Midterm 2 KEY words

Modern Theory:

Adaptive radiation - cluster of closely related species that are each adaptively specialized to a
specific habitat or food source.
- groups of organisms filling ecological niches
Advanced characters - a new version of a trait found in the most recent common ancester of a
group.
-more recently evolved
-opposite of primitive characters
- "derived" character

Allopatric speciation a reproductive isolating mechanism that results from geographical
separation between two populations
-a prezygotic mechanism
- Populations evolve independently and diverge into different species
-caused by glaciers, continental shifts, etc

Behavioural isolation -a prezygotic isolation process
-2 species do not mate because of differences in courtship behavior
-also known as ethological isolation
-ex: songs of bullfrogs, fireflies example used in class (sequences of bursts of
light vary for different species of fireflies within males and females)

Biological species the concept of a species based on the ability of populations to interbreed
and produce fertile offspring
-basically a reproductively isolated gene pool
-no universal agreement to what it is
-problems with the concept: how do you define a fossil species?
how do you define populations that reproduce asexually? (ex archaea and
bacteria)

Cladogram a dichotomous phylogenetic tree that branches repeatedly
- end points of branches represent different species

Diploid an organism that contains 2 sets of chromosomes
-grow through cell division (mitosis) and reproduce by meiosis (production
of gametes)
-ex: animals

Ecological isolation a prezygotic isolation mechanism
-species that live in the same geographic region occupy different habitats
-thus making it difficult for them to mate with one another
-ex: a marsh species vs. a woodland species

Ecological species the species concept where a group of organisms is adapted to a particular
set of resources (niche) in the environment
-the ecological & evolutionary processes that control how resources are
divided up produce these clusters
-good for ecological foodwebs
-PROBLEM: the observations are just as subjective as the morphospecies
concept

Gametic isolation -prezygotic reproductive isolating mechanism
-is the incompability of the sperm of one species and the egg of another
species to join together
-ex: giant clams/ sponges/organisms that release their egg and sperm into
the water column recognize only each other and dont end up combining
with other species

Hybrid breakdown a post zygotic isolation mechanism
-hybrids are capable of reproduction, but the offspring have reduced
fertility or reduced viability (fitness)
-the hybrids eventually die out from the population
-this ensures speciation b/c the species in the long run do not mix
successfully

Hybrid viability whether or not the hybrid organism will be able to come to term
-the zygote may form, but may end up being destroyed
-if the hybrid is inviable, this ensures speciation because the hybrid will
never exist
-or the hybrid will survive, but not to a reproductive age
-this is because the developmental programs of the parent organisms are
incompatible
Ex: goats and sheep can fertilize each other but their ova will never come to
term

Hybridization when 2 species interbreed and produce fertile offspring
-can be the interbreeding between 2 homozygous individuals that creates a
heterozygote
-ex: more hardy and disease resistant crops can be formed from
hybridization
-leads to speciation

Mechanical isolation pre-zygotic reproductive isolation mechanism
-differences between reproductive organs make it physically impossible for
the sperm and egg of different species to join (this also applies to undesired
species ex what type of insect will pollinate a certain flower)
ex: the comet orchid has its reproductive organs behind the petals --12
inch long tube so only a month with a 12 inch long tongue will be able to
fertilize it

Microevolution small-scale genetic changes within populations
-often in response to shifting environmental circumstances or change
events
-this type of evolution occurs only in ONE species
-i.e. the frequency of alleles in a population changes
-ONLY genetic changes
-due to: genetic drift, gene flow, mutation, natural selection, non-random
mating
Monophyletic - group of organisms that includes a single ancestral species and all of its
descendants

*** Morphospecies - Species, distinguishable from others ONLY by morphology
- E.g. Yellow Throated Warbler vs. Yellow Rumpled Warbler

Parapatric speciation Speciation between populations with adjacent geographic distributions.
-Evolution, like allopatric speciation without geographical speciatioin.
-SUBSTANTIAL reproductive isolation b/w spatially adjacent populations
have LIMITED gene exchange
-population on outskirts of zones

Phylogenetic species A group of organisms bound by unique ancestry
- smallest branch at the end of a cladogram
- can place fossils bacteria and archaea
-branches can be neverending, subspecies, etc. (Are they species, families,
orders?)

Phylogeny evolutionary history of a group of organisms
***Plesiomorphy - Sharing a character state with an ancestral clade
- Primitive

Postzygotic isolation
mechanisms
A reproductive isolating mechanism that acts after zygote formation.
Hybrid inviability, hybrid sterility and hybrid breakdown
Prezygotic isolation
mechanisms
A reproductive isolating mechanism that acts prior to the production of a
zygote, or fertilized egg.
Ecological/habitat, temporal, behavioural, mechanical and gametic

Reproductive
isolation
A biological characteristic that prevents the gene pools of two species from
mixing.
Ex: genitalia of a bird do not match that of a horse

Ring species A species with a geographic distribution that forms a ring around an
uninhabitable terrain.
Gene flow between distant population occurs only through intermediary
populations
Example: Salamanders of California, rattle snake
Still capable of interbreeding on border between zones (transition zone)
These become different sub species, each zone is a different sub species,
but the all under the same species

Speciation Species formation
3 types:
Allopatric (isolation)
Parapatric (barrier spanning)
Sympatric (contiguous/touching populations)
Ex. Rape seed oiltoxic seed removed creating the subspecies, Canola Oil.

***Subspecies Taxonomic subdivision of species
Local variants of a species

Sympatric speciation Speciation that occurs without the geographic isolation of populations,
based on environment
Sympatric = Species that occupy the same space at the same time
Evolves between distinct subgroups that arise within one population
Ex. Hybrid offspring has a lower fitness and generations eventually die off

Temporal isolation A prezygotic reproductive isolating mechanism
Species live in the same habitat (and sometimes could interbreed)
Breed at different times of day or different times of year


Hadean eon and Archean eon:

Viroids
Pathogens without a protein component,
they are pure RNA. They are small
molecules of RNA that act as RNA
silencers. They silence mRNA translation
into proteins therefore proteins cannot be
produced and the cell begins to die.
Human viroid: Hepatitis D. Accompanies
Hep B virus, replicates and packages itself
when Hep B does. Hides inside the capsid
of Hep B.
(virus that can replicate itself and is
composed of RNA {RNA world})
Prion
Pathogens that do not have any heritable
component ( RNA or DNA) Prions exist
as a protein with a tertiary structure and
can invert itself into the
aberrant/pathogenic form which is mostly
composed of pleated sheets. The aberrant
form will induce normal prions to invert
into the aberrant form. As it inverts
proteins, they stick together and form
branching fibres. The ends of the fibres
act as catalytic sites and can invert normal
prions. The fibres gown spontaneously
and manifest themselves in vacuoles or
spaces between cells. They can become
large enough to push cells apart. Mainly
effects the nervous system, pushes nerve
cells apart and destroys neural function
(mad cow disease)
In the aberrant form they are very stable
and immune to protease.
Heterotroph
Organisms that grow/build using carbon
that already exists as part of an organic
carbon-carbon bond/
Absorbtive heterotroph
Organism which excretes enzymes into its
external environment to digest organic
materials which are then absorbed ( ex.
Vicariance The fragmentation of a continuous geographic distribution by non-
biological factors. Allopatric by speciation
Species become completely separated
Results in the formation of new species
Ex. marsupials

fungi, many protista and monera)
Ingestive heterotroph
An organism or protist that obtains its
nutrients by injestive organic material and
then digesting it.
Autotroph
Organism with a metabolic process that is
capable of building organic carbon using
atmospheric carbon dioxide.
Chemolithoheterotroph
Organism that use inorganic redox pairs as
a source of energy and use inorganic
carbon.
Chemolithotrophs,
Organisms that use inorganic redox pairs (
iron oxide) to trap the high energy
electron and use the energy.
Chemoorganoheterotrophs,
Organisms that use inorganic redox pairs
as a source of energy and use organic
carbon source.
Chemoorganotrophs,
Chemoorgano-Organisms or metabolisms
that use high energy organic bonds.
Chemoorganotrophs - organisms that use
covalent bonds in organic chemicals as a
source of energy.
Chemoorganoheterotrophs- organisms that
use covalent bonds in organic chemicals
as a source of energy and use organic
carbon.
Phototrophs
Organisms that use light energy to build
carbon-carbon bonds (light energizes
electrons into a higher state, the energy is
transferred through redox pairs- used to
build a gradient or high energy molecules
( NADH etc))
Photoheterotrophs
Organisms that use light energy as an
energy source and use organic carbon as a
carbon source.

Bacterial flagellum
The structure used by bacteria for
locomotion, the same structure is present
in all bacteria who have a flagellum. The
flagellum itself (the tail/whip) is
thousands of copies of just one protein.
The flagellum is connected to the
motor(basal structure) by the hook. The
motor is composed of a series of proteins
that span the plasma membrane to form
rings. The number of rings depends if the
bacteria is gram-negative or gram-
positive. The motor is driven by a proton
gradient; in order to move down the
gradient, the protons must fall through the
opening of the motor proteins. The energy
moves the central rotor attached to the
hook, spinning the ring which whips the
flagellum into circular motion. Switch
proteins attached to the motor can change
the direction of spinning
(clockwise/counterclockwise). The whole
motor system is composed of 20 proteins.
Binary fission
The simplest form of bacterial
reproduction. The genome is duplicated,
each copy attached itself to the cell wall.
As the cell divides, a copy ends up in each
daughter cell. The plasmid and other
cytoplasmic inclusions are partitioned
randomly between the 2 daughter cells. If
the plasmid is incorporated into the
genome, it is replicated at the same time
as the genome.
Conjugation
The presence of a "fertility gene" on the
plasmid produces pili on the surface of the
cell wall. When encountering a bacterium
without the F-factor, the two become
connected and a single stranded copy of
the plasmid is transferred from the F-
positive cell into the F-negative cell.

The plasmid is capably of incorporating
itself into the genome of the bacterial host
and can also snip itself out anytime. When
snipping out, the plasmid can snip pieces
of the bacterial DNA which are
incorporated into the plasmid. During
conjugation, a copy of the plasmid
including pieces of bacterial DNA is
transferred into the F-negative cell. This is
a form of horizontal gene transfer.
Transduction
During viral infections by bacteriophage,
the bacterial DNA generally disappears
but occasionally a piece may remain intact
which may be encapsulated during the
assembly phase instead of viral DNA. The
result is a bacteriophage with bacterial
DNA instead of viral DNA. When
infecting another bacterium, that DNA is
injected into the cell which the bacterial
can incorporate into its own DNA.
Transformation
A bacterium can absorb a DNA strand
from the external environment and splice
it into its own DNA. Sometimes the
process is successful and a new gene
sequence is inserted and becomes active.
Sometimes, the new DNA is degraded and
salvaged for nucleotides.
Methanogens
Anaerobic bacteria. They combine
hydrogen and carbon dioxide to build
organic in a process which results in
methane as a by-product. Abundant in the
Archean eon and were trapped in pockets
of water in the earths crust, they continued
metabolizing and producing large
quantities of methane gas which is stored
as methane hydrates.
Can recycle organic material and produce
fuel.
Bacterial cell wall
Composed of peptidoglycan which is a
series of repeating units of two different
sugars that form dimers which are strung
together. Every second sugar contains a 4
amino peptide which allows 2 different
peptidoglycan fibres to interact. An
enzyme forms a covalent linkage between
the 2 terminal amino acids of the small
peptide chains of 2 different
peptidoglycan molecules.
Gram-positive
Peptidoglycan layer is thick and on
outermost surface of bacterium and can be
stained.
Gram-negative
Peptidoglycan layer is thin and
sandwiched between an inner and outer
plasma membrane(periplasm between the
membranes) the additional outer
membrane prevents staining and often
contains endotoxins. The outer membrane
also prevents penicillin from damaging
peptidoglycan.
Viral Infections
Virus infects host cell and insert own
genetic material. Genetic material
compromises replication, transcription
and translation machinery. Viral DNA is
replicated and viral protein parts are
created by host cell and assembled
together into viral cells inside the host cell
and they burst out by lysing the host cell
(lytic cycle)
In the lysogenic cycle, the Viral DNA is
inserted into bacterial chromosome and
remain dormant for long periods of time
and is replicated along with host cell
DNA. Spontaneous induction occurs
where viral DNA is released from host
DNA and then completes the lytic cycle.
Enveloped virus
During infection makes proteins
associated with viral parts. Inserts proteins
into plasma membrane of the host cell,
performs exocytosis and wrapping itself
in host membrane. When infecting, they
fuse their plasma membrane with host
plasma membrane.
Non-enveloped virus
Not covered with a membrane. Use their
capsid to attach themselves to host cell.

Key words Hadeon Eon

Adhesion
The ability of a substance to stick to an
unlike substance
Bio monomers
Identical or nearly identical subunits that
link together to form biological polymers
during polymerization ( glucose, amino
acids...)

Amino acids, pyruvate, basic hydrocarbons,
glucose, nucleotides etc.
- Believe to be created from Interstellar
organics or Prebiotic soup
- Miller-Urey Apparatus proved that it is
possible to produce these organic compounds

biopolymers/macromolecules
- polymers produced by living organisms+
biodegradable
- monomer units covalently
bonded(repeatingly) to form larger
structures
-polynucleotides( DNA/RNA),
polypeptides (short polymers of amino
acids) , polysaccharides ( glucose,
fructose, galactose)
- have well defined structures, shapes
(how they fold) determines function

Macromolecules: proteins, lipids,
carbohydrates, nucleic acids
- Created through chemical evolution: the
binding of biomonomers
- Questions: panspermia, ribozymes,
importance of clays (+ive and ive charged)


Building phase of the earth
-Explosion that formed the sun propelled
lighter materials (gases) to the outer edges
of the solar system and the heavier
materials (iron) stayed near the sun. As a
result, the inner planets have iron cores
while outer planets are mainly composed
of gases.
-Planets, asteroids, and other
extraterrestrial material crashing around,
creating the formation seen today.
Formation of the moon from a chunk of
the earth that was blown off due to a
collision with an other body.
Stabilizing phase of the earth
- once orbits of planets stabilized,
meteorites, asteroids and other
extraterrestrial bodies were not being
thrown about as violently and frequently.
Though impacts still occurred on earth,
they did not cause global damage. Dense
iron core remained molted and lighter
gases escaped into the atmosphere through
out-gassing. Initial atmosphere composed
of methane gases, sulphur gases and no
oxygen. As the earth cooled, water vapor
began to liquify and rain down, the planet
was covered in a blanket of water but the
earth could not sustain life due to sterility
of water and the extreme heat from core
of planet.
Carbon
-universal building block. forms perfect
tetrahedron. can be stitched together into
any form. most abundant element on
earth.

Essential element in all organic compounds,
very abundant
- Perfectly symmetrical, stable tetrahedral
bonds
- Excellent for forming chains, only other
candidate is less abundant silicon

Cenozoic
Chemical evolution
organic molecules associated with life
have to be created
Central Dogma
DNA ----> RNA --->Proteins
The central dogma basically states that
Proteins are derived from RNA which is
derived from DNA. But the question is
what was the first self-replicating
molecule? For DNA to be the first self-
replicating molecule is problematic
because DNA is too complex a molecule.
Through the discovery of HIV Aids,
which was the first RNA virus, it was also
discovered that RNA could replicate itself.
RNA can turn itself into DNA and has
catalytic abilities, ribozymes.
RNA world
Ribozymes: strands of RNA with catalytic
properties and can replicate themselves
and make proteins. It can be suggested
that the first self-replicating molecule was
an RNA strand with catalytic ability to
assemble nucleotides and replicate itself.
The strand can fold itself to form an active
site where the nucleotides would be
stitched together. If somehow, during this
process, catalytic RNA began stitching
together amino acids and makes proteins
with a catalytic site, that protein can be
used to make more RNA strands. This
process separates the coding from the
work. RNA can use this process to
assemble nucleotides into base-pairs,
creating DNA strand for storage purposes.
This makes RNA the intermediate with
ribozomes controlling everything.

1) Replication DNA copies itself to make
more DNA
2) Transcription Parts of DNA copied into
RNA strands
3) Translation RNA codes translated by
ribosome to produce a protein

Clays
Superfine sediments with charged groups
on them. Clay molecules interact with
each other to form lattices. Clays are
organizers of charged substances. If the
primordial soup is placed on clays, the
clays will align the amino acids head to
tail, in sequence. In the shallows of the
oceans or perhaps where water splashed
on land, nucleotides were likely being
stitched together on clays.
This could potentially be the source of the
first RNA strand.
Cohesion
- The attraction between polar and
non-polar parts of water
molecules. Form H-bonds with
itself. Water molecules, as a result,
try to lock into one another ( even
in liquid form ) and form a spongy
matrix on which a small degree of
weight can be applied. This
property is called surface tension,
when a small weight is placed on
it, the water molecules will push
back with equal force, holding the
object that is applying weight in
place. This is how some insects are
able to walk on water.
Behaviour of water molecules to stick together
- Result of the polarity of the molecule,
hydrogen bonds form between molecules
- Creates a surface tension across surface of
water (can support some insects)

Crystal lattice of water
-as water freezes, it forms a uniform
lattice that is less dense than liquid water.
therefore, it rises to the top (ex. icebergs
float in water). During periods of intense
cold (ice ages) the surface oceans would
be completely covered with ice but there
would be water present deep beneath the
ice. The ice acts as an insulator and
creates and environment in the water
beneath that could sustain life. therefore,
during ice ages, some species were able to
survive and from them, the earth would be
repopulated again.

Solid H2O (ice) has a crystalline structure and
a lower density than liquid H2O (water)
- At 4
o
C, water arranges itself with
neighboring molecules into a honeycomb
shape
- This is due to hydrogen bonds, in liquid the
lattice breaks, in ice the lattice is solid
- Biological importance: Ice (less dense) forms
at tops of bodies allowing the lower volume of
liquid water to continue supporting life

Emergence
-a property that comes about from
interactions between substances (ex.
molecules, proteins etc.) that is not
present in the substances in themselves.
ex. the ability to produce and utilize
energy, in living organisms is the product
of the interactions between proteins,
sugars, enzymes and all the other factors
that make the energy production
mechanism in living organisms.

Complex systems and patterns arise out of
relatively simple interactions
- Examples: swarming of animals, chemical
bonds to produce complex organics
- Life is a major source of complexity, and
evolution is the major principle or driving force
behind life

Eukaryote
- living organisms that posses cells with
the genetic material contained inside a
separate unit called the nucleus.
Mesozoic
Geological time scale
Habitable zone
- Earth's distance form the sun allows a
range of temperatures that allows water to
remain in the liquid state, liquid water is
the fundamental prerequisite for the
development of life.
- because of the size of the planet, earth's
gravitational pull is strong enough to hold
an atmosphere around the planet.
Hadeon eon
-the first eon, characterized by earth's
initial formation. The planet was initially
solid and water was present on large
celestial bodies.
Dust and gasses were gradually
accumulating on the planet and there were
frequent collisions with extraterrestrial
bodies (this released extreme amounts of
heat, keeping the planets surface molten
for period of time), there was intensive
volcanic and seismic activity. Overtime
heat was radiated off and the surface
layers of gasses, dust and molten rock
cooled and formed the crust. At the end of
Hadean eon, first forms of life were
appearing.

The Nice Model (late heavy
bombardment)
The initial solar system was somewhat
unstable and ordered as Jupiter, Saturn,
Neptune, and Uranus with J in more or
less in it's present orbit and the positions
of Neptune and Uranus inverted from the
present ordering. The asteroid belt (
composed of icy bodies) was in orbit
outside U. Interactions between the orbits
of the planets altered their orbits little by
little. When the orbits of J and S came into
2:1 resonance, the orbital forces ( of J + S)
exerted disrupted the orbits of N and U,
inverting them(to where they are now)
and dispersing the asteroid belt.

Dispersion of the asteroid belt results in
the bombardment of the inner planets.
Called the late heavy bombardment, it is
also how water originated on Earth; it was
carried by an asteroid(s). Craters on the
planets and the moon also believed to
have resulted from the bombardment.


Archean Eon
- Second eon, began with the formation of
the earth's crust. The environment was
completely anoxic; all the oxygen on the
earth's surface was bound in water. The
first bacteria arise and all are anaerobic.
Special anaerobic cyanobacteria arose that
could oxidize water to generate protons
and high energy electrons to produce ATP
with oxygen gas being a waste product,
this is the most efficient way of gaining
electrons. Oxygen gas produced escapes
into the atmosphere where it oxidizes
minerals. For a period of time, all the
surface of the earth was rusted, causing
massive changes to the strata.

Archean oceans likely formed by the
condensation of water vapour from the
out-gassing of volcanoes. The iron
released by the out-gassing combined with
oxygen to form ferric iron hematite (
Fe2O3) which resulted in banded iron
formations on the flanks of volcanoes
unique to the Archean eon.

Green house gas effect:
The concentration of carbon dioxide in the
atmosphere reached extremely high levels
due to out-gassing from volcanoes,
causing a green house gas effect. Warming
the surface of the planet and likely
preventing the development of glaciation.
Reducing Atmosphere
Hypothesis that claimed that the early
atmosphere was a reducing atmosphere
due to the lack of any oxygen and the
presence of large quantities of methane,
ammonia, hydrogen and carbon dioxide.
These molecules an abundance of
electrons and hydrogen and would have
reacted with one another to yield larger,
more complex molecules. The lack of any
oxygen also meant that their was no ozone
layer, UV rays from the sun were then
also available to provide energy(along
with lightning) for reactions.
Miller-Urey experiment
Components of a reducing atmosphere,
hydrogen, methane, ammonia and water
vapour were added to a closed apparatus,
and energy was provided in the form of
sparking electrodes. The electrodes
mimicked lightning, in primordial earth
there was a lot of volcanic activity which
is always accompanied by lightning
therefore light would have been a major
source of energy for chemical reactions.
This mixture was heated and cooled (
water <--> vapour) and allowed to cycle
for a week. The resulting concoction
contained many organic compounds,
including amino acids, lactic acid, formic
acid and ascetic acid. 15% of the carbon
initially in methane had be converted into
organic molecules essential for life. The
addition of formaldehyde and hydrogen
cyanide resulted in the formation of amino
acids, fatty acids, purine and pyrimidine,
sugars and phospholipids.
This was the first experiment to
demonstrate the abiotic formation of
molecules critical to life.
Results in the early oceans being a
primordial soup of organic molecules:
provides an environment in which an
extraterrestrial LUCA could have
metabolized.

CO2 + H2O + CH4 + SO2 + other inorganics
organic compounds
- Evidence of how life may have originated,
pre-biotic soup

Hydrothermal vents
Complex organic molecules could have
occurred under the sea at the site of deep
sea vents. At the level, weight of the water
column keeps water in liquid form
despite extremely high temperatures.
Reduced gases such as methane,
ammonia, hydrogen sulfide, are produced
by the crack in the ocean floor. The
extreme temperature and pressure could
provide the environment necessary to
react the gases and form basic organic
molecules.

Vents at the bottom of ocean that spew out
hot noxious gases, such at SO2
- Contingent for the origin of life due to high
energy and presence of organics

Extreme bacteria- thermophile-are known
to thrive in these environments. They
posses the criteria necessary for space
travel and potentially enhance the
feasibility of LUCA being extraterrestrial.
Hydrophilic
Charged/polarized molecules, can be
dissolved in water and other polar
solvents.
Hydrophobic
Non-polar molecules that prefer neutral
and non-polar solvents. Tend to form
clusters in water ( lipids). Do not dissolve
in water.
Panspermia
The hypothesis that "seeds" of life exist
already all over the Universe
- Life on Earth may have originated through
these "seeds"
- Other habitable bodies may have had life
delivered to them as well

Extraterrestrial origins for life on earth.
Small bacteria can be found on asteroids
with morphological forms similar to
bacteria on earth. Possible it arrived on
earth on an asteroid that collided with
earth during the late heavy bombardment.
Liposome
when lipids are fragmented and mixed
with water, they cannot come back
together into their original form but
instead, form a sphere composed if a
bilayer of lipid molecules containing
aqueous environment inside.
Micelles: sphere composed of a single
layer of lipid molecules.
Prokaryote
Living organisms with cells that do not
have genetic material contained inside a
nucleus.
Probionts/protocells
Precursors to prokaryotic cells.
A group of abiotically produced organic
molecules that are surrounded by a
membrane or membrane-like structure.
Reverse transcriptase
Enzyme that functions as an RNA
dependant DNA polymerase.
Proterozoic eon
Stable continents appeared. First evidence
of oxygen build-up in atmosphere. Fossils
of living organisms from this eon are good
Specific heat
The amount of heat that is required to
raise the temperature of a substance by
one degree.
Spontaneous origins
All life appeared on earth as is.
The idea that life spontaneously was created
by no physical-chemical means

Surfactant
Compounds that lower the surface tension
between two liquids or between a liquid
and a solid. Includes detergents, wetting
agents, emulsifiers.

Wetting agents that lower the surface tension
of a liquid, amphiphilic
- Allows for easier spreading, and lower the
interfacial tension between two liquids

Eons Largest division of time
Eras Division of eons

Or


Absorbtive
heterotroph

Aerobic Aerobic - Requirement of oxygen
- Usual necessity for oxygen is in the respiration processes
- Oxygen acts as an electron acceptor

process by which molecules are oxidized to produce ATP via an
electron transport chain and ATP synthase.
- Chemoorganoheterotrophs, break chemical bonds and use them for
energy via glycolysis, kreb cycle, they all trap energy and use it to
build sugars

Algae
Anaerobic No requirement of oxygen
- Usual dependence on oxygen is from the organisms metabolic
processes
- Other inorganic molecules, such as sulphur, can be used as electron
acceptors

process by which molecules are oxidized to produce ATP via an
electron transport chain and ATP synthase.
- Chemoorganoheterotrophs, break chemical bonds and use them for
energy via glycolysis, kreb cycle, they all trap energy and use it to
build sugars

Animalia - The taxonomic Kingdom that includes all living and extinct animals
Antibody - highly specific soluble protein molecule that circulates in the blood
- recognizes and binds to antigens to clear them from body.
Antigen - foreign molecule that triggers an immune response.
- antibodies bind to these molecules.
- ex: the antigens on the surface of blood cells
Antibiotic resistance - Type of drug resistance where microrganisms are able to survive
exposure to antibiotic
- Spontaneous or induced genetic mutation in bacteria may confer
resistance to antimicrobial drugs
- genes that resist can be transfer between bacteria horizontally by
conjugation, transduction, or transformation.
- Gene for antibiotic resistance which had evolved via natural
selection may be shared.
Archaea - Unusual group of bacteria, that can survive in extreme conditions
(extremophiles)
- single celled microorganisms
- have no nucleus or any other membrane-bound organelles w/ in
their cells.
-Phototrophs, chemolithotrophs, chemorganotrophs
- No peptidoglycan, plasma membrane=branched w/ ether links, has
operon genes, translation via complex RNA polymerase, no nuclear
envelope, circular chromosome, DNA histones

One of the three domains, from Linnaeus taxonomic hierarchy
- These prokaryotic organisms can survive in extreme conditions,
extremophiles
- Survives as either Halophiles, Thermophiles, can also be
methanogens

ATP synthetase
(synthase)
- enzyme that provides energy for the cell by using ATP (most common
energy currency)
- Formed from ADP+Pi
- in glycolysis, and kreb cycle
- E coli atp Synthase is the simplest from of Atp synthase

Membrane-spanning protein complex, couples reactions:
- Energetically favouring transport of protons across a membrane with
the synthesis of adenosine triphosphate (ATP) from adenosine
diphosphate (ADP) and a phosphate group

Autotroph - makes energy from the sun or light photons
- produces complex organic compouns like carbs from inorganic
compound (photosynthesis)
- inorganic chem reactions chemosynthesis
- Algae and plants
- Phototrophs and lithotrophs
- Get carbons from carbon oxides

An organism that produces its own food from CO2, simple inorganics,
and energy
- The energy could come from the sun, photo, or from the oxidation of
other organic, organo, or inorganic litho compounds

Bacteria (Eubacteria) Multicellular
- Metabolism (photo, chemolitho,organothrops)
- Gram-positive bacteria very dormant and resistant endospores

One of the three domains, from Linneaus taxonomic hierarchy
- These prokaryotic organisms are the most metabolically diverse
- All six -troph options are possible

Bacterial flagellum - Motor embedded in gram negative
- Motorized by the flow of H+ ions, protons nudge ATP synthase-like
molecules that spin the flagellum. (tail spins)
- Powered by ATP
- Flagellum = bio chem motor
- shaft sits against molecular motor at bottom
- hook: sleeve that attaches shaft and flagellum
- different than animal flagellum
Bacteriophage - Number of viruses that infect bacteria
- Consist of outer protein capsid enclosing genetic material
- Lytic or lysogenic cycle
- Viron assembly
Binary fission - subdivision of a cell into two or more parts and regeneration of
those parts into separate cells.
- Asexual reproduction and cell division used by prokaryotes and
some eukaryotes
- Results in reproduction of a living prokaryotic cell
- Takes place without spindle fibres
- DNA mol replicates, then attaches each copy to different part of cell
membrane to build identical clones

One mode of prokaryotic reproduction
- DNA replicates in cell, and cell splits in half
- This method yields no genetic variation from parent to daughter cells

Capsin protein
Capsule





Cellular Respiration
- may be a polysaccharide or polypeptide
- ex. Bacillius or streptococci
- detected by special stain
- antigenic
- antiphagocytic determines virulence of many bacteria


Cellular respiration - The process by which high-energy molecules are
converted to ATP
- Takes place aerobically or anaerobically, depending on organism and
environment
- Takes place in all living organisms

Chemolithotrophs









Chemorganohetrotrophs
- consume carbon already in inorganic compound
- Use sulfur and ammonia to get energy
- Carbon fixation

Class of organisms that fix their own source of carbon
- These organisms get energy from the oxidation of inorganic
compounds
- These organisms can only be bacteria

Class of organisms that consume other organisms as a source of
carbon
- These organisms get energy from the oxidation of organic
compounds
- These organisms can be bacteria, some protists, fungi, or animals

Chemoorganotrophs - Break C-c bonds to make energy
- Pull together CO2 to make organic compounds
- Ex. Bacillius

Class of organisms that fix their own source of carbon
- These organisms get energy from the oxidation of organic
compounds
- These organisms can only be bacteria

Chitin - Polymer derived from glucose
- Cell wall of fungi and exoskeleton of athropods (crabs, squids,
octopods, lobsters, shrimps) mollusks
Circular genome
Conjugation - Transfer of genetic material between bacterial cells by direct cell to cell
contact
- Donor cell provides a conjugative or mobile genetic element that is most
often a plasmid or transposon
- plasmid replicates and through the pilli, some plasmid migrates to the
other cell.
- may take a bit of the genome by accident, creating a unique new cell
- plasmid is the key in recombinant DNA
- Mechanism of horizontal gene transfer as are transformation and
transduction
- Genetic material transferred is often beneficial to the recipient.
- Benefits may include antibiotic resistance

One mode of prokaryotic reproduction
- Part of DNA of a donor cell moves through a cytoplasmic bridge into
recipient cell
- Genetic recombination occurs and yields genetic variation
- In ciliate protozoa, this is the form of sexual reproduction

Cyanobacteria - obtain energy through photosynthesis
- blue-green algae
- capable of splitting H2O molecule and taking CO2 to make C-C bonds
- perform oxygenic photosynthesis by reducing atmosphere into an
oxidizing one
- rocks and minerals became oxidized and began to rust.

A phylum of bacteria that obtain their energy through photosynthesis
- Due to its high efficiency, these bacteria flourished filling the
atmosphere with O2
- Involved in the marine nitrogen cycle and a primary producer in areas
of the ocean

Daughter cell - cell resulting from the replication and division of a single parent cell
- genetically identical
- only in eukaryote cells
Domains - Highest taxonomic category
- group of cellular organisms w/ distinct characteristics that set it apart
as a main branch of evolutionary tree.
Electron donor - donates electrons to another compound (reducing agent)
- thus it is oxidized
- transfer of an electric charge during cell respiration
- results in release of energy
- microorganisms like bacteria obtain energy in ET processes

A molecule which has easily relievable electrons (electron pair)
- This is caused by an accessible atom of low electronegativity, usually
H
- Useful in biochemical redox reactions such as NADH ->NAD+ + H+ +
2e-

Electron receptor - accepts electrons it is an (oxidized agent)
- thus it is reduced
- during cellular respiration and photosynthesis
- during process of ETC

A molecule which has a high affinity for electron pairs
- This is caused by an accessible atom with a high electronegativity,
usually O
- Useful in the electron transport chain: 2H+ + 2e- + O2 ->H2O

Electron transport chain - in chloroplasts light drives the conversion of water to oxygen and
NADP+ w/ transfer of H+ ions across chloroplast membranes
- in mitochondria its the conversion of oxygen to water, NADH to NAD+
- more complex in bacteria
- use more than one ETC

Stage in cellular respiration where high-energy electrons are used to
make ATP
- Occurs in mitochondria as well as chloroplasts of eukaryotic cells
- Electrons pass through a protein complex creating an electrochemical
gradient
- As H+ diffuses back across membrane, ATP-synthase generates
ATP

***Endospore - dormant state bacteria; can withstand extreme conditions
Enveloped virus - a lipid bilayer comes from the cell that the virus infected
- that bilayer then envelops the virus, and protects because of the
antigens found on the surface of the bilayer.
Eukaryota - nucleus or nuclear envelop containing genetic material
- cell wall chitin in fungi
Extremophiles

- the weird archaea
- thrive in extreme physical conditions that are determental to most
life on earth
- Ex. Chemolithoautotrophs; thermo= heat loving; halo= salt loving
- may be precursors of life on this planet
- Encompasses majority of Archaea

Another name for archaea bacteria
- Can survive in hypertonic solutions (salt water) as halophiles
- Can survive in very hot conditions (hydrothermal vents) as
thermophiles

Flagellar hook - Sleeve that Connects the flagellar motor to the long filament acting as a
helical propeller
Flagellar motor - Hook made from 120 copies of a single protein
Fungi - Heterotrophic difference lies where food is ingested
- they are ingestive heterotrophs
- food digested externally and absorbed.
Gram-negative bacteria - Bacteria that do not retain crystal violet dye in the gram staining
protocol. (become pink or red)
- Pathogenic ability associated with the lipopolysaccharide layer.
- LPS triggers problems in the immune system b/c of cytokine production.
Inflammation is a common result
- Cytoplasmic bacteria
- Thin peptidoglycan layer (thinner than gram positive bacteria)
- Ex. E.coli

Description of bacterial cell walls
- Capsule may not be present, if present it is curved
- Peptidoglycan layer is thin, does not show on test, outer membrane
present
- This is the form of most pathogen bacteria

Gram-Positive bacteria - Bacteria that are stained dark blue or violet by gram staining
- Able to retain the purple colour because of a high amount of
peptidoglycan in the cell wall.
-Typically lack the outer membrane found in Gram-neg

Description of bacterial cell walls
- Capsule present, not curved
- Peptidoglycan layer is large, thick, shows up on test, no outer
membrane

Halophiles - extremophiles that thrive in environments with high concentrations of
salt
- can be found anywhere with salt concentration 5 times greater than the
ocean

Heterotroph - An organism that acquires energy and nutrients by eating other
organisms or their remains.
- get energy from breaking carbon bonds
- ex: dogs, humans

An organism that consumes its own food and energy from other
organisms
- Additional energy could come from the sun, photo, or from the
oxidation of other organic, organo, or inorganic litho compounds

Histones - A small, positively charged protein that is complexed with DNA in the
chromosomes of Eukaryotes.
Horizontal gene transfer - transformation, the genetic alteration of a cell resulting from intro,
uptake, and expression of foreign genetic material
- transduction, process in which bacterial DNA moved from one
bacterium to another by a virus (bacteriophage)
- bacterial conjugation, process in which a bacterial cell transfers genetic
material to another cell by cell to cell contact
- gene transfer agents, virus like elements encoded by most host that are
found in the alphaproteobacteria
Ingestive heterotroph - like heterotrophs, they get energy from breaking C-C bonds in
molecules, the difference is in the digestion.
- food digested externally and absorbed.
- Ex: fungi are ingestive heterotrophs
Latent viral phase
Lysogenic cycle - Cycle in which the DNA of the bacteriophage is integrated into DNA of
the host bacterial cell and may remain for many generations.
Lithotrophs - an organism that uses inorganic substrate (minerals) to obtain carbon
fixation or energy by anaerobic respiration
- utilize inorganic compounds as energy sources
- deep sea worms and plastids
- often extremophiles
Lytic cycle - phage inserts its DNA into the host cell
- the virus takes over the cells replication machinery to reproduce viral
DNA and proteins
- Viral particles are assembled inside
- The cell lyses, erupting and freeing the new phages
Methanogens - microbes that produce methane as a metabolic byproduct in anoxic
conditions
- responsible for the methane content in belching
- some are extremophiles found in hot springs
- in anaerobic environments remove excess hydrogen produced by other
forms of anaerobic respiration
Monera - A kingdom that includes all prokaryotes
- Unicellular organisms without a nucleus
- Cyanobacteria classified under monera
Nitrogen fixation - at beginning of the planet, N was only available as a gas.
- natural process, either biological or abiotic, by which nitrogen in the atm
is converted into ammonia
- Fixed nitrogen is part of essential subunits (DNA, A.A, proteins)
- cyanobacteria play key role in the nitrogen cycle of the biosphere
use inorganic sources of combined nitrogen

A metabolic process in which molecular nitrogen is converted to
ammonia
- Certain bacteria, specifically cyanobacteria, perform this
- Can take form of a symbiotic relationship with a plant that uses the
ammonia

Nonenveloped virus - A virus that is not encased in host cell phospholipid bilayet.
-
Nucleoid - area with a prokaryote cell where majority of the genetic material is
found

The central region of a prokaryotic cell where DNA is located
- No membrane bounds this region
- Replication and transcription occur here

Oxidized - loses an electron
- reducing agent is oxidized

Process of a substance losing electrons
- Occurs during oxidation reactions
- These substances are called reducing agents

Pandemic - widespread occurrence of a disease
Pathogen - virus bacterium prion or fungus that causes disease in its animal or
plant host
- small amount of bacteria actually harmful
- cause infectious diseases ex. Tuberculosis
- which is causes by other bacterias like streptococcus and
pseudomonas and food borne illnesses

a biological agent that causes disease or illness to its host
- could be viral, bacterial, fungal, or prionic
- Not all pathogens are negative

Penicillin - Group of antibiotics derived from penicillium fungi
- First drug that was affective in fighting many diseases
- Ex. Syphilis
- Still widely used today even though many bacteria now resistant
- Used in treatments of gram-positive bacteria
Peptidoglycan - Polymer of sugars and aminoacids formas a mesh like layer outside
the plasma membrane of bacteria (not archaea)
- In the bacterial cell wall is a crystal lattice structure
- Formed by linear chains of two amino sugars
- interacts with stains

The primary structural molecule of bacterial cell walls
- A polymeric substance formed from a polysaccharide backbone +
short polypeptides

Periplasm - Space between the peptidoglycan cell wall and the inner membrane of
gram negative bacteria
- Space outside the inner membrane for gram-positive bacteria
- May be 40% of total cell volume in gram negative and significantly less
in gram-positive
- Includes nutrient binding transport and alteration of substances toxic to
the cell.
- Clinical importance when considering antibiotic resistance
Phage - bacteriophage
- virus particle made up of a head unit (a capsid), a tail unit and and a
strand or two of nucleic acids.
- to infect, it injects its DNA into a host cell.
- looks like an alien space pod.
Photoheterotrophs - Break carbon carbon bonds as a source of carbon
- Use photonic energy from light to do this

Class of organisms that consume other organisms as a source of
carbon
- These organisms get energy from the sun
- These organisms can only be bacteria

Photosynthesis - Conversion of light energy (in the form of photons) to chemical energy
(in the form of sugars and other organic molecules).
- Can occur in species with chloroplasts
- Occurs in autotrophs

Highest efficiency method of carbon fixation and energy capture
- CO2 + H2O (CH2O)n + H2O + O2
- Used in plants and cyanobacteria

Phototrophs - Light as source to generate high energy electrons
- Transfer electrons from inorganic carbons
- Ex. Plant
- See them in proterozones and bacteria do this too

Class of organisms that fix their own source of carbon
- These organisms get energy from the sun
- These organisms can be bacteria, certain protists, or plants

Pilli - Hair like structures found on the surface of many bacteria
- Composed of proteins
- Some bacterial viruses attach receptors on pili at the start of their
reproductive cycle
- They are antigentic
Plantae - A kingdom that includes multicellular plant organisms
Plasmid - DNA molecule that is separate from, and can replicate
independently of the chromosomal DNA
- They are stranded and in many cases circular
- Occur naturally in bacteria
- Sometimes found in eukaryotic organisms

Separate DNA molecule in certain prokaryotes, usually circular or
double stranded
- Often contains gene which supplement those in the nucleoid
- Replicates independent of nucleoid DNA

Prions - Pathogen that does not involve nuclear material
- Infectious protein molecules
- has an aberrant form: a flipped orientation that induces normal protein
to flip into aberrant/pathogenic form.
- aberrant form sticks together forming a fibrous chain that flips other
proteins and pushes other cells (ex: neurons) apart.
- Ex: mad cow disease
Prokaryote -
- organisms that lack a nucleus and othe membrane-bound organelles
- most are unicellular
- no nucleus ex: mitochondria etc
- no organelles
- belong in two taxonic domains: archaea and bacteria
Protista - Kingdom that includes several groups of unicellular eukaryotes
- single celled organisms
- animal like protists (protozoans)
- plant like protists (algae)
Proton gradients - gradient of protons (duh)
- Used to power ATP synthase
- sources include: splitting H2O molecules
Protozoa - organisms of the Protozoa group
- a phylum/group of phyla that includes single celled microscopic
animals, (including amebas, flagellates, ciliates, etc)
- belong to kingdom Protista
Redox pair - 2 species between which an electron is gained or lost.
- gain= reduction
- loss= oxidization
- ETC creates p+ gradient that can then generate ATP via ATP synthase
Reduced - Gain of electrons
- Oxidizing agent gets reduced

Process of a substance gaining electrons
- Occurs during reduction reactions
- These substances are called oxidizing agents

Reverse transcriptase - An enzyme that uses RNA as a template to make a DNNA copy of the
retrotransposon
- used to make DNA copies of RNA in test tube reactions.
Ribosome - location of protein production
- Three binding sites for tRNA
- builds chains of amino acids

Saprophytic - organism that lives on dead or decaying matter.
Stromatolites - layers formed in shallow water by trapping, binding, and
cementation of sedimentary grains by biofilms of microorganisms,
especially cyanobacteria
- found on shorelines
- provide some of the most ancient records of life on earth
- fossil record
Thermophiles - type of extremophile that thrives at high temps between 45 to 122
Celsius
- found in various geothermally heated regions of the earth ex: hot
springs and deep sea vents
- their enzymes allow then to function at such high temps
- Ex. DNA polymerase, TAQ polymerase
Transduction - (related to topic) virus: a protein container w/ pieces of DNA.
- protein shuts down transcription/translation of cell
- lands, injects, destroys. Protein copies, makes cases, lysis.
- sometimes bacterial fragments survive.
- these fragments can end up in other cells from injection, increasing
biodiversity.

One mode of prokaryotic reproduction
- DNA is transferred from a donor to a recipient by means of a
bacteriophage
- This method yields variable genetic variation
- The DNA may kill the bacteria and reproduce more bacteriophages or
- The DNA may combine with host cell DNA and the message will be
passed on

Transformation - bacteria can take chunks of DNA from the external environment
and add it into the genome.
- uptake integration either stable or unsuccessful
transformation

One mode of prokaryotic gene transfer
- Bacterial cell can intake DNA from the surrounding environment
- The DNA may prove useful or useless and be passed on or
- The DNA may prove detrimental and kill the bacteria
- This method yields genetic variation depending on survival of bacteria

Vaccine - creates antibodies in out body
- we inject a small amount of capsid protein so that our body recognizes it
as a foreign particle
- we create antibodies so that if the virus enters our system, the virus can
be destroyed
Virion - a complete infective form virus particle outside of the cell
Viroids - Pure RNA in circular loops
- Plant pathogens.
- RNA silencers silence mRNA in cells and inhibit transcription.
- Ex: Hepatitis D
- virus that has a function made of RNA
Virus

- NOT cells (non living) [no membrane, ribosomes, mitochondria, DNA is
wrapped in a protein coat]
- virus: a protein container w/ pieces of DNA.
- only reproduces by injecting into cells
- protein shuts down transcription/translation of cell
- lands, injects, destroys. Protein copies, makes cases, lysis.
- characterized initially based on morphology

Proterozoic eon:

9+2 organization - Orientation of cilia and flagella in eukaryotes
- Position of 9 microtubules surrounding two central ones
- Differs from prokaryotic flagella which acts as a micro motor

Alternation of generations - Life cycle that switches between haploid and diploid between
generations
- Haploid generation: haploid spores undergo mitosis making haploid gametophytes
- Diploid generation: gametophytes fertilize zygote sporophyte meiosis

Amoeboid movement - Type of protist locomotion where pseudopods use actin and myocin to
move
- ATP can change the density of the protein solution to solid or liquid states
- The solid ectoplasm makes the outer structure of the pseudopod for liquid
endoplasm channel to flow through causing movement

Antibody - Type of protein found in the blood plasma
- Binds to specific antigens found of cell surfaces, or foreign invaders
- Destroys the cells with the antigen markers as a part of our immune system

Antigen - Substances which prompt the production of antibodies
- Surface markers on cells

Archaea - One of the domains of life
- Extremophile prokaryotes with many biochemical similarities with eukarya
- Believed to be one of the first organisms on earth due to extremophility

Asexual reproduction - Process of self-reproduction
- No genetic variation occurs through this method
- Single organism gives rise to offspring without genetic input from another

Bacteria - One of the domains of life
- Consists of the most metabolically diverse prokaryotes
- Also the most reproductively diverse domain

Bacteriophage - A complex virus that infects bacterial, prokaryotic cells, not eukarya
- Consists of a protein capsid surrounding genome as well as characteristic tail and
sheath for bacterial cell wall penetration
- These viruses are enveloped, meaning they have a phospholipid bilayer surrounding

Capsid protein - Protein coat which protects genome
- Found in all viruses
- May or may not be enveloped

Chloroplast - Unique organelle in plants and plant-like protists
- Contains photosynthetic pigments used to capture energy from light
- Origin results from endosymbiosis of ancestral protists of cyanobacteria

Cilia - Motile extension of the cell surface
- Structurally identical to flagella in eukaryotes (9 + 2 organization or microtubules)
- Used for cell locomotion in protists, and sweeping of debris or other cells

Contractile vacuole - Specialized cytoplasmic organelle that is used for locomotion or feeding
- Pumps fluid in cyclical manner from inside the cell to outside
- Alternately fills and contracts vacuole at various points on cell surface

Diploid - Organism or cell with two copies of each chromosome in nucleus
- Common to most kingdom life cycles at some point

Diplontic - Life cycle of animal-like protists
- Consists of purely diploid asexual reproductive phase
- And partially haploid sexual reproductive phase (gametes are haploid)

Ectoplasm - Insoluble protein solution in pseudopods used for stability and walls of channel

Endomembrane system - System of interconnected membranous sacs in eukaryotes
- Nuclear membrane, endoplasmic reticulum, Golgi apparatus, and derived elements

Endoplasm - Soluble protein solution in pseudopods used in amoeboid channel for locomotion

Endosymbiosis - Engulfing of an organism leads to symbiotic relationship as opposed to
predation
- Hypothetical scenario supported by mitochondrial and plastid organelles

Enveloped virus - Virus surrounded by a phospholipid bilayer for easy entrance/exit of cells
- Envelop surrounds capsid of virus

Epidemic - Widespread disease

Eukarya - One of the domains of life
- Consists of all organisms with eukaryotic cells
- Has the 3 kingdoms of multicellular life: animals, plants, fungi {+ protists}

Flagellum - Long, threadlike, cellular appendage responsible for movement
- Possible derivative of composed cilia
- Found in both eukaryotic and bacterial cells, but with different structures

Gametocyte (phyte?) - Gametophytes are individuals from the alteration of generation life cycle
- Haploid individuals produced as spores (n) undergo mitotic divisions
- Can be male and develop sperm or female and develop eggs

Haploid - Organism or cell with one copy of chromosomes
- Common to all life cycles at some point

Haplontic - Life cycle of fungal-like protists
- Consists of purely haploid asexual reproductive phase
- And partially diploid sexual reproductive phase (zygotes are diploid)
Histone proteins - Small positively charged protein that complexes DNA in formation of
chromosomes
- DNA literally wraps around 8 histones (twice wrapped in a 2x2x2 arrangement)

Host - Any cell with its own functioning genetic material, nutrients, taken over by another
- Species is fed upon by parasites (or viruses)

Immune system - The combined defences, acquired or innate, that a body uses to eliminate
infection
- Consists of while blood cells as well as other phagocytotic cells
- Intrinsically controlled in all organisms; extrinsically or intrinsically compromised

Latent viral phase - Phase of viral life cycle where its genome replicates with host cells
- Viral protein are not synthesized at this stage

Lysogenic replication - Viral replication where virus first remains dormant for a period of time
- As viral gene replicates with host cell, number of infected cells increase
- At a point, genome separates and proteins and synthesized, many host cells die

Lytic replication - Virus is never dormant
- Viral gene immediately takes over host cell and viral proteins synthesized
- Ends, as with lysogenic cycle, with lysis of host cell and virus spreads

Malaria - Disease caused by the parasite Plasmodium sp.
- Causes high fever, sweating, which attracts mosquitoes
- Protist parasite has life cycle in mosquito and human liver and red blood cells

Meiosis - Eukaryote gamete production
- The division of diploid cells into haploid progeny
- Consists of two round of nuclear and cellular division

Merozoite - During the life cycle of Plasmodium sp. these are the reproducing form
- Found in human red blood cells

Metachronal wave - Synchronized wave motion of cilia on a ciliate
- This motion produces a power and recovery stroke, though power stroke is
stronger, it is not 100% efficient as protist moves back slightly

Mitochondria - Membrane bound organelle responsible for synthesis of ATP in eukaryotic cells
- Possible origin through endosymbiosis by ancestral protist of a bacterium

Mitosis - Nuclear division that produces daughter nuclei
- These nuclei are exact genetic copies of the parental nucleus
- This process precedes cytokinesis where the cytoplasm divides

Nonenveloped virus - Virus with no phospholipid bilayer surrounding its capsid

Nuclear envelope - Membrane separating cytoplasm from the nucleus
- Continuous with the rough endoplasmic reticulum
- Possible origin through inward extension of plasma membrane
Parasite - An organism that feeds on, or otherwise exploits its host

Peptidoglycan - A polymeric substance formed from a polysaccharide backbone tied together by
short polypeptide
- The primary structural molecule of bacterial cell walls
- Can be stained in gram-tests, testing gram-positive, indicating no capsule

Phage - Synonymous with bacteriophage

Phytoplankton - General name for microscopic, free-floating aqueous protists and plants

Planar flagellar beat - Motion of flagella on some flagellated protists
- Flagellum moves back and forth along a plane in space
- This primitive motion eliminates problem of recovery stroke in ciliated protists

Plasmodium - The composite mass of plasmodial slime moulds
- Individual nuclei are suspended in common cytoplasm
- Surrounded by single membrane

Plastid - Chloroplast double membrane bound organelle
- Contain pigment chlorophyll responsible for capturing energy from the sun
- Possible origin through endosymbiosis

Primary consumers - A member of the second trophic levels
- Usually herbivores, consumers of the primary producers

Primary producers - A member of the first trophic level
- Autotrophic, usually a photosynthetic organism

Proterozoic - Third major eon of earths history
(2,500 550 Ma) - Oxygen atmosphere, single celled aerobic organisms
- Introduction of first eukarya, the protists

Protist - Organism classified in the kingdom protista
- Unicellular eukaryotes which are likely ancestors of all multicellular life
- Diverse kingdom with animal, plant, and fungal-like properties

Pseudopod (Pseudopodium) - A temporary cytoplasmic extension of a cell
- Concept used by amoebas for locomotion

Reverse transcriptase - An enzyme that uses RNA as a template to make a DNA copy of the
retrotransposon
- Paradox of the central dogma in that RNA is producing DNA

RNA polymerase (simple and complex) - An enzyme that catalyzes the assembly of nucleotides
into an RNA strand

Secondary endosymbiosis - A non-photosynthetic eukaryote engulfed a photosynthetic eukaryote
- The smaller photosynthetic protist, algae, formed a symbiotic relationship

Sexual reproduction - The mode of reproduction in which male and female parents produce
offspring
- Offspring arise as zygotes from fertilization of an egg by a sperm from a male
- This method allows for genetic variation

Spiral flagellar beat - Motion of flagella on some flagellated protists and spirillium bacteria
- Flagellum moves in a corkscrew motion propelling cell through space
- This motion is the most efficient method of individual cell locomotion

Sporozoite - During Plasmodium sp. life cycle, these are the form which enter human blood
through mosquito saliva

Trophozoite - During Plasmodium sp. life cycle, these are the form which live and feed in human
red blood cells

Vaccine - Substance administered which is a weaker form of a pathogen to patients
- Purpose is to raise their immunity by getting used to form and antigens

Virion - A complete virus particle

Virus - An infectious agent that contains either DNA or RNA surrounded by a capsid

Zooplankton - Small, usually microscopic animals that float freely in aquatic habitats

Zygote - A fertilized egg

or



Proterozoic eon

Autapomorphies
Origins of Mitochondria
The primitive eukaryotic cell was only
capable of anaerobic metabolism to
generate ATP, one of the intermediates of
which is 3 carbon organic molecule
pyruvate. Bacteria was used as a food
source and would normally be digested
but for some reason, one bacterium was
not digested and it continued metabolizing
inside the eukaryotic cell. The bacteria
used the pyruvate molecules produced by
the cell to produce ATP and any surplus
ATP would diffuse out of the
mitochondria and could be used by the
eukaryotic cell as an energy source. A
symbiosis developed in which the
eukaryotic cell would provide pyruvate
and mitochondria would provide ATP.
This high efficiency energy production
system allowed the eukaryotic cell to
dedicate more energy to growth and
development, one of the reasons
eukaryotic cells are so large.
The mitochondrial DNA sequence has
been preserved for long periods of time
due to its efficiency. The membrane
surrounding mitochondria is characteristic
of prokaryote membrane and its DNA is
characteristic of prokaryote DNA.
Endomembrane System
Invaginations of the plasma membrane to
increase surface:volume ratio and create
complex endomembrane system that has
specialized organelles and surfaces for
different cellular activities.. Provides
compartments within the cell which are
separate from the cytoplasm. System
contains nuclear envelopes, endoplasmic
reticulum, golgi comples, vesicles and
lysosomes.
The genetic material was first to be
wrapped in endomembrane system. The
invagination creates a double lipid bilayer
with pores in it used for communication
and transport of ribosomes and RNA. The
genetic material, events of the genome,
transcription were separated from the rest
of the cellular components and were given
a specialized cellular component. This
allows for the modification of mRNA
(removal of introns) before translation.
Chromosomes
Storage of genetic material in multiple
linear strands rather than in a single
circular loop. This characteristic allows
fast replication of a large genome because
there are replication points on multiple
chromosomes rather than only one
replication point on a single bacterial
chromosome.
Centrosome
Important role in mitosis and meiosis.
System of microtubules extending from
the centrosome pull the chromosomes
apart. The cytoskeleton is also composed
partly of microtubules.
Microtuble networks extend throughout
the cell from the centrosome and are
responsible for positioning the nucleus
and other organelles, also creates overall
polarity of the cell. The centrosome
implements the cell's 3D architectural
plan which is encoded in the centriole of
the centrosome and passed to the daughter
cells when they duplicate. Molecular
motors (kinesin and dyenin) move along
the microtubles and are responsible for
intracellular transport. They can speed
materials across the cell which overcomes
the limitations of passive diffusion.
Kinesin and dyenin
Molecular motors that interact with
tubulin dimers in cytoskeleton. Burns ATP
and moves down the tubulin, also has a
binding site on which things attach as they
move down the fibres they move things
around. Kinesin moves towards the
centrioles and dyenin move away.
Transport vesicles and increase the speed
of functions happening in the cell.
Origin of cellular mobility
Cell gliding. The centrioles build
cytoskeleton at one end and retract at the
other end with motors transporting
cytoplasmic material.
Endosymbiosis
Chloroplast (plastid) arose by
endosymbiosis, a photoautotroph, likely a
cyanobacteria, was internalized by a
eukaryote. There's a double plasma
membrane around the plastid ( bacterial
membrane and eukaryote membrane) The
plastid contains bacterial DNA and
bacterial ribosomes. In some algae, the
plastid still has traces of peptidoglycan.
Certain algal groups have a third lipid bi-
layer membrane surrounding the plastid.
This would have resulted from a
secondary endosymbiotic event in which a
small eukaryote algae is engulfed by a
larger eukaryote.