Structure and Function of the Cell

Introduction to the cell

Both living and non-living things are composed of molecules made from chemical elements such as Carbon,
Hydrogen, Oxygen, and Nitrogen. The organization of these molecules into cells is one feature that
distinguishes living things from all other matter.

The cell is the smallest unit of matter that can carry on all the processes of life.

1. Every living thing, from the tiniest bacterium to the largest whale, is made of one/more cells
2. Before the C17th, no one knew that cells existed, since they are too small to be seen with the naked
eye. The invention of the microscope enabled Robert Hooke, (1665) and Anton van Leuwenhoek
(1675) to see and draw the first 'cells', a word coined by Hooke to describe the cells in a thin slice of
cork, which reminded him of the rooms where monks lived.
3. The idea that all living things are made of cells was put forward in about 1840 and in 1855 came
'Cell Theory' – i.e. 'cells only come from other cells' – contradicting the earlier theory of
‘Spontaneous Generation’.

Cell Theory consists of three principles:

1. All living things are composed of one or more cells.

2. Cells are the basic units of structure and function in an organism.
3. Cells come only from the replication of existing cells.

Cell diversity

Not all cells are alike. Even cells within the same organism show enormous diversity in size, shape, and
internal organization. Your body contains around 1013 to 1014 cells of around 300 different cell types,
which we broadly classify into 4 groups.

Cell size

1. A few types of cells are large enough to be seen by the unaided eye. The human egg (ovum) is the
largest cell in the body, and can (just) be seen without the aid of a microscope.
2. Most cells are small for two main reasons:
a. The cell’s nucleus can only control a certain volume of active cytoplasm.
b. Cells are limited in size by their surface area to volume ratio. A group of small cells has a
relatively larger surface area than a single large cell of the same volume. This is important
because the nutrients, oxygen, and other materials a cell requires must enter through it
surface. As a cell grows larger at some point its surface area becomes too small to allow these
materials to enter the cell quickly enough to meet the cell's need. (= Fick’s Law – something
you need to learn well.)

Rate of diffusion α Surface Area x Concentration

Difference Distance

Cell shape

 Cells come in a variety of shapes – depending on their function

 The neurones from your toes to your head are long and thin
 Blood cells are rounded disks, so that they can flow smoothly

Internal organisation

1. Cells contain a variety of internal structures called organelles

2. An organelle is a cell component that performs a specific function in that cell
 3. Just as the organs of a multicellular organism carry out the organism's life functions, the organelles
of a cell maintain the life of the cell
4. There are many different cells; however, there are certain features common to all cells
5. The entire cell is surrounded by a thin cell membrane
All membranes have the same thickness and basic structure
6. Organelles often have their own membranes too – once again, these membranes have a similar
structure
7. The nucleus, mitochondria and chloroplasts all have double membranes, more correctly called
envelopes
8. Because membranes are fluid mosaics, the molecules making them up – phospholipids and proteins -
move independently. The proteins appear to ‘float’ in the phospholipids bilayer
9. Membranes can thus be used to transport molecules within the cell e.g. endoplasmic reticulum.
10. Proteins in the membrane can be used to transport substances across the membrane
– e.g. by facilitated diffusion or by active transport.
11. The proteins on the outside of cell membranes identify us as unique.

Prokaryotes vs. Eukaryotes

Organisms whose cells normally contain a nucleus are called Eukaryotes; those (generally smaller)
organisms whose cells lack a nucleus and have no membrane-bound organelles are known as Prokaryotes.

Prokaryotes Eukaryotes
Typical
Bacteria Protoctista, fungi, plants, animals
organisms
Typical size ≈1-10 µm ≈10-100 µm (sperm cells) apart from the tail, are smaller)
Nuclear body Real nucleus with nuclear envelope DNA circular (ccc DNA) linear
Type of nucleus
No nucleus molecules (chromosomes) with histone proteins
Ribosomes 70S 80S
Cytoplasmatic
Very few structures Highly structured by membranes and a cytoskeleton
structure
Flagellae/cilia
Cell movement Flagellae and cilia made of tubulin
made of flagellin
Mitochondria None 1 - 100 (though RBC’s have none)
Chloroplasts None In algae and plants
Single cells, colonies, higher multicellular organisms with
Organization Usually single cells
specialized cells
Binary fission Mitosis (normal cell replication)
Cell division
(simple division) Meiosis (gamete production)

Parts of the eukaryotic cell

The structures that make up a Eukaryotic cell are determined by the specific functions carried out by the
cell. Thus, there is no typical Eukaryotic cell. Nevertheless, Eukaryotic cells generally have three main
components: A cell membrane, a nucleus, and a variety of other organelles.

The cell membrane

1. A cell cannot survive if it is totally isolated from its environment. The cell membrane is a complex
barrier separating every cell from its external environment.
2. This "Selectively Permeable" membrane regulates what passes into and out of the cell.
3. The cell membrane is a fluid mosaic of proteins floating in a phospholipid bilayer.
 4. The cell membrane functions like a gate, controlling which molecules can enter and leave the cell.
5. The cell membrane controls which substances pass into and out of the cell. Carrier proteins in or on
the membrane are specific, only allowing a small group of very similar molecules through. For
instance, α- glucose is able to enter; but β – glucose is not. Many molecules cannot cross at all. For
this reason, the cell membrane is said to be selectively permeable.
6. Cell membranes are made mostly of phospholipid molecules. They have only two fatty acid ‘tails’ as
one has been replaced by a phosphate group (making the ‘head’).
7. The head is charged and so polar; the tails are not charged and so are non-polar.
8. The two ends of the phospholipid molecule have different properties in water. The phosphate head is
hydrophyllic and so the head will orient itself so that it is as close as possible to water molecules.
9. The fatty acid tails are hydrophobic and so will tend to orient themselves away from water.
10. So, when in water, phospholipids line up on the surface with their phosphate heads sticking into the
water and fatty acid tails pointing up from the surface.
11. Cells are bathed in an aqueous environment and since the inside of a cell is also aqueous, both sides
of the cell membrane are surrounded by water molecules.
12. This causes the phospholipids of the cell membrane to form two layers, known as a phospholipid
bilayer. In this, the heads face the watery fluids inside and outside the cell, whilst the fatty acid tails
are sandwiched inside the bilayer.
13. The cell membrane is constantly being formed and broken down in living cells.

Cytoplasm

1. Everything within the cell membrane which is not the nucleus is known as the cytoplasm.
2. Cytosol is the jelly-like mixture in which the other organelles are suspended, so cytosol + organelles
= cytoplasm.
3. Organelles carry out specific functions within the cell.
4. In Eukaryotic cells, most organelles are surrounded by a membrane, but in Prokaryotic cells there are
no membrane-bound organelles.

Fluid mosaic model of cell membranes

1. Membranes are fluid and are rather viscous – like vegetable oil.
2. The molecules of the cell membrane are always in motion, so the phospholipids are able to drift
across the membrane, changing places with their neighbour.
3. Proteins, both in and on the membrane, form a mosaic, floating in amongst the phospholipids.
4. Because of this, scientists call the modern view of membrane structure the ‘Fluid Mosaic Model’.
5. The mosaic of proteins in the cell membrane is constantly changing.

Membrane proteins

1. A variety of protein molecules are embedded in the basic phospholipid bilayer

2. Some proteins are attached to the surface of the cell membrane on both the internal and external
surface. These may be hormone receptors, enzymes or cell recognition proteins (or antigens)
3. Other proteins are embedded in the phospholipid bilayer itself. These are often associated with
transporting molecules from one side of the membrane to the other and are referred to as carrier
proteins.
4. Some of these form channels or pores through which certain substances can pass (facilitated
diffusion), whilst others bind to a substance on one side of the membrane and carry it to the other
side of the membrane (active transport)
5. Proteins exposed to the cell's external environment often have carbohydrates attached to them which
act as antigens (e.g. blood groups A & B – group AB has both; group O has neither).
6. Some viruses may also bind here too.

The nucleus (pl. nuclei)

1. The Nucleus is normally the largest organelle within a Eukaryotic cell. But it is NOT the ‘BRAIN’ of
the cell!!
 2. Prokaryotes have no nucleus, having a nuclear body instead. This has no membrane and a loop of
DNA (and no chromatin proteins)
3. The nucleus contains the cell’s chromosomes (human, 46, fruit fly 6, fern 1260) which are normally
uncoiled to form a chromatinic network, which contain both linear DNA and proteins, known as
histones. These proteins coil up (dehydrate) at the start of nuclear division, when the chromosomes
first become visible.
4. Whilst most cells have a single nucleus some cells (macrophages, phloem companion cells) have
more than one.
5. Fungi have many nuclei in their cytoplasm – they are coenocytic (= common cytoplasm throughout)
6. The nucleus is surrounded by a double membrane called the nuclear envelope.
7. The nuclear envelope has many nuclear pores through which mRNA, and proteins can pass. These
dimples make it look like a golf ball.
8. Most nuclei contain at least one nucleolus (plural, nucleoli). The nucleoli are where ribosomes are
synthesised. Ribosomes, you remember, translate mRNA into proteins.
9. When a nucleus prepares to divide, the nucleolus disappears.

Nucleus

The nucleus is the control centre of the cell. It is surrounded by a nuclear membrane that allows molecules to
enter and leave the nucleus similar to the plasma membrane.

The nucleus contains DNA (deoxyribonucleic acid). The DNA is arranged in groups called chromosomes.
This is the genetic material of the cell. Every organism has a specific number of chromosomes in each
nucleus of each of its cells. Humans have 46 chromosomes in every cell while roundworms have 2. When
not dividing the chromosomes are called chromatin. They become elongated and interwoven at this stage.

A molecule of DNA when the cell is not dividing (in chromatin form):

A chromosome as seen at the start of cell division:

Genes are located on the chromosomes. These are the structures that control the production of protein. In
this way the genes determine the characteristics of the living thing.
The nucleus of a cell contains chromosomes, on which are the genes consisting of the DNA that codes for
proteins, the main ingredients of living beings.

Nuclear Pores

Nuclear pores are openings through which materials enter and leave the nucleus. Large molecules can pass
between the cytoplasm and the nucleus through these pores. 1 example is RNA from nucleus to cytoplasm
and nucleotides from cytoplasm to nucleus. This will be discussed later in another chapter of your text.

The arrows show a nuclear pore.

Nucleolus

The nucleolus is the area where ribosomes are made. Ribosomes are made of RNA. The nucleolus contains a
lot of rRNA (ribosomal RNA)

Comparison of structures between animal and plant cells

Typical animal cell Typical plant cell

Organelles  Nucleus  Nucleus
o Nucleolus (within nucleus) o Nucleolus (within nucleus)
 Rough ER  Rough ER
 Smooth ER  Smooth ER
 80S Ribosomes  80S Ribosomes
 Cytoskeleton  Cytoskeleton
 Golgi apparatus  Golgi apparatus
 Cytoplasm  Cytoplasm
  Mitochondria  Mitochondrion
 Vesicles  Vesicle
 Vacuoles  Chloroplast and other plastids
 Lysosomes  Central vacuole
 Centrioles o Tonoplast (central vacuole
membrane)

Additional  Cilia  Plasma membrane

structures  Flagellae  Cellulose cell wall
 Plasma membrane  Plasmodesmata

Mitochondria

1. Mitochondria are found scattered throughout the cytosol, and are relatively large organelles (second
only to the nucleus and chloroplasts)
2. Mitochondria are the sites of aerobic respiration, in which energy from organic compounds is
transferred to ATP. For this reason they are sometimes referred to as the ‘powerhouse’ of the cell
3. ATP is the molecule that most cells use as their main energy ‘currency’
4. Mitochondria are more numerous in cells that have a high energy requirement - our muscle cells
contain a large number of mitochondria, as do liver, heart and sperm cells
5. Mitochondria are surrounded by two membranes, indicating that they were once free-living
organisms that have become mutualistic and then a part of almost every eukaryotic cell (not RBC’s
and xylem vessels)
a. The smooth outer membrane serves as a boundary between the mitochondria and the cytosol.
b. The inner membrane has many long folds, known as cristae, which greatly increase the
surface area of the inner membrane, providing more space for ATP synthesis to occur.
6. Mitochondria have their own DNA, and new mitochondria arise only when existing ones grow and
divide. They are thus semi-autonomous organelles.

Ribosomes

1. Unlike most other organelles, ribosomes are not surrounded by a membrane

2. Ribosomes are the site of protein synthesis in a cell
3. They are the most common organelles in almost all cells
4. Some are free in the cytoplasm (Prokaryotes)
others line the membranes of rough endoplasmic reticulum (rough ER)
5. They exist in two sizes: 70S are found in all Prokaryotes, chloroplasts and mitochondria, suggesting
that they have evolved from ancestral Prokaryotic organisms. They are free-floating. 80S found in all
eukaryotic cells – attached to the rough ER (they are rather larger)
6. Groups of 80s ribosomes, working together, are known as a polysome.

Endoplasmic reticulum (ER)

1. The ER is a system of membranous tubules and sacs

2. The primary function of the ER is to act as an internal transport system, allowing molecules to move
from one part of the cell to another
3. The quantity of ER inside a cell fluctuates, depending on the cell's activity. Cells with a lot include
secretory cells and liver cells
4. The rough ER is studded with 80s ribosomes and is the site of protein synthesis. It is an extension of
the outer membrane of the nuclear envelope, so allowing mRNA to be transported swiftly to the 80s
ribosomes, where they are translated in protein synthesis
5. The smooth ER is where polypeptides are converted into functional proteins and where proteins are
prepared for secretion. It is also the site of lipid and steroid synthesis, and is associated with the
Golgi apparatus. Smooth ER has no 80s ribosomes and is also involved in the regulation of calcium
levels in muscle cells, and the breakdown of toxins by liver cells
6. Both types of ER transport materials throughout the cell.
Golgi apparatus

1. The Golgi apparatus is the processing, packaging and secreting organelle of the cell, so it is much
more common in glandular cells.
2. The Golgi apparatus is a system of membranes, made of flattened sac-like structures called cisternae.
3. It works closely with the smooth er, to modify proteins for export by the cell.

Lysosome

1. Lysosomes are small spherical organelles that enclose hydrolytic enzymes within a single membrane
2. Lysosomes are the site of protein digestion – thus allowing enzymes to be re-cycled when they are
no longer required. They are also the site of food digestion in the cell, and of bacterial digestion in
phagocytes
3. Lysosomes are formed from pieces of the Golgi apparatus that break off
4. Lysosomes are common in the cells of Animals, Protoctista and even Fungi, but rare in plants.

Cytoskeleton

1. Just as your body depends on your skeleton to maintain its shape and size, so a cell needs structures
to maintain its shape and size
2. In animal cells, which have no cell wall, an internal framework called the cytoskeleton maintains the
shape of the cell, and helps the cell to move
3. The cytoskeleton consists of two structures: a) microfilaments (contractile). They are made of actin,
and are common in motile cells. b) microtubules (rigid, hollow tubes – made of tubulin).
4. Microtubules have three functions:
a. To maintain the shape of the cell
b. To serve as tracks for organelles to move along within the cell
c. They form the centriole

Centriole

1. This consists of two bundles of microtubules at right-angles to each other

2. Each bundle contains 9 tubes in a very characteristic arrangement
3. At the start of mitosis and meiosis, the centriole divides, and one half moves to each end of the cell,
forming the spindle
4. The spindle fibres are later shortened to pull the chromosomes apart

Cilia and flagellae

1. Cilia and Flagellae are structures that project from the cell, where they assist in movement
2. Cilia (sing. cilium) are short, and numerous and hair-like
3. Flagellae (sing. flagellum) are much longer, fewer, and are whip-like
4. The cilia and flagellae of all Eukaryotes are always in a ‘9 + 2’ arrangement that is characteristic (see
diagram)
5. Protoctista commonly use cilia and flagellae to move through water
6. Sperm use flagellae (many, all fused together) to swim to the egg
7. Cilia line our trachea and bronchi, moving dust particles and bacteria away from the lungs

Plant cell structures

1. Most of the organelles and other parts of the cell are common to all Eukaryotic cells. Cells from
different organisms have an even greater difference in structure
2. Plant cells have three additional structures not found in animal cells:
a. Cellulose cell walls
b. Chloroplasts (and other plastids)
c. A Central Vacuole
Cellulose cell wall

1. One of the most important features of all plants is presence of a cellulose cell wall.
2. Fungi such as Mushrooms and Yeast also have cell walls, but these are made of chitin.
3. The cell wall is freely permeable (porous), and so has no direct effect on the movement of molecules
into or out of the cell.
4. The rigidity of their cell walls helps both to support and protect the plant.
5. Plant cell walls are of two types:
a. Primary (cellulose) cell wall - While a plant cell is being formed, a middle lamella made of
pectin, is formed and the cellulose cell wall develops between the middle lamella and the cell
membrane. As the cell expands in length, more cellulose is added, enlarging the cell wall.
When the cell reaches full size, a secondary cell wall may form
b. Secondary (lignified) cell wall - The secondary cell wall is formed only in woody tissue
(mainly xylem). The secondary cell wall is stronger and waterproof and once a secondary cell
wall forms, a cell can grow no more – it is dead!

Vacuoles

1. The most prominent structure in plant cells is the large vacuole.

2. The vacuole is a large membrane-bound sac that fills up much of most plant cells.
3. The vacuole serves as a storage area, and may contain stored organic molecules as well as inorganic
ions.
4. The vacuole is also used to store waste. Since plants have no kidney, they convert waste to an
insoluble form and then store it in their vacuole - until autumn!
5. The vacuoles of some plants contain poisons (eg tannins) that discourage animals from eating their
tissues.
6. Whilst the cells of other organisms may also contain vacuoles, they are much smaller and are usually
involved in food digestion.

Chloroplasts (and other plastids)

1. A characteristic feature of plant cells is the presence of plastids that make or store food.
2. The most common of these (some leaf cells only!) are chloroplasts – the site of photosynthesis.
3. Each chloroplast encloses a system of flattened, membranous sacs called thylakoids, which contain
chlorophyll.
4. The thylakoids are arranged in stacks called grana.
5. The space between the grana is filled with cytoplasm-like stroma.
6. Chloroplasts contain ccc DNA and 70S ribosomes and are semi-autonomous organelles.
7. Other plastids store reddish-orange pigments that colour petals, fruits, and some leaves.

Multicellular organization

In a unicellular organism, one cell carries out all of the functions of life. In contrast, most cells in a
multicellular organism are specialized to perform one or a few functions – more efficiently. Because of cell
specialization, the cells of multicellular organisms depend on other cells in the organism for their survival.

Tissue, organs, and organ systems

1. In most Multicellular Organisms, we find the following organization:

o Cellular Level: The smallest unit of life capable of carrying out all the functions of living
things.
o Tissue Level: A group of cells that performs a specific function in an organism.
o Organ Level: Several different types of tissue that function together for a specific purpose.
o Organ System Level: Several organs working together to perform a function. The different
organ systems in a multicellular organism interact to carry out the processes of life
2. Plants also have tissue and organs, although they are arranged somewhat differently from those of
animals – e.g. vascular tissue.
 3. The four plant organs are: Roots Stems Leaves and Flowers

Colonial organizations

1. A colonial organization is a collection of genetically identical cells that live together in a closely
connected group.
2. Many of the cells of the colony carry out specific functions that benefit the whole colony.
3. Colonial organisms (e.g. sponges, coral) appear to straddle the border between a collection of
unicellular organisms and a true multicellular organism. They lack tissues and organs, but do exhibit
the principle of cell specialization.

ORGANELLE LOCATION DESCRIPTION FUNCTION

Outer layer rigid, strong, Support (grow tall) protection allows
Cell wall Plant, not animal
stiff made of cellulose H2O, O2, CO2 to pass into and out of cell
Plant - inside cell wall Support protection controls movement of
Cell animal - outer layer; materials in/out of cell barrier between
Both plant/animal
membrane cholesterol selectively cell and its environment maintains
permeable homeostasis
Nucleus Both plant/animal Large, oval Controls cell activities
Nuclear Surrounds nucleus Controls movement of materials in/out of
Both plant/animal
membrane selectively permeable nucleus
Clear, thick, jellylike
Cytoplasm Both plant/animal material and organelles Supports /protects cell organelles
found inside cell membrane
Endoplasmic
Network of tubes or
reticulum Both plant/animal Carries materials through cell
membranes
(E.R.)
Small bodies free or attached
Ribosome Both plant/animal Produces proteins
to E.R.
Bean-shaped with inner
Mitochondrion Both plant/animal Breaks down sugar molecules into energy
membranes
Plant - few/large Store food, water, waste (plants need to
Vacuole Fluid-filled sacs
animal - small store large amounts of food)
Plant -
Small, round, with a Breaks down larger food molecules into
Lysosome uncommon
membrane smaller molecules digests old cell parts
animal - common
Green, oval usually
Uses energy from sun to make food for
Chloroplast Plant, not animal containing chlorophyll
the plant (photosynthesis)
(green pigment)

This page has been written by Ian White.

 Eukaryotic Cell: Structure and Function

Introduction to eukaryotic cells

By definition, eukaryotic cells are cells that contain a membrane-bound nucleus, a structural feature that is
not present in bacterial or archaeal cells. In addition to the nucleus, eukaryotic cells are characterized by
numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts,
mitochondria, and others.

In previous sections, we began to consider the Design Challenge of making cells larger than a small
bacterium—more precisely, growing cells to sizes at which, in the eyes of natural selection, relying on
diffusion of substances for transport through a highly viscous cytosol comes with inherent functional trade-
offs that offset most selective benefits of getting larger. In the lectures and readings on bacterial cell
structure, we discovered some morphological features of large bacteria that allow them to effectively
overcome diffusion-limited size barriers (e.g., filling the cytoplasm with a large storage vacuole maintains a
small volume for metabolic activity that remains compatible with diffusion-driven transport).

As we transition our focus to eukaryotic cells, we want you to approach the study by constantly returning to
the Design Challenge. We will cover a large number of subcellular structures that are unique to eukaryotes,
and you will certainly be expected to know the names of these structures or organelles, to associate them
with one or more "functions", and to identify them on a canonical cartoon representation of a eukaryotic cell.
This memorization exercise is necessary but not sufficient. We will also ask you to start thinking a bit
deeper about some of the functional and evolutionary costs and benefits (trade-offs) of both evolving
eukaryotic cells and various eukaryotic organelles, as well as how a eukaryotic cell might coordinate the
functions of different organelles.

Your instructors will, of course, propose some functional hypotheses for you to consider that address these
broader points. Our hypotheses may sometimes come in the form of statements like, "Thing A
exists because of rationale B." To be completely honest, however, in many cases, we don't actually know all
of the selective pressures that led to the creation or maintenance of certain cellular structures, and the
likelihood that one explanation will fit all cases is slim in biology. The causal linkage/relationship implied
by the use of terms like "because" should be treated as good hypotheses rather than objective, concrete,
undisputed, factual knowledge. We want you to understand these hypotheses and to be able to discuss the
ideas presented in class, but we also want you to indulge your own curiosity and to begin thinking
critically about these ideas yourself. Try using the Design Challenge rubric to explore some of your ideas. In
the following, we will try to seed questions to encourage this activity.
Figure 1. These figures show the major organelles and other cell components of (a) a typical animal cell
and (b) a typical eukaryotic plant cell. The plant cell has a cell wall, chloroplasts, plastids, and a central
vacuole—structures not found in animal cells. Plant cells do not have lysosomes or centrosomes.

The plasma membrane

Like bacteria and archaea, eukaryotic cells have a plasma membrane, a phospholipid bilayer with embedded
proteins that separates the internal contents of the cell from its surrounding environment. The plasma
membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell.
Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane,
usually with some help of protein transporters.

Figure 2. The eukaryotic plasma membrane is a phospholipid bilayer with proteins and cholesterol
embedded in it.

As discussed in the context of bacterial cell membranes, the plasma membranes of eukaryotic cells may also
adopt unique conformations. For instance, the plasma membrane of cells that, in multicellular organisms,
specialize in absorption are often folded into fingerlike projections called microvilli (singular = microvillus);
(see figure below). The "folding" of the membrane into microvilli effectively increases the surface area for
absorption while minimally impacting the cytosolic volume. Such cells can be found lining the small
intestine, the organ that absorbs nutrients from digested food.

An aside: People with celiac disease have an immune response to gluten, a protein found in wheat, barley,
and rye. The immune response damages microvilli. As a consequence, afflicted individuals have an impaired
ability to absorb nutrients. This can lead to malnutrition, cramping, and diarrhea.

Figure 3. Microvilli, shown here as they appear on cells lining the small intestine, increase the surface area
available for absorption. These microvilli are only found on the area of the plasma membrane that faces the
cavity from which substances will be absorbed. Credit: "micrograph", modification of work by Louisa
Howard

The cytoplasm
The cytoplasm refers to the entire region of a cell between the plasma membrane and the nuclear envelope.
It is composed of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (see
figure below). Even though the cytoplasm consists of 70 to 80 percent water, it nevertheless has a semisolid
consistency. It is crowded in there. Proteins, simple sugars, polysaccharides, amino acids, nucleic acids,
fatty acids, ions and many other water-soluble molecules are all competing for space and water.

The nucleus

Typically, the nucleus is the most prominent organelle in a cell (see figure below) when viewed through a
microscope. The nucleus (plural = nuclei) houses the cell’s DNA. Let’s look at it in more detail.

Figure 4. The nucleus stores chromatin (DNA plus

proteins) in a gel-like substance called the nucleoplasm.
The nucleolus is a condensed region of chromatin
where ribosome synthesis occurs. The boundary of the
nucleus is called the nuclear envelope. It consists of two
phospholipid bilayers: an outer membrane and an inner
membrane. The nuclear membrane is continuous with
the endoplasmic reticulum. Nuclear pores allow
substances to enter and exit the nucleus.

The nuclear envelope

The nuclear envelope, a structure that constitutes the outermost boundary of the nucleus, is a double-
membrane—both the inner and outer membranes of the nuclear envelope are phospholipid bilayers. The
nuclear envelope is also punctuated with protein-based pores that control the passage of ions, molecules, and
RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semisolid fluid inside the
nucleus where we find the chromatin and the nucleolus, a condensed region of chromatin where ribosome
synthesis occurs.

Chromatin and chromosomes

To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the
nucleus that are made up of DNA, the hereditary material. You may remember that in bacteria and archaea,
DNA is typically organized into one or more circular chromosome(s). In eukaryotes, chromosomes are
linear structures. Every eukaryotic species has a specific number of chromosomes in the nuclei of its cells.
In humans, for example, the chromosome number is 23, while in fruit flies, it is 4.

Chromosomes are only clearly visible and distinguishable from one another by visible optical microscopy
when the cell is preparing to divide and the DNA is tightly packed by proteins into easily distinguishable
shapes. When the cell is in the growth and maintenance phases of its life cycle, numerous proteins are still
associated with the nucleic acids, but the DNA strands more closely resemble an unwound, jumbled bunch
of threads. The term chromatin is used to describe chromosomes (the protein-DNA complexes) when they
are both condensed and decondensed.

Figure 5. (a) This image shows various levels of the organization of

chromatin (DNA and protein). (b) This image shows paired
chromosomes. Credit (b): modification of work by NIH; scale-bar data
from Matt Russell

The nucleolus

Some chromosomes have sections of DNA that encode ribosomal RNA.

A darkly staining area within the nucleus called the nucleolus (plural =
nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are
then transported out to the cytoplasm through the pores in the nuclear envelope.

Note: possible discussion

Discuss amongst yourselves. Use the Design Challenge rubric to consider the nucleus in more detail. What
"problems" does an organelle like the nucleus solve? What are some of the qualities of a nucleus that may be
responsible for ensuring its evolutionary success? What are some of the trade-offs of evolving and
maintaining a nucleus? (Every benefit has some cost; can you list both?) Remember, there may be some
well-established hypotheses (and it is good to mention these), but the point of the exercise here is for you to
think critically and to critically discuss these ideas using your collective "smarts".

Ribosomes

Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron
microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the
cytoplasm. They may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of
the endoplasmic reticulum and the outer membrane of the nuclear envelope (cartoon of cell above).

Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist
of two subunits, aptly called large and small (figure below). Ribosomes receive their "instructions" for
protein synthesis from the nucleus, where the DNA is transcribed into messenger RNA (mRNA). The
mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases
in the mRNA into a specific order of amino acids in a protein. This is covered in greater detail in the section
covering the process of translation.

Figure 6. Ribosomes are made up of a large subunit

(top) and a small subunit (bottom). During protein
synthesis, ribosomes assemble amino acids into
proteins.

Mitochondria

Mitochondria (singular = mitochondrion) are often

called the “powerhouses” or “energy factories” of a cell
because they are the primary site of metabolic
respiration in eukaryotes. Depending on the species and
the type of mitochondria found in those cells, the
respiratory pathways may be anaerobic or aerobic. By
definition, when respiration is aerobic, the terminal electron is oxygen; when respiration is anaerobic, a
compound other than oxygen functions as the terminal electron acceptor. In either case, the result of these
respiratory processes is the production of ATP via oxidative phosphorylation, hence the use of terms
"powerhouse" and/or "energy factory" to describe this organelle. Nearly all mitochondria also possess a
small genome that encodes genes whose functions are typically restricted to the mitochondrion.

In some cases, the number of mitochondria per cell is tunable, depending, typically, on energy demand. It is
for instance possible muscle cells that are used—that by extension have a higher demand for ATP—may
often be found to have a significantly higher number of mitochondria than cells that do not have a high
energy load.

The structure of the mitochondria can vary significantly depending on the organism and the state of the cell
cycle which one is observing. The typical textbook image, however, depicts mitochondria as oval-shaped
organelles with a double inner and outer membrane (see figure below); learn to recognize this generic
representation. Both the inner and outer membranes are phospholipid bilayers embedded with proteins that
mediate transport across them and catalyze various other biochemical reactions. The inner membrane layer
has folds called cristae that increase the surface area into which respiratory chain proteins can be embedded.
The region within the cristae is called the mitochondrial matrix and contains—among other things—
enzymes of the TCA cycle. During respiration, protons are pumped by respiratory chain complexes from the
matrix into a region known as the intermembrane space (between the inner and outer membranes).
Figure 7. This electron micrograph shows a mitochondrion as viewed with a transmission electron
microscope. This organelle has an outer membrane and an inner membrane. The inner membrane contains
folds, called cristae, which increase its surface area. The space between the two membranes is called the
intermembrane space, and the space inside the inner membrane is called the mitochondrial matrix. ATP
synthesis takes place on the inner membrane. Credit: modification of work by Matthew Britton; scale-bar
data from Matt Russell

Note: possible discussion

Discuss: Processes like glycolysis, lipid biosynthesis, and nucleotide biosynthesis all have compounds that
feed into the TCA cycle—some of which occurs in the mitochondria. What are some of the functional
challenges associated with coordinating processes that have a common set of molecules if the enzymes are
sequestered into different cellular compartments?

Peroxisomes

Peroxisomes are small, round organelles enclosed by single membranes. These organelles carry out redox
reactions that oxidize and break down fatty acids and amino acids. They also help to detoxify many toxins
that may enter the body. Many of these redox reactions release hydrogen peroxide, H2O2, which would be
damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down
the H2O2 into oxygen and water. For example, alcohol is detoxified by peroxisomes in liver cells.
Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into
sugars.

Vesicles and vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact
that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them: the
membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the
cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The
membrane of a vacuole does not fuse with the membranes of other cellular components.

Animal cells versus plant cells

At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes,
mitochondria, peroxisomes, and in some, vacuoles. There are some striking differences between animal and
plant cells worth noting. Here is a brief list of differences that we want you to be familiar with and a slightly
expanded description below:

1. While all eukaryotic cells use microtubule and motor protein the based mechanisms to segregate
chromosomes during cell division, the structures used to organize these microtubules differ in plants versus
animal and yeast cells. Animal and yeast cells organize and anchor their microtubules into structures called
microtubule organizing centers (MTOCs). These structures are composed of structures called centrioles that
are composed largely of α-tubulin, β-tubulin, and other proteins. Two centrioles organize into a structure
called a centrosome. By contrast, in plants, while microtubules also organize into discrete bundles, there are
no conspicuous structures similar to the MTOCs seen in animal and yeast cells. Rather, depending on the
organism, it appears that there can be several places where these bundles of microtubules can nucleate
 from places called acentriolar (without centriole) microtubule organizing centers. A third type of tubulin, γ-
tubulin, appears to be implicated, but our knowledge of the precise mechanisms used by plants to organize
microtubule spindles is still spotty.
2. Animal cells typically have organelles called lysosomes responsible for degradation of biomolecules. Some
plant cells contain functionally similar degradative organelles, but there is a debate as to how they should be
named. Some plant biologists call these organelles lysosomes while others lump them into the general
category of plastids and do not give them a specific name.
3. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas
animal cells do not.

The centrosome

The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of
centrioles, two structures that lie perpendicular to eachother (see figure below). Each centriole is a cylinder
of nine triplets of microtubules.

Figure 8. The centrosome consists of two

centrioles that lie at right angles to each other.
Each centriole is a cylinder made up of nine
triplets of microtubules. Nontubulin proteins
(indicated by the green lines) hold the
microtubule triplets together.

The centrosome (the organelle where all

microtubules originate in animal and yeast)
replicates itself before a cell divides, and the
centrioles appear to have some role in pulling
the duplicated chromosomes to opposite ends of
the dividing cell. However, the exact function of
the centrioles in cell division remains unclear, as cells that have had their centrosome removed can still
divide, and plant cells, which lack centrosomes, are capable of cell division.

Lysosomes

Animal cells have another set of organelles not found in plant cells: lysosomes. Colloquially,
the lysosomes are sometimes called the cell’s “garbage disposal”. Enzymes within the lysosomes aid the
breakdown of proteins, polysaccharides, lipids, nucleic acids, and even "worn-out" organelles. These
enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is
more acidic than the pH of the cytoplasm. In plant cells, many of the same digestive processes take place in
vacuoles.

The cell wall

If you examine the diagram above depicting plant and animal cells, you will see in the diagram of a plant
cell a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that
protects the cell, provides structural support, and gives shape to the cell. Fungal and protistan cells also have
cell walls. While the chief component of bacterial cell walls is peptidoglycan, the major organic molecule in
the plant cell wall is cellulose (see structure below), a polysaccharide made up of glucose subunits.

Figure 9. Cellulose is a long chain of β-glucose molecules connected by a 1-4 linkage. The dashed lines at
each end of the figure indicate a series of many more glucose units. The size of the page makes it impossible
to portray an entire cellulose molecule.
Chloroplasts

Chloroplasts are plant cell organelles that carry out photosynthesis. Like the mitochondria, chloroplasts have
their own DNA and ribosomes, but chloroplasts have an entirely different function.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a
chloroplast’s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs called
thylakoids (figure below). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed
by the inner membrane that surrounds the grana is called the stroma.

Figure 10. The chloroplast has an outer membrane,

an inner membrane, and membrane structures called
thylakoids that are stacked into grana. The space
inside the thylakoid membranes is called the
thylakoid space. The light harvesting reactions take
place in the thylakoid membranes, and the synthesis
of sugar takes place in the fluid inside the inner
membrane, which is called the stroma. Chloroplasts
also have their own genome, which is contained on a
single circular chromosome.

The chloroplasts contain a green pigment

called chlorophyll, which captures the light energy
that drives the reactions of photosynthesis. Like plant
cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their
chlorophyll is not relegated to an organelle. Evolution connection: Endosymbiosis

We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you
wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species depend on each other for their
survival. Endosymbiosis (endo- = “within”) is a mutually beneficial relationship in which one organism
lives inside the other. Endosymbiotic relationships abound in nature. For instance, some microbes that live
in our digestive tracks produce vitamin K. The relationship between these microbes and us (their hosts) is
said to be mutually beneficial or symbiotic. The relationship is beneficial for us because we are unable to
synthesize vitamin K; the microbes do it for us instead. The relationship is also beneficial for the microbes
because they receive abundant food from the environment of the large intestine, and they are protected
both from other organisms and from drying out.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know
that bacteria have DNA and ribosomes, just as mitochondria and chloroplasts do. Scientists believe that host
cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and
autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution,
these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming
mitochondria and the autotrophic bacteria becoming chloroplasts. There will be more on this later in the
reading.

The central vacuole

Previously, we mentioned vacuoles as essential components of plant cells. If you look at the cartoon figure
of the plant cell, you will see that it depicts a large central vacuole that occupies most of the area of the cell.
The central vacuole plays a key role in regulating the cell’s concentration of water in changing
environmental conditions.

Silly vacuole factoid: Have you ever noticed that if you forget to water a plant for a few days, it wilts?
That’s because as the water concentration in the soil becomes lower than the water concentration in the
plant, water moves out of the central vacuoles and cytoplasm. As the central vacuole shrinks, it leaves the
cell wall unsupported. This loss of support to the cell walls of plant cells results in the wilted appearance of
the plant.

The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the
cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm.