified stem consisting of a swollen base of a stem axis enclosed by dry, scalelike leaves. These usually have fibrous and contractile roots.
 pseudobulb - unique to orchids, these are thickened, bulblike stems that store both water and nutrients.
 cladophyll - flattened stem that serves the photosynthetic function of a leaf. Another example: various species of cactus). From the Greek clad, meaning "branch" and phyll,
meaning "leaf".
 thorn - Although not all spines you see on a plant are modified stems, thorns are shortened stems modified to form sharp, protective spikes. (Other types of spines can be
extensions of the periderm, or even modified leaves, as in cactus spines. They are not always modified stems.)
The Root This organ is the first to emerge from a seed.

Its functions are

 anchor the plant to its substrate

 absorb water and inorganic substances from the substrate
 conduct the above upwards to the rest of the plant
 production (in meristems) of certain hormones that are transported other parts of the plant
 production of secondary metabolites (e.g., nicotine in tobacco, which is transported to the leaves for deposition as an herbivore deterrent)
 storage of nutrients as carbohydrates and/or lipids

Origin of the Root The primary root is the first root that forms in and emerges from the seed.

In most other plants, the primary root develops into a taproot, a large, central root from which lateral roots emerge.
 Root depth depends on environment
 Porous soil - deep roots; rocky soil - shallower roots
 Temperature and soil water content also affect root depth.
 And of course, different species have different root characteristics

 spruce, beech, poplar, tend to have relatively shallow roots

 oaks, most pines, maples, sycamores, etc, tend to have taproots almost as tall as the aboveground portion of the plant.
 What about southern Florida root depth? The dilemma of hurricanes!
 record root depth is held by the mesquite: just over 53 METERS. (Why mesquite?)

 The main "feeder roots" spread in the topmost soil layers, usually no deeper than about a meter.
 Roots tremendously increase plant surface area where the plant needs it: for water absorption.
 Root surface area is much greater than shoot surface area.
 Root and shoot are balanced: If the roots are damaged, the shoot may die back.
If the shoot is damaged, there's less photosynthate available for new root growth. In the most derived plants (monocots), the taproot is replaced by a system of fibrous roots that all
emerge in a bunch at the base of the stem.
Root Growth and Development Let's have a look at where it all begins: The Root Tip.

Again, note the relative locations of the apical and three primary meristems.

Can you see the quiescent center? Labeled with a radioactive nucleoide, the tip shows up on an autoradiograph with actively dividing nuclei showing dark (taking up the marker),
and relatively inactive cells with invisible nuclei (not taking up marker).
 The root cap is a protective cap of live parenchyma cells

 it is produced by the apical meristem behind it

 it protects the root meristem as it grows through the soil
  outermost cells are sloughed off as the root tip "pushes" through the soil
 root cap cells produce a slimy lubricant (mucilage or mucigel)
o it's the plant equivalent of mucus
o hydrophilic polysaccharide (a type of pectin)
o produced in the Golgi and packaged in vesicles that attach to the cell wall and empty their contents.
o the goo passes through the cell wall and oozes out onto the root cap surface.
o mucigel allows greater ease of transporting ions from interstitial soil water to the root surface, where it can be absorbed.
o mucigel is friendly to nitrogien-bacteria, and may help them colonize roots of nitrogen-fixing plant species (primarily in the Pea Family, Fabaceae)
o may provide some protection against desiccation.
 root cap cells last 4-9 days, depending on plant species and growth rate
 root cap facilitates geotropism via the columella, a central column of cells that contain starchy amyloplasts. These fall to the bottom of the cells, attracting hormones that
promote growth in the direction of the amyloplasts. (more on this later)

Root Meristems The apical meristem (from the Greek merismos, which means "division") is found at the very tip of the root, just behind the root cap.
As in all meristems, the apical meristem contains some cells that will always remain meristematic: one daughter cell remains in the meristem (the initial) and continues to divide,
whereas its sister cell (the derivative) stays behind as the meristem grows out. The derivative differentiates into some type of cell, depending on its gene expression. This is known
as primary growth.

The very end of the root tip contains the initials and the immediate derivatives, and is known as the promeristem. Note the relative locations of the apical and three primary
meristems.
(What's different about this quiescent center? Why?)

 Region of Cell Division - the apical meristem

 Region of Elongation - growing cells elongating (primary meristems)
 Region of Maturation - cells mature, no longer elongating (mature tissues)

Root Primary Structure Recall that any plant organ has three main layers:

 epidermis (and derivatives)

 vascular tissue
 ground tissue
Root Anatomy: Cross Sectional View

From outermost layer to innermost:

 epidermis
 cortex
 endodermis - selectively permeable layer; unique to roots
 pericycle - a secondary/lateral meristem that gives rise only to side branch roots; unique to roots
  vascular cylinder (a.k.a. stele)

Root Epidermis Root epidermis is the surface that meets the environment, and it is the first selectively permeable membrane the plant uses to filter uptake.

Surface area is increased by trichomes that form root hairs:

These are found primarily in the Region of Maturation, and die off once the cells age. Although the cell walls contain suberin, water and minerals can pass easily between the cells
of the epidermis, so further filtration is needed down the line.

Mycorrhizae This is a symbiotic relationship between a fungus and a plant root. (What does each partner get out of the relationship?)

 Vesicular Arbuscular Mycorrhizae (V.A.M.) - association between a zygomycete fungus ("Black Bread Mold") and a plant
 Ectomycorrhizae - association between ascomycete (Sac Fungus) or basidiomycete (Club Fungus) and a conifer or flowering plant (usually large trees).

Some of the most valuable edible organisms in the world are TRUFFLES, various species of mycorrhizal (ascomycete and basidiomycete) fungi that partner with plants.
In mycorrhizal plants, root hair surface area is negligible compared to that provided by the interface of mycorrhiza, plant and fungus. Most absorption is done via the mycorrhizal
hyphae.

Recent research suggests that mycorhizzal associations may be a symbiotic partnership between not two, but three species, including special bacteria that live inside the gungus
and are essential to the establishment of the symbiosis.

The Cortex Just internal to the epidermis lies the cortex, composed primarily of parenchyma.

Cortex plastids are primarily for storage (fats, carbs). Only in some species with photosynthetic roots (which types of plants would you expect these to be?) are there chloroplasts
in these cells.

In woody plants, the cortex is shed off once woody growth begins. In herbaceous plants, the cortex is maintained throughout the life of the plant.
Most of the cortex is airy, with a lot of space (filled with fluid and or air) between the cells.

Fluids travel via:

 symplast - the connection formed by plasmodesmata

 apoplast - the continuous surface formed by adjoining cell walls

(recall: the tonoplast is the continuous fluid pathway formed by the plasma membrane of the vacuoles)

The innermost layer of the cortex is the endodermis, the main "filtration" surface of the root.

The Casparian strips banding each endodermal cell are made of suberin (sometimes lignin, as well), and prevent interstitial entry of water into the stele (central core of vascular
tissue). Thus, water cannot travel via the apoplast, and must pass through the selectively permeable plasma membrane of the endodermal cells before it reaches the vascular
system.
Pericycle This is a layer of pluripotent parenchyma cells located just inside the endodermis. Pericycle gives rise to side branch roots.

The Stele Root morphology is fairly well conserved across plant taxa. Therefore, differences in the morphology of the stele can be an important tool for classifying plants and
determining evolutionary relatedness.

The stele consists (from outermost to innermost layers):

 phloem from three to many bundles, alternating with xylem

 xylem - central core
The number of xylem "arms" in the stele determines its classification as a...
o diarch - two arms (uncommon)
o triarch - three arms
o tetrarch - four arms
o pentarch - five arms
o hexarch - six arms
o polyarch - more than six arms ...stele.

 In young roots, the phloem and xylem are nested in a central core of parenchymal pith
  In monocot roots only the xylem core surrounds a central cylinder of parenchymal pith. This is the simplest way to tell the difference between a typical root and the highly
derived monocot root.

The Variety of Roots

Roots of various plant species have evolved various specializations.

 food storage roots - used by the plant to store starch for metabolic activities later in the season. Typical examples: carrot, beet, sweet potato.
 water storage roots - found in arid regions, these are roots that collect large amounts of water during rainy season for the plant to use during dry season. These are most
often found in xeriphytes (sometimes spelled xerophyte). Local examples include the East Indian Rosewood and the Starburst.
 propagative roots - have meristematic regions from where new, genetically identical plantlets can grow. These regions are not the same as nodes: they do not contain a true
apical meristem.
Local examples include the East Indian Rosewood and the Starburst.
 pneumatophores - gas exchange surfaces on root tips protruding from water-logged soil. Certain species of mangrove have these. But, contrary to popular myth, cypress
"knees" apparently have no gas exchange function. (Cypress trees with knees removed do not suffer from any apparent lack of oxygen.
 prop roots - These grow from the lower part of a stem or trunk down to the ground, and providing extra support for the plant. These tend to be more common in plants with
a tall, soft stem structure, as well as in plants that live in softer soils.
Common examples include corn (Zea mays), Screw "Pine" (Pandanus tectorius), various species of palms, and red mangroves (Rhizophorus mangle.
 aerial roots - typical of epiphytes such as orchids (in which these roots are called velamen, with a spongy outer surface very good at absorbing and holding water)
and bromeliads.
 buttress roots - wall-like extensions off the base of the trunk which provide support against physical assault from high winds.
Our local Ficus spp. and the Royal Poinciana (Delonix regia tend to develop these in certain environments.
 contractile roots - these specialized roots, usually found at the base of an underground organ (e.g., a bulb) actually contract to perform such functions as getting a bulb to its
proper soil dept for growth
 haustoria - parasitic plant roots that invade the tissues of a host plant and transfer nutrients from host to parasite.
Examples of plants that have haustoria are dodder and mistletoe
 adventitious roots - are roots that grow anywhere they are not "expected." Examples are the adventitious roots that grow so prodigiously from some of our native and
introduced species of Ficus trees. Several of the root types listed above (e.g., prop roots, aerial roots) can also be considered adventitious.

Life-sustaining Root Symbiosis: Nitrogen Fixation Nitrogen is one of the four main elements most common in biological macromolecules, and yet no eukaryotes are
capable of fixing atmospheric nitrogen , N2, into its usable forms, such as ammonium (NH4+) with other species changing it into nitrite (NO2-) and nitrate (NO3-).

Certain nitrogen-fixing bacteria, however, are capable of converting gaseous nitrogen into its biologically useful forms, and some of these have formed symbiotic
relationships with plants, notably in the Fabaceae (Pea Family), commonly called legumes.
The roots of legumes are covered with swellings called nodules within which reside symbiotic bacteria that fix nitrogen. Various strains of a bacterial species
named Rhizobium form this association.

Nitrogen fixation into ammonium requires an anaerobic environment such as that found in the root nodules. The root nodule surfaces are highly lignified, helping to prevent
gas exchange. Also, root nodules often contain leghemoglobin, a hemoglobin-like molecule with high affinity for free oxygen. This protein provides a sort of "buffer" for
oxygen, allowing the bacteria enough oxygen to produce ATP for the very energy-expensive reactions of nitrogen fixation without allowing too much oxygen to build up in
the nodule tissues and interfere with nitrogen fixation itself.

The figure below shows the sequence of events leading to nodule formation.
How does this symbiosis develop? It's amazing...

o The plant root emits flavonoids into the soil.

o Certain species of Rhizobium take up these flavonoids (the strain of Rhizobium colonizing each plant species is different, and determined by the exact structure of
the flavonoid messenger.)
 o The flavonoid activates a transcription factor protein, the activity of which results in the activation of a bacterial operon known as nod (for "nodule").
o The genes in the nod group produce enzymes that catalyze Nod proteins, specific to the bacterial strain.
o The Rhizobium secrete the Nod molecules into the soil, and these signal to the plant root to elongate root hairs and form the infection thread that the bacteria will
use to enter the root.

There is some evidence to suggest that early mycorrhizal fungus/plant communication pathways (which also employ flavonoids) led to the evolution of the bacteria/plant
communications resulting in nitrogen fixation symbiosis. Crop Rotation Most agricultural crops severely deplete soil nitrogen. Hence, good farming technique usually
includes crop rotation, in which the farmer will grow a non-legume crop in a field for one or more years, and then plants a legume crop for a year to help restore soil fixed
nitrogen.

Water Movement

First, a bit of review, and a few definitions:

 bulk flow: overall movement of water in response to differences in the potential energy of water.
 water potential: difference in water energy between two regions containing water.

Think of the control of

 water behind a dam

 water in your bladder

These require the constant input of energy.

As you should already know, water (like any other substance) always moves from an area of relatively high water potential to an area of relatively low water
potential.

Water potential is usually measured in units of the pressure needed to stop water movement, or hydrostatic pressure. Common units include
the bar or megaPascal

By convention, 100% H2O is said to have a potential of zero.

 This is the maximum possible water potential, since 100% water contains the maximum possible density of water molecules per unit volume.
 If you were to dissolve any substance into the pure water, the water potential of that solution decreases, as it now contains fewer water molecules per
unit volume than 100% water does. This new solution has relatively lower water potential than 100% water.
  HENCE, any aqueous solution has negative (less than zero) water potential.

Recall:

 Any liquid dissolving a substance is known as a solvent

 Any substance dissolved in a solvent is known as a solute.

Water, being a polar substance, is an excellent solvent for polar (hydrophilic) solids. In solution, water molecules cluster around a polar solute molecule,
creating a hydration shell:

A few more definitions to recall:

 A hypotonic (= hypoosmotic) solution is one which has relatively more water molecules (and fewer solutes) than a solution to which it is being
compared.
 A hypertonic (= hyperosmotic) solution is one which has relatively fewer water molecules (and more solutes) than a solution to which it is being
compared.
 Two or more isotonic (=isoosmotic) solutions have equal concentrations of solutes.
 diffusion: the movement of water from a hypotonic area to a hypertonic area, following the potential gradient
 osmosis: Diffusion of water across a selectively permeable membrane.
 dialysis: movement of solute molecules from an area of relatively high concentration to an area of relatively low concentration across a selectively permeable membrane.

Water molecules are highly cohesive (they stick together) and adhesive (they stick to other polar substances).

Osmotic pressure is a measure of the tendency of a solution to take up water molecules when separated from pure water by a selectively permeable membrane.

In living cells, the plasma membrane serves as the selectively permeable membrane.

A plant cell in a very hypertonic solution, left long enough, may lose so much internal water (via osmosis) that it becomes plasmolyzed (i.e., torn away from the cell wall) beyond
repair.

In an isoosmotic solution, a plant cell is somewhat flaccid (i.e., it's walls have a bit of "give" and "bounce").

In a hypoosmotic solution, a plant cell will take up water and become turgid. (If the solution is too hypoosmotic, the cell may rupture).

As long as the plasma membrane is intact, the turgor pressure of a cell is equal and opposite to the wall pressure. This is the main source of structural support in herbaceous plants)

Water Movement Through Xylem

 Plants imbibe (take up) and transpire (release via the stomates) more water than animals do, as they have no re-circulation system. About 99% of all water entering the roots
leaves the leaves via the stomates without ever taking part in metabolism.
 Water movement is due to differences in potential between soil, root, stem, leaf and atmosphere.
 Under normal circumstances, the water potential in soil is higher than that in root cell cytosol.
 For example, here's a hypothetical array of water potentials in a soil and plant system:
Water follows the potential gradient from soil to atmosphere, and is pulled together by the cohesiveness and adhesiveness of the molecules themselves. The pressure in the xylem
tubes so generated is known as shoot tension.
As water enters the root from the soil, it may travel via the

 apoplastic route - soil solution is taken up by the hydrophilic walls of the root hairs, which provide access to the apoplast (continuum formed by the cell walls). Water and
minerls diffuse intot he cortex along the matrix of cell walls.
 symplastic route - minerals and water cross the plasma membranes of root hair cells and enter the symplast (continuum of cytoplasm formed via plasmodesmata)
 transmembrane (tonoplast) route - some water and minerals traveling along the apoplast are actively transported into the protoplasts of epidermal and cortical cells, and
then move inward via the symplast.
 endodermis - Casparian strips block interstitial entry of water and minerals into the stele. Only solutions already in the symplast or entering it via the plasma membrane of
the endodermal cells can get into the xylem.
  Endodermal and living cells in the stele discharge water and minerals into their apoplast. The xylem vessels then transport the apoplastic water and minerals upward into
the shoot system.

Generation of transpirational pull

 Water diffuses from the xylem into the spaces inside the spongy mesophyll--> stomates-->atmosphere.
 Water coating the surface of the mesophyll spaces forms crescent-shaped menisci as it enters the air spaces.
 As water molecules are pulled from between the cells, the menisci become more curved, and water tension increases (due to the cohesiveness of the water molecules).
 Meniscus tension is inversely proportional to the radius of its curved surface: as the meniscus becomes more concave, its radius decreases and the tension increases.
 Tension thus generated is a negative pressure: it essentially "pulls" water from areas of greater hydrostatic pressure (i.e., fluid-filled areas such as xylem vessels and interstitial
areas filled with water) into the areas of lower hydrostatic pressure (stomates).

This is the basis of "transpirational pull".

Bubbles sometimes can form in the water column in the xylem (this is more common in vessel elements than in tracheids--why?).

cavitation: rupture of the water column embolism: filling of a vessel or tracheid with air.
The shoot tension generated by transpirational pull is capable of lifting water up to 500 feet from the ground, which is more than enough to account for the tallest land trees'
(redwoods) ability to lift water all the way to their tips (about 350 feet).

Root Pressure Of lesser importance in moving water through xylem is root pressure.

 at night, stomates are usually closed and transpiration stops.

 endodermis-ringed root stele cannot "leak" ions, so water potential decreases as water from the soil osmoses into the stele.
 this root pressure effectively "pushes" water up the stem and into the leaves.
 Some herbaceous plants have special openings on the leaf margins called hydathodes. These allow root pressure water to escape, forming lovely little "beads" of "dew"
overnight, and preventing cell rupture due to too much water pressure. This process is known as guttation, and its results are generally observable only in the early morning, when
humidity is relatively high.

Water and Nutrient Movement Through Phloem

Unlike movement of xylem sap, movement of phloem sap requires energy expenditure on the part of the plant.

Recall that substances have three different pathways by which they can cross a plasma membrane:

 diffusion - passive transport; molecules simply move across the membrane following the potential gradient.
 facilitated diffusion - also passive; substances must pass through a protein "filter" in the membrane, though they are still following the potential gradient.
 active transport - the cell uses energy (stored and "delivered" by ATP, adenosine triphosphate) to pump cells into or out of the cell against a gradient.
Recall the proton pump:

 Left to their own devices, protons will travel from areas of high to low potential until they reach equilibrium, with equal concentration of protons on either side of a membrane.
 Living cells can hydrolyze ATP and use the energy thus released to transport portons out of the cytoplasm, through the plasma membrane and into the extracellular
spaces against the proton potential gradient.
 The enzymatic machinery and the process itself are known as the proton pump.
 The action of the proton pump causes the interstitial spaces to become crowded with protons (relative to the cytoplasm), and also to be relatively more positively charged than
the cytoplasm.
 The difference in potential energy of the protons inside and outside the cell comprise the membrane potential.

 The effect is like pushing more and more water behind a dam. The water "wants" to push past the dam, but if the dam is strong enough, it can hold the water back. MOST
dams, however, have gates that can be opened to varying degrees, allowing some water through.
 A hydroelectric plant at a waterfall captures the energy of falling water (as it changes from potential on the upper side of the waterfall to kinetic, as falling water). That
energy turns turbines which convert the water's kinetic energy into electrical energy.

 Pretty much the same thing is happening at the proton pump. The crowded protons (like the water behind the dam) "want" to pour back into the cell against the plasma
membrane (the dam). But they can pass through the membrane only through the selectively permeable protein channel "gates".
 Many protein channels use the energy of the protons bumping around at the gates to carry various of substances into the cell.
 As a proton zips through an open gate back into the cell from the outside, its potential energy changes to kinetic energy (like the water coming through the dam), and that energy
can be packaged by the cell, not as electricity, but as chemical energy in the bonds of ATP.
 The membrane potential also can be used to do work such as bringing positively charged ions into the cell following the gradient.

Negatively charged ions can be brought into the cell via cotransport:

 Some protein channels transport not only protons, but also can carry a particular negative ion (e.g., nitrite or nitrate) into the cell, using the membrane potential energy (the
inrushing protons) to do the work.
 This is how sugars are loaded into plant cells.
 Phloem sap is a thick, aqueous solution containing up to 30% sugars (sucrose), amino acids, hormones etc. (In contrast, xylem sap is relatively thin and watery, containing
mostly dissolved inorganics)
 Plants need to mobilize stored carbohydrates in order to perform cellular work via cellular respiration:
  convert starches/stored carbs into simple sugars
 load simple sugar (usually sucrose) into phloem
 transport sugar to wherever it needs to go

Definitions:

 source: any location in a plant where sugar is either produced or stored

 sink: location in a plant where sugar is used

How does a plant get sugars from the source to the sink? 1. load sugar into sieve elements at the source and into the phloem via:

 apoplast (along the outside of the cell walls)

 symplast (between protoplasts via plasmodesmata)
 tonoplast: (along the vacuole membranes)

The driving force causing this water movement is water potential.

2. Transfer cells (recall these specialized, high surface area parenchyma cells) facilitate the movement of water/solutes from apoplast to symplast and vice versa and into the
phloem conducting cells (sieve cells and sieve tube elements).

3. Sugar accumulating in phloem transport cells may concentrate up to 2-3 times its concentration in regular mesophyll. Hence, ATP is needed to load the sugar. Transfer cells are
very metabolically active.

4. Sucrose is cotransported into sieve tubes by proton pumps.

5. Phloem sap can move at a rate of about 1m/hour, which is too fast for simple diffusion. It's moved via bulk flow: differences in pressure at opposite ends of a conduit cause
movement with the potential gradient.

6. As sugar concentration increases in certain areas of the phloem (sink), water potential drops. This causes water from areas of higher water potential to flow towards those areas
of lower potential.

7. Result: water flows under pressure, somewhat like water through a hose.

8. Potential gradient goes from source to sink.

9. Once the sugars are unloaded at the source, the water will diffuse into the xylem and be carried up to the stomates the plant in xylem sap.
Photosynthesis: The Breath of Life Recall...

 First Law of Thermodynamics: Energy cannot be created or destroyed, but it can be changed in form.
 Second Law of Thermodynamics: All systems tend to go from a state of greater organization to a state of lesser organization with a concommitant loss
of usable energy.

Photosynthesis, the conversion of inorganic water (H2O) and carbon dioxide (CO2) into organic sugar is the plant personification of these two Laws. During the
process of photosynthesis...
 randomizing solar energy intercepted by plants, and instantaneously changed (transduced) into electrical energy (the kinetic energy of electron flow). It is then "packaged"
as chemical energy (the potential energy stored in the covalent bonds of sugar molecules). (First Law)
 No energy transformation is 100% efficient. Not all solar energy captured by a plant cell is converted to electrical and then chemical energy. Some of it is lost as heat or other
randomizing energy that cannot be used to do work (entropy). (Second Law)

Like cellular respiration, photosynthesis proceeds via a series of orderly enzymatic reactions.

Recall Baby Chemistry:

 An enzyme is a proteinaceous biological catalyst.

 A catalyst is a molecule that increases the rate of a reaction without being consumed or permanently changed by that reaction.
 A substrate is a molecule upon which the catalyst acts.
 The active site of an enzyme is a (usually) three-dimensional "pocket" into which a substrate is chemically bonded for catalysis of its particular reaction.
 An endergonic reaction absorbs energy as it proceeds.
 An exergonic reaction releases energy as it proceeds.
 In a catabolic reaction, a substrate is broken down.
 In an anabolic reaction, a substance is constructed from one or more substrates.
 In an oxidation reaction, a molecule loses one or more electrons, and becomes more positively charged. (A positively charged ion is a cation.)
 In a reduction reaction, a molecule gains one or more electrons, and becomes more negatively charged. (A negatively charged ion is an anion.)
 In biological systems, oxidation and reduction reactions are most often paired, resulting in a redox reaction: as one molecule is oxidized, the molecule that accepts its
electrons is reduced.

Keep these familiar terms in mind as we follow the course of photosynthesis in overview.

The Nature of Light Energy: Physics 101 By now we should all know that the sun provides most of the earth's energy in the form of electromagnetic radiation.
(Can you think of any energy on earth that's not solar in origin?)

The smallest unit of light energy is known as a quantum, which has properties of both a particle (it can be deflected by solid matter) and a wave (it travels through space in an up
and down pattern at a specific wavelength).

Not all quanta are the same. Although they all travel through space at the speed of light (299,792,458 m/sec), they may do so at different wavelengths...
...and different frequencies.
Different wavelengths of electromagnetic energy correspond to different physical entitles which react with matter in different ways.

Visible Light: Quanta that Stimulate your Central Nervous System

 The quanta that we can perceive as light are called photons, and photons of different wavelengths comprise the visible spectrum.
Humans can see photons ranging in wavelength from about 380 nm (violet) to about 700 nm (red), and a photon will be perceived by your brain as a certain color depending on its
wavelength when it hits the color-sensing photoreceptors of your retina.
(Note: A nanometer = 10-9 meters, or 0.000000001 meters.)

 The shorter the wavelength, the higher the frequency, and the higher the energy.
 The highest energy photons are in the violet region; the lowest energy ones are in the red region

The Wonder of Photosynthesis Recall that an autotroph (auto = "self" and troph = "feeding") is an organism that captures energy and stores it in the chemical bonds of organic
molecules that it manufactures from inorganic molecules. They are also known as producers or primary producers. The greatest autotroph biomass on earth is comprised of
plants.
(A heterotroph (hetero = "other" and troph = "feeding") is an organism that eats other organisms to obtain energy. They are also known as consumers.)
The most common means by which autotrophs make organic molecules (sugar) is via photosynthesis.
(Autotrophs that capture light energy are called photoautotrophs, though there are other kinds of autotrophs.)

Plants are photoautotrophs that absorb photons only in a specific region of the spectrum.
A pigment is any substance that absorbs light. The main pigments responsible for the initiation of photosynthesis are chlorophylls and carotenoids which absorb light in different
regions of the visible spectrum. And these pigments, as you already know are embedded in the thylakoid membranes of the chloroplasts.
Photons interact with matter--including plant pigments--in one of three ways. A photon striking matter (liquid, gas or solid) can be

 transmitted (it passes through the matter)

 reflected (it bounces off the matter and changes direction)
 absorbed (its energy is converted into the energy of the molecule it hits)

Only when absorbed can photons initiate biological activity.

 Plant pigments absorb photons in the violet/blue region and in the red region.
 Thus, only violet, blue and red light will drive photosynthesis.
 All other wavelengths are reflected, which is why plants look green. They are reflecting or transmitting the green light, not using it to make sugar.

You should already know the overall chemical reaction of photosynthesis:

It takes...

 six molecules/mole of carbon dioxide (0.037% of the atmosphere) plus

 12 molecules/mole of water

in the presence of light and the proper enzymes in the cell, to make

 one molecule/mole of glucose

 6 molecules/moles of oxygen
 6 molecules/moles of water

The sugar (glucose) is the storage form for energy in plants, and it's often converted into long chains for long-term storage as carbohydrate, which forms the body of the plant.
The oxygen and water are side products that are not used by the plant in this reaction.

Why Photosynthesis? What does the plant do with the sugar molecules, once it has them?
  body structure (cellulose and other macromolecules)
 energy storage (for cellular work)

The latter, of course, is done via cellular respiration, the overall chemical equation for which is exactly the opposite of photosynthesis:

It takes...

 one molecule/mole of glucose in the presence of

 six molecules/moles of oxygen and
 six molecules/moles of water

can be "burned" to release stored energy as well as the "waste" products of

 6 molecules/moles of carbon dioxide and

 12 molecules/moles of water

Chlorophyll All photoautotrophs use an isomer of chlorophyll known as chlorophyll a as the primary photosynthetic pigment. This is the only type of chlorophyll that can pass
excited electrons to the primary electron acceptor protein in the thylakoid membrane. But there are other isomers of chlorophyll. The one present in all members of the
monophyletic taxon known as Viridaeplantae also contain chlorophyll b and carotenoids as accessory pigments.
The accessory pigments cannot pass excited electrons to the PEA protein, but they can pass them to the "team captain," chlorophyll a. What do you suppose might be the
advantage of accessory pigments? Consider...

 absorption spectrum - range of wavelengths absorbed by a particular pigment

 action spectrum - range of wavelengths capable of driving a particular biological process

Isolated chlorophyll molecules in solution and exposed to light will absorb light, resulting in an excitation of the chlorophyll's electrons. In a live cell, the excited electron would be
sent along a transport chain, and its energy harvested in a stepwise fashion.

The isolated chlorophylls, with no place to send their electrons, exhibit a phenomenon known as fluorescence. (And if you didn't come to class for the explanation, you're just
going to have to read and figure this out on your own. Hint: Check out your old BIL 151 lab on Photosynthesis pigments!)
 absorption spectrum - range of wavelengths absorbed by a particular pigment
 action spectrum - range of wavelengths capable of driving a particular biological process

The action spectrum of photosynthesis was first reported in 1883 by T. W. Engleman, who did an experiment now considered classic.

Absorption of photons is the first step in the... Light-dependent Reactions of Photosynthesis Before we go any further, let's watch a short movie, which we'll see again at the end.
 Overview of Photosynthesis

The essential steps in the light reactions are...

 water molecules are split, producing electrons, protons, and oxygen gas (O2).
 electrons from the water molecules are passed along the electron transport system on the thylakoid membranes
 as electrons are passed along the chain of proteins, energy is lost at each transfer, and this is packaged in the high-energy phosphate bonds of ATP.
 some of the protons from the split water molecules reacts with another energy courier molecule, NADP (nicotinamide adenine dinucleotide phosphate) to form NADP-H,
which stores the energy of the proton.
 both ATP and NADP-H shuttle the energy of captured photons, now stored as chemical energy, to the stroma (the thick gel matrix of the chloroplasts) where it will be
transduced yet again and stored in the covalent bonds of sugars.

Heart of the Light Reactions: The Photosystems A photosystem is a light-gathering complex composed of a proteinaceous reaction center complex surrounded by several light-
harvesting complexes. These are embedded in the thylakoid membranes.

 Each light-harvesting complex consists of various pigment molecules (chlorophyll a, chlorophyll b, carotenoids) bound to proteins in the thylakoid membrane.
 The systems are spread out over the surface of the thylakoid, providing a large surface area for light harvesting as well as a variety of pigments with different absorbance
spectra.
 Antenna pigments, such as carotenoids and chlorophyll b, pass their excited electrons to one another until the e- reaches the reaction center complex.
 The reaction center complex contains a pair of chlorophyll a molecules associated with a large protein, the primary electron acceptor.
 As the chlorophyll a molecules accept excited electrons from other pigments in the photosystem, they pass them along to the primary electron acceptor (a redox reaction).
 The primary electron acceptor passes the excited electron to a small "shuttle" protein that carries it to a cytochrome complex of proteins that form an <.b>electron
transport chain.
 And you know what happens when an excited electron passes along such a chain: at each transfer, energy is lost. But in a live photosystem, it isn't puffed off into space.
There are small, energy-courier molecules just waiting to package that energy: ADP and NADP. These are converted to energy-storing ATP and NADP-H, respectively.
 The ATP and NADP-H travel to the stroma, where their energy will be packaged in the covalent bonds of sugar.

Photosystems I and II There are two types of photosystems (named in order of their discovery, not in order of their function) in the thylakoid membranes:

 Photosystem II (PS II) -

o reaction center contains chlorophyll a molecules (P680) that have peak absorbance (λmax) of 680nm.
 Photosystem I (PS I) -
o reaction center contains chlorophyll a molecules (P700) that have λmax of 700nm.

The chlorophyll a molecules of the two photosystems are nearly identical, but each is associated with different proteins in their respective reaction centers.
Here's how it works...
 A photon is absorbed by a chlorophyll or carotenoid molecule in the thylakoid membrane. As it falls back to its ground state, its energy is transferred to the electron of an
adjacent pigment, raising it to an excited state. This continues until the excited electron belongs to the famous P680 chlorophyll of PS II.
 The excited P680 electron is transferred to a primary electron acceptor protein. The oxidized P680 is now P680<sup+< sup="">.</sup+<>
 Nearby, an enzyme splits water to yield

 two electrons - these replace those lost by the two P680<sup+< sup=""> molecules in the reaction center</sup+<>
 one oxygen atom - this combines with another oxygen atom from a different split water molecule to form oxygen gas (O2)
 two protons (hydrogen ions) - some will combine with NADP (to form NADP-H) to store energy to be shuttled to the stroma for the light-independent reactions.

 The excited electrons from PS II travel to PS I via an electron transport chain (similar components as those found in the mitochondrial electron transport chain) consisting of a
cytochrome complex known as plastoqinone (Pq) and another protein, plastocyanin (Pc).
 As electrons "fall" exergonically from one component of the electron-transport chain to the next, our old pal the Second Law of Thermodynamics rears its head: energy is
released at each transfer, but quickly captured and packaged in the high-energy phosphate bonds of ATP. (Electrons passign through teh cyctochrome comlex results in the
pumping of protons out of the membrane, and the resulting potential difference is used in chemiosmosis.
 Meanwhile, back at PSI, chlorophylls and carotenoids are behaving in a similar manner, doing the wave, and transferring photon energy (not converted to electrical energy--the
flow of electrons) to the pair of P700 chlorophylls at the reaction center.
 P700 transfers its excited electron to its own primary electron acceptor, and becomes P700+ (redox again!).
 The electron reaching the "bottom" of the electron transport chain in PSII is shuttled to PSI, where it replaces the lost electron of P700+, restoring it to its original
P700 configuration.
 PSI excited electrons travel along a different electron transport chain via the protein ferredoxin ((Fd). There is no proton pump at the PSI electron transport chain, so no ATP is
produced there.
 A special enzyme, NADP+ reductase, catalyzes the transfer of two electrons from Fd to one NADP+, reducing it to energy-storing NADP-H.

One picture is worth a lot of words.

The flow of electrons from PSII to PSI has been called linear electron flow or non-cyclic electron flow to distinguish it from a less common phenomenon...

Cyclic electron flow Once in a while, an excited electron from PSI's primary electron acceptor will "short circuit" and pop over to Fd and back into the electron transport chain
between PSII and PSI, instead of to NADP+ reductase.

This will produce more ATP (and is a good supplement), but no NADP-H.
It's probably an accident of the proximity of the various molecules, but because it's not deleterious there has been no selection pressure against it. It just happens.

The Calvin Cycle: An Anabolic Cycle During the light-independent reactions of photosynthesis, a.k.a., The Calvin Cycle, the energy stored in ATP and NADP-H during the
light-dependent reactions is briefly released and then repackaged into the covalent bonds of sugar.

 The sugar first produced by the Calvin Cycle is not 6-carbon glucose (this is constructed later), but a 3-carbon sugar known as glyceraldehyde-3-phosphate or G3P.
 The Calvin Cycle "spins" three times to make this 3-carbon sugar from three molecules of CO2. The conversion of inorganic carbon from CO2 into the carbons of an organic
molecule, G3P, is known as carbon fixation.
 Remember that there are many Calvin Cycles going on in the stroma at any given time, so many atoms of carbon are constantly being fixed quickly into sugar.
 The Calvin Cycle can be reduce to three phases:
  I. Carbon Fixation

One CO2 molecule is attached to a 5-carbon sugar named ribulose biphosphate (RuBP) by an enzyme named rubisco. (Rubisco may be the most abundant protein
on earth! It is certainly the most abundant protein in the chloroplasts.)

The resulting 6-carbon sugar is extremely unstable, and it immediately splits in half, forming two molecules of 3-carbon 3-phospho glycerate.

 II. Reduction
o A phosphate group (from ATP) is attached to each 3-phospho glycerate, forming 1,3-phosphoglycerate (guess where the phosphates are attached!)
o NADP-H swoops in and reduces 1,3-phosphoglycerate, which loses its phosphate group (in addition to gaining electrons) to become our old pal, G3P.
o For every six G3Ps made by the Calvin Cycle, five are recycled back to regenerate new molecules of RuBp. Only ONE leaves the cycle to be packaged for use by
the plant.
o It takes two molecules of G3P (3 carbons) to make one molecule of glucose (6 carbons).
o ADP and NADP+ formed during the Calvin Cycle are shuttled back to the photosystems to be "recharged" with energy, and converted to ATP and NADP-H,
respectively.
 III. Regeneration of RuBP

Five molecules of G3P from the Calvin Cycle's Reduction phase pass through a complex series of enzymatic reactions to yield three molecules of RuBP. This costs
the cell 3 more molecules of ATP, but provides new "machinery" for the Calvin Cycle to continue spinning

What's the cost of making carbohydrate? To make one molecule (or mole) of G3P, the plant must expend the energy of nine ATP molecules (or moles) (at 7.3kcal/mole) and six
molecules of NADP-H. Some of this is packaged in the sugar, of course. But because of our old pal The Second Law of Thermodynamics, some is also lost as entropy.

(A good question might be...How many CO2 molecules, ATP molecules and NADP-H molecules are needed to make one molecule of glucose?)

And here again is our nice Overview of Photosynthesis that will tie all this together.

Plants that produce 3-carbon G3P via the Calvin Cycle are called C3 plants. But there are some plants that have an alternative mechanism for carbon fixation, and this is
particularly true in plants that evolved in hot, arid climates.

The Balancing Act: Water Loss vs. Photosynthesis Carbon dioxide for photosynthesis enters via the stomates. But during the hottest part of the day, stomates often close to prevent
water loss. Even with stomates partially open, CO2 levels drop rapidly, fostering photorespiration.
Photorespiration: a wasteful relic?

 As CO2 levels drop, the Calvin Cycle becomes "starved" for raw material.
 Rubisco has an affinity for O2 (albeit lower than for CO2).
 In a scarcity of CO2, rubisco binds to O2, and begins to feed oxygen into the Calvin Cycle instead of CO2.
 The "deformed" product of this metabolic cycle is unstable, and "splits" to form a 2-carbon compound that diffuses out of the chloroplast.
 When this product enters the peroxisomes or mitochondria, it is further split to release CO2.
 This process is called photorespiration because it occurs in the light and generates CO2. But unlike cellular respiration, it generates no ATP. (In fact, it consumes ATP!)

Why does photorespiration persist? Some suggest it's evolutionary baggage left over from an era when there was far more CO2 in the atmosphere than oxygen.

However, mutant plants that cannot perform photorespiration (mutant rubisco) often suffer more damage from intense light than non-mutant plants. Though it's not well
understood, it may be that photorespiration may neutralize potentially damaging products of the light reactions.

Still, in some plants (and notably in many agricultural crops), photorespiration steals away up to 50% of the carbon fixed by the light reactions! Not a big deal for the plants, but
potentially a big deal for heterotrophs (us!) using those plants for their own energy.

C4 Plants Some plants, across about 19 different families, have a clever trick that allows photosynthesis while stomates are closed while minimizing photorespiration. These plants,
known as C4 plantsmanufacture a 4-carbon compound that serves as a "shuttle" for CO2 to the Calvin Cycle's initial carbon fixation phase when plants can't access atmospheric
carbon dioxide.

A unique leaf anatomy is associated with the C4 pathway: C4 plants have two types of photosynthetic cells, bundle-sheath cells and mesophyll cells, arranged in the leaf as shown
here:
  The Calvin Cycle occurs only in the bundle-sheath cells.
 The mesophyll cells act as a "carbon dioxide pump," concentrating carbon dioxide by transporting CO2 cleverly bound to other compounds.

But how?
 In the mesophyll cells, an enzyme known as PEP carboxylase binds free CO2 to phosphoenolpyruvate (PEP) to form 4-carbon oxaloacetate and other 4-carbon compounds
(e.g., malate).
 PEP carboxylase has a very high affinity for CO2, but NONE for oxygen gas. So when rubisco is bamboozled by stomatal closure and oxygen, PEP carboxylase can still
sequester carbon dioxide.
 Via plasmodesmata, mesophyll cells transport their 4-carbon, CO2-carrying products to the bundle-sheath cells.
 The 4-carbon compounds release their precious CO2 passengers, which then enter the Calvin Cycle and can be incorporated into G3P and other products in a normal fashion.
 This CO2 release generates pyruvate, which travels back to the mesophyll cells and is converted to PEP (with energy expended).
 So this process is not without cost, but it keeps the Calvin Cycle going even when CO2 concentration in the cell is low, while minimizing photorespiration.

But where do we get that extra ATP?

 Bundle sheath cells have only Photosystem I, which generates ATP, but no NADP-H. Only cyclic electron flow is used to generate ATP in these cells.
In essence, C4 plants pump enough extra CO2 into the bundle sheath cells to keep rubico loaded with CO2, at a cost of ATP.

This mechanism would be particularly advantageous in a hot, arid climate, where stomates must close during the day to prevent desiccation, and it is in these areas that C4 plants
first evolved and still thrive.
CAM Plants Many succulent plants have evolved a different way to allow normal photosynthesis even when stomates are closed. The plants in which this pathway was first
discovered are members of Family Crassulaceae, and the pathway, named for them is known as crassulacean acid metabolism, or CAM.

During the day, CAM plants' stomates are closed. But at night they open, taking up CO2 and incorporating it into a variety of organic acids for storage. These acids are stored in the
vacuoles of leaf mesophyll cells until daybreak.

As the light reactions start up in response to light, CO2 is released from the organic acids. The energy from ATP and NADP-H from the light reactions can now be used to fix that
carbon, even though the stomates are closed.

 C4 and CAM are similar in that they use organic intermediates to store CO2 for later release, concentrating it when the plant isn't open to the atmosphere.
 C4 and CAM are different in that C4 plants have two types of cells, and they separate carbon dioxide storage cells (mesophyll) from Calvin Cycle-performing cells (bundle-
sheath). CAM plants perform both functions in the same (mesophyll) cells).
PLANT NUTRITION An essential nutrient is one required by an organism for normal growth and development, but which it cannot manufacture on its own.
These vary widely across species.
Animals, for example, have many essential organic nutrients (fatty acids, amino acids, vitamins, etc.) that they cannot manufacture themselves, and so must
ingest them as other organisms containing those finished products.

Because PLANTS manufacture all the organic nutrients they need, they have no essential organic nutrients. However, plants do require very specific
INORGANIC nutrients in order to grow, develop and thrive.

Macronutrients
These are elements (usually taken up in the form of compounds) required by plants in relatively large quantities. They are often major components of the
plant's body. In plants, six of the main inorganic nutrients required are the six main components of organic molecules:

 carbon
 hydrogen
 oxygen
 nitrogen
 sulfur
 phosphorus

Three additional macronutrients needed by plants are:

 potassium
 calcium
 magnesium

Micronutrients
These are the elements (often taken up as compounds) needed in relatively small quantities.

 chlorine
 iron
 boron>
 manganese
 zinc
 copper
 molybdenum
 nickel
The main function of these micronutrients is to serve as coenzymes in various enzymatic pathways.

Some of the functions of the various macro- and micronutrients, as well as physical symptoms of their deficiencies are listed in your text, in Table 29-2. Be
sure to review it!

A shortage of any of these nutrients will often have characteristic symptoms in the plant, with older plant parts showing the effects sooner than younger parts.
(Younger organs act as nutrient sinks, drawing more incoming material to themselves than the older parts do; they are the last to suffer from nutrient
deficiencies.)

WHERE DOES THE PLANT GET ITS NUTRIENTS? One of the major sources, of course, is SOIL.
Organic versus Inorganic Farming Techniques

 What is the difference between ORGANIC and INORGANIC farming?

  inorganic fertilizer is applied as the name implies: in the form of inorganic compounds of nitrogen, phosphorus
and potassium (N-P-K) as well as trace elements, in lower quantities.
 These may leach out of soil rather quickly, though they are instantly available to plants.
 organic fertilizer, as its name implies, consists of complex organic material that's in the process of decomposing.
 Although it takes longer to become available to plants (depending on the speed with which decomposers release
inorganic forms to the plants), it will stay in the soil much longer.

 Decaying organic matter within soil is often called humus. The more humus there is in the soil, the less likely it is to
be compacted, the more likely it is to retain water (humus has a spongelike capacity to hold water), and the more
gradual (and permanent) the release of nutrients.
 Read the special "box" in your text on Composting (page 664). Very important!
 Soil is also composed of inorganic components named by their particle size. From largest to smallest granule, these
are
sand --> clay --> silt
 Because sand, clay, and silt are slightly negatively charged, they help to retain postively charged nutrient ions such
as potassium, calcium, and magnesium.
 In very acid soils, negatively charged ions become bound to the soil particles, and are difficult for plants to take up.
Example: very marshy areas where the organic component of the soil is extremely high, making the soil very acid.
(Some plants growing here have special adaptations for obtaining nitrogen. What are they?)

 What role do you suppose water/precipitation plays in affecting nutrient content of soil? (Think: Rainforest)
 Soils tend to leach anions, but retain cations, as the colloidal surface of clay and humus tend to have an excess of
negative charges that hang onto the cations in interstitial water.
The Importance of Nitrogen
As we have already mentioned, nitrogen fixation by bacteria is vital to the survival of all life on earth.

Recall that some plants (notably those in the Family Fabaceaea, the Pea Family) have specialized root nodules that
house symbiotic nitrogen-fixing bacteria. This is one reason that legumes are so high in protein: no shortage of nitrogen
for building it!
Rhizobium and other nitrogen-fixing prokaryotes are able to reduce elemental nitrogen to ammonium via the activity of
an enzyme known as NITROGENASE. The fixation of a single N2 molecule into two molecules of ammonia requires
16 ATPs. This is an expensive process!
Let's follow the Amazing and Wonderful communication cycle between the symbiotic nitrogen-fixing bacterial
genus Rhizobium (each legume species has its own specific symbiotic species of Rhizobium) and the leguminous plant
they call home...
This results in growth of root nodules like so:
 The mechanism by which bacteria initially attach to the root hairs is not yet well understood, but may involve the
activity of sugar-binding proteins known as lectins.
 Root nodules are perfectly evolved to be hospitable to prokaryotic symbionts. Legumes even produce a form of
hemoglobin (leghemoglobin) that retains oxygen and acts as a slow-release "buffer" source of O2 for the metabolically
very active nitrogen fixers as they make and use all that ATP to fix nitrogen.
 The host/symbiont relationship is highly species specific; each legume has its own species of Rhizobium that will
generally not colonize other species of plants.

A Link to the Evolution of Mycorrhizal Associations Recall:

 Ectomycorrhizae - usually found in large trees, and is often an association with a basidiomycete (or sometimes an
ascomycete) fungus.
 Endomycorrhizae - common in many plants, this is an association between the plant's roots and a zygomycete
fungus.
What does each partner get out of this mutually beneficial symbiotic relationship? Let's figure it out.

 Mycorrhizal plants deprived of their fungal symbionts do not thrive, and grow far more slowly than their mycorrhizal
conspecifics.
 Cytokinin (a hormone we'll discuss shortly) appears to activate the nod genes.
 Both symbiotic bacteria and mycorrhizal fungi cause an increase in cytokinin production in roots.
 Cytokinins are evidently part of this complex signalling process, though the exact mechanism is not yet known.
 The Nod proteins secreted by Rhizobium are chemically similar to chitin. What other Famous Microorganism also
contains chitin? And how might this be related to the evolution of root nodule formation?
Amazing sidelight: The nodulin (nod) genes involved in the formation of root nodules are the same ones activated in
mycorrhizal associations, to form the fungus/plant connections.
 Mycorrhizae appear to date back at least 400 million years
 Root nodules are probably no older than 160 million years
It's probable that the nod gene function was an exaptation just "waiting" for the nitrogen fixation symbiosis to develop.

Review the Nitrogen Cycle...

as well as the pathway of all other elemental nutrients, as exemplified by the Phosphorus Cycle...
...and treat your plants well.
Internal Control: Plant Hormones

Unlike animals, plants can manufacture all the chemical substances they need for survival, given only light, water, carbon dioxide and trace elements from the
soil. They manufacture all the amino acids, proteins, carbohydrates, nucleic acids and other compounds , and among these are hormones (from the
Greek horman, meaning "to stimulate").

By definition (originally from animals), a hormone

 is manufactured in a particular part of the body

 is transported to another part of the body
 induces a chemical responses that controls a specific physiological event

In plants, some hormones operate in the same tissues in which they are manufactured, and others are transported for use to different locations.

Plants don't have glands to produce hormones: various tissues throughout the plant body produce hormones.

Recall the generalized model for a hormone-triggered signal transduction pathway:

 a hormone binds to a specific protein receptor, either embedded in the plasma membrane or in the cytoplasm (depending on the receptor and the system).
 binding of the hormone to the receptor causes the protein's conformation to change
 this stimulates the production of "relay molecules" in the cytoplasm
 relay molecules trigger various responses to the original signal

A given plant hormone may:

 elicit different responses in different tissues

 elicit different responses at different times of development in the same tissue
 directly affect the activity or production of other hormones
 elicit different responses depending on concentration in a given tissue

The sensitivity of a plant tissue to a given hormone may be altered either by

 changing hormone concentration in the target tissue

 altering receptor sensitivity to that hormone in the target tissue
Meet the Hormones Mature and growing plants' growth and development is governed primarily by five major classes of HORMONES

 auxins - responsible for cell division and growth in cell size

 cytokinins - responsible for increase in cell division
 ethylene - responsible for senescence (aging) processes
 abscisic acid - responsible for dormancy of various types
 gibberellins - responsible for cell division and growth in cell size

Be sure to study Table 27-1 in your text: Major Plant Hormones, Their Nature, Occurrence and Effects for an overview.

In addition to the five classes above, other chemical substances exhibiting hormone-like activity have more recently been discovered.

 brassinosteroids
These are required for normal tissue growth. First reported in 1970 by Mitchell, et al., these steroids were first isolated from Brassica napus pollen. (B. napus, commonly
known as Rapeseed, a member of the Mustard Family (Brassicaceae), for which this class of chemicals is named.)
 salicylates and jasmonates
These are involved in a complex cascade of chemical events that, stimulated by herbivory, can help the plant mount a chemical defense against its predators. The two
chemicals operate by stimulating the production of allelochemicals that are toxic to herbivorous insects. Some herbivorous insect larvae have recently been shown to
activate a gene (P450) responsible for coding cytochrome enzymes that detoxify the allelochemicals. (The Cold War is Everywhere.)
 polyamines
These small, basic molecules are ubiquitous in living organisms, and are involved in mitosis and meiosis control via regulation of apoptosis (programmed cell death).
 systemin
A small polypeptide (18 amino acids long!) that acts as a transcription factor (an inducer) to stimulate production of at least 15 different genes that code for protective
chemical compunds. Systemin is transported from the site of herbivore damage to other tissues where it induces gene transcription of defense factors, including jasmonate.
 Nitric Oxide (NO)
As in animals, NO has recently been shown to be an important chemical signal in plant growth, development, and defense.

The Original Big Five As mentioned before, the original five classes of hormones (the only ones known for many decades) were...

 auxins
 cytokinins
 ethylene
 abscisic acid
 gibberellins
Let's meet them in more detail. Auxin Darwin & Darwin (1881) did the first experiments to study the effects of the mysterious growth factor.

Additional experiments by Frits Went (1926) demonstrated that the mystery factor was produced in shoot meristems. Went named the compound auxin (from the
Greek auxein meaning "to increase")
We now know that light causes transport of auxins away from an area exposed to light, and in that area, auxins cause cell elongation.
The most common naturally occurring auxin is Indole Acetic Acid (IAA), but other forms occur, and many IAA-like compounds are used commercially because they are more
stable than natural IAA, which is readily broken down by plant enzymes, fungi and bacteria.
The compound shown in the middle is the infamous Agent Orange, widely used as a defoliant during the Vietnam War (along with similar compounds "Agent Purple," "Agent
Green" and "Agent Pink", collectively known as the "Rainbow Herbicides" and so named for the identifying stripe of color painted on the barrels containing them), was
contaminated with and breaks down into highly toxic and carcinogenic dioxin.

The compound on the far right is the active ingredient in commercial preparations such as "RootTone." It is used to stimulate the growth of adventitious roots and to reduce fruit
drop in commercial crops. This synthetic auxin, too, can break down into toxic, carcinogenic compounds.

Site of Production - primarily leaf primordia, meristems, and maturing seeds, though all plant tissues can produce small amounts of this hormone.

Transport - IAA is the only plant hormone known to be transported in a polar (i.e., unidirectional) fashion. Transport takes place via the vascular parenchyma cells, and may be

 basipetal - moving towards the plant base from higher parts (shoots and stems)
 acropetal - moving towards upper parts of the plant from lower parts.

IAA also may be transported in a non-polar fashion via the phloem conducting cells.

Effects

 differentiation of meristem into vascular tissue

 promotes leaf formation and arrangement
 induces flowering
 inhibits leaf abscision
 inhibition of lateral bud growth via stimulation of a "nutrient sink" in the growing tip (this results in apical dominance).
 stimulation of pericycle to produce lateral roots (although a high concentration applied to already growing roots will inhibit their growth)
 fruit development and ripening (from auxins produced by maturing seeds). (Parthenocarpic (seedless) fruit can be induced to ripen with application of IAA, and some mutant
commercial forms produce IAA in their tissues, ripening without the aid of seeds.

A note on seedless fruit...

Ever wonder how your banana, pineapple, watermelons, oranges or grapes can develop without seeds? Wonder no more.
Parthenocarpy - in some species, fruits mature without ovule fertilization. In some species, pollination is required to stimulate fruit production, in others, pollination produces
larger, tastier parthenocarpic fruit, and in still others, pollination is not required. (Most seedless citrus must be pollinated; bananas and pineapples need not be.)

Parthenocarpic fruits do occur in nature, and some species produce both parthenocarpic and seeded fruit in the same crop. Why waste the energy? It could be an important defense
against fruigivorous insects.

Stenospermocarpy - This process requires both pollination and fertilization, because it results from the abortion of the developing embryo in the seed, at which point the seed
stops developing. Seedless grapes are a result of stenospermocarpy, and you can see teh remnant of the aborted seed in most seedless grapes.

Seedless grapes are usually smaller than seeded grapes because the developing seeds produce another hormone, gibberellin, that promotes the fruits increase in size and sugar
content. By spraying seedless grapes with gibberellins artificially, the farmer can produce large, marketable grapes.
Cytokinins The cytokinins were first discovered in the liquid endosperm of coconuts (coconut water, not coconut milk) by Johannes van Overbeck in 1941. Applied to growing
plant embryos, the mystery substances in the coconut endosperm stimulated growth of both tissues and cells.

After about another decade of fruitless (har!) research, Folke Skoog was able to purify, but not isolate the substance. Carlos Miller later analyzed a DNA breakdown product that
had similar activity to the mystery coconut substance, and this led to the discovery that the substance he found (kinetin) was related to the plant hormones (though probably not
found naturally in plants) that were later named cytokinins for their role in promoting cell division. Miller isolated a natural cytokinin from corn and named it zeatin, after the corn
genus. It is still the most active and powerful of the known plant cytokinins.
Where found? - Growing tissues and wounded areas.

Transport - Acropetal, from root to shoot, via the vascular tissues. Effects

 delays senescence (loss of chlorophyll) in leaf tissues

Check out the two tobacco plants. The one on the left was genetically engineered to contain a gene for biosynthesis of cytokinins, but the gene activates only in older
leaves. The plant on the right is the untreated control.

 Interacts with IAA to facilitate plant cell growth and differentiation.

A growing plant cell has two pathways
1. enlarge and divide repeatedly
2. elongate

In the former case, the cell tends to remain meristematic. In the latter, it begins the genetic cascade towards differentiation and maturation into a specific cell type.

In tissue culture, a plant cell given

 IAA only - enlarges without dividing

 kinetin only - no effect
 [IAA] = [kinetin] yields rapid cell division giving rise to small, undifferentiated cells (meristem!)
  [IAA] > [kinetin] callus (undifferentiated mass of plant cells) develops roots
 [IAA] < [kinetin] callus develops shoot buds

Ethylene The effects of ethylene on plants were known long before Darwin discovered auxin. In the late 1800s, when streets were lit at night with gas lights, it was noted that
leaves on trees growing near leaking gas mains lost their leaves. Dimitry Neljubov (1901) demonstrated that the causative agent was a simple hydrocarbon, ethylene:

Later experiments revealed that ethylene governs a number of plant functions, including

 growth of most tissues

 fruit maturation
 leaf and fruit abscission
 senescence

Source/Transport - Ethylene's natural precursor is the amino acid methionine, and the biosynthetic pathway is relatively simple:
Note the interesting things that will stimulate ACC to break down into the active form, ethylene.

Effects

 antagonist to IAA, it inhibits cell enlargement in most species

 triggers stem elongation in many aquatic species (keeps them from drowning!)
 triggers an increase in air space development in the submerged tissues of mesophytes caught in a flood! (a stop-gap emergency supply of oxygen!). The air spaces are generated
by the destruction of parenchyma tissues in the stem cortex.
 promotes leaf, flower, and fruit abscission by causing degeneration of cells in the abscission zone of these structures. (Auxin will reverse or inhibit this function.)

 promotes ripening of fruit

What is fruit ripening?

o removal/degredation of chlorophyll
o deposition of other pigments (e.g., xanthophylls, carotenoids)
o fleshy portions soften due to dissolution of pectin in middle lamellae
o starches, organic acids and oils are synthesized into sugars

Many ripening fleshy fruits will undergo a notable increase in the rate of cellular respiration, and are known as climateric fruits (e.g., Solanaceous fruit such as tomatoes,
pome fruits (apples; pears), avocados). Others undergo a gradual reduction in respiration as they ripen, and are known as non-climateric fruits (e.g., citrus, grapes,
strawberries).

In climateric fruits, ethylene synthesis increases as ripening commences, and ethylene promotes many of the ripening features.
 Commercially, fruits that are picked green (e.g., tomatoes, bananas, etc.) can be gassed with ethylene in transport so that they ripen as they travel, and are thus less easily
bruised during transport.

 Family Cucurbitaceae: ethylene is involved in the sex determination in monoecious members of the cucumber family. High [gibberellin] leads to maleness, and high [ethylene]
leads to femaleness.

Abscisic Acid (ABA) The "abscisic" part is a misnomer. This hormone is not responsible for leaf, flower or fruit abscission. ABA is, rather, the Hormone of Dormancy.

Transport - ABA is produced in leaves, root cap and stems. It is transported via xylem, phloem to the target tissues.

Effects

 inhibits plant growth: it is the opponent to cytokinin

 young, developing seeds contain high concentrations of ABA which

 promotes production of storage proteins

 inhibits germination

ABA is water soluble: a good rinse is sometimes all that's necessary to leach ABA from the seed coat tissues and allow germination.

 under water-stress conditions, ABA causes stomatal closure

The full membrane channel course of events can be found in your text (pages 619-620). In essence, ABA stimulates ion channels such that K+, Cl-, and malate are rapidly
pumped from the cytosol to the cell wall. The resulting change in potential causes water to leave the cytosol, as well. As the guard cells lose turgor, they shrink, closing the
stomatal opening.
 promotes bud scale formation in preparation for dormancy
 gibberellin reverses the effects of ABA.

Gibberellins In 1926, Japanese pathologist E. Kurosawa was studying a parasitic fungus (Gibberella fujikuroi) that caused "Foolish Seedling Disease." Affected plants would
"bolt"--grow pale, long, weak stems very quickly, then topple and die. Kurosawa discovered that it was a substance produced by the fungus that made the plants bolt.
The substance was isolated in 1934 by chemists T. Yabuta and Y. Sumiki, who named it gibberellin (gibberellic acid, or GA), after the fungus. It was later discovered that almost
all plants produce gibberellins, and that they are present in various concentrations in various plant tissues. At least 125 naturally occurring gibberellins have so far been identified.

Effects

 Some GAs promote stem elongation, but their mechanism is different from that of auxin; they enhance cell elongation
Some dwarf mutant plants supplied with GA grow as tall as normal plants, indicating that the dwarfing is due to an inborn error of GA metabolism in these plants.)
 artificial gibberellin application to seeds can replace the "after-ripening" necessary for some species before germination can begin
 in some species, gibberellins are involved in the mobilization of stored protein and starch in the endosperm for use by the embryo
 can stimulate parthenocarpic fruit (even in some species in which auxin cannot, such as mandarin oranges, almonds, and peaches).
 involved in promoting flowering in some species

As mentioned at the start of this lecture, most hormones operate at the molecular level by acting as transcription factors or by affecting transcription factors, and hence, DNA
transcription and translation.

As you'll learn in Genetics (if you haven't already), it's All About RNA. Stay tuned.
Plants and the Environment: Tropisms, Circadian Rhythms and More If you're rooted to the spot, you need means other then physical movement of existing
tissues to respond to environmental stimuli. The hormones we met last time are intimately involved in triggering the physiological responses exhibited by
plants.

For a cell to be able to respond to a stimulus, it must have an appropriate receptor (a molecule affected by the stimulus).

(CONSIDER: Why are humans unable to see UV radiation that other organisms can see and use to forage?)

(On the other hand, why do humans physiologically respond to the tetrahydrocannibanol (THC) manufactured by Cannabis--despite the fact we don't
manufacture or need this compound ourselves?)

Recall the generalized model for a hormone-triggered signal transduction pathway:

 a hormone binds to a specific protein receptor, either embedded in the plasma membrane or in the cytoplasm (depending on the receptor and the system).
 binding of the hormone to the receptor causes the receptor protein's conformation to change
 this stimulates the production of "relay molecules" in the cytoplasm
 relay molecules trigger various responses to the original signal
 plants have a wide variety of signal transduction pathways, each triggered in response to specific environmental stimuli.

Etiolation: An Example of Hormone-mediated Response What happens to a potato if you wrap it up in a brown paper bag and then forget about it?

Etiolation is the term applied to the morphological adaptations exhibited by a plant growing in the dark:

 long, spindly stems (why is this adaptive?)

 lack of chlorophyll (why is this adaptive?)
 stunted leaves (why is this adaptive?)

Upon reaching light, de-etiolation ("greening") takes place:

 stem elongation slows

 chlorophyll is manufactured
 leaves expand to normal proportions

...but how does the plant sense the light?

The receptor in this case is a pigment known as PHYTOCHROME.

Phytochromes are proteinaceous molecules with a sulfur-linked (covalently bonded) pigment active group (the chromophore) consisting of a linear tetrapyrrole.

The pigment absorbs primarily in the red and far-red region of the spectrum, and so appears blue-green to our eyes.

The chromophore portion of the molecule can exist in one of two forms, PR or PFR:
The functional phytochrome consists of two identical proteins, each with a chromophore. One part of the protein acts as the photoreceptor, and the other as a kinase, which
triggers cellular responses.

 When the chromophore absorbs light, it isomerizes from one form to the other. This change in configuration results in a slight change in the kinase portion of the protein.
 The kinase is the biologically active region of the molecule, and its interaction with other biological molecules elicits a physiological response.

Let's take a tour of the signal transduction pathway for de-etiolation, triggered by the isomerization of phytochrome:
It's all about gene expression. Ultimately, the signal transduction pathway results in the activation (or, in some cases, the suppression) of genes involved in the production of a
specific, environmentally-induced phenotype.

 a signal transduction pathway usually involves the increase in the activity of enzymes specific to a particular physiological response, either by
  stimulating transcription of the mRNA coding for that enzyme (transcriptional control)
OR
 activating existing enzymes (post-translational control)

Note:

A single phytochrome isomerization can trigger the production of hundreds of secondary messenger molecules, thus amplifying the response to what might have been a
very weak initial environmental stimulus (i.e., it can take very little light to trigger de-etiolation.)
 Several different phytochrome genes have been discovered, each coding for a slightly different protein. The chromophore is the same in all known phytochromes, but because
the proteins differ, the phytochromes have different sensitivities to red light.

(Note: These genes were discovered in Arabadopsis thaliana (commonly known as "Thale Cress"; Family Brassicaceae). This little guy is the plant equivalent of Caenorhabditis:
it is one of the most highly utilized plant models in studies of botanical molecular and cellular processes.)

Other Responses to Light: The Hard-working Phytochromes and Blue Light Receptors Light is one of the most critical environmental factors for plant survival and growth.
Evolution has provided them with at least two different classes of photoreceptors:

 phytochromes (whom we've met already)

 blue light photoreceptors

Blue Light Photoreceptors

Blue light stimulates

 phototropism
 opening of stomates
 slowing of hypocotyl elongation upon breaking ground

The blue light receptor was so difficult to find that for a long time researchers referred to it as "cryptochrome!" But in the last decade, three blue-absorbing receptors have been
found:

 cryptochromes (inhibit hypocotyl elongation)

 phototropin (its name implies its function)
 zeaxanthin (induces stomatal opening)

Phytochromes and Germination

Germination is the critical starting point of a plant's life. Especially if you're a small seed (with little endosperm), it you germinate too early, when you're buried too deeply in the
soil, or when you're in a spot that's too shady, you're OUT OF THE GENE POOL.
In the 1930s, USDA researchers used lettuce seeds to determine the effects of light on germination rate. Seeds were soaked, and then:

 kept in the dark (control)

 exposed to a flash of red light, then kept in dark

 exposed to a flash of red light, then far red light, then kept in dark

 exposed to a flash of red light, far red, red, then kept in dark

 exposed to a flash of red light, far red, red, far red

Seeds last exposed to red light had the highest germination--and the effect was reversible (as indicated by the last protocol). Red light stimulated germination, and far red light
inhibited it.

(What's the adaptive significance of this?)

Remember:

Given this information, which phytochrome (PR or PFR) might you expect to promote germination?

Which might inhibit germination?

Tropisms A tropism is a permanent, directed movement (growth) in response to an external stimulus. Tropisms may be positive (going towards a stimulus) or negative (going
away from a stimulus).
Plant tropisms are changes in growth pattern in response to stimuli.

 phototropism - growth in response to light. (In plants, this is mediated by auxin, as we saw in the previous lecture; we won't cover it again here.)
 gravitotropism - growth in response to gravity
 hydrotropism - growth in response to moisture/water
 heliotropism - growth in response to the sun's movements
 thigmotropism - growth in response to physical touch

...and you can think of more tropisms, no doubt (halotropism, chemotropism, etc.)

Gravitotropism
Lay a plant on its side, and--given enough time--it will reorient both its shoots and roots in the proper position.

 Roots exhibit positive gravitotropism.

 Shoots exhibit negative gravitotropism.

But how does the plant know which way is up, and which way is down? It starts with germination (remember the little song). As you might guess, auxin is a key player in
gravitotropism.

Amyloplasts
Starch-filled plastids called amyloplasts (a.k.a. statoliths) tumble downwards in response to gravity in specific cells of the shoots and the roots.
  In shoots (and in coleoptiles), the amyloplast-rich cells form a starch sheath around the vascular tissues.
 In roots, the amyloplast-rich cells are located in the root cap, and especially in its central axis (the columella).

When a root or shoot is placed on its side, the amyloplasts slide to the formerly vertical cell wall and rest there. A few hours later, the shoot or root begins to bend/grow vertically
(up or down, depending on whether it's a shoot or a root). When the horizontal wall becomes more vertical again, the amyloplasts slide back to their position on the "bottom" wall
of the cell.

Why does the displacement of the amyloplasts result in differential growth? Several hypotheses have been proposed...

1. Calcium/Auxin Redistribution Hypothesis

The aggregation of amyloplasts at the lowest points in the cells triggers a redistribution of Ca+ ions, and this, in turn triggers the (active) lateral transport of auxin within the root.
But--counterintuitively to what you might expect--the auxin and calcium accumulate on the BOTTOM side of the displaced root.

Recall: At HIGH concentrations, auxin actually inhibits cell elongation. Hence, growth on the lower side of the root slows down, and proceeds as normal on the upper side. Once
the root is growing straight down (or shoot straight up), the statoliths take up their usual position on the "bottom" cell wall, and growth direction stabilizes.

2. Protoplast Pressure Hypothesis

Mutant Arabidopsis and tobacco planst lacking statoliths are still capable of gravitotropism, albeit more slowly than wild type plants. So there must be more to this phenomenon
than just the starch granules.

Some investigators have suggested that the entire protoplast is involved in sensing a change in gravity: cytoskeletal components may "tug" on the proteins that bind the protoplast
to the cell wall, causing

 stretching of the proteins on the "up" side

 compression of the proteins on the "down" side

This could explain how plants "sense" gravity, but not how the cell responds on a molecular level.

3. Tensegrity Model
Tension integrity, or "tensegrity", (a term used in architecture to describe structural integrity generated by the tension among interconnected parts of a building or other structure)
has been suggested as another mechanism by which plants sense gravity.

Proponents of this model suggest that actin filaments stretched by the plant's orientation stimulate an increase in local [Ca+2]. It has been noted that

 Ca+2 ions move upwards in shoots turned on their sides

 Ca+2 ions move downwards in roots turned on their sides

As we've seen, Ca+2 ion concentration changes are part of many signal transduction pathways. But the specific way in which this one works is not yet known.
Hormonal Involvement in Gravitotropism

 cytokinin apparently stimulates rapid cell division on the lower surface of the very tip of a gravitostimulated root, causing it to grow downwards.
 auxin causes cell elongation farther away from the apex, resulting in the bending of the root away from the meristem.

Thus, two types of altered cell growth may contribute to the end result: the root bending downwards towards gravity.

Response to Mechanical Stimuli An organism rooted to the spot has an adaptive advantage if it can alter its growth in response to mechanical touch, if it's unable to physically
move its existing cells and tissues.

Thigmomorphogenesis
Recall our earlier discussion of ecotypes.

The Jeffrey Pine (Pinus jeffreyi) is one of the most striking examples of showing two distinct ecotypes, one growing on flat lowland areas, and the other on high cliffs (Yosemite
National Park) where winds are strong and constant.
The morphological differences can be explained by a phenomenon known as thigmomorphogenesis.

As we've already hinted, plants are extremely sensitive to mechanical stimuli.

 measuring a leaf with a ruler will affect its subsequent growth

 rubbing the stems of a young plant daily will stunt its growth (relative to controls)

(What do you suppose might be the adaptive advantage in an individual able to alter its growth form in this particular way?) (Recall the devastation of Hurricane Wilma, which
came from the WEST.)

Mechanical stimulation of plants in this way results in an increase in Ca+2 ions in the cytosol. As we saw previously, this can trigger/mediate gene expression. In the case of
thigmomorphogenesis, the genes activated encode enzymes that affect the physical properties and construction of the cell walls themselves, increasing lignification and reducing
cell elongation.
Thigmotropism
Certain plants (especially vining plants) are very sensitive to touch, and will grow in response to mechanical touch.

Vines (and their tendrils) will usually grow straight until they are touched. At that point, they will curve and coil in the direction of the touch (differential growth on either side of
the stem) until they are able to attach to whatever solid thing attracted them.

Fast Responses to Mechanical Stimuli Turgor movements are relatively quick plant movements that result from changes in internal water pressure.
Examples include stomatal opening and closure, as well as the sudden movements of the sensitive plant's leaves or the Venus flytrap's insect-capturing leaves. (They are not
tropisms.)
Turgor movements are also known as thigmonastic movements because they usually occur in response to touch, shaking, or even electrical stimuli.

In Mimosa pudica, specialized cells within the pulvinus at the base of each leaflet and the main petiole rapidly lose water in response to a change in potassium ion potential in the
apoplast. This, in turn, appears to be triggered by the loading of sugar into the apoplast from the phloem, all in response to a small environmental stimulus!

Definition: A pulvinus is a sort of plant motor organ. It is an an enlarged area at the base of a movable plant structure (petiole, leaflet attachment to rachis, node, etc.) that can
produce movement by a change in turgor pressure in some of its cells.
Long a mystery, the means by which the Venus Flytrap closes its specialized leaves in response to touch may be close to discovery. It took an international team of

 mathematicians
 engineers
 biologists

Lakshminarayanan Mahadevan (Professor of Applied Mathematics, Harvard University) explains...

 the open leaf trap is somewhat akin, physically, to a tennis ball cut in half and pushed inside out
 the leaves are held in place by regions of cells with high turgor pressure that apply enough tension to the open leaves to keep them in place
 mechanical stimulus of tiny hairs inside the trap cause a change in ion potential, and water shifts out of the turgid cells
 the slight change in curvature releases the tension holding the leaves open, allowing them to snap shut.
(The original paper appears in the January 2007 issue of Nature, for those who wish to read further.)

The Venus Flytrap discriminates:

 at least two hairs must be stimulated for it to close

 or one hair can be touched within a certain span of time
 this reduces the chances of false alarms springing the trap

Circadian Rhythms Circadian Rhythms are adaptations in response to environmental changes over the course of 24 hours.

In most organisms, these rhythms are timed by internal mechanisms that collectively function as a biological clock that synchronizes the organism's metabolism in response to
environmental changes. This allows the organism to optimize its functions over a 24-hour day, or over the course of changing seasons. Circadian flowering rhythms can be vital to
the evolutionary fitness of a given individual.

Plants...

 close their leaves and flowers daily in a sleep cycle

 go dormant (in temperate latitudes) over the winter
 flower at different times of the year (photoperiodism)

...and perform other Circadian "tasks".

The exact timing of the cycle is variable (about 21-27 hours, depending on the particular Circadian response), but these will synchronize with the environmental day/night cycle in
an outdoor plant (or animal) and shift with the seasons and other stimuli (think: jet lag).

Photoperiodism: How do Plants Know When to Flower? Some plant species bloom in the summer (when days are long), whereas others bloom in the winter (when days are short).
Others bloom at times in between. Plants that bloom only when there is a specific day to night ratio are said to be photoperiodic.

How does each individual "know" how to flower exactly when its conspecifics are flowering, thus increasing its likelihood of pollination? What might be the evolutionary
significance of plant species that have developed these differences in the timing of their reproduction?

What factors might induce plants to flower?

 temperature?
 moisture?
 oxygen?
 light period?

Which of these is the most reliable gauge of the season in temperate latitudes?

Although temperature, water, and other environmental conditions may vary from year to year, the duration of daylight is predictable.

The Secret of Flowering

In 1920, Garner and Allard reported two species of plants that would not flower unless their daylight hours were of a certain, critical shortness. Even a flash of light during the
critical dark period would inhibit flowering. They called this phenomenon photoperiodism.

There are three "flavors" of plants with respect to photoperiodicity:

 short day plants flower in early spring or fall; they need daylight shorter than a particular, critical length, or they will not flower.
 long day plants flower in summer; they need daylight longer than a particular, critical length, or they will not flower.
 day neutral plants flower without respect to day length (flowering mechanisms are various, and some are not well understood)

Particular species tend to be one type, but

 ecotypes of differing flowering stimulus periods are known in species that have a broad north/south distribution
 the number of days of critical period depends on species. (Some species need only one day of the critical period, whereas others need several weeks of a critical period
before they will flower.)

How does it work? It's our Old Pal phytochrome.

Recall the Two Phytochromes

The PR form:

 has a λmax (maximum absorbance) at 666nm (red)

 is synthesized in dark-grown seedlings
 is converted to PFR in the presence of red light
 is the more stable of the two forms

The PFR form:

 has a λmax of 730nm (far red)

 is biologically active, eliciting a physiological response in the plant
 is converted to PR in the presence of far red light
 is the less stable form, and will spontaneously revert to PR in darkness (dark reversion)
 can be destroyed by proteases in the cell
 Because PFR absorbs some red light, there is usually a proportion of about 85% PFR to 15% PR in the cell when the cell is exposed to red light.
 However, because PR is not very sensitive to far red wavelengths, in far red or darkness, the cell has about 97% PR to 3% PFR.

Got all that? Here are a thousand words...

In all photoperiodic plants,

 In the winter when days are short, [PR] > [PFR]

 In the summer when days are long, [PR] < [PFR]

The critical difference is...

 In short-day (i.e., winter flowering) plant species, PFR inhibits flowering.

 In long-day (i.e., summer-flowering) plant species, PFR induces flowering.

Therefore,

 In WINTER, PFR when concentration is low, the flowering inhibition it exerts in winter-flowering plants is "lifted." They bloom!
 In SUMMER, PFR when concentration is high, the flowering induction it exerts in summer-flowering plants starts working. They bloom!
Hormonal Control of Flowering
The putative receptor stimulated by the phytochrome isomerization is known as florigen. It may be a hormone--or even a team of hormones--but it has not yet been identified.

In any case, the physical result of photoperiodism is the expression of genes in meristem cells that cause differentiation of the cells into the tissues and various parts of the flower
we now know so well. Signal transduction pathways that trigger these gene expressions are still under study. Stay tuned!

Plant Responses to Environmental Stress Flooding, drought, extreme temperatures (abiotic), pathogens, herbivores and competition (biotic) are all selective factors that have
resulted in a marvelous array of plant responses.

Drought
Plants need water to survive, of course. But they do have mechanisms by which they can survive short periods of drought.

 loss of water from cells reduces turgor, closing stomatal guard cells
 in some species, leaves roll into a water-loss reducing shape (e.g., grasses)
 loss of turgor will inhibit further plant growth (photosynthesis slows!)
 drought inhibits the formation of surface roots, promotes deep root formation

Flooding
Overwatering kills plants because of oxygen deprivation (drowning). But plants have some short-term survival strategies that can allow them to cope with temporary inundation.

 low oxygen concentration in tissues stimulates ethylene production

 ethylene triggers apoptosis in some root cortex cells
 this creates air spaces and even air tubes continuous with the non-submerged plant parts (snorkels!)

Salt Stress
Excess salts in the soil can prevent water uptake (simply due to differential water potential), and can be directly toxic in high concentrations.

 some plants can produce organic solutes (non-toxic, even in high concentrations) that help equalize water potential
 a halophyte is a plant evolutionarily adapted for life in soils with relatively high salt content. These have other mechanisms (e.g., salt-excretion glands) for reducing water
potential between root and soil.

Heat Stress
Excessive heat can denature enzymes and cause other metabolic damage.

 In times of extreme heat, increased transpiration can effect evaporative cooling

  special "chaperone" proteins known as heat shock enzymes which may link to other enzymes and structural proteins, preventing them from denaturing in the heat--at least
temporarily.

Cold Stress
Cold temperatures increase cytosol viscosity (slowing things down). I don't need to tell you that freezing ruptures cells and causes biological havoc.

 lipid composition in plasma membranes changes in response to cold: unsaturated lipids (which have a lower freezing point) increase, and saturated lipids decrease
 this change can take hours or even days
 hence, plants are often more sensitive to cold than they are to other environmental stresses: there's sometimes not enough time to respond
 freezing temperatures can be mitigated by solutes in the cytosol which lower its freezing point (sometimes simply removing water from the cell is the method!)
 in this case, resistance to dehdration is the key to survival

Plant Defenses Against Herbivores Physical defenses against herbivores can be obvious: thorns, pubescent leaves, sticky resins, etc. Chemical defenses can be more subtle.

Canavanine is an unusual amino acid that closely resembles arginine. If an insect eats enough tissue from a plant containing canavanine, the compounds replaces arginine in many
of the insect's newly forming proteins, rendering them inactive. Death ensues!

Calling in the Cavalry

When a corn plant is munched by a caterpillar, the physical damage and certain chemicals in the caterpillar's saliva combine to elicit release of volatile compounds from the corn
leaf. This attracts parasitoid wasps that lay their eggs in the hapless caterpillars' bodies.
Warning the Neighbors
A damaged plant can even send warning to its nearby conspecifics.
Lima beans suffering attack by spider mites release volatile compounds that elicit the expression of genes that encode enzymes that make the plant

 less susceptibel to spider mites

 attractive to another species of mites that preys on spider mites

Some of the genes involved above are also activated by jasmonic acid, which we already know is an important component of plant defense signal transduction pathways.

Plant Defenses Against Pathogens Pathogens can be

 virulent - causing disease in a plant because the plant has little or no genetic defense
 avirulent - causing mild harm, but not death (a result of a coevolutionary "Cold War")

Gene-for-gene Resistance

This form of protection, utilized by many plants, is the production of protein by specific plant disease resistance genes (collectively called R genes) that can recognize
molecules produced by pathogens (often encoded by the pathogen's Avr, or "avirulence" genes).
 Different R genes respond to different pathogens, but if a plant does not have an R product that matches the Avr of a pathogen, then that pathogen may be virulent in that
plant species.

Hypersensitive Response
Pathogen-produced molecules known as elicitors can induce a less specific type of defense response.

Cell wall damage can cause fragments of cellulose to convert to oligosaccharins can act as elicitors, and can stimulate the production of antimicrobial phytoalexins.

Other microbe infections can elicit the cell to produce compounds that

 attack bacterial cell walls

 increase lignification of plant cell walls

An avirulent pathogen (i.e., one that has an R-Avr match in that plant species) will elicit a particularly strong response, and the plant will actually wall off the localized
infection. This Hypersensitive Response (HR) will produced small lesions where the infection has been corralled. The leaf will be ugly, but it will survive.

Systemic Acquired Resistance

A Hypersensitive Response will also set up signal transduction pathways that result in SAR - Systemic Acquired Resistance.

Recall that the activation of the SAR response requires accumulation of endogenous salicylic acid, which is triggered by the presence of a pathogen.

In Arabidopsis, a high concentration of salicylic acid activates a molecular signal transduction pathway that is identified by a gene called nim1 (also known
as npr1 or sai1). The pathway results in heightened immunity to all pathogens in uninfected parts of the plant, sometimes for many days after the attack.

Because the SAR elicits production of various phytoalexins and PR proteins, it tends to be non-specific, and can afford protection against a variety of pathogens.

An overview of plant defense against an avirulent pathogen...

Key:

 1 - Plant R protein (receptor) and pathogen Avr protein (ligand) join

 2 - signal transduction pathway is initiated
 3 - HR response: cells seal off pathogens and then undergo apoptosis
 4 - dying cells release a chemical signal (salicylate)
 5 - salicylate is transported to the other parts of the plant
 6 - signal transduction pathways are initiated in distant parts of the plant
 7 - SAR is achieved when phytoalexins and PR proteins are produced in those remote tissues.
Evolution: A Natural Process

"Do you believe in evolution?"

"What is the theory of evolution?"
What is wrong with these two questions? Are they valid?

For an excellent tutorial on evolutionary processes and ideas, visit the University of California at Berkeley site,
"Understanding Evolution". (We'll refer to this a few times here.)

 EVOLUTION - change over time

 ORGANIC EVOLUTION - genetic and physical change in living populations over time.
 MICROEVOLUTION - genetic change within a population without reproductive isolation between population
members
 MACROEVOLUTION - genetic change among members of a population that leads to reproductive isolation
(speciation)
To understand evolutionary processes is to understand the genetic composition of a population and the forces that
determine and change that genetic composition.
REMEMBER: Populations--not individuals--evolve.

Recall a few important definitions.

 species: a group of similar organisms that can interbreed in nature to produce fertile, viable offspring (biological
species definition)
 population: all individuals of the same species living in a defined geographic area. (anything from your eyebrows
to the Himalayas).
 deme - partially isolated subset of a population.
 gene pool: all the genes at all loci in every member of an interbreeding population.

If you really do not recall any of your genetics, then please be sure to review this very simple genetics primer before
proceeding.
Measuring Relative Allele and Genotype Frequencies
Genetic and phenotypic variability in a population arises from the existence of multiple alleles at different gene loci. A
fundamental measurement useful in studies of changing genetic composition of populations is the frequency with
which known alleles occur at a given locus.
In 1908, Godfrey H. Hardy, a British mathematician, and Wilhelm Weinberg, a German physician.

independently reported a mathematical rule that describes allele frequencies in a population.

For a population segregating two alleles at a particular locus in which
 A is the dominant allele and
 a is the recessive allele
the total frequency of both alleles, A + a = 1.0.
The total number of either allele is equal to:
 # of allele (A or a)/total # of alleles in the population
Standard shorthand:
 The frequency of A is represented as p.
 The frequency of a is represented as q.
 Hence, p + q = 1.0
Hardy and Weinberg independently noted that at any given starting relative frequency of A and a the relative
frequencies of the three possible genotypes in an idealized, non-evolving population can be predicted with an
expansion of the binomial equation:
p2 + 2pq + q2
...in which
 p2 = frequency of homozygous dominant individuals
 q2 = frequency of homozygous recessive individuals
 2pq = frequency of heterozygous individuals

 If observed relative genotype frequencies match the expected, the population is said to be in Hardy Weinberg
equilibrium, which means that the population is not evolving at the monitored gene locus.
 If the observed relative genotype frequencies do not match the expected, the population is not in Hardy Weinberg
equilibrium. This means that the population is undergoing microevolution at that gene locus.

Mechanisms of Change
Five different factors can cause a population to evolve (and not remain in HW equilibrium):
 mutation - the raw material of evolution
 small population size - this can lead to genetic drift
 non-random mating - this can lead to a disproportionate number of homozygotes (in the case of positive
assortative mating) or heterozygotes (in the case of negative assortative mating)
 migration into or out of the population (no gene flow with other demes) will change the allele frequencies of the
population from which individuals leave, or individuals arrive from other populations.
 natural selection - That is, if one allele or genotype confers a reproductive advantage over the others, evolution
will occur.
Any heritable trait can be...
 adaptive - it increases the likelihood of its bearer to leave offspring
 maladaptive - it decreases the likelihood of its bearer to leave offspring
 neutral - it does not affect the likelihood of its bearer to leave offspring
But note that it is not a single gene locus that is necessarily the only focus of natural selection. The whole
organism carries multiple alleles at thousands of loci, and various factors can result in maladaptive traits being passed
on and adaptive ones being lost from the population. Random processes play a large role in evolution.

Mechanisms of Speciation
The definition of a biological species states that a species shares a gene pool that is not shared with other species. But
how do those gene pools become separated? Several mechanisms may be involved...
 allopatric speciation
  peripatric speciation
 parapatric speciation
 sympatric speciation
Although animals rarely undergo sympatric speciation, in plants this is not at all uncommon, especially via
two genetic mechanisms,
 autopolyploidy
 allopolyploidy
Polyploid individuals are often larger and physically more robust than the parent plants, and if they are self-fertile
(which they are, once the process is complete), they can give rise to a population that is partly or completely
reproductively isolated from the original population.
A famous example is that of Goat's Beard. Wild Tragopogon dubius, Tragopogon porrifolius, and Tragopogon
pratensis were imported from Europe and became established in the Western U.S. (Washington and Idaho).
Promiscuous and fertile, the three species interbred, producing infertile interspecies that went through allopolyploid
reproduction to become self-fertile.
See the original abstract.
And then see how pretty they are. The European Ancestors (from left to right, T. dubius, T. porrifolius, and T.
pratensis.
The crosses and doublings:

The Tragopogon phenomenon is of great interest to evolutionary biologists because it is one of the first times that the
evolution of genomes has been observed in recorded, recent history.
Reproductive Isolation
Once two populations have diverged and are two different species, there are several ways in which gene flow between
them can be thwarted. Reproductive isolation (which maintains two species as separate entities) can be in effect at the
following PREZYGOTIClevels...
 temporal (sibling species have differently timed mating cycles or seasons)
 ecological (sibling species live in different microhabitats)
 geographic (sibling species are separated by geographical obstacles)
 mechanical (sibling species mating apparati are not compatible)
 behavioral (sibling species do not recognize each other's courtship behaviors)
 gametic (sibling species' gametes are chemically incompatible)
...and at the following POSTZYGOTIC levels.
 hybrid inviability (hybrids between sibling species do not survive)
 hybrid sterility (hybrids between sibling species cannot produce viable offspring)
 hybrid breakdown (hybrids can produce offspring, but those offspring suffer reduced fertility with each
subsequent generation)
An overview (for those of you who haven't heard this before) can be found HERE.

Coevolution
When populations of two or more species interact so closely that each one affects the evolution of the other,
coevolution is said to be occurring. This most often results in different types of symbioses that we discussed in the first
lecture.
Pollination is one of the most important examples of coevolved symbiosis on earth, and it is threatened.

Adaptation
The term adaptation must be used with care, as it has several biological definitions. It can be
 the state of being adjusted to a particular environment
For example, a guppy can be adapted to live in salt water, if the salinity in its environment is gradually increased.
 a characteristic that changes in response to environmental changes (a short term, individual response)
For example, a snowshoe hare changes the color of its fur seasonally by shedding out brown summer fur and
replacing it with white winter fur, and so on. This is a seasonal adaptation to changes in weather and
environmental conditions. (The ability to adapt is a result of evolution, though the adaptation cycle itself is an
individual phenomenon.)
 an evolutionary response to natural selection, producing a population better suited to its environment than previous
generations
For example, populations of modern Jackrabbits have evolutionary adaptations (huge ears; curly fur, long, thin
limbs, etc.) that allow them to survive desert temperatures that their non-desert-dwelling ancestors could not have
survived.

Developmental Plasticity
Genes determine phenotypic potential. Environmental influence can affect the development of many different heritable
traits to attain varying degrees of their genetic potential.
Because of plants' indeterminate growth, environmental influence can impact plant morphology throughout the
lifespan.

 Leaves growing in the shade or sun on the same plant may look different.
 Cloned plants may look different if they are grown with different nutrients, water, mycorrhizae or not, etc.
 Plants of the same species can develop completely different growth forms, depending on whether they live in a
relatively moderate environment, or a very windy one.
When environmental conditions vary gradually along a geographic range, plant morphologies may also mirror that
gradual shift. Such shifts are called clines.
Some widespread species may grow in very different climate conditions, and have very different growth forms, even
though they are genetically very similar. Populations that have distinct morphologies in response to such climatic
pressures are known as ecotypes.
The Jeffrey Pine (Pinus jeffreyi) is one of the most striking examples of showing two distinct ecotypes, one growing on
flat lowland areas, and the other on high cliffs (Yosemite National Park) where winds are strong and constant.
A tale of Edelweiss...
Ecotypes are physiologically different, with measurable variation in metabolism, photosynthesis rates, growth rates,
etc. Developmental plasticity plays an early role in establishing these permanent variations in the adult organisms.

The Species Concept

To this point, you probably have usually been given the definition of "species" that I introduced at the beginning of this
lecture. This is known as the biological species concept. Plants, in particular, make this definition sometimes very
difficult to apply, as gene flow does occur regularly between morphologically distinct species. Hence, there are other
concepts of what defines a species.
Investigators using the morphological species concept classify species not solely on the basis of genetic isolation, but
also on the basis of morphological distinctness.
Long-lived trees and shrubs that share a relatively recent common ancestor may look very different, and be classified as
different species, but they are still able to cross-pollinate to produce fertile, viable hybrids. This is not unique to plants,
but it is quite common in plants.
Sometimes hybrids are sterile, but if they are very adept at asexual reproduction (e.g., like the widespread Equisetum
hyemale x Equisetum laevigatum hybrid E. x ferissii, who needs sex?

Aren't plants amazing?

Systematics and Taxonomy
 Systematics - the study of evolutionary relationships between living things
 Taxonomy - the classification and naming of living things

The greater goal: Discover how the branches of the Tree of Life connect and diverge, giving a history of the evolution of life on earth.

For the next few lectures, we will be concerned with the GREEN branches of the tree: the ancestors and descendants of the taxonomic group commonly known as Plantae. Let's
take a brief tour of the Tree of Life as it stands this minute.

You are no doubt familiar with the taxonomic hierarchy and naming system devised by Swedish botanist Carl Linne, who Latinized his own name to Carollus Linnaeus.
The system he devised, published in 1735, is known as Systema naturae, and is still used today by all branches of systematics, including zoology, botany, mycology, and
microbiology.

In the Linnaean system, every scientific name consists of an organism's Genus and species, the names of which are always GREEK, LATIN or LATINIZED versions of other
languages or terms.

Example: Delonix regia is the scientific name of the Royal Poinciana Tree

Its name is from the Greek delo, meaning "visible" and the Latin regi, meaning "royal". An appropriate name.

Each species is nested within successively more inclusive taxa. From MOST inclusive to LEAST inclusive, the major taxonomic ranks are:

'
  Domain
 Kingdom
 Phylum
 Class
 Order
 Family
 Genus
 species

Within each of the above taxonomic categories there are larger and smaller subgroups such as subkingdom, superphylum, subphylum, subclass, etc., to allow "fine tuning" of
classification. Taxonomic groups of any rank may be generically referred to as a taxa (singular: taxon).

The Aspects of a Taxon 1. The taxon's name. For example, the taxonomic name of all domestic corn plants is Zea mays. The family to which all corn species belong (along with
all other grasses) is Poaceae, in the Order Cyperales, etc.

The scientific name of a group of similar organisms has no more significance than any other convenient label used to describe a group of similar items. Taxonomic names such as
"Bacteria," "Chlorophyta" and "Zea mays" are similar in function to descriptive names of similar objects, such as "shoes" or "cars."

2. The taxon's rank. For example, the taxon Nymphaeaceaea (Water Lilies) is assigned the taxonomic rank of Family. Like the taxon's name, the taxon's rank has no true
biological significance. It serves only to help the systematist locate the taxon within the hierarchy.

3. The taxon's content. For example, all of the obvious organisms in this lecture hall are (probably) members of the genus Homo and the species Homo sapiens. To the
systematist, this is perhaps the most important aspect of the taxon. By grouping certain individuals within a single species, certain species within a single genus, certain genera
within a single family and so on, the systematist tells us which organisms are believed to be most closely related to one another, in terms of common evolutionary ancestry.

A taxon has dimensions in both space (geographical range) and in time (its evolutionary history).

Any taxon's evolutionary history and phylogenetic relationships can be diagrammed with a phylogenetic tree such as this one showing the relationships of the major groups of
green plants.

Note that the only taxon that has any biological reality is the species. All other taxonomic ranks are human constructs.

A species full scientific name consists of its Genus and species, italicized:

Psychotria nervosa Sw. var. lanceolata (Nutt.) Sarg.

Raphanus sativa L.
 So what's that other stuff?

The International Code of Botanical Nomenclature (ICBN) has all the rules you'll ever need for naming your very own new plant species.
 A few interesting/important notes from the ICBN:

 Fossils may be treated as morphotaxa. A morphotaxon is a taxonomic group constructed on the basis of morphology, and may not reflect evolutionary relationships (given
the absence of DNA or other data).
 Asexual forms also may be classified as morphotaxa.
 Every individual plant is treated as belonging to an indefinite number of taxa of consecutively subordinate rank, among which the rank of species is basic.
 Since some plants hybridize and are fertile, hybrid taxa (also known as nothotaxa) are nothogenus and nothospecies. These ranks are the same as genus and species. The
addition of "notho" indicates the hybrid character.
 The secondary ranks of taxa in descending sequence are
o tribe between family and genus
o section and series between genus and species
o variety and form below species
 A greater number of ranks of taxa can be made by adding the prefix "sub-" to the terms denoting the principal or secondary ranks.A plant may thus be assigned to taxa of
the following ranks (in descending sequence):
o regnum, subregnum
o divisio or phylum, subdivisio or subphylum
o class, subclass
o order, suborder
o family, (suffix is "-aceae") subfamily (suffix is "-oideae")
o tribe, (suffix is " -eae")subtribe (suffix is "-inae")
o genus, subgenus
o section, subsection
o series, subseries
o species, subspecies
o variety, subvariety
o form, subform

Plant families are named for the type genus: the first genus to be described in that family. For example:

 Asteraceae (Daisy family) is named for type genus Aster

 Fabaceae (Legumes) is named for genus Faba
 Rosaceae (Rose family) is named for genus Rosa
 Poaceae (Grass Family) - Poa
 Solanaceae (Tobacco Family) - Solanum
 Orchidaceae (Orchid Family) - Orchis
 Pinaceae (Pine Family) - Pinus

...and so on.
 Tools of Classification Early taxonomists (such as Linnaeus) used external morphology as the most important means by which to classify organisms. Today, of course, we have
more sophisticated ways to determine actual common ancestry, and avoid the trap of accidentally classifying superficially similar organisms that are actually similar only because
of convergent evolution.

Today's evolutionary biologists uses...

 Comparison of morphology
 Comparison of biochemistry and physiology
 Comparison of chromosomes
 Comparison of cell ultrastructure
 Comparison of cellular metabolism and pathways
 Comparison of nucleic acid sequences and protein composition
 Studies of geographical distribution (biogeography)
 Comparison of ontogeny (embryo development)

...to build a complete catalog of evidence showing that two species are derived from single common ancestor.

Primitive versus Derived Characters A character that is not much changed from the same character in an ancestral form is said to be primitive, and is also called a plesiomorphy.
One that has been modified from the same character in an ancestral form is said to be derived with respect to the more primitive form, and is also called an apomorphy.

A primitive character shared between two or more taxa is known as a symplesiomorphy (literally "shared primitive character"). A derived character shared between two or more
taxa is known as a synapomorphy (literally "shared derived character").

Let's consider some examples.

Homologous versus Analogous characters If similarity between two characters in two different taxa can be attributed to their presence in a common ancestor, then those two
characters are said to be homologous.

Characters that have evolved similar form and function from different ancestral sources are said to be analogous. Analogous characters are also called "homoplasies" or
"homoplastic characters."

For example...

Let's have a LOOK.

Constructing Phylogenies That Reflect Common Ancestry The goal of the systematist is to construct phlogenies that show recency of common descent. This means that all valid
taxa must be MONOPHYLETIC.
  Monophyletic taxon: includes only those taxa derived from a single common ancestor.

In some cases, phylogenies do not accurately reflect evolutionary relationships, as in the case of (invalid) taxa that are POLYPHYLETIC or PARAPHYLETIC.

 Polyphyletic taxon: includes taxa derived from more than one common ancestor.
 Paraphyletic taxon: includes only some of the descendants of a common ancestor, but not all of them.
In some cases, true evolutionary relationships cannot be determined with the data available, or a group may be in the process of being classified. In this case, members of a group
may be placed (hopefully temporarily!) into a FORM TAXON.

Form taxon, also known as a morphotaxon: a taxon whose members are included in the group more on the basis of shared, known similarities in morphology, physiology, etc.
than on known evolutionary relationships. (e.g., "Kingdom" Protista, "Kingdom" Monera, "Phylum" Deuteromycota)

Three Schools of Thought in Evolutionary Biology

 Classical Evolutionary
 Phenetic
  Cladistic

Classical Evolutionary System

 Until recently, this was the accepted method of classification

 both common ancestry and time of evolutionary diversification since splitting from a common ancestor were considered important aspects in classifying a taxon
 specialization after a branch point is considered relevant to classification
 monophyletic & paraphyletic groups are acceptable

The Phenetic System

 a system of convenience, somewhat akin to the library's Dewey Decimal System.

 classifications are based on measurable, morphological characters, not evolutionary relationships
 all morphological features are considered equally important in this system (no characters are "weighted" with more significance)
 characters are chosen at random, to eliminate bias.
 classifications made on the basis of overall % of shared similarity.
 Problem: any rank higher than species is often polyphyletic, due to convergence of morphological characters.
 monophyly, paraphyly and polyphyly have no meaning to the pheneticist (a.k.a. "numerical taxonomist"). The hard core pheneticist might assert that because true
evolutionary relationships are not possible to know (we can't go back and make sure), that such terms are irrelevant and impossible to confirm.

The Cladistic System

 Devised by German biologist Willi Hennig and published in 1950, this is the most commonly used systemi in almost all institutions of higher learning today.
 The name of the system comes from the Greek clad, meaning "branch" and genesis, meaning "origin." Literally, it refers to the origin of branching of an ancestral
taxon into two sister taxa.

Four Tenets of Cladism:

1. Cladogenesis (speciation) is the only quantifiable feature of evolution.

2. All taxa must be monophyletic

3. All evolutionary relationships must be measured in terms of recency of descent from a common ancestor.
 4. The rank of a taxon is automatically determined by the age of the common ancestor.

Phyla had all branched off by the pre-Cambrian

Classes, by the Cambrian and Devonian

Orders by the Carboniferous and Permian

Families by the Triassic & Early Cretaceous

Tribes by the Late Cretaceous and Oligocene

Genera by the Miocene

If you don't remember the timeline of these periods, here's a handy reference Geological Time Scale.

Consider: All cladogenesis now taking place is at the species level.

In the Cladistic System:

 only derived characters are informative in determining evolutionary relationships.

 The more shared, derived characters two taxa exhibit, the more recent their common ancestry.
 degree of specialization after a branch point gives no further useful information about evolutionary relationships (or classification)
 Over time, an ancestral stem taxon gives rise to daughter (= sibling) taxa.
 The branching of a single, ancestral taxon into two new taxa is known as cladogenesis.
 Fossils are treated the same as extant taxa: a fossil organism cannot be said to be ancestral to an extant taxon. It can be said ONLY that a particular fossil taxon shares a
common ancestor with a particular extant taxon.
 In the ICBN, fossil taxa are considered to be morphotaxa (based on morphology only), since DNA, physiology, and other characters of the living organisms cannot be
known for certain.
 The Cladist uses shared, derived characters to devise a phylogenetic tree that is (hoped to be) based on recency of descent from a common ancestor.
 Such a phylogenetic tree is called a CLADOGRAM.
 More than one cladogram may be consistent with available data. In this case the systematist chooses the most parsimonious (i.e., the simplest; the tree with the fewest
steps, which is thus the simplest explanation of the relationships) to be the "working hypothesis."
 This doesn't mean that the cladist believes that evolution is always parsimonious. But until more data become available, the simplest explanation is the model of choice.
 organisms are ranked and classified SOLELY on the basis of recency of common ancestry.
 The time dimension of the phylogenetic tree is the most important; physical differentiation after cladogenesis is relatively unimportant.
 Where Classical Evolutionary Taxonomy and Cladistics Part Ways...

It's easiest to use an animal example:

In the Classical system, birds were accorded separate Class status (Class Aves), even though they share a most recent common ancestor with crocodilians and dinosaurs. The
Classical Evolutionary Taxonomist would say that characters such as feathers (modified scales), homeothermy(the ability to maintain constant body temperature metabolically)
and endothermy(the ability to produce body heat metabolically) make birds sufficiently different from other reptiles that they should be placed in their own class.

In the Cladistic system, birds are considered part of Reptilia because of their common ancestry with other reptiles. To give them separate status simply because of their
specializations obfuscates true evolutionary relationships. To the Cladist:

 feathers are a synapomorphy that link all birds together, with respect to all other vertebrates (none of which have scales modified to form feathers).
 If one considers only birds, however, feathers become a symplesiomorphy common to all birds. Their presence in birds offers no further useful information for classifying
different kinds of birds into smaller, less inclusive taxa.

 The bird example above illustrates how the degree of specialization after a branch point GIVES NO FURTHER USEFUL INFORMATION in terms of elucidating common
ancestry. In fact, common ancestry can be obscured if such specializations are used to justify separate taxonomic status for a group with such specializations. (e.g., assigning birds
to a separate Class (Aves) simply because they are "so different" from other descendants of the reptilian ancestor).

A recent cladogram of "green plant" relationships can be seen here, at the Tree of Life.
 These trees were devised by determining character states (in this case, presence or absence of a particular character), as shown below:

Characters that are common/widespread are usually considered to be ancestral/primitive states. But when two or more character states are compared, an outgroup is used: a taxon
that is closely related to, but not included in, the taxa being classified.

(What might be a good outgroup for the cladograms shown above?)

Analysis of rRNA sequences has yielded a universal evolutionary tree (always subject to revision, as more data become available!):
You already should be familiar with the two most commonly cited models for Eukaryote evolution, the Endosymbiont Model and the Autogenous Model...
It's probable that the photosynthetic eukaryotes evolved after the original heterotrophic ones, when photosynthetic prokaryotes were phagocytized, but not digested, by those first,
primitive heterotrophs.

Beginning next time, the introduction to Protists and Other Beasts. Don't miss it!
Prokaryotic Precursors
A word of warning right at the outset: The phylogenies in any textbook are usually
out of date. If there is a conflict, use Tree of Life Web Project, and your class notes.
As you should already know, prokaryotes are distinct from eukaryotic cells in many
ways. Notably...
 prokaryotes lack membrane-bounded organelles
 DNA in the form of a single, circular chromosome (and sometimes plasmids), not
linear chromosomes, as in eukaryotes.
 the flagellum is composed of flagellin, and is analogous--not homologous--to the
eukaryote flagellum (or cilium, which is essentially a shortened flagellum) Both have
the characteristic "nine surrounding two" microtubule arrangment in cross section.
 the cell wall, if present, is composed primarily of peptidoglycan, not cellulose (or
chitin, as in the fungi)
 they store energy primarily as glycogen (same starch that animals and fungi store)
Prokaryotes were once classified on the basis of shape, though this has long since fallen
by the wayside with new molecular techniques. But do recall the basic bacterial shapes
of coccus (round), bacillus (rod-shaped), or spirillum (curved rod or spiral), as these are
useful descriptive terms, if not always helpful for phylogenetic analysis.
Prokaryotes share genetic material via conjugation (analogous to
mating), transformation (taking up compatible DNA from the environment),
and transduction (transfer of genetic material via a viral intermediate), and reproduce
asexually via fission, simple division of the parent cell into two identical daughter cells.
(NOTE: fission is NOT the same as mitosis, as the chromosome of a prokaryote is
circular, not linear!).
Prokaryotes show tremendous diversity of metabolism with respect to...
Need for oxygen:
 aerobic
 anaerobic
 facultative anaerobic
Temperature tolerance:
 psychrophyles (extreme cold; can grow at 0oC and survive at much colder
temperatures)
  thermophiles (hot springs) and extreme thermophiles (deep sea vents)
and other environmental factors.
Metabolites from bacteria are used to produce many commercial products, from
antibiotics to products for milk fermentation (yogurt and cheese).
Some prokaryotes are pathogens. Most are gram-negative rods, and about a hundred
prokaryotic species are known to cause disease in plants. Of these, perhaps the most
devastating are the mycoplasmas and mycoplasma-like organisms (MLOs).
 smallest known living organisms
 genome is tiny
 lack a cell wall, so may assume different shapes
 may be free-living in soil and sewage
 may be intracellular parasites
 may be intracellular pathogens, and thus very hard to kill without harming the host
o Citrus Stubborn Disease (caused by a mycoplasma named Spiroplasma citri) is

transmitted by leaf hoppers, and causes severe stunting of growth

o X-disease, caused by an MLO, in peaches
o pear decline, caused by an MLO, spread by a psyllid fly vector

o Lethal Yellowing in Coconuts and other palms

Plant Precursors: Photosynthetic Prokaryotes

Of greatest interest to the botanist, perhaps, are the prokaryotes the echo the early
beginnings of the symbiosis that gave rise to the plants. These are the cyanobacteria,
once known as "blue green algae."
Cyanobacteria are ecologically important because they are
 photosynthetic
 nitrogen fixers
They are of great interest to evolutionary biologists because...
 their photosynthetic pigments (chlorophyll a, carotenoids) are also found in plants
 they have unique accessory pigments called phycobilins (phycoerythrin,
and phycocyanin)
 they have extensive internal membranes (thylakoids) similar to those in chloroplasts,
as seen in the famous ascidian symbiont, Prochloron.

As you already know, Earth was formed 4.5 - 5 billion years ago and the earliest life on
earth appeared between 3.5 - 4 billion years ago.
The oldest known fossils are STROMATOLITES--sedimentary rock (calcium carbonate
deposits) with striations very similar to those made even now by extant cyanobacteria.

The Evolution of Chlorophyll a:

Origin of our Oxidizing Atmosphere

 chlorophyll a first appeared about 3 billion years ago, in ancestral cyanobacteria.

 about 1 billion years ago, the first green algae appeared
 by the start of the Cambrian (0.6 billion years ago), oxygen was present in only about 1% of its present concentration.
(PAL = Present Atmospheric Level)

The Result:

 Anaerobic respiration gradually gave way to aerobic respiration as the major metabolic pathway.
 The upper levels of the ocean could be colonized because of the generation of a protective ozone layer.
  By 0.4 billion years ago (when land plants present), the oxygen was about 10% PAL
 It took about 1.2 billion years of photosynthesis to oxidize all the Fe in earth's crust, before oxygen could begin to enter the atmosphere.

The Earliest Eukaryotes were Protists

The oldest known eukaryote fossils (2.1 billion years old, found in pre-Cambrian fossil beds in Michigan) are called acritarchs.

from the Greek acrit = "confused" and arch = "origin"

What do "protists" have in common?

Other than their unicellularity, few characters link them as a large group. Rather, they are now being divided into the candidate kingdoms we see above.

Protists may be

 unicellular
 colonial
 colonial with a division of labor among cells
 planktonic (free-floating in a marine or freshwater water column)
 terrestrial
 photoautotrophic
 chemoheterotrophic, including
o predatory
o parasitic
o commensal
o mutualistic
o detritivorous (feeding on dead, organic matter and turning it into smaller organic molecules, but NOT decomposing it)

But always refer to The Tree of Life Web Project to keep track of how phylogenies are now viewed at any given nanosecond in time.

The Plant Clade: Archaeplastida

 Rhodophyta (red algae)
It is now believed that at least a billion years ago, an ancestral heterotrophic eukaryote took up a symbiotic relationship with a cyanobacterium-like prokaryote, and the
ancestor of Rhodophyta was "born." That early Rhodophyte lineage is later believed to have branched, giving rise to today's Rhodophyta and Chlorophyta.
 (What do you suppose might be the significance of having a red pigment (phycoerythrin) as a photosynthetic accessory pigment? Hint: what wavelengths would such a
pigment (1) absorb and (2) reflect. And which of those wavelengths goes deeper into water?)

 Green Algae Relatives of land plants

Eukaryotes have been around for a long time. But what we now commonly call "protists" are probably derived from many different ancestral lineages, and systematists are only
now beginning to sort out the mess that was once "Kingdom Protista" into eight or more candidate new kingdoms.

You learned about most of these in BIL 160, so we will concentrate today only on the protists that are now included with plants in a monophyletic taxon briefly known
as Viridaeplantae, but now often referred to as "Green Plants" until we figure out the relationships and monophyly of its component taxa.

The Green Plants (Viridaeplantae?)

This descriptive group name now includes more than just the familiar land plants. Using cladistic techniques to determine common ancestry, plant systematists have disposed of
the archaic "Kingdome Plantae" and redefined "green plants" as a broad (putatively monophyletic) assemblage of eukaryotes that share the following apomorphies, unique to this
group

 chlorophylls a and b
 carotenoids as accessory photosynthetic pigments
 chloroplasts with a double membrane
 energy stored as starch inside the chloroplast in which it is produced
 cell walls composed of cellulose

Included in the "green plants" are several thousand species of green algae and hundreds of thousands of species of land and aquatic plants.

Within the Green Plants are less inclusive taxa, which we will visit in turn.

Zygnematales
The Zygnematales are (haploid) green algae that undergo sexual reproduction via conjugation: haploid vegetative cells in the algal adult form non-flagellated gametes.
Complementary (+ and - types) gametes fuse to form a zygote. There are many variations on the conjugation theme, but one example is nicely shown in Spirogyra:
Each zygote undergoes meiosis to produce four new haploid propagules, which are released from the cell wall of the former vegetative cell to grow into new, haploid filaments of
algae.

Charales
The Charales, also known as stoneworts or brittleworts, are common in slow-moving, often eutrophic freshwater habitats, and are found on every continent except Antarctica.

The plant body (a.k.a. thallus) consists of large cells that may be several centimeters long. The algae may branch at nodes made up of smaller cells.

As in true plants, growth occurs at the apex (though there are no true tissues, and hence, no true meristems). The base of the plant and along the length contacting substrate sprouts
clear rhizoids, rootlike structures that are not absorptive, but primarily for anchoring the organism.
The algae has separate sex organs (male = antheridia; female = oogonia), which grow at the nodes.

The name of these algae comes from the crust of white calcium carbonate seen in some species, which gives them a crunchy feel. Some species have a strong, icky smell, and are
sometimes given the nickname "skunkweed" or "musk grass".

Chara is a species of particular interest in southern Florida, as it is a problematic invasive exotic that chokes canals and waterways throughout the area.

Early Cousins of Land Plants: Coleochaetales

There are fifteen extant species of Coleochaete, of interest to systematists because they appear to be the closest living relatives of land plants. What characters do they share?

 Zygotes are retained in the oogonium, where they grow and develop into new plants.
 Oddly, they do not undergo an alternation of generations, which other green plants do.

Coleochaetes are abundant, often found attached to the leaves of aquatic flowering plants and other firm substrates in fresh water. Land Plants, Zygnematales, Coleochaetales
and Charales share important synapomorphies:

 Cellulose synthesis takes place inside rose-shaped hexameric proteins known as rosettes anchored in the plasma membrane. (Land plant and charophyte cell walls contain
more cellulose than do those of other green algae.)
 Their cell walls contain lignin-like compounds
 o along with the complex carbohydrate cellulose (the most abundant organic molecule on earth), lignin is a major structural component of many types of plant cell
walls.
o lignin is most often a component of woody plant bodies, and less common in herbaceous (i.e., non-woody) plants
o lignin is a very large organic molecule that confers compressional strength to plant parts.
 Zygote cell walls contain sporopollenin, once thought to be unique to land plants.
o Many algae (including charophyceans) live in ephemeral ponds that dry up.
o Natural selection favored individuals with traits that best enabled them to survive and/or produce offspring despite drought.
o Charophyceans produce a tough polymer, sporopollenin, that covers the zygotes (which are still attached to the mother plant) and protects them from desiccation.
o Sporopollenin is also found in plants, where it is a component of the protective covering of plant spores.
o Because sporopollenin allowed plants to survive in drier habitats, it facilitated their early colonization of land.
 Peroxisome enzymes

Recall that peroxisomes contain enzymes that manufacture H2O2 from various substrates, and use it to oxidize large molecules (e.g., fatty acids) into smaller
molecules that can be transported to the mitochondria for use in cellular respiration.

Only charophycean and land plant peroxisomes also contain enzymes that reduce the loss of the organic products via that old evolutionary relic, photorespiration.

 Similar flagellated sperm - its structure is different from that found in other algal groups.
 A phragmoplast forms near the end of mitosis.

Recall: the phragmoplast is composed of microtubules and microfilaments, and appears late in mitosis. Vesicles derived from the Golgi gather at the equator of the
nascent daughter cells, forming a network of tubules and vesicles filled with cell wall precursors. This "cell plate" gradually expands towards the perimeter of the
cells, and joins with the original cell wall, separating the two daughter cells from each other.

Embryophyta: The Land Plants

Several synapomorphies link all land plants together and distinguish them from their relatives:

 heteromorphic [alternation of generations] (note the meaning of "heteromorphic")

 [true tissues]
 waxy cuticle (to prevent desiccation)
 stomates (microscopic openings on the leaf for gas exchange)
 apical meristems (plant "stem cells" at the tip of every shoot and root)
 multicellular [gametangia] - antheridia in males, archegonia in females
 walled spores produced in sporangia
 embryo develops inside mother's archegonium
  secondary metabolites such as alkaloids, terpenes, tannins, phenols, flavonoids (which we've met before)

Items above that appear in [brackets] are found in all plants, but may also appear in a few highly derived green algae and/or charophytes.

Embryophyta: An Overview
 The Bryophytes - Non-vascular Plants
These include the Marchantiomorpha (liverworts), Anthocerophyta (hornworts), and Bryophyta (true mosses). Bryophytes lack an internal vascular system for transport: no
xylem, no phloem.

In Bryophytes, the haploid gametophyte phase is the dominant life cycle phase, living more than one season.
The diploid sporophyte generation is small and ephemeral.

 Hepatophyta (Marchantiomorpha) - the liverworts

 Anthocerophyta - the hornworts
 Bryophyta - the mosses

 Tracheophyta - The Vascular Plants As the name implies, these plants have an internal transport system consisting of

 xylem
...which transports water and dissolved minerals
from the roots to the rest of the plant, and
 phloem
...which transports photosynthetically produced sugars, proteins, and other biological macromolecules
throughout the plant, in varying (and changing) directions.

In Tracheophytes, the diploid sporophyte phase is dominant, living more than one season;
the haploid gametophyte generation is small and ephemeral.

 The Seedless Vascular Plants

o Lycopsida - club misses, spike mosses, and quillworts
o Filicopsida - ferns, horsetails, whisk ferns
 The Spermatopsida (Seed Plants)
o Gymnosperms (the naked seed plants)
 Cycadophyta - the cycads ("sago palms")
 Ginkgophyta - maidenhair trees
  Coniferophyta - the conifers
 Gnetophyta - the gnetophytes
o Angiosperms (the flowering plants)

The Non-vascular Plants: Amphibians of the Plant World The Non-vascular plants, commonly known as bryophytes (from the Greek bryo, meaning "moss"
and phyt, meaning "plant") are the descendants of the first true land plants. Some of them have remained relatively unchanged from those ancestors, retaining
many primitive characters that keep them from becoming truly independent of water (though some species live in extremely dry habitats). They definitely
make our world more beautiful.

An overview of Embryophyte relationships, featuring the Bryophytes...

An appropriate outgroup for this cladogram would be the Charophytes, the green-algae like plants that exhibit oogamy (as do plants): the fertilization of a
sessile egg (retained within the female's tissues) by a motile sperm (the only flagellated cell ever produced by Bryophytes).

Reminder:

 isogamy - gametes are physically indistinguishable

 heterogamy - gametes are physically distinguishable
 oogamy - special case of heterogamy

Molecular, ultrastructural, and morphological data confirm that the Bryophytes are monophyletic with the rest of the Embryophyta, and their characteristics can
thus give us insights into the very first evolutionary adaptations that allowed plants to colonize land.

Sporopollenin
 Many algae, including charophyceans, live in ephemeral ponds that dry up.
 Natural selection favored individuals with traits that best enabled them to survie and/or produce offspring despite drought.
 Charophyceans produce a tough polymer, sporopollenin, that covers the zygotes (which are still attached to the mother plant) and protects them from desiccation.
 Sporopollenin is also found in plants, where it is a component of the protective covering of plant spores.
 Because sporopollenin allowed plants to survive in drier habitats, it facilitated their early colonization of land. Why would a terrestrial existence be an advantage?

 air filters less sunlight than water. There's more light for photosynthesis.
 air has more CO2 than water. There's more fuel for photosynthesis.
 early terrestrial habitats lacked pathogens or predators/herbivores.
 terrestrial soil is richer in nutrients than aquatic soil (why?)

All this meant that individuals who could best survive on land had a reproductive advantage. Sporopollenin, evidently first produced by the ancestor of Charophytes and Land
Plants, was one of the earliest exaptations that allowed plants to withstand the harsher environment of land. The conversion of earth to a plant-based planet had begun.

Bryophytes...

 lack xylem and phloem (hence, lack true organs)

 have a very thin waxy cuticle
 have stomates fixed in the open position; they cannot be closed
 release flagellated sperm directly into the environment (and so need water--at least a thin film--for reproduction)
 have a dominant gametophyte generation, and a short-lived, ephemeral sporophyte

 Bryophytes that lack true vascular tissue do not have true leaves, stems and roots.
 The relatively undifferentiated body of such plants is known as the thallus, the term used to describe a plant (or fungal) "body".
 The three major bryophyte taxa are

 Hepatophyta - The Liverworts

 Anthocerophyta - The Hornworts
 Bryophyta - The True Mosses

(NameNote: The suffix "wort" is from the ancient Anglo Saxon word wyrt meaning "herb".)

Let's meet them.

Hepatophyta (Marchantiomorpha): The Liverworts The earliest clade to branch from the other embryophytes was the ancestral liverwort. These are thalloid plants, as their body
consists of a relatively undifferentiated thallus that branches dichotomously. To the creative eye, the liverwort thallus bears a faint resemblance to a certain animal organ that gets
very little respect...

The Doctrine of Signatures is an ancient belief that the shape, color and other properties of plants can tell the herbalist which ones can be used to heal ailments of specific parts of
the body. Liverworts, as you might guess, were often used to treat liver ailments, though no data exist to suggest that such treatments were (or are) effective.

Liverworts live in moist, shady places such as stream banks, and there are many species in the tropics, subtropics (not here, though!), and temperate forests.

The more primitive liverworts are thalloid, and the more derived are termed "leafy" because of their small, leaflike projections.
The top portion of the thallus is rich in chloroplasts, whereas the bottom layer (thicker) is devoid of any chloroplasts or pigment. This is where the rhizoids sprout, anchoring the
thallus to the substrate.

Liverworts have primitive, stomate-like pores but they cannot open and close as the stomates of higher plants can.

Reproduction Reproduction may be asexual, via gemmae:

Or sexual:

Liverwort gametophytes:
 The male (left) bears stalks called antheridiophores that bear the sperm-generating antheridia
 The female (right) bears stalks called archegoniophores that bear the ovum-bearingarchegonia
 When the environment is wet, the antheridia release sperm, which swim up the archegoniophore and into the archegonium.
 Fertilization takes place inside the archegonium, and the resulting zygote then grows into a sporophyte, in situ.
 Still attached to the archegoniophore, the sporophyte grows a single sporangium, within which meiosis takes place.

 The resulting spores are released into the environment, where the lucky ones will germinate and grow into gametophytes (either male or female).

 The sporophyte and archegoniphore then wither and die, leaving the gametophyte thallus to grow and prosper.
 Here's the whole cycle...
Mosses and Hornworts have very similar life cycles, though the plants look somewhat different.
In all Bryophytes, the gametophyte is the long-living stage, whereas the sporophyte is ephemeral.

Don't miss the exciting new film, Explosive Liverwort Sperm!.

Anthocerophyta: The Hornworts Hornwort gametophytes superficially resemble thalloid hornworts, but their cellular structure suggests that they are not particularly closely
related. In many species (but not all):

 Cells usually have one large chloroplast

 Chloroplast contains a pyrenoid (similar to that seen in the Charophycean Coleochaete)
 Many hornworts are mutualistic with cyanobacteria, which fix nitrogen in the hornwort tissues.
 Like Liverworts, Hornworts undergo fertilization inside the female archegonium, and the sporophyte sprouts from the gametophyte thallus.
At maturity, the curled sporangium splits open to release the haploid spores.

The Hornwort sporophyte is of interest in the journey to the dominant sporophyte seen in vascular plants because
  It has a meristem between the foot (point of attachment to the gametophyte) and the sporangium, and so grows continually as long as conditions are good. This results in a
very elongate sporophyte.
 The sporophyte has numerous stomates with guard cells.
 It has a waxy cuticle

Bryophyta: The True Mosses The mosses are the most diverse non-vascular plants, and are economically and ecologically important for many reasons. There are three Classes of
mosses now accepted:

 Sphagnidae - The Peat Mosses (Sphagnum)

 Andreaeidae - The Granite Mosses (Andreaea, about 120 species; Andraeobryum, one species)
 Bryidae - The "True" Mosses (about 9500 species)

Alone among the bryophytes, mosses sometimes contain a thin strand of conducting tissue in the center of the erect portion of the plant body. This makes the stalklike structure an
early stem. In some species, the leaflike structures also contain a small, central thread of vascular tissue, and so some species of mosses also have the early beginnnings of true
leaves.

Mosses have a life cycle very similar to that of the liverworts (and hornworts)
...although the male and female gametophytes are not as obviously morphologically distinct. Sphagnidae - The Peat Mosses The most primitive mosses are the peat mosses, all
contained in the genus Sphagnum which has about 400 species.

The Sphagnum sporophyte is different from that of all other mosses, forming a red or black sphere raised up on a haploid pseudopodium (it's part of the gametophyte).
As the spores inside mature, the sporangium gradually dries up, internal tissues shrink, and the air pressure inside builds up to about 5 bars (about what you'd find in the tire of a
large truck). When the pressure is sufficient, the top of the sporangium (the operculum) pops off violently, spraying spores all over the place!

The Strangeness of the Sphagnum protonema. Unlike the protonema of other mosses, which resembles filamentous algae, Sphagnum protonema is a plate of cells, one layer
thick, that looks a LOT like Coleochaete. The marginal cells are meristematic, and divide either sideways or outwards, increasing the size of the protonema. Eventually, the erect
stalk of Sphagnum grows from one of the marginal cells. It contains an apical meristem that gives rise to the stem and leaves.

Ecological Importance of Sphagnum A whopping 1% of the earth's surface (about half the area of the U.S.) is occupied by peat bogs, making Sphagnum one of the most abundant
plants on earth. The peat bogs store huge amounts of carbon (400 billion metric tons), and so may mitigate the effects of anthropogenic climate change.

Because peat bogs (made up of dead Sphagnum plus all the grasses and other plants that grow within the moss) are highly acidic, they are not hospitable to bacteria, and decay
occurs extremely slowly, making the sequestered CO2 therein stable and not likely to be released quickly. This can be seen clearly in the preservation of the Bog People of
Denmark.

Dried peat is an important fuel for domestic and industrial use in many northern countries. So much for sequestered carbon!

Andreaeidae - The Granite Mosses These ancient mosses grow mostly in high, mountainous and arctic regions, often on solid rock (which is where they get their name).
What's unusual about them?

 The protonema consists of a double row of cells, rather than the typical single row
 The rhizoids, too, consist of two rows of cells (unlike the single row of other bryophytes)
 The sporangium capsule ruptures via splitting at four places along the side, rather than popping an apical operculum, as in most mosses.

Bryidae - The True Mosses The vast majority of moss species belong to this taxon. They usually grow as short, upright plants that form "cushion" mats, or in a more creeping,
"feathery" form.
Mosses may grow on soil, rocks, or as epiphytes, and are found at almost all latitudes.

Leaves usually grow in a spiral arrangement along the stem.

"True" mosses show several evolutionary advances over the liverworts, hornworts, and other mosses are seen in various species of bryids, such as

 multicellular rhizoids
 leaves with a distinct midrib, sometimes containing conducting cells
 stems of some species contains a central strand of conducting tissue known as the hadrom, consisting of individual cells called hydroids. These are elongate, tapering cells
that lack a protoplast at maturity.
 in some species, nutrient-conducting leptoid cells surround the hydroids, comprising a nutrient-conducting tissue called leptom.
 The sporangium of the mature sporophyte is capped by the haploid calyptra, derived from the gametophyte.
  At spore maturity, the calyptra falls off, revealing the operculum. When the operculum popps off, the peristome becomes visible as a ring of tiny "teeth" alternating with
open areas through which the spores escape into the world.

The peristome is different in morphology across species, and is used as a classification tool. In all species, however, it opens and closes in response to changes in humidity (when
do you suppose it opens?)

And speaking of changes with humidity, let's have some fun with mosses.
The Tracheophytes: Vascular Plants In the bryophytes, the haploid gametophyte is the conspicuous, long-lived generation, and the diploid sporophyte is
attached to the maternal gametophyte for its entire, relatively short lifespan.

In Tracheophytes, the opposite is true. The gametophyte is short-lived and may be either free-living (the more primitive condition) or attached to the parent
sporophyte for its entire, short lifespan. Most of the plants you see in your day-to-day travels are the sporophytes of vascular plants.

Tracheophytes have several evolutionary advances that made them better suited for a fully terrestrial existence than are the Bryophytes.

 xylem and phloem

 lignin (not only structural in and of itself, but allows greater turgor pressure)
 thick waxy cuticle
 fully functional stomates (open and close with turgor pressure)
 profuse branching via apical meristems
o increased young tissues for photosynthesis
o increased areas for sporangia (as opposed to only one sporangium per sporophyte in the Bryophytes)
 highly differentiated plant tissues and organs
The Body of the Vascular Plant
The earliest vascular sporophytes were plants consisting only of stems, lacking leaves or roots. They were dichotomously branched, and relatively
undifferentiated.

Later, the root system and shoot system evolved, making the plant body parts more versatile, and allowing a division of labor.

Recall the general types of tissue and their functions:

 vascular
 ground
 dermal
 meristematic

...as well as the difference between primary growth and secondary growth.

Vascular Tissues
Both tracheids and vessel elements are known as tracheary elements, although the two types of cells evidently evolved independently. (Any morphological
similarity is due to convergence.)
Stem Evolution
The earliest vascular plants were little more than an elongate axis with a core of vascular tissue. This axis can be considered the primordial stem, from which
the other plant organs evolved.

One can see the progression of complexity in the plant axis reflected in the arrangement of vascular tissues in the cross section of the stem (and now, in the
root). The central core of vascular tissue in the plant root or stem is known as the stele, and there are several different types that can be identified by their
morphology in cross section.

 The Protostele: A central core of xylem surrounded by a ring of phloem.

  haplostele - found in most roots, this is a solid core of xylem surrounded by phloem. It is the most primitive type of protostele.
 actinostele - named for its shape (from the Greek actinos, meaning "ray"), this one is rare. The whisk fern, Psilotum is one extant plant having an actinostele. (You'll
meet Psilotum shortly.)
 plectostele - interconnected regions of xylem are collectively surrounded by a mass of phloem. Club mosses (Lycopodiopsida) often exhibit this type of stele arrangement.

 The Siphonostele: A central pith is surrounded by a ring of xylem, which is, in turn, surrounded by a ring of phloem.

 solenostele - the most primitive type of siphonostele, this is a pith surrounded by xylem and phloem. Some primitive ferns show this type of arrangement.
 dictyostele - similar to the solenostele, but with multiple gaps in the xylem/phloem ring surrounding the pith where numerous leaf gaps occur. Found only in ferns.
  eustele - The rings of xylem and phloem are now arranged in bundles, forming a circle around the central pith. This is the most common type of stele in seed plant stems.

Here's an illustration of how leaf gaps cause gaps in the xylem/phloem rings in some types of siphonosteles (depending on where the cross section is taken).

Root Evolution
Roots evolved from the underground portions of the plant, but retained many primitive characteristics. For example, all roots except those of monocots retain the haplostele
configuration.

Leaf Evolution
The first leaves were merely scales that "peeled away" from the ancient plant axis, lacking any trace of vascular tissue. These were known as enations, and are still found in a few
living plants (e.g., the Whisk Fern, Psilotum).

Further evolution resulted in somewhat larger scales growing out from the stem, and taking a core of protostele along with it. These early leaves were probably very similar to
the microphylls of the living Club Mosses (whom you'll meet shortly). Microphylls contain a single strand of vascular tissue, and do not leave leaf gaps as larger leaves do.

Megaphylls are larger leaves, and are found in plants with siphonosteles or eusteles. Most living plants have megaphylls, though many of these are highly derived and may have
lost their original leafy shape (e.g., cactus spines; pine "needles").

The Life Cycle of Seedless Vascular Plants One picture is worth lots of words. Let's locate the Smurfs and Humans in this life cycle of a fern, which is typical of most other
seedless tracheophytes.
Note the reversal of fortune, relative to the bryophytes: the sporophyte is now the long-lived generation, and the gametophyte is short-lived and ephemeral. In the seedless vascular
plants, the gametophyte is free-living, and not dependent on the parent sporophyte.

Evolution of the Seedless Vascular Plants Three phyla of extinct seedless vascular plants are of interest to evolutionary botanists

 Rhyniophyta - named for the Scottish village of Rhynie, where abundant fossils were found.
 Zosterophyllophyta - Named for their resemblance to modern marine anthophytes in the genus Zostera, which superficially resemble grasses.
 Trimerophytophyta - Probably provided the ancestral lineage from which both the pteridophytes and the early gymnosperms arose.
The three extinct phyla above were relatively small in stature, and flourished from the Silurian (about 425 mya) to the middle of the Devonian (about 370 mya).

Rhyniophyta
These were relatively small, undifferentiated plants consisting of upright and underground axes that branched dichotomously, and (when reproducing) ended in a single
sporangium that produced homospores. Rhizoids sprouted from the underground axes. The plants had a waxy cuticle and stomata.
The axis anatomy was similar to today's vascular plants: epidermis surrounding a cortex surrounding a stele of central xylem and peripheral phloem. The tracheids were
more similar to moss conducting cells than to vascular plant tracheids, but had more lignin in their cell walls.
In the rhyniophytes, xylem cells matured first in the center of the stem, with younger cells found progressively outwards, toward the periphery of the stele. This process is
known as centrifugal differentiation.

Zosterophyllophyta
Also leafless and consisting of dichotomously branching stemlike axes, these small plants had stomates only on the upper surface, suggesting they were nestled in mud or
sludge.
Sporangia were borne on small, lateral branches, and like Rhyniophytes, zosterophyllophytes were homosporous.
Unlike the xylem of rhyniophytes, zosterophyllophyte xylem matures first at the periphery of the stele, with younger, less differentiated cells found in the center of the
stele. This "opposite" type of maturation from most plants is called centripetal differentiation, and is seen in today's Club Mosses. Because of this similarity and because
lycophyte sporangia and sporangia-bearing branches are so similar, Zosterophyllophyta is believed to share a most recent common ancestor with today's Lycophyta.
Trimerophytophyta
Trimerophyta specimens are believed to be the sister taxon of Rhyniophyta. They were leafless, but more profusely branched than Rhyniophyta. Reproductive branches terminated
in clusters of elongate sporangia, each borne on a smaller, shorter stem. Xylem differentiates centrifugally, as in rhyniophytes.

Still no leaves, but these plants were larger (more than a meter tall) and more complex than the Rhyniophytes and Zosterophyllophytes.

Still homosporous, but reproductive branches ended in clusters of elongate sporangia.

The features of the three extinct phyla give us clues to the orgins of the two extant phyla of seedless tracheophytes

 Lycopodiophyta - The Club "Mosses"

 Pteridophyta - The Ferns and their relatives

Lycopodiophytes and Pteridophytes became dominant from about the late Devonian (about 375 mya) and were dominant through the Carboniferous (about 290 mya).

Seed plants first appear in the fossil record in the late Devonian (about 380 mya), and underwent an explosion in diversity through the Permian and Mesozoic.

When the first flowering plants appeared about 125 mya, it took only about 40 million more years for them to diversify and colonize habitats so successfully that they out-
competed other plants in almost every habitat. They retain this dominance today.

Phylum Lycopodiophyta - The Club Mosses Around the mid-Devonian, a major evolutionary split separated the lycophyte lineage from the ancestors of all other vascular plants
(euphyllophytes).

Though today's lycophytes are small and herbaceous, ancient ones were the size of large trees, and were the major plant form in the Carboniferous.

Club Mosses are characterized by a stem with a protostele, underground rhizoids, and microphylls.

The more primitive family of extant lycophytes is Lycopodiaceae, the most diverse genus of which is Lycopodium.
The structures you see in two of the species above are called strobili (singular, strobilus. A strobilus is a whorl of sporophylls, and is also sometimes known as a "cone."

The spores are homospores, giving rise to gametophytes that are either (depending on species)

 photosynthetic, lobed masses of cells somewhat reminiscent of liverworts

 or

 underground, non-photosynthetic mycorrhizal symbionts

The gametophytes of some species take 6-15 years to develop mature antheridia and archegonia, and once they mature, they may produce a series of sporophytes as they grow
vegetatively. They tend not to self-fertilize, predominantly cross-fertilizing. (Why is this best?).

The genus Selaginella includes familiar species such as the Resurrection Plant (Selaginella lepidophylla), but contains about 750 other species, as well.
Like Lycopodium, the stems of Selaginella bear microphylls, and the sporophylls are arranged in strobili. But this time the plant is heterosporous, producing microspores and
megaspores, which develop into male and female gametophytes, respectively.

Megasporangia are borne on megasporophylls, and microsporangia are borne on microsporophylls in the strobilus, which you see in longitudinal section here:
The microgametophyte develops inside the microspore, and at maturity consists of one vegetative cell and an antheridium which produces multiple, biflagellate sperm. This
ruptures when environmental conditions are right for sex.

The megagametophyte grows within the megaspore, but ruptures its wall when it reaches a certain size. Only the segment producing archegonia protrudes from the megaspore
cell wall, making it available for sperm.

Fertilization takes place once the male and female spores have been shed from the strobilus, and the sporophyte grows inside the archegonium. In some species of Lycopodium and
Selaginella, a stalklike suspensor connects the embryo to the gametophyte, and in some of those, the suspensor pushes the sporophyte embryo into the nutrient-rich gametophyte
tissues where it feeds, grows, and eventually becomes an independent sporophyte.

Phylum Pteriodiophyta - Ferns and their Relatives This is a very diverse group, with more than 11,000 species, second only to the angiosperms in variety.

The most familiar pteridophytes are the ferns, which can be classified on the basis of the type of sporangia they grow:

 eusporangia
 leptosporangia

as shown here...
Only two orders (Ophioglossales; Marattiales) produce eusporangia; all others produce leptosporangia. Of these, the most widespread and well known are the grape ferns
(Botrychium and the Adder's Tongue Ferns (Ophioglossum)
The gametophytes of these genera are non-photosynthetic, subterranean and form symbiotic relationships with fungi that live within their tissues. The gametophytes are
homosporous.

Fun Fact for Botanical Trivial Pursuit: Ophioglossum reticulatum has more chromosomes--1260--than any other living organism. And yet how tiny!

The vast majority of ferns, however, produce leptosporangia and are homosporous. The largest taxon is Order Filicales, with at least 10,500 of the 11,000 species of ferns.

Most filicale ferns have stems with a siphonostele, and produce megaphylls. The underground portion of the plant is a rhizome (also with a siphonostele), and this sprouts
numerous, true roots with a protostele.

The fern leaf is usually pinnate with a central rachis (the extension of the petiole in pinnate leaves), and young leaves in most species emerged as coiled structures known
as fiddleheads
Some make a tasty addition to salads, and others are distasteful or even poisonous (renal toxins are common in ferns!). So be sure you can properly identify a fern before you eat it!
Sporophylls are not borne in strobili, but are individual fronds that grow sporangia on their undersides, when mature. The sporangia occur in clusters called sori (singular = sorus),
and in some species the sorus is covered with small, protective plate (an outgrowth of the leaf), called an indusium.
Spores grow into a bisexual gametophyte, again reminiscent of a liverwort.
Note the locations of the antheridia and the archegonia. The new sporophyte will sprout from the notch in the "heart," eventually obliterating the gametophyte.
The Psilotales The Whisk Ferns were once believed to be the most primitive tracheophytes because of their superficial resemblance to the Rhyniophytes. Aboveground and
belowground parts of the plant contain a protostele, and are considered to be simple stems. However, molecular data now reveal that they are fern relatives that have secondarily
lost their fernlike features.
The life cycle is similar to that of other ferns, with a bisexual gametophyte that resembles the Psilotum rhizome. It is subterranean, and forms symbiotic relationship with fungi in
the plant tissues.

Equisetales - The Horsetails These ancient fern relatives were once placed in their own phylum, but it is now known that they share a common ancestor with other ferns, and so are
subsumed into the Pteridophyta.

The plants consist of hollow stems with rings of dry, scalelike leaves at each node.
The only surviving genus, Equisetum, is essentially unchanged from its Carboniferous fossil relatives, making this perhaps the oldest named genus.

These live in moist areas and bogs. The hollow stems are highly impregnated with silica, which makes them rough and tough. Native Americans are said to have used them to
scour pottery, and hence their other common name, "Scouring Rushes."
The strobilus of Equisetum is composed of a whorl of small, sporangium-bearing modified branches called sporangiophores.

The homospores have thickened bands of the cell wall known as elaters wrapped around the spore, and these expand and contract, depending on humidity.
These germinate into bisexual gametophytes that are photosynthetic, free-living, and ranging in size from a few millimeters to about 3.5 millimeters in length.
...and the cycle begins again.

Spermatopsida: The Seed Plants The seed plants are the dominant plant life forms on the planet today, and the arose from numerous branchings of the plant
clade. Collectively, the seed plants are classified in Spermatopsida.

Five phyla of seed plants still exist today.

 Cycadophyta - the cycads, or sago "palms"

 Ginkgophyta - the ginkgos
 Coniferophyta - the conifers
 Gnetophyta - the gnetophytes (yes, that's the best I can do)
 Anthophyta - the flowering plants

Of these, the first four above are gymnosperms, and the last comprises the angiosperms. In this lecture, we'll concentrate on the gymnosperms.

The Gymnosperms: Plants with Seeds, but no Flowers or Fruit The gymnosperms (from the Greek gymnos, meaning "naked" and sperm, meaning "seed") are
the first seed plants. The seed conferred a major selective advantage because it not only protects the growing sporophyte embryo from the environment (the
seedless plant sporophyte embryo is exposed and helpless in comparison), but also provides nutrients and, in many cases, a means by which the new
sporophtyes can be dispersed very far from the parent organism.

The Magical Seed Unlike the seedless tracheophytes, which are mostly homosporous, all gymnosperms are heterosporous, producing male microspores and
female megaspores. Seeds amplify heterospory, with megaspores developing inside an ovule which will eventually become a seed.

Over the course of seed plant evolution, the following events each conferred a selective advantage. They led to the evolution of the ovule as we know it today.

 Megaspores were retained inside the megasporangium, instead of being released.

 The megasporangium became fleshy and filled with nutrients. In seed plants, the megasporangium tissue is known as nucellus
 Megaspore mother cells in each sporangium were reduced to only ONE, instead of many.
 Only one of the four megaspores produced via meiosis is retained (similar to oogenesis in animals. Why is this advantageous?)
 The megagametophyte remains and develops entirely within the megaspore, and never becomes free-living.
 The sporophyte embryo remains and develops within the megagametophyte.
 Sporophyte tissues enclosed the megasporangium, forming integuments around it that will eventually become a protective seed coat. The integuments
have only one opening, the micropyle, via which the male can reach the megasporangium.
 The micropylar apex of the megasporangium is chemically and morphologically modified to better receive microspores/pollen grains.
We don't know which of these events occurred first, but fossil evidence suggests that the integuments evolved from fleshy lobes of sporophyte tissue
(the cupule) that originally surrounded the megasporangium. Their gradual fusion left only the micropyle as an opening.
The earliest cupule is seen in the late Devonian plant Elkinsia polymorpha:

And later fossils show a progression of cupule fusion that probably led to today's ovule:
Progymnosperms Phylum Progymnospermophyta is an extinct taxon of woody plants that had characteristics intermediate between the seedless tracheophytes
and the seed plants. Like the seedless plants, they

 produced spores that gave rise to free-living gametophtyes

 most species were homosporous

Like seed plants, they

 produced true wood made of secondary xylem (fossils look like conifer wood!)
 produced secondary phloem
 had a bifacial (i.e., growing xylem in one direction and phloem in the other) vascular cambium
 had flattened structures that apparently were true leaves
 had a protostele
 a few species were heterosporous These plants formed large trees (some 17 meters tall!), and were found in dense forests. Some have called them the "first modern trees". They
likely share a common ancestor with all modern seed plants.
Extinct Gymnosperms Recall that fossil plants taxa are almost always considered to be morphotaxa, since we cannot examine them closely enough to determine ultrastructure and
DNA sequences that would reveal true evolutionary relationships. One such group is the "seed ferns" (Pteriodpsermales), and another is the Cordaitales (coniferlike seed plants).
The former is almost certainly polyphyletic. Both groups reached their peak of dominance in the Carboniferous.

"Coal Age" plants are of great ecological importance, especially today with mounting evidence of anthropogenic climate change.

 Today, photosynthesis takes up about 100 billion metric tons of CO2 per year.
 This is only about 10% of total atmospheric CO2
 Respiration returns about the same amount of CO2 to the atmosphere as what is removed via photosynthesis. (The difference is about 1 part in 10,000)
 This slight loss of CO2 is due to dead, organic matter being buried and put out of reach of decomposition.
 Plant matter so buried becomes peat.
 If peat is further buried under many layers of sedimentary rock, and comes under pressure, it can transform into coal.
 Certain periods in earth's history saw much greater deposition of "fossil fuel" than others, and one is the aptly named Carboniferous. Carbon-based organic matter was present in
huge quantities in the Carboniferous:

 The earth was warmer than it is now, fostering photosynthesis and plant growth
 Lands were low, and sometimes covered by warm water
 The equator was farther north, allowing tropical and subtropical conditions to promote plant growth farther north (where most land masses are) than now.

Five groups of plants dominated the lands at this time. Three of them--the lycophytes, equisetophytes and ferns--were seedless vascular plants, and the other two weee the seed
ferns and the cordaites.

Extant Gymnosperms Recall the four phyla of gymnosperms that still grace our planet today:

 Cycadophyta - the cycads, or sago "palms"

 Ginkgophyta - the ginkgos
 Coniferophyta - the conifers
 Gnetophyta - the gnetophytes (yes, that's the best I can do)

Let's meet them.

Coniferophyta - The Conifers The most familiar gymnosperms are the conifers. Pine, spruce, fir, redwoods, cedar, cypress, juniper...the list goes on. But one thing they share is a
life cycle that's a bit more complex than that of the seedless tracheophytes. A few important notes:

 The female gametophyte (megagametophyte) produces several archegonia

  More than one ovum may be fertilized, and more than one embryo in the ovule may begin to develop (polyembryony), but in the end, only one embryo out-competes its
siblings and survives. Very few seeds ever contain more than one viable embryo.
 Gymnosperms no longer need environmental water for fertilization. The male gametophyte that develops from the microspore is a windborne pollen grain that is delivered
directly to the female's "door" (micropyle).
 The process of the pollen being delivered to the close vicinity of the megagametophyte is known as pollination.
 After pollination, the microgametophyte (pollen) grows a pollen tube through which two sperm are delivered to the megagametophyte. There are no antheridia in the seed
plant male gametophyte!

The Diversity of Conifers Seventy genera include the approximately 630 species included in the Coniferophyta. The largest living organisms ever known, the Giant Redwoods
(Sequoia sempervirens) belong to this group, as do the oldest living things, the Bristlecone Pines (Pinus longaeva).

And as we tumble farther into autumn and the winter holiday season, it's interesting to note that the Christmas Tree had its origin as a phallic symbol adopted from the seasonal
fertility rites of the pagan Germanic and Roman people of ancient Europe.
The approximately 80 species of pines dominate the biome known as coniferous forest or taiga. Here they dominate because of the slight advantage they have of being able to
photosynthesize--albeit at a very low rate--even during the harsh winter months, which deciduous flowering trees cannot.

Pine Leaves: Unique Arrangement In a pine seedling, the leaves (long, thin modified leaves often called "needles") are borne singly, and whorl around the branches.

As the tree matures, the pine starts to produce the needles in bunches. These needle clusters are called fascicles, and may have from 1-8 needles (depending on species) held
together at the base by a small collar of scalelike leaves. The needles (leaves) are born on an extremely short shoot within the fascicle base, in which growth of the meristem has
been suspended. The fascicle is actually an extremely short branch with determinate growth.
The leaves are evolved to allow the pine to survive and thrive in dry, often very cold climates. The cuticle is very thick, and stomates are usually recessed into grooves that protect
them from wind and desiccation. Leaves, stems and roots are all impregnated with resin, which not only deters insects, but also has a lower freezing point than water.
Although most conifers are known as "evergreens," they do shed their needles and change them out every 2-4 years, though usually not all at once.

Pine Stems and Wood The stem of conifers is typical of the woody stems we already have studied, and all conifers produce secondary growth via a vascular cambium.

In the timber industry, the wood of conifers is known as softwood, and the wood of angiosperm trees is known as hardwood. Comprised primarily of tracheids, not the more
highly lignified vessel elements, conifer wood is indeed less rigid than anthophyte wood. Life Cycle of the Pine The life cycle of Pinus is a good example, and is very similar to
that of all other gymnosperms.
In pines, this process takes two years.

Male and female cones are distinctive in appearance, with male cones lasting only a few months (just long enough for pollination), and female cones taking two years to mature.
Other familiar and economically important conifers include the firs, larches, spruces, redwoods, yews, cypresses, and junipers.
The toxic Yew is a source of important chemicals of use for treating tumors. Its seeds are not borne in strobili, but rather surrounded by a fleshy cup called an aril, which attracts
birds, which disperse the seeds.

Text reading assignment of note: Pay special attention to the material on Family Araucariaceae, and the "living fossil" Wollemia nobilis on pages 424-426.

Cycadophyta - The Cycads The common name "Sago Palm" is misleading, because these are not palms at all, but ancient gymnosperms that have been around since before the
dinosaurs. There are 11 extant genera, and most do very well in southern Florida's mild climate.
Above, our native "coontie", Zamia pumila and its endangered butterfly (for which it is a larval host plant), the Atala Eumaeus atala.

Interesting Life Cycle Note:

Cycad pollen tubes are haustorial. That is, they are modified for penetration of tissues and absorption of nutrients. Some botanists suggest that the pollen tube evolved from a
structure that was originally meant to allow the microgametophyte to collect nutrients from the sporophyte for sperm production, and that the structure only later became a sperm
delivery apparatus.

Ginkgophyta - The Ginkgo Trees The only living species of this mostly extinct phylum is the famous Ginkgo biloba. Its fan-shaped leaves are easily recognized and distinct among
conifers.
Virtually extinct in the wild in their native China, these are widely cultivated as ornamentals, and are very resistant to smog.

Life Cycle Note:

Like those of cycads, Ginkgo pollen tubes are haustorial. This suggests that both cycads and ginkgos are more primitive in this respect than pines or gnetophytes.

Gnetophyta - The Gnetophytes Believed to be the closest relatives to the flowering plants, there are only three living genera:

 Ephedra
 Gnetum
 Welwitschia

The only Gnetophyte native to the U.S. is Ephedra viridis, commonly known as "Mormon Tea" or "Joint Fir."
Ephedra (sinica) is perhaps most famous recently because of its powerfully stimulant alkaloid, Ephedrine, which was marketed as a weight-loss aid until people started dying of
heart attacks after taking it.

Male and female strobili are borne on separate branches on these monoecious plants.
Genus Gnetum has members with several morphological similarities to angiosperms, such as

 leaf shape

 similarity of strobili to inflorescences (flower clusters) of angiosperms

  vessel elements in xylem
 lack of archegonia in female gametophytes of Gnetum and Welwitschia (though this may be due to convergence)
 double fertilization seen in Ephedra, though this produces extra embryos, and not nutritive endosperm

Gnetophytes and Angiosperms very likely share a common ancestor. Molecular data support this monophyly. So next time, we'll meet the Big, Successful Cousins, the
Angiosperms.

Spermatopsida: The Seed Plants The most recent and most derived of the Spermatopsida comprise Phylum Anthophyta. These are the angiosperms, or
Flowering Plants.

This clade has undergone a great deal of revision with molecular data, and the taxon is now divided very differently from its original classification. Let's take a
quick look at the Current Classification of the Anthophytes.

Angiosperms are the most diverse and successful plants, numbering anywhere from 300,000-450,000 species, with many yet to be scientifically named and
described. Their morphological diversity is unmatched among living things, with some species of Eucalyptus exceeding 100 meters in height, and others being
nearly microscopic.
Anthophytes can be herbaceous or woody, upright or vines, annuals or perennials, shrubs or trees...you name it. Flowering plants have been the dominant life
form on earth for over 100 million years.

What synapomorphies set angiosperms apart from other plant phyla?

 flowers
 fruit
 female gametophyte is an 8-nucleate mass of cytoplasm
 unique pollination
 double fertilization resulting in one embryo and a mass of 3n endosperm
 placentation
 vessel elements dominant in xylem
 sieve tube elements (with companion cells derived from the same cell) dominant in phloem

...and so many others that it's clear these plants are monophyletic, since it's not likely that so many shared, derived characters would arise together via simple
convergence.

Anthophytes were once divided into two main groups, "dicots" and "monocots," but more recent data reveal that this was an artificial separation based mainly
on the high degree of derived character states seen in the monocots. As you can see from the phylogenetic tree of anthophytes we viewed before, the "dicots"
are actually not all derived from a single ancestor.

The Flower: Vocabulary-o-Rama! We already have seen the basic anatomy of a typical flower:
...and you should still be able to recognize and name all the basic parts.

Like a pine needle fascicle, a flower is actually a determinate shoot that terminates in leaves. But these leaves are all highly specialized for reproductive, and
even the sterile portions (stamens, petals) may assist in this regard.

Flower Anatomy Be sure you remember the meaning and significance of...
  petal and corolla
 sepal and calyx
 perianth
 stamen and androecium (literally, "male house")
 anther and filament
 carpel and gynoecium (literally, "female house")
 stigma and style and ovularly
 pistil (a group of fused carpels)
 In a pistil, the ovulary chambers (equivalent to the carpels) are called locules

Placentation The placenta the point of attachment of the ovule to the ovulary wall. Placentation can be an important classification character, and in various
plant taxa, placentation may be

 parietal (ovules are connected to the inner surface of the outer wall)
 axile (ovules are attached to the central column connected to ovulary walls by partitions (number of chambers = number of carpels))
 marginal - ovules lined up in a row on one side of the ovulary
 basal (ovule(s) attached to the base of the ovulary)
 apical (ovule(s) attached to the apex of the ovulary)
 free central (ovules attached to a central column not connected to the rest of the ovulary
Parts Gone Missing: Complete and Incomplete, Perfect and Imperfect Flowers A flower can have four types of specialized leaf whorls, the (1) calyx and (2)
corolla (sterile) as well as the (3) androecium (microsporophylls) and (4) gynoecium (megasporophylls). Most flowers have all four, but in some cases, one or
more of the whorls has been secondarily lost. A flower that has

 sepals
 petals
 stamens
 carpels

...is said to be a complete flower. A flower that lacks one or more of these whorls is said to be an incomplete flower.

A loss of the reproductive whorls has special terminology. A flower with both stamens and pistil(s) is said to be a perfect flower, whereas one missing either
of those is said to be an imperfect flower. Recall that if a single plant has only male or only female flowers, then that species is dioecious, but if a single plant
has either separate male and female flowers or perfect flowers, that species is monoecious.
(A special note about mangos and avocados...)

Inflorescences Flowers may be borne singly, on a peduncle, or in a cluster called an inflorescence. The tiny stalk of an individual flower in an inflorescence is
called a pedicel.

Inflorescence morphology is another useful classification character, and of course we have a massive vocabulary to describe them!

I. Indeterminate Inflorescences
An indeterminate inflorescence has new buds growing at the apex while mature flowers appear on lower pedicels. Buds open first from the base of the
inflorescence.
 spike - an elongate, unbranched, indeterminate inflorescence with sessile (i.e., lacking pedicels) flowers

 spikelet - a small spike (found in grasses (Family Poaceae) and sedges (Family Cyperaceae)
 raceme - an elongate, unbranched, indeterminate inflorescence with flowers on pedicels

 panicle - a branching raceme

 corymb - a flattened raceme (elongate pedicels at the margins of the inflorescence grow to reach the same level as the internal pedicels)

 compound corymb - a branching corymb

 umbel a flattened or rounded inflorescence with the pedicels radiating from a central, common point(may be determinate or indeterminate)

 compound umbel - a branched umbel. Secondary umbels arise from the tips of the primary stalks
 capitulum - (literally "head") - this inflorescence, characteristic of the Daisy Family (Family Asteraceae) is dense, vertically compressed and bears sessile flowers on a single
receptacle. In many species, sterile ray flowers form a ring around a dense mass of central, fertile flowers. The entire inflorescence is subtended (held upon) an involucre (cluster
of bracts) of phyllaries (small, scale-like bracts). May be determinate or indeterminate.
 thyrse - main inflorescence is an indeterminate raceme; determinate cymes branch from the central raceme.
II. Determinate Inflorescences
A determinate inflorescence has new buds growing at the base while mature flowers appear on upper pedicels. Buds open first at the top of the inflorescence.
 simple cyme, a.k.a. dichasium - two dichotomous lateral branches and pedicels of equal length

 compound dichasium - a branched dichasium

 compound cyme - a determinate thyrse
 helicoid cyme, a.k.a. bostryx - a determinate cyme in which the branches develop only on one side due to abortion of opposing paired bud
 cincinnus - a tight, modified helicoid cyme in which the pedicels are very short

 scorpioid cyme, a.k.a. rhipidium - a zig-zagging, determinate cyme with alternate branches due to abortion of opposing paired buds at each rachis node
Ovulary Position And it just gets worse. The position of the ovulary attachment--with respect to the other whorls--is another way to classify the plant you're trying to identify.

As we'll see, this will affect the morphology of the fruit that develops from the ovulary and associated structures.
The Life Cycle Once again, the alternation of generations appears, but now the female gametophyte reaches her most reduced form, lacking even archegonia.

A closer look at the female gametophyte:

And from this, comes the seed, whom you've already met.

Anthophyta: Evolutionary Wonders The early Cretaceous saw the first appearance of flowering plants in the fossil record. By the mid Cretaceous, about 90 million years ago,
flowering plants were the dominant life form on earth. This is a tremendously quick rise to dominance, geologically speaking. What is it that made the Anthophytes so successful?
There are several hypothetical explanations, all of which probably contributed.

 evolution of the flower

 coevolution of the flower and pollinators
 evolution of fruits (and their dispersal mechanisms)
 evolution of certain secondary metabolites unique to flowering plants

Determining Evolutionary Relationships The earliest evolutionary botanists relied primarly on morphology and the fossil record to try and make sense of flowering plant
relationships. But as we know, the fossil record is incomplete, and cannot yiel important molecular and cellular information that may be more relevant to determining actual
common ancestry.

To this day, morphology is still a major tool in plant cladistics, though more and more molecular data are helping to clarify relationships. Let's once again remind ourselves of
the current (and subject to revision!) Classification of the Anthophyta.

Synapomorphies that link the angiosperms are

  flowers
 fruit
 rolled and closed megasporophylls (carpels)
 double fertilization (and the resulting triploid endosperm)
 three-nucleate microgametophyte (pollen)
 eight-nucleate megagametophyte
 absence of archegonia in megagametophyte
 anthers with two pairs of pollen chambers
 sieve tubes and companion cells in the phloem

(Meaning that these characters were present in the common ancestor of all angiosperms.)

Recall that the old phylogeny divided plants into "dicots" and "monocots." We now know that there are some plants that are neither (as long as you are following cladistic
classification methods that allow only monophyletic taxa).

One symplesiomorphy shared by some anthophytes with cycads and ginkgos is pollen with a single aperture through which sperm exit. Hence, single-aperture pollen is a primitive
character with respect to anthophytes. It is found in all anthophytes except the Eudicots, which have pollen with three apertures, a synapomorphy that links all the eudicots and
separates them from all other anthophytes.

Let's Meet the Anthophytes... The most primitive flowering plants were once called "dicots," but we now know that this term is not monophyletic. Several groups have been
removed and placed in separate taxa.

The earliest known angiosperm, a fossil discovered in China, is the appropriately named Archaefructus.

 It was a marsh-dweller, with its roots in muddy sludge

 It had highly dissected, feathery leaves
 It had very simple versions of angiosperm stems, roots, etc.
 It was herbaceous
 Its flowers were small, but its many stamens might have attracted pollinators.

...suggesting that these characters could be primitive with respect to all angiosperms.

Amborellaceae - A Unique Living Fossil The living anthophytes that retain the most archaic characters are found in New Caledonia. Of these, the most primitive is Amborella
trichopoda, the only species in the most primitive anthophyte family, Amborellaceae. It's a short, evergreen shurb that has undifferentiated perianth parts (no distinct petals or
sepals). It's dioecious, with separate sexes, and having relatively primitive sporophylls. It produces small, red fruits (drupes, which you'll meet later) and it's seeds have resin
deposits reminiscent of the more primitive seed plants.
Let's remind ourselves of where we are on the Tree of Life.

Nymphaeaceae - Water Lilies and Their Relatives These plants returned to a watery existence some time in the late Cretaceous, essentially reproductively isolating themselves.
They have remained relatively unchanged since that time.
More details on the Nymphaeaceae.

Magnoliidae Once believed to be the most primitive of all flowering plants, the magnolias and their allies are now accorded separate status. There are several commercially
important groups, such as the Lauraceae (Laurel Family), the Piperaceae (Piper Family), and the Magnoliaceae.

Until 1991, most botanists believed that the earliest flowers resembled those of the magnolia, with large, numerous, spirally arranged (not whorled) petals. We now know
that Archaefructus preceded magnolia-like flowers by 10-20 million years. Showy flowers came later!

Monocots The monocots are probably the most distinctive and easily recognized of all angiosperms. they have

 flower structures arranged in multiples of three

 perianth not differentiated into calyx and corolla
 fibrous root systems (as opposed to taproots)
 parallel leaf venation
 vascular tissue arranged in scattered bundles throughout the stem (as opposed to rings)
 a central pith in the root stele
 no vascular cambium (except in the most primitive group, the Joshua Trees)
These include many economically important plants, including all the grasses (corn, wheat, oats, rice, etc.), palms, sedges, orchids, lilies, etc.

The monocots have traditionally been paired with the eudicots as the two major lineages of flowering plants, and may be sister taxon to them. This has yet to be resolved.

Eudicots The term "eudicot" was first coined by J. A. Doyle and C. L. Hotton in 1991. Things have never been the same.

This group contains the vast majority of flowering plant families, though many relationships within this taxon remain unresolved. A discussion of all the eudicots could span many
semesters. So we must content ourselves with discussing the diversity of their most defining characters: flowers and fruit.

Evolution of Anthophytes: Flowers and Fruit and Bugs, oh my. Two synapomorphies that unite all anthophytes and separate them from the other plant lineages
are

 The Flower

A whorl of specialized megasporophylls (carpels) surrounded by a whorl of specialized microsporophylls (anthers) surrounded by sterile,
specialized leaves comprising the perianth.

 The Fruit

A mature ovulary (and sometimes associated structures derived from other flower parts) containing the seeds.

The anatomy of both these structures can tell you not only about their natural history, but also about their evolutionary relationships.

Evolution of the Flower The flowers of a given plant family generally have specific characteristics that set them apart from other families, but these characters
tend not to vary much within a family. The earliest flowers did not have distinct sepals and petals, and probably were not showy.

As insects discovered the riches of pollen, a coevolutionary marvel took place. The undifferentiated leaves surrounding the reproductive parts of some flowers
changed in response to selective pressure, becoming different from the sepals, and attractive to pollinators. Although in some groups petals are believed to have
derived from sepals (e.g., in water lilies and magnolias, the sepals gradually "segue" into showy petals), in most angiosperms they are derived from stamens
that lost their sporangia and became sterile. (Remember Archaefructus!) How can we tell?

 sepals generally have the same number of vascular strands as the leaves of the same plant.
 petals, like stamens, usually have only one vascular strand

Early angiosperm stamens were diverse in structure and purpose. The carpels, on the otehr hand, tended to be rather uniform and unspecialized, perhaps
constrained in morphology by natural selection, as they were the carriers of the next generation.

Trends in Flower Evolution

As insect pollinators drove the earliest evolutionary radiations of angiosperm flowers, four major trends took place:

1. A reduction in metamerism. Earliest flowers had many copies of each part, and did not have a definite number of each. More derived flowers have
shown a reduction in the number of each flower part, and have a specific number of each, depending on species.

2. A reduction in the number of floral whorls from an original four to three, two, or even one. The floral axis has become shortened. In many cases,
flower parts are fused.
3. Ovary position is inferior, rather than superior, in more derived flowers. There has been a gradual shift from hypogyny to epigyny.

4. Actinomorphy has been replaced by zygomorphy. In their primitive condition, flowers are actinomorphic, with their parts radiating from a central
point. Some species have evolved flowers with a zygomorphic shape, which are bilaterally symmetrical.
Success Stories: Asteraceae and Orchidaceae The two largest plant families also show the greatest degree of flower specialization.

Asteraceae With more than 22,000 species, this is the largest of all eudicot families, and each species tends to be numerous in its given habitat. Asteraceae
(Daisy Family) is characaterized by compositeflowers : they are bunched together in a tight head.
Each of the fertile, actinomorphic flowers in a composite flower has

 an inferior ovary
 five fused stamens
 stamens fused to the corolla, composed of five fused petals
 pistil is composed of two fused carpels, each containing one ovule in one locule

These are surrounded by the ring of sterile ray flowers that are zygomorphic. Because the flowers in the inflorescence open from the margins to the center,
different pollinators will visit, and the resulting seeds will have greater potential genetic diversity than if all of them opened at once, and were pollinated by the
same pollinator.

Orchidaceae This monocot family is the most diverse of all plant families, with at least 24,000 species. Unlike the asters, however, these tend not to be
individually numerous, and some are extremely rare.

The orchid flower has

  a pistil consisting of three fused carpels with an inferior ovary
 each locule is filled with thousands of tiny ovules
 one stamen, fused with the stigma to form the column
 the contents of the anther are dispersed as a single unit, the pollinium
 the perianth consists of three distinct petals forming two "wings" and one "lip"
 three additional sepal/petals subtend the upper three, and are usually colorful

Orchids are zygomorphic, and--as you already know--can be very strange in appearance.

Orchid culture is practically a cult, with breeders seeking the rarest and most bizarre orchids for culture. The genus Vanilla is commercially cultivated to
produce the famous flavoring agent.

Pollination: A Driving Force in Anthophyte Evolution Not all anthophytes have large, showy flowers. Species pollinated by wind usually have small,
inconspicuous flowers, leading many people to believe that they lack flowers altogether. For example, here are the male and female flowers of the wind-
pollinated oak (Quercus sp.):
Wind pollination is most effective when the plants in question are numerous and not too far apart (as in a forest or grassland).

Flowers pollinated by animals have the comparative luxury of being able to be farther apart, as long as their mobile and/or volant (flying) pollinators have a
long distance range. This promotes not only outcrossing, but the freedom to colonize outlying areas that might otherwise be out of the reach of wind-carried
pollen.

Conspicuous flowers are the specialty of species whose pollen is distributed by animals such as insects, birds or mammals. These generally have flower
structure and colors modified to attract their own particular pollinator(s). And of these, insects have been the most common, and perhaps one of the most
important forces for natural selection and coevolution of plant and pollinator.

What are the advantages of being pollinated by an animal?

The bisexual flower was a major advantage when animal pollination first took hold: it meant that each pollinator visit was doubly efficient. The pollinator
could deliver and collect pollen in a single visit.
Some flowers are pollinator generalists, whereas others have coevolved such specificity that if either member of the coevolutionary pollination "team" were to
go extinct, so would the other.

Of prime importance in specializing to attract a particular type of pollinator are

 flower shape
 flower hue (color)
 flower brightness (pale to dark)
 quantity of pollen
 quantity of nectar
 type of fragrance (if any)
 other secondary metabolites

Flower Color Flower color is produced mainly by two groups of compounds, carotenoids and flavonoids.

 Carotenoids - yellow to orange pigments, oil soluble, stored in plastids. These first evolved as accessory pigments for photosynthesis, but have evolved more functions as
pigments for flowers and fruits.
 Flavonoids - ranging in color from pale ivory to blue to purple and red, these are water-soluble ring compounds stored in the central vacuole. One class of flavonoids, the
anthocyanins, are red (phycoerythrin) or blue (phycocyanin), and are especially important in the coloration and patterns in many species of flowers.

You can often tell the type of pollinator a plant has evolved to attract by the nature of its flowers...

Beetles
Magnolias and many other archaic flowering plants are pollinated by beetles, which were probably among the first animal pollinators. Originally making their way as herbivores
and scavengers, beetles move primarily by walking and munching. Hence, beetle-pollinated flowers tend to produce copious pollen, some of which will be sacrificed as a meal for
the beetle while the rest sticks to its legs and body and is transported to another flower.

Although beetles have good vision and diurnal species can see a wide range of colors, they tend to be attracted more to odors than to color or shape. Beetle-pollinated flowers tend
to have very strong scents, ranging from sweet and fruity to rotting flesh.

Because many beetles are nocturnal, some of their night-blooming flowers are white--easily spotted at night.

Flies
Flies have good vision and can see color, but they, too, are more drawn to scent than color. Flies move about by flying, and because they have relatively short tongues, the flowers
that use them as pollinators tend to be shallow, with easy to reach nectar.
Fly flowers tend to be pale, and may have a sweet scent. (Male mosquitoes are important pollinators: they don't suck blood!). Others putrid scent, reminiscent of rotting flesh, and
may be dark and hirsute, since blowflies and other carrion-eating flies are attracted to dark red, purple, and maroon (Now why, do you suppose?).

Although flies first appear in the fossil record about 200 mya, their diversity exploded when they began to pollinate anthophyts, about 100 mya.

Bees
Bees are the most important pollinators in the world, and almost all of the 20,000 bee species feed on nectar and pollinate flowers.

A bee flower usually has a somewhat fused corolla. It is usually not so deep that the bee's short tongue can't reach the nectaries, but just deep enough to require the bee to crawl
inside and smear pollen all over its body.

 a honey bee will visit 50-100 flowers on a single foray.

 a worker honey bee can carry more than half her weight in nectar and pollen payload
 honey is processed nectar: aged, oxidized, and regurgitated with a lot of bee spit enzymes
 the compound eye of the bee is conducive to short wavelengths, and they cannot see beyond orange. Bee flowers tend to be white, yellow, blue, violet, and may have ultraviolet
nectar guides.
Lepidopterans
Butterflies and moths are important pollinators. The former are diurnal, and the latter are primarily nocturnal. Both butterflies and moths sip nectar through a long, flexible tube
called a proboscis, which is coiled when the insect is not feeding. Before they even uncoil it, they sample the flower with chemoreceptors on their feet.

Butterflies are highly visual, and can see the entire spectrum visible to humans, as well as UV. They are particularly attracted to reds, oranges and pinks. Butterfly flowers are often
orange, red or dark pink with very long, fused corollas that prevent other pollinators from stealing nectar. (Butterflies will also feed on shallow flowers; they're not picky.)

Moths are also visual, but they rely largely on chemoreception to not only find mates, but food. Moth flowers are usually night-blooming, pale in color (usually white), and have a
strong, sweet smell. Like butterfly flowers, they tend to be tubular.

Birds
Very few species of birds have much of a sense of smell. Flowers evolved to attract them rely on color and shape. Bird flowers are usually very brightly colored, and may be
ornate. They tend to produce copious, watery nectar (birds have a high liquid requirement!), and are large and heavy, to be able to support the weight of a bird. They tend to extend
beyond the leaves of the plant, to allow easier access for the bird.

Few birds hover, so bird-pollinated flowers often have perches or landing pads (heavy, fleshy petals or bracts) that facilitate the bird's feeding and getting dusted with nectar.

Hummingbird flowers are usually highly specialized for these unique pollinators. The corolla tends to be deep, fused, and hanging so that only a hovering animal can reach the
nectar. They tend to be spaced in such a way that the bird's wings don't damage adjacent flowers as it feeds on one.

Mammals
Bats find food by smell and/or sight. Many cactus are pollinated by bats; they hav large, showy white flowers with sweet fragrance and LOTS of pollen and nectar to feed their
high-metabolism pollinators.

The flowers tend to be large enough to accomodate a bat's face or even its entire head and, like bird flowers, they tend to extend beyond the leaves for easier access for a large
pollinator.

 Some flowers are pollinated by birds during the day, and bats at night.
 Bats not only pollinate, but are major seed dispersers.
 Different species of bats are specialized to feed on pollen, nectar, fruit.
 Bats have reasonably good vision, but nocturnal species can't see colors.

Some flowers, such as certain species of Proteus are pollinated by rodents, and hang their flowers close to the ground for easier access.

In Australia, pollen- and nectar-feeding marsupials such as the honey opossum and sugar glider are major pollinators of various species of Myrtaceae (Eucalyptus family).
Flowers evolved to attract large pollinators with high energy requirements (e.g., bats, birds), must provide a large quantity of nectar and/or pollen. But they also must evolve means
by which to exclude smaller pollinators who might enter the flower and fill up all in one go. No visit to another flower means no pollination!

The End Result: Fruit A fruit is a mature ovulary containing seeds.

The propagule of an anthophyte is composed of tissue from two different generations, grandma sporophyte (the fruit and seed coat) and grandchild sporophyte (the seed, comprised
of a diploid sporophyte embryo and its "sibling," the triploid endosperm). The short-lived 8-nucleate embryo sac gametophyte is pretty much gone by the time the fruit is ripe
enough for you to eat.

A fruit is a three-layered structure. The outermost layer is known as the exocarp, the middle layer is the mesocarp and the inner layer surrounding the seed is the endocarp. Taken
together, these three layers comprise the pericarp.
Fruits may be

 simple
 aggregate
 multiple

A simple fruit is formed from a single flower with a single pistil. Remember, though, that a pistil may have one or many carpels per receptacle. Common examples of simple fruits
are blueberries, citrus, tomatoes and melons.
An aggregate fruit is formed from a single flower with many pistils borne on the same receptacle. That is, there's only one peduncle per fruit. Common examples are strawberries
(an aggregate of achenes), raspberries (an aggregate of tiny drupes), and corn (an aggregate of grains).

A multiple fruit is formed from a cluster of individual flowers in a single inflorescence. Each "fruitlet" has its own receptacle and its own pedicel. Common examples are
pineapples, bananas, kiwi fruits. All of these have fused fruitlets, which appear to comprise a single, fleshy fruit. But they're actually a cluster of fused fruit.

Accessory Fruit An accessory fruit is one in which the fleshy pericarp is composed of floral tissue in addition to the walls of the ovularies. For example, the pistil of an apple
blossom (an epigynous flower) develops into the papery apple "core" and a bit of adjacent tissue. The fleshy, edible part of the fruit is derived from the receptacle, which has
grown up to surround the pistil.

Similarly, the "seeds" on the outside of a strawberry are the actual fruits. The fleshy, sugar-filled "fruit" designed to attract seed dispersers such as birds, monkeys or yourself is
actually the receptacle that has evolved the function of attracting animal seed dispersers.

Types of Fruits Fruits may be fleshy or dry at maturity (i.e., when the seeds are ready to be dispersed).
A fleshy fruit is defined as one in which the mesocarp is moist and pulpy at seed maturity. Three basic types are the

 berry
 drupe
 pome

A dry fruit is defined as one in which the mesocarp is definitely dry at seed maturity.
 Dry fruits may be either dehiscent or indehiscent.
 A dehiscent fruit splits open at seed maturity to release the seeds.
 An indehiscent fruit does not split open at seed maturity.

Dry, dehiscent fruits include

  follicles (which split along one side or seam)
 legumes (these split along two seams and are unique to the Pea Family, Fabaceae)
 siliques (which split along two sides to reveal seeds attached to a central partition)
 capsules(the most common dry fruit, which consist of at least two carpels which may split in a variety of ways).

Dry, indehiscent fruits include

 achenes (a single seed attached to its pericarp only at the base)

 nuts (similar to the achene, but with a harder, thicker pericarp)
 grain (a single seed tightly fused to its pericarp)
 samara (a single-winged fruit)
 schizocarp (unique to the parsley & carrot family, Apiaceae, these split into two fruits at seed maturity)

Each of these fruit types may be modified by a number of dispersal mechanisms designed to carry the offspring as far away from the parent as possible. (Why is this a good idea?)
Seeds may be dispersed by wind, water, animals or other mechanisms.

Fleshy Fruits The Berry

A vast number of superficially different fruits are botanically classified as berries. What makes a berry a berry? The entire pericarp is fleshy when the seeds are mature. There are
three basic types of berries. . .

 A true berry has a fleshy endocarp, mesocarp and exocarp (which may sometimes be tough and rind-like) surrounding one to many seeds. Common examples are
blueberries, grapes, tomatoes, cucumbers, squash, melons, kiwis and bananas.
 A pepo has a thick, somewaht rigid pericarp separated from numerous seeds. Bell peppers, jalapenos and other "peppers" are examples.
 A hesperidium has an aromatic, leathery exocarp (the "rind") and mesocarp and endocarp compartmentalized into sections (each representing a carpel), each of which
contains one to several seeds. This type of berry is unique to the genus Citrus, which produces fruits such as oranges, grapefruit, lemons, limes and tangerines.

(Surprise! Strawberries, raspberries, blackberries and mulberries are not berries at all! What are they?)

The Drupe
A drupe has a single seed enclosed in a hard endocarp, often called a "stone" or "pit." The rest of the pericarp is fleshy or pulpy. A drupe usually develops from a single-ovule
flower with a superior ovary.

A large number of fruits commonly called "nuts" are actually drupes, or parts of drupes, including

 coconuts
 almonds
 walnuts
 pecans
The "shells" of these "nuts" is actually the stony endocarp.

More easily recognizable as drupes are those whose exo- and mesocarps are edible, such as

 cherries
 apricots
 peaches
 plums
 mangos
 olives

The "pit" of these fruits is actually the endocarp containing the seed. Crack open the stone of a peach and you'll find a seed that looks just like an almond. (Caution: cyanide!)

Fruits such as raspberries, blackberries and mulberries are not berries, but aggregates of miniature drupes ("drupelets"). The crunchy nuggets in your raspberry jam are the "pits"
of the drupelets that gave their lives for your toast.

The Pome
A pome is a fleshy fruits with a thin exocarp, fleshy mesocarp and somewhat papery or leathery endocarp that is shaped like a five-pointed star in cross section (it has five carpels).
It develops from a flower with an inferior ovulary surrounded by the flower's receptacle (a epigynous flower).

The the bulk of the pome is comprised of fleshy tissue derived from the receptacle, so it's an accessory fruit. Common pome fruits include

 apple
 pears
 quinces Most pome-forming plants are members of Family Rosaceae, the Rose family. Next time you eat an apple (especially Golden Delicious), notice the faintly rose-like
scent.

Dry, Dehiscent Fruits The Pea Family (Family Fabaceae) is large, diverse and economically important. A great number of ecologically vital tropical rainforest trees are members of
this family, commonly called "leguminous" plants or just "legumes."

The family's common name is derived from the type of fruit produced by all its members. The pericarp is dry at seed maturity, and splits along two longitudinal seams to release
the seeds. Examples include

 peas (actually the seeds, if they're not in their pod)

 various beans
 lentils
 carob
  mesquite
 kudzu
 Royal Poinciana
 Our Friend the Peanut

(You may note that many store-bought legumes, such as string beans, are green and fleshy. That's because they're harvested before the seeds are mature. If left in the field long
enough, they would dry and split.) Peanuts are a bit unusual for legumes: once the flowers have been pollinated, the stems droop and the developing fruit actually are pulled
underground by specialized stems. Rather than dehiscing, as most legumes do, the pericarp is broken open via bacterial action.

The Capsule The capsule is the most common type of dry, dehiscent fruit. Capsules display a wide variety of morphologies but all consist of at least two carpels that split in
various ways at maturity.

Like the legume, the capsule is dry at maturity. Depending upon the species, some capsules split between carpels, others split through the carpel cavities and others form a caplike
structure which pops off to release the mature seeds.

Capsules may be smooth, or stubbled with stickers or long projections which may catch on fur and aid in seed dispersal. Mature capsules often rattle when touched or shaken by
the wind.

Some common plants that form capsules include

 star anise
 irises
 orchids
 lilies
 poppies
 snapdragons
 Our local mahogany, Swietenia mahogani
 Brazil "nuts" are actually the seeds of a gigantic capsule

Dry, Indehiscent Fruits The Achene

An achene has a thin, dry pericarp attached only at the base to the single seed within. The pericarp is indehiscent: it does not split open at maturity to release its seed.

Examples include

 sunflower "seeds"
 buckwheat
  strawberry "seeds"

All members of the Asteraceae form achenes. When you make a wish with a dandelion, you are blowing achenes all over the neighborhood.

As mentioned before, a strawberry flower is actually an inflorescence of many small flowers, each of which matures into a tiny achene. The "seeds" on the outside of the
strawberry are not seeds at all--they're the fruits! The "hair" on each "seed" is what's left of the stigma.

After fertilization, the pedicels of the strawberry flowers fuse and become fleshy. As the seed within each achene matures, it produces a plant hormone (a gas known as ethylene)
which causes the fused pedicels to ripen (become red and filled with sugar). You've seen strawberries that are red and ripe all over except for one little gnarled green area? That's
because the ovules on the green area of the "berry" didn't get fertilized, don't mature and and so don't produce ethylene.

A strawberry is not only an aggregate fruit (a cluster of achenes), but also an accessory fruit (made up of floral tissue in addition to the walls of the ovulary). The fleshy red stem
bearing the achenes is designed to attract seed dispersers such as a bird or primate. The achenes pass rapidly through the digestive tract (at least the ones you didn't crush with your
teeth. . . ) and are eventually deposited in a nice patch of organic fertilizer.

The Nut
A nut is a one-seeded fruit similar to an achene, but generally larger and with a much harder, thicker pericarp. It develops in a cup formed by fused bracts at the base of the fruit.
(Imagine the "cap" of an acorn.) True nuts include

 Acorns
 hazelnuts
 hickory nuts
 macadamia nuts
 chestnuts

Remember: many things commonly called "nuts" are not nuts in the botanical sense. Peanuts are (odd) legumes. Coconuts, walnuts, pecans, and almonds come from drupes. Brazil
nuts are the seeds of a large capsule.

The Grain
Seventy five percent of the world's human population relies upon rice--a grain--as its major staple food source. Corn, another grain, supplies the United States with a multi-billion-
dollar-a-year industry, with products ranging from the coating on the pages of your textbook to the high-fructose corn syrup in your cola to part of the gasoline in your gas tank.
Wheat, oats, barley, rye are all grains. A grain is a one-seeded indehiscent fruit whose pericarp is completely fused to the seed. Because the pericarp and seed are so tightly united,
you eat a lot of indigestible cellulose ("dietary fiber") when you eat whole grains.

Grains are produced by members of the grass family (Poaceae). Another name for a grain is a caryopsis, a term used by those who wish to sound more learned at farm gatherings.
PLANT ECOLOGY AND HUMAN INTERACTIONS

Predation/herbivory is one of the major driving forces in plant evolution, especially when
it comes to morphology and chemical warfare.
As we learned early in the semester, one of the most important ways a plant defends itself
is by producing secondary metabolites such as alkaloids, terpenoids, phenolics, quinones
and compounds that create physical deterrent, such as needlelike crystals of calcium
oxalate (raphides).
Plant families that produce specific compounds are often fed upon only by certain types
of insects that have coevolved to be immune to their defenses. Examples include:
 Brassicaceae (Mustard Family) and certain species of beetles, hemipterans, and sulfur butterflies
 Asclepidaceae (Milkweed Family) and aposematic insects such as Monarch butterflies (and a few related species), chrysomelid beetles, cerambycid beetles, which sequester the
toxins in their own tissues and use them to deter predators.

When an insect group specializes on a particular family that's toxic to others, it suffers little competition for that resource.

Mimicry of toxic animals by non-toxic animals also has evolved as a result of such specialization on poisonous plant families. (e.g., the Monarch Butterfly and its harmless
Viceroy mimic)

Numerous alkaloids have evolved to deter herbivores. But it's That Amazing Primate who just doesn't seem to get the message who always seems able to subvert evolution and
turn it to His/Her own purposes.

 religious/spiritual uses (e.g., Peyote, Cannabis, etc.)

 medicines (antibiotics, hormone mimics, etc.)
 recreation (Cannabis, Papaver somniferum, Coca)
Angiosperms have a greater variety of complex secondary metabolites than any other type of organism, and it has been these, in part, that have spurred the success of this group,
along with the flower and fruit.

Ethnobotany is a field within the biological sciences that bridges across to anthropology. It is the study of the use of indigenous plants by indigenous human cultures, Particular
interest often lies in the discovery of how plants and plant compounds are used in medicinal and religious practice, as these can have commercial application.

Ecological Succession
Ecological succession is the observed process of change in the species structure of an ecological community over time. Within any community some species may become less
abundant over some time interval, or they may even vanish from the ecosystem altogether. Similarly, over some time interval, other species within the community may become
more abundant, or new species may even invade into the community from adjacent ecosystems. This observed change over time in what is living in a particular ecosystem is
ecological succession.

Every species has a set of environmental conditions under which it will grow and reproduce optimally. In a given ecosystem, and under that ecosystem's set of environmental
conditions, those species that can grow the most efficiently and produce the most viable offspring will become the most abundant organisms. As long as the ecosystem's set of
environmental conditions remains constant, those species optimally adapted to those conditions will flourish.

The "engine" of succession, the cause of ecosystem change, is the impact of established species have upon their own environments. A consequence of living is the sometimes
subtle and sometimes overt alteration of one's own environment. The original environment may have been optimal for the first species of plant or animal, but the newly altered
environment is often optimal for some other species of plant or animal. Under the changed conditions of the environment, the previously dominant species may fail and another
species may become ascendant.

Ecological succession may also occur when the conditions of an environment suddenly and drastically change. A forest fires, wind storms, and human activities like agriculture all
greatly alter the conditions of an environment. These massive forces may also destroy species and thus alter the dynamics of the ecological community triggering a scramble for
dominance among the species still present.
Sample diagram of ecological succession. Pioneer species include a variety of annual plants. This successional stage is then followed by communities of perennials and grasses,
shrubs, softwood trees and shrubs, and finally hardwood trees and shrubs. This succession takes about 120 years to go from the pioneer stage to the climax community in a typical
North American deciduous forest community.

Definition of a virgin forest is...

Biomes: How Plants Affect the Structure of Major Ecosystems

A BIOME is a major ecosystem spread over a wide geographic area, and characterized by certain types of flora and fauna, as determined by climate. Climate and soil determine
the flora, which, in turn, largely determine what type of other organisms live in that biome.

Major Terrestrial Biomes

 Arctic Region at the north and south poles

o Located above 60o North and South latitudes
 o Arid (for the reasons described in the section on climate)
o Bitterly cold temperatures
o Day length varies tremendously, with 24 hour daylight or night at the respective solstices.
o Low animal diversity
o Most photosynthetic organisms are marine, and most sun energy is captured in the water.
o Some typical vertebrates you might find here: penguins (Antarctic only; no penguins in the North), seals, walruses, whales of various species, polar bear.
o Typical plants: Not much here but some diatoms in the ocean and ice, and possibly some floating algae.
 Tundra. See more beautiful images of the tundra.
o Located just south of the polar regions in the northern hemisphere.
o Arid (as are the polar regions)
o Characterized by PERMAFROST: a permanently frozen layer of soil, which may be deeper in summer than in winter, but still prevents the growth of large trees
with deep root systems.
o most plants are scrubby and small
o lichens (fungus/algae symbiosis) are a major photosynthetic food source
o High winds and cold temperatures prevail
o Very short days in winter, very long days in summer
o Typical vertebrates: reindeer/caribou, Snowy Owls, Grizzly Bear, Brown Bear, Wolf, Arctic Fox, Ptarmigan (a partridge-like bird), migratory birds, lemmings
(small rodents), voles (another rodent).
o Typical Plants: Small, shrubby perennials; profusion of flowering annuals visible in the spring and summer; small trees with shallow roots due to
permafrost. Lichen, a symbiotic relationship between fungus and a protist or bacterial autotroph, is one of the major primary producers in the arctic tundra, and a
vital source of food for the tundra's herbivores.
 Coniferous (Boreal) Forest (also known as "taiga") . See more images of the taiga/boreal forest.
o Found south of the arctic and tundra regions, primarily in the northern hemisphere
o Northern boreal forest receives tremendous snowfall in winter; the conical shape of pines may help them shed snow and avoid damage to their branches from the
weight of snow.
o Highly endangered, these ecosystems are being rapidly logged out, especially in North America.
o Also found along the the Andes of South America
o Major plant form: evergreen, coniferous trees such as pines, firs, spruce, etc. (Cone-bearing trees). Under the trees grow shrubs, mosses, ferns, etc.
o Relatively high levels of rainfall, but short days in the winter.
o Typical vertebrates: deer, wolf, bear, foxes, many migratory birds, squirrels, rabbits, etc. Higher species diversity than tundra.
 Temperate Deciduous Forest
o Found south of the coniferous forest in areas of relatively high rainfall and relatively high elevation, but with longer day length than in coniferous regions
o Major plant form: deciduous (i.e., trees that seasonally drop their leaves) flowering trees and shrubs.
o Typical temperate deciduous forest areas are the northeastern U.S. and most of Europe.
o Typical vertebrates: deer, wolf, bear, foxes, many migratory birds, squirrels, rabbits, etc. Somewhat higher species diversity than coniferous forest. Some species
hibernate through the winter, when food is scarce in the snowy landscape.
 Prairie (Temperate Grassland) and more beautiful shots of Prairie can be seen HERE.
o Characterized by distinct seasonal changes, moderate rainfall, extremely rich, organic soil.
 o Major plant forms: annual grasses and flowering plants; some areas with more standing water become marshes characterized by small trees such as willows,
cottonwoods, etc.
o Very fertile land, but with harsh seasonal variations: hot summers, cold winters
o The "veldt" of South Africa, the "puszta" of Hungary, the "pampas" of Argentina, the steppes of Central Asia and Russia, and the plains of the central U.S. are all
examples of this highly productive biome.
o Most of these grasslands have been converted to farmland for human use, but some native grasslands have been preserved.
o Typical vertebrates: American Bison (sometimes erroneously called "buffalo"), prairie dog, jackrabbit, fox, coyote, deer, many migratory birds (especially predatory
birds such as hawks and falcons), etc. Many animals undergo winter hibernation.
 Savanna (Tropical/Subtropical Grassland)
o Characterized by distinct seasonal changes, highly seasonal rainfall (very harsh dry season), extremely rich, organic soil.
o Major plant forms: annual grasses and flowering plants; Trees are generally very drought tolerant and have high canopies due to herbivory by large animals such as
elephants and giraffes.
o Fire is a major abiotic component of this biome, and most plant species are evolved to withstand periodic fires
o Very fertile land, but with harsh seasonal variations: very wet season followed by extremely harsh dry season (during which most animals migrate away)
o Lush grass and shrubbery growth in the rainy season provides ample food for large animals, but they must migrate to greener pastures during drought.
o Typical vertebrates: grazing hoofed mammals (gazelles, antelopes, etc.), lions, leopards, cheetahs, elephants, giraffes, true buffalo (Water Buffalo, Cape Buffalo),
rhino, hippopotamus, etc.
 Chaparral (Mediterranean Scrub Forest)
o Found in arid regions with Mediterranean climate (e.g., southern California, Spain, European and African areas bordering the Mediterranean Sea; southern tip of
Africa, southwestern tip of Australia)
o Winters are rainy and mild; summer days are long, hot, and very dry
o Characterized by periodic, seasonal fires
o Major plant forms: Dense, spiny, evergreen shrubs (some of these produce seeds that will germinate and grow only after they've been through a fire.)
o Typical vertebrates: coyote, mule deer, various rodents, many lizards, snakes, migratory birds, etc.
 Tropical Rainforest
o Found worldwide (at least in times past) around the equator
o Extremely high levels of rainfall
o Poor nutrient content in soils due to high levels of rainfall
o Tremendous plant diversity; large trees have shallow root systems evolved to be able to quickly absorb nutrients as soon as they become available (due to decay of
dead things), before the rains wash them away.
o Very dense plant growth and very high level of productivity
o In mature rainforest, the forest floor is relatively clear of plants, since the upper canopy of trees blocks most sunlight. Only when there's a large treefall does a new
growth of shrubby "pioneer species" germinate from the soil and provide cover for the forest to re-grow.
o Typical vertebrates: You name it! More than 50% of all the earth's terrestrial animal species are found in the tropical rainforest. Picture: monkeys, toucans, parrots,
reptiles of all types, amphibians, and representatives of just about any major animal group.
 Desert (plus a view of Joshua Tree National Monument and Death Valley National Park.
o Extremely arid. Very hot in the daytime; in some regions, extremely cold at night
o High nutrient levels in the soil due to very little rainfall
o Sparse plant life due to very low humidity and available water
 o Plantlife is XERIPHYTIC (from the Greek xeri, meaning "dry" and phyt meaning "plant"): evolved to have special adaptations to store and avoid losing water.
o typical plants: cactus, Yucca, xeriphytic shrubs of various species, spectacular explosion of flowering annuals comes with the spring rains
o typical vertebrates: drought-tolerant mammals such as desert foxes, burros, jackrabbits, high diversity of snakes and lizards, tortoises, Roadrunner and some other
desert-adapted birds (plenty of hawks and eagles)

Recall the link between soil nutrient content and precipitation.

 Which of these biomes has the highest productivity?

 Which has the highest and lowest soil nutrient content?
 Which are most useful to humans for agriculture?