Chapter 7.

A TOUR OF THE CELL

From Campbell BIOLOGY

The cell is as fundamental to biology as the atom is to chemistry: All organisms are
made of cells. In the hierarchy of biological organization, the cell is the simplest
collection of matter that can live. Indeed, there are diverse forms of life existing as
single-celled organisms. More complex organisms, including plants and animals,
are multicellular; their bodies are cooperatives of many kinds of specialized cells
that could not survive for long on their own. However, even when they are
arranged into higher levels of organization, such as tissues and organs, cells can
be singled out as the organism’s basic units of structure and function. The
contraction of muscle cells moves your eyes as you read this sentence; when you
decide to turn this page, nerve cells will transmit that decision from your brain to
the muscle cells of your hand. Everything an organism does is fundamentally
occurring at the cellular level. This chapter introduces the microscopic world of
the cell.

This text takes a thematic approach to the study of life, and the cell is a microcosmic
model of many of the themes introduced in Chapter 1. We will see that life at the
cellular level arises from structural order, reinforcing the themes of emergent
properties and the correlation between structure and function. For example, the
movement of an animal cell depends on an intricate interplay of structures that
make up a cellular skeleton. Another recurring theme in biology is the interaction
of organisms with their environment. Cells sense and respond to environmental
fluctuations. As open systems, they continuously exchange both materials and
energy with their surroundings. And keep in mind the one biological theme that
unifies all others: evolution. All cells are related by their descent from earlier cells,
but they have been modified in various ways during the long evolutionary history
of life on Earth. For example, if one unicellular organism lives in fresh water and
another inhabits the sea, we can expect these cells to be somewhat differently
equipped as a result of their divergent adaptations to disparate environments.

Perhaps the greatest obstacle to becoming acquainted with the cell is imagining how
something too small to be seen by the unaided eye can be so complex. How can cell
biologists possible dissect so small a package to investigate its inner workings?
Before we actually tour the cell, it will be helpful to learn how cells are studied.
Microscopes provide windows to the world of the cell

The evolution of science often parallels the invention of instruments that extend human
senses to new limits. The discovery and early study of cells progressed with the
invention and improvement of microscopes in the 17th century. Microscopes of
various types are still indispensable tool for the study of cells.

The microscopes first used by the Renaissance scientists, as well as the microscopes you
are likely to use in the laboratory, are all light microscopes (LMs). Visible light is
passed through the specimen and then through glass lenses. The lenses refract (bend) the
light in such a way that the image of the specimen is magnified as it is projected into the
eye.

Two important values in microscopy are magnification and resolving power, or

resolution. Magnification is how much larger the object appears compared to its real size.
Resolving power is a measure of the clarity of the image; it is the minimum distance two
points can be separated and still be distinguished as two separate points. For example,
what appears to the unaided eye as one star in the sky may be resolved as twin stars with
a telescope.

Just as the resolving power of the human eye is limited, the resolving power of telescopes
and microscopes is limited. Microscopes can be designed to magnify objects as much as
desired, but the light microscope can never resolve detail finer than about 0.2 µm, the
size of a small bacterium. This resolution is limited by the wavelength of the visible light
used to illuminate the specimen. Light microscopes can magnify effectively to about
1000 times the size of the actual specimen; greater magnifications increase blurriness.
Most of the improvements in light microscopy since the beginning of this century
involved new methods for enhancing contrast which makes the details that can be
resolved stand out better to the eye. Shinya Inoué, the scientist you met in the interview
that precedes this chapter, has pioneered videomicroscopy and other improvements in
light microscopy.

Although cells were discovered by Robert Hooke in 1665, the geography of the cell was
largely uncharted until the past few decades. Most subcellular structures, or organelles,
are too small to be resolved by light microscopes. Cell biology advanced rapidly in the
1950s with the introduction of electron microscope. Instead of using visible light, the
electron microscope (EM) focuses a beam of electrons through the specimen. Resolving
power is inversely related to the wavelength of radiation a microscope uses, and electron
beam have wavelengths much shorter than the wavelengths of visible light. Modern
electron microscopes can achieve a resolution of about 0.2 nanometer (nm), a
thousandfold improvement over the light microscope. Biologists use the term cell
ultrastructure to refer to cell’s anatomy as resolved by an electron microscope.

There are two types of electron microscopes: the transmission electron microscope
(TEM) and the scanning electron microscope (SEM). The TEM aims an electron beam
through a thin section of the specimen, similar to the way the light microscope transmits
light through a slide. However, instead of using glass lenses, which are opaque to
electrons, the TEM uses electromagnets as lenses to focus and magnify the image by
bending the trajectories of the charged electrons. The image is ultimately focused onto a
screen for viewing or onto photographic film. To enhance contrast in the image, very thin
sections of preserved cells are stained with atoms of heavy metals, which attach to certain
places in the cells. Cell biologists use the TEM mainly to study the internal ultrastructure
of cells.

The SEM is especially useful for detailed study of the surface of the specimen. The
electron beam scans the surface of the sample, which is usually coated with a thin film of
gold. The beam excites the electrons on the sample surface itself, and these secondary
electrons are collected and focused onto a screen. This forms an image of topography of
the specimen. An important attribute of the SEM is its great depth of field, which results
in an image that appears three-dimensional.

Electron microscopes reveal many organelles that are impossible to resolve with the light
microscope. But the light microscope offers many advantages, especially for the study of
live cells. A disadvantage of electron microscopy is that the chemical and physical
methods used to prepare the specimen not only kill cells but also may introduce artifacts
structural features seen in micrographs that do not exist in the living cell.

Microscopes of various kinds are the most important tools of cytology, the study of cell
structure. But simply describing the diverse organelles within the cell reveals little about
their function. Modern cell biology developed from an integration of cytology with
biochemistry, the study of life’s chemical processes, or metabolism. A biochemical
approach called cell fractionation has been particularly important in this multidisciplinary
synthesis of cell biology.

Cell biologists can isolate organelles to study their functions

The objective of cell fractionation is to take cells apart, separating the major organelles
so that their individual functions can be studied. The instrument used to fractionate cells
is the centrifuge, a merry-go-round for test tubes capable of spinning at various speeds.
The most powerful machines, called ultracentrifuges, can spin as fast as 80,000
revolutions per minute (rpm) and apply forces on particles of up to 500,000 times the
force of gravity (500,00 g).

Fractionation begins with homogenization, the disruption of cells. The objective is to

break the cells without severely damaging their organelles. Spinning the soupy
homogenate in a centrifuge separates the parts of the cell into two fractions: the pellet,
consisting of the larger structures that become packed at the bottom of the test tube; and
the supernatant, consisting of smaller parts of the cell suspended in the liquid above the
pellet. The supernatant is decanted into another tube and centrifuge again. The process is
repeated, increasing the speed with each step, collecting smaller and smaller components
of the homogenized cells in each successive pellet.

Cell fractionation enables the researcher to prepare specific components of cells in bulk
quantity in order to study their composition, and functions. By following this approach,
biologists have been able to assign various functions of the cell to the different
organelles, a task that would be far more difficult if they had to study intact cells. For
example, one cellular fraction collected by centrifugation has enzymes that function in
the metabolic process known as cellular respiration. The prevalent organelles in that
fraction match the structures called mitochondria, as visualized in the electron
microscope. This helped cell biologists determine that mitochondria are the sites of
cellular respiration. Cytology and biochemistry complement each other in the correlation
between cellular structure and function.

A panoramic view of the cell

Prokaryotic and Eukaryotic Cells

Every organism is composed of one of two structurally different types of cells:
prokaryotic cells or eukaryotic cells. Prokaryotic cells are found only in the kindom
Monera, the bacteria. Protists, plants, fungi, and animals—four of the five kingdoms of
life—are all eukaryotes.

The two types of cells differ markedly in their internal organization. One difference is
denoted by their names. The prokaryotic cell has no nucleus (The word prokaryote is
from the Greek pro, “before,” and karyon, “kernel,” referring here to the nucleus). Its
genetic material (DNA) is concentrated instead in a region called the nucleoid, but no
membrane separates the region from the rest of the cell. In contrast, the eukaryotic cell
Gr. eu, “true,” and karyon) has a true nucleus enclosed by a membranous nuclear
envelope. The entire region between the nucleus and the membrane bounding the cell is
called the cytoplasm. It consists of a semifluid medium called the cytosol, in which are
suspended organelles of specialized form and function, most of them absent in
prokaryotic cells. Thus, the presence or absence of a true nucleus is just one example of
the disparity in structural complexity between the two types of cells. The prokaryotic cell
will be described in detail in Chapters 17 and 25, and the possible evolutionary
relationships between the two types of cells will be discussed in Chapter 26. Most of the
discussion of cell structure that follows in this chapter applies to eukaryotes.

Cell Size
Size is a general feature of cell structure that relates to function. The logistics of carrying
out metabolism set limits on the size range of cells. The smallest cells known are bacteria
called mycoplasmas, which have diameters of between 0.1 and 1.0 micrometer (µm).
These are perhaps the smallest packages with enough DNA to program metabolism and
enough enzymes and other cellular equipment to carry out the activities necessary for a
cell to sustain itself and reproduce. Most bacteria are 1 to 10 µm in diameter, about ten
times larger than mycoplasmas. Eukaryotic cells are typically 10 to 100 µm in diameter,
ten times larger than bacteria.

Metabolic requirements also impose upper limits on a size that is practical for a single
cell. As an object of a particular shape increases its size, its volume grows
proportionately more than its surface area. (Area is proportional to the linear dimension
squared, whereas volume is proportional to the linear dimension cubed.) For objects of
the same shape, the smaller the object is, the greater its ratio of surface area to volume.

At the boundary of every cell, the plasma membrane functions as a selective barrier that
allows sufficient passage of oxygen, nutrients, and wastes to service the entire volume of
the cell. For each square micrometer of membrane, only so much of a particular
substance can cross per second. The need for a surface sufficiently large to accommodate
its volume helps explain the microscopic size of most cells.

The Importance of Compartmental Organization

The complexity of a eukaryotic cell is another structural feature correlated with function.
Internal membranes partition the cell into compartments and also participate directly in
much of the cell’s metabolism; many enzymes are built right into the membranes.
Because the compartments of the eukaryotic cell provide different local environments
that facilitate specific metabolic functions, processes that are incompatible can go on
simultaneously in separate subcellular compartments.

Membranes of various kinds are fundamental to the organization of the cell. In general,
biological membranes consist of a double layer of phospholipids and other lipids.
Embedded in this lipid bilayer or attached to its surfaces are diverse proteins. However,
each membrane has a unique composition of lipids and proteins suited to that
membrane’s specific functions. For example, enzymes that function in cellular respiration
are embedded in the membranes of the organelles called mitochondria.

Before continuing with the chapter, examine the overviews of eukaryotic cells. These
figures and their legends introduce the various organelles and provide a map of the cell
for the detailed tour upon which we will soon embark. As eukaryotic cells, they have
much more in common with each other than either has with any prokaryote. As you will
see, however, there are important differences between plant and animal cells.
FIGURE 7.7
Overview of an animal cell. This drawing of a generalized animal cell combines the most common structures found in
animal cell. No single cell looks like this. Within the cell are a variety of components collectively called organelles
(“little organs”). Some organelles are bounded by membranes, while others lack membranes. The most prominent
organelle in an animal cell is usually the nucleus, in which inherited genes reside in the form of DNA. The chromatin
consists of this DNA along with proteins. The chromatin is actually a collection of separate structures called
chromosomes, which are visible as separate units only in a dividing cell. Also present in the nucleus are one or more
nucleoli (singular, nucleolus). Nucleoli are involved in the production of particles called ribosomes, which function in
protein synthesis. The nucleus is bordered by a porous envelope consisting of two membranes.

Most of the cell’s metabolic activities occur in the cytoplasm, the entire region between the nucleus and the plasma
membrane surrounding the cell. The cytoplasm is full of specialized organelles suspended in a semifluid medium called
the cytosol. Pervading much of the cytoplasm is the endoplasmic reticulum (ER), a labyrinth of membranes forming
flattened sacs and tubes that segregate the contents of the ER from the cytosol. The ER takes two forms: rough (studded
with ribosomes) and smooth. Many types of proteins are made by ribosomes attached to ER membranes, and the ER
also plays a major role in assembling the other membranes of the cell. The Golgi apparatus, another type of
membranous organelle in the cytoplasm, consists of stacks of flattened sacs that play an active role in the synthesis,
refinement, storage, sorting, and secretion of chemical products by the cell.

Other classes of organelles enclosed by membranes are: lysosomes, which contain mixtures of digestive enzymes that
hydrolize macromolecules; peroxisomes, a diverse group of organelles containing specialized enzymes that perform
specific metabolic processes; and vacuoles, which have a variety of storage and metabolic functions. The mitochondria
(singular, mitochondrion) are organelles that generate ATP from organic fuels such as sugar in the process of cellular
respiration.

Nonmembranous organelles within the cells include microtubules and microfilaments. They form a framework called
cytoskeleton, which reinforces the cell’s shape and functions in cell movement. The cell in the drawing has a flagellum,
an organelle of locomotion, which is an assembly of microtubules. Also made of microtubules are centrioles, located
near the nucleus. These play a role in cell division.
FIGURE 7.8
Overview of a plant cell. This drawing of a generalized plant cell reveals the similarities and differences between an
animal cell and a plant cell. Like the animal cell, the plant cell is surrounded by a plasma membrane and contains a
nucleus, ribosomes, and Golgi apparatus, mitochondria, peroxisomes, and microfilaments and microtubules. However,
a plant cell also contains membrane-enclosed organelles called plastid. The most important type of plastid is the
chloroplast, which carries out photosynthesis, converting sunlight to chemical energy stored in sugar and other organic
molecules. Another prominent organelle in many plant cells, especially older ones, is a large central vacuole. The
vacuole stores chemicals, breaks down macromolecules, and by enlarging, plays a major in plant growth. The
membrane of the vacuole is called the tonoplast. Outside a plant cell’s membrane (as well as in fungi and some protists)
is a thick cell wall, which helps maintain the cell’s shape and protects the cell from mechanical damage. The cytosol of
adjacent cells connects through trans-wall channels called plasmodesmata.
 The first stop on our detailed tour of the cell is one of the membrane-enclosed
organelles, the nucleus.

The nucleus contains a cell’s genetic library

The nucleus contains most of the genes that control the cell (some genes are located in
mitochondria and chloroplasts). It is generally the most conspicuous organelle in a
eukaryotic cell, averaging about 5µm in diameter. The nuclear envelope encloses the
nucleus, separating its contents from the cytoplasm.

The nuclear envelope is a double membrane. The two membranes, each a lipid bilayer
with associated proteins, are separated by a space of about 20-40nm. The envelope is
perforated by pores that are about 100nm in diameter. At the lip of each pore, the inner
and outer membranes of the nuclear envelope are fused. The pore complex regulates the
entrance and exit of certain large macromolecules and particles. The nuclear side of the
envelope is lined by the nuclear lamina, a netlike array of protein filaments that
maintains the shape of the nucleus. There is also growing evidence for a nuclear matrix, a
framework of fibers distributed throughout the nuclear interior.

Within the nucleus, the DNA is organized along with proteins into material called
chromatin. Stained chromatin appears through both light microscopes and electron
microscopes as a diffuse mass. As a cell prepares to divide (reproduce), the stringy,
entangled chromatin condenses, becoming thick enough to be discerned as separate
structures called chromosomes. Each eukaryotic species has a characteristic number of
chromosomes. A human cell, for example, has 46 chromosomes in its nucleus; the
exceptions are the sex cells—eggs and sperms—which have only 23 chromosomes in
humans.

The most visible structure within nondividing nucleus is the nucleolus, which synthesizes
molecular ingredients of ribosomes. These ribosomal components pass through the
nuclear pores to the cytoplasm, where their assembly is completed. Sometimes there are
two or more nucleoli; the number depends on the species and the stage in the cell’s
reproductive cycle. The nucleolus is roughly spherical, and through the electron
microscope it appears as a mass of densely stained granules and fibers.

The nucleus controls protein synthesis in the cytoplasm by sending molecular messengers
in the form of ribonucleic acid (RNA). This messenger RNA (mRNA), as it is called, is
synthesized in the nucleus according to instructions provided by the DNA. The mRNA
then conveys the genetic messages to the cytoplasm via the clear pores. Once in the
cytoplasm, the mRNA attaches onto the ribosomes, the sites where the genetic message is
translated into the primary structure of a specific protein. The process of translating
genetic information is described in detail in Chapter 16.
Ribosomes build a cell’s proteins

Ribosomes are the sites where the cell assembles proteins. Cells that have high rates of
protein synthesis have a particularly great number of ribosomes, another example of cell
structure fitting function. For example, a human liver cell has a few million ribosomes.
Cells acting in protein synthesis also have a prominent nucleoli, which function in
ribosome production.

Ribosomes build proteins in two cytoplasmic locations. Free ribosomes are suspended in
the cytosol, while bound ribosomes are attached to the outside of a membranous network
called the endoplasmic reticulum. Most of the proteins made by free ribosomes function
within the cytosol; examples are enzymes that catalyze metabolic processes localized in
the cytosol. Bound ribosomes generally make proteins that are destined either for
inclusion into membranes, for packaging within certain organelles such as lysosomes, or
for export from the cell. Cells that specialize in protein secretion, for instance, the cells of
pancreas and other glands that secrete digestive enzymes—frequently have a higher
proportion of bound ribosomes. Bound and free ribosomes are structurally identical and
interchangeable and the cell can adjust the relative numbers of each as its metabolism
changes. You will learn more about ribosome structure and function in Chapter 16.

Many organelles are related through the endomembrane system

Many of the different membranes of the eukaryotic cell are part of an endomembrane
system. These membranes are related either through direct physical continuity or by the
transfer of membrane segments through the movement of tiny vesicles (membrane-
enclosed sacs). These relationships, however, do not mean that the various membranes
are alike in structure and function. The thickness, molecular composition, and metabolic
behavior of a membrane are not fixed, but may be modified several times during the
membrane’s life. The endomembrane system includes the nuclear envelope, endoplasmic
reticulum, Golgi apparatus, lysosomes, various kinds of vacuoles, and the plasma
membrane (not actually an endomembrane in physical location, but nevertheless related
to the endoplasmic reticulum and other internal membranes). We have already discussed
the nuclear envelope and will now focus on the endoplasmic reticulum and the other
endomembranes to which it gives rise.

The endoplasmic reticulum manufactures membranes

and performs many biosynthetic functions
The endoplasmic reticulum (ER) is a membranous labyrinth so extensive that it
accounts for more than half the total membrane in many eukaryotic cells. (The word
endoplasmic means “within” the cytoplasm, and reticulum is derived from the Latin for
“network.”) The ER consists of a network of membranous tubules and sacs called
cesternae (L. cisterna, “box” or “chest”). The ER membrane separates its internal
compartment, the cisternal space, from the cytosol. And because the ER membrane is
continuous with the nuclear envelope, the space between the two membranes of the
envelope is continuous with the cisternal space of the ER.

There are two distinct, though connected, region of ER that differ in structure and
function: smooth ER and rough ER. Smooth ER is so named because its cytoplasmic
surface lacks ribosomes. Rough ER appears rough through the electron microscope
because ribosomes stud the cytoplasmic surface of the membrane. Ribosomes are also
attached to the cytoplasmic side of the nuclear enveloope’s outer membrane, which is
confluent with rough ER.

Functions of Smooth ER
The smooth ER of various cell types functions in diverse metabolic processes, including
synthesis of lipids, metabolism of carbohydrates and detoxification of drugs and other
poisons.

Enzymes of the smooth ER are important to the synthesis of fatty acids, phospholipids,
steroids, and other lipids. Among the steroids produces by smooth ER are the sex
hormones of vertebrates and the various steroid hormones secreted by the adrenal glands.
The cells that actually synthesize and secrete these hormones—in the testes and ovaries,
for example—are rich in smooth ER, and the structural feature that fits the function of
these cells.

Liver cells provide one example of the role of smooth ER in carbohydrate metabolism.
Liver cells store carbohydrate in the form of glycogen, a polysaccharide. The hydrolysis
of glycogen leads to the release of glucose from the liver cells, which is important in the
regulation of sugar concentration in the blood. However, the first product of glycogen
hydrolysis is glucose phosphate, an ionic form of the sugar that cannot exit the cell and
enter the blood. An enzyme embedded in the membrane of liver cell’s smooth ER
removes the phosphate from the glucose, which can leave the cell and elevate blood sugar
concentration.

Enzymes of the smooth ER help detoxify drugs and other poisons, especially in liver
cells. Detoxification usually involves adding hydroxyl groups to drugs increasing their
solubility and making it easier to flush the compounds from the body. The sedative
Phenobarbital and other barbiturates are examples of dugs metabolized in this manner by
smooth ER in liver cells. In fact, barbiturates, alcohol, and many other drugs induce the
proliferation of smooth ER and its associated detoxification enzymes. This in turn
increases tolerance to the drugs, meaning that higher doses are required to achieve a
particular effect, such as sedation. Also, because some of the detoxification enzymes
have relatively broad action, the proliferation of smooth ER in response to one drug can
increase tolerance to other drugs as well. Barbiturate abuse, for example, may decrease
the effectiveness of certain antibiotics and other useful drugs.

Muscle cells exhibit still another specialized function of smooth ER. The ER membrane
pumps calcium ions from the cytosol into the cisternal space. When muscle cell is
stimulated by a nerve impulse, calcium rushes back across the ER membrane into the
cytosol and triggers contraction of the muscle cell.

Rough ER and Protein Synthesis

Many types of specialized cells secrete proteins produced by ribosomes attached to rough
ER. For example, certain cells in the pancreas secrete the protein insulin, a hormone, in to
the bloodstream. As a polypeptide chain grows from a bound ribosome, it is threaded
through the ER membrane into the cisternal space, possibly through a pore. As it enters
the cisternal space, the protein folds into its native conformation. Most secretory proteins
are glycoproteins, proteins that are covalently bonded to carbohydrates. In the cisternal
space, the carbohydrate is attached to the protein by specialized molecules built into the
ER membrane. The carbohydrate appendage of a glycoprotein is an oligosaccharide, the
term for relatively small polymer of sugar units.

Once the secretory proteins are formed, the ER membrane keeps them separate from the
proteins produced by free ribosomes that will remain in the cytosol. Secretory proteins
depart from the ER wrapped in the membranes of vesicles budded like bubbles from a
specialized region called transitional ER. Such vesicles in transit from one part of the cell
to another are called transport vesicles, and we will soon learn their fate.

Rough ER and Membrane Production

In addition to making secretory proteins, rough ER is a membrane factory that grows in
place by adding proteins and phospholipids. As membrane proteins elongate from the
ribosomes, they are inserted into the ER membrane itself and are anchored there by
hydrophobic portions of the proteins. The rough ER also makes its own membrane
phospholipids; enzymes built into the ER membrane assemble phospholipids from
precursors in the cytosol. The ER membrane expands and can be transferred in the form
of transport vesicles targeted for other components of the endomembrane system.

The Golgi apparatus finishes, sorts, and ships many product of the cell

After leaving the ER, many transport vesicles travel to the Golgi apparatus. We can
think of the Golgi as a center of manufacturing, warehousing, sorting, and shipping. Here,
products of the ER are modified and sorted, and then sent to other destinations. Not
surprisingly, the Golgi apparatus is especially extensive in cells specialized for secretion.
The Golgi apparatus consists of flattened membranous sacs, looking like a stack of pita
bread. A cell may have several of these stacks, all interconnected. Each cisterna in a stack
consists of a membrane that separates its internal space from the cytosol. Vesicles
concentrated in the vicinity of the Golgi apparatus are engaged in the transfer of material
between the Golgi and other structures.

The Golgi apparatus has a distinct polarity, with the membranes of cisternae at opposite
ends of a stack differing in thickness and molecular composition. The two poles of a
Golgi stack are reffered to as the cis face and trans face; these act, respectively, as the
receiving and shipping departments of the Golgi apparatus. The cis face is usually located
near ER. Transport vesicles move material from the ER to the Golgi. A vesicle that buds
from the ER will add its membrane and contents of its lumen (cavity) to the cis face by
fusing with a Golgi membrane. The trans face gives rise to vesicles, which pinch off and
travel to other sites.

Products of the ER are usually modified during their transit from the cis pole to the trans
pole of the Golgi. Proteins and phospholipids of membranes may be altered. For example,
various Golgi enzymes modify the oligosaccharide portions of glycoproteins. When first
added to proteins in the ER, the oligosaccharides of all glycoproteins are identical. The
Golgi removes some sugar monomers and substitutes others, producing diverse
oligosaccharides.

In addition to its finishing work, the Golgi apparatus manufactures certain

macromolecules by itself. Many polysaccharides secreted by cells are Golgi products,
including hyaluronic acid, a sticky substance that helps the animal cells

The Golgi manufactures and refines its products in stages, with different cisternae
between the cis and trans ends containing unique teams of enzymes. Products in various
stages of processing are transferred from one cisterna to the next by vesicles.

Before the Golgi apparatus dispatches its products by budding vesicles from the trans
face, it sorts these products and targets them for various parts of the cell. Molecular
identification tags, such as phosphate groups that have been added to the Golgi products,
aid in sorting. And vesicles budded from the Golgi may have external molecules on their
membranes that recognize “docking sites” on the surface of specific organelles.

Lysosomes are digestive compartments

A lysosome is a membrane-enclosed sac of hydrolytic enzymes that the cell uses to digest
macromolecules. There are lysosomal enzymes that can hydrolyze proteins,
polysaccharides, fats, and nucleic acids—all the major classes of macromolecules. These
enzymes work best in an acidic environment, at about pH 5. The lysosomal membrane
maintains this low internal ph by pumping hydrogen ions from the cytosol into the lumen
of the lysosome. If the lysosome should break open or leak contents, the enzymes would
not be very lysosomes can destroy a cell by auto digestion. From this example, we can
see once again how important compartmental organization is to the function of the cell:
The lysosome provides a space where the cell can digest macromolecules safely, without
the general destruction that would occur if hydrolytic enzymes roamed at large.

Hydrolytic enzymes and lysosomal membrane are made by rough ER and then
transferred to a Golgi apparatus for further processing. Lysosomes probably arise by
budding from the trans face of the Golgi apparatus. Proteins of the inner surface of the
lysosomal membrane and the digestive enzymes themselves are probably spared from
self-destruction by having three-dimensional conformations that protect vulnerable bonds
from enzymatic attack.

Lysosomes function in intracellular digestion in a variety of circumstances. Amoeba and

many other protests eat by engulfing smaller organisms or other food particles called
phagocytosis (Gr. phagein, “to eat,” and kytos, “vessel,” referring here to the cell). The
food vacuole formed in this way then fuses with a lysosome, whose enzymes digest the
food. Some human cells also carry out phagocytosis. Among them are macrophages, cells
that help defend the body by destroying bacteria and other invaders.

Lysosome also use their hydrolytic enzymes to recycle the cell’s own organic material, a
process called autophagy. This occurs when a lysosome engulfs another organelle or a
small parcel of cytosol. The lysosomal enzymes dismantle the ingested material, and the
organic monomers are returned to the cytosol for reuse. With the help of lysosomes, the
continually renews itself. A human liver cell, for example, recycles half of its
macromolecules each week.

Programmed destruction of cells by their own lysosomal enzymes is important in the

development of many organisms. During the transforming of a tadpole into a frog, for
instance, lysosomes destroy the cells of the tail. And the hands of human embryos are
webbed until lysosomes digest the tissue between the fingers.

Variety of inherited disorders called storage diseases affect lysosomal metabolism. A

person afflicted with a storage disease lacks one of the active hydrolytic enzymes
normally present in lysosomes. The lysosomes become engorged with indigestible
substrates, which begin to interfere with other cellular functions. In Pompe’s disease, for
example, the liver is damaged by an accumulation of glycogen due to the absence of a
lysosomal enzyme needed to break down the polysaccharide. In Tay-Sachts disease, a
lipid-digestive enzyme is missing or inactive, and the brain becomes impaired by an
accumulation of lipids in the cells. Fortunately, storage diseases are rare in the general
population. In the future, it might be possible to treat storage diseases by injecting the
missing enzymes into the blood along with the adaptor molecules that target the enzymes
for engulfment by cells and fusion with lysosomes. It might be possible to repair a
disorder directly by inserting genes (DNA) for the missing enzyme into the appopriate
cells.
Vacuoles have diverse functions in cell maintenance

Vacuoles and vesicles are both membrane-enclosed sacs within the cell, but vacuoles are
larger than vesicles. Vacuoles have various functions. Food vacuoles, formed by
phagocytosis, have already been mentioned. Many freshwater protists have contractile
vacuoles that pump excess water out of the cell. Mature plant cells generally contain a
large central vacuole enclosed by a membrane called tonoplast, which is part of their
endomembrane system.

The plant cell vacuole is a versatile compartment. It is a place to store organic

compounds, such as the proteins that are stockpiled in the vacuoles of storage cells in
seeds. The vacuole is also the plant cell’s main repository of inorganic ions, such as
potassium and chloride. Many plant cells use their vacuoles as disposal sites for
metabolic by-products that would endanger the cell if they accumulated in the cytoplasm.
Some vacuoles are enriched in pigments that color the cells, such as the red and blue
pigments of petals that attract pollinating insects to flowers. Vacuoles may also help
protect the plant against predators by containing compounds that are poisonous or
unpalatable to animals. The vacuole has a major role in the growth of plant cells, which
elongate as their vacuoles absorb water, enabling the cell to become larger with minimal
investment in new cytoplasm. And because the cytoplasm occupies a thin shell between
the plasma membrane and the tonoplast, the ratio of membrane surface to cytoplasmic
volume is great, even for a large plant cell.

The large vacuole of a plant cell develops by the coalescence of smaller vacuoles;
themselves derive from the endoplasmic reticulum and Golgi apparatus. Through these
relationships, the vacuole is an integral part of the endomembrane system. FIGURE 7.16
reviews the endomembrane system. We’ll continue our tour of the cell with three
organelles that are not closely related to the endomembrane system: proxisomes,
mitochondria, and chloroplasts.
 FIGURE 7.16
Review: relationships among
endomembranes. The nuclear envelope
is an extension of the rough ER, which is
also confluent with smooth ER.
Membrane produced by the ER flows in
the form of transport vesicles to the
Golgi. The Golgi, in turn, pinches off
vesicles that give rise to lysosomes and
vacuoles. Even the plasma membrane
expands by the fusion of vesicles born in
the ER and Golgi. (Coalescence of
vesicles with the plasma membrane also
releases secretory proteins and other
products to the outside of the cell.) As
membranes of the system flow from ER
to the Golgi and then elsewhere, their
molecular compositions and metabolic
functions are modified. The
endomembrane system is a complex and
dynamic player in the cell’s
compartmental organization.

Peroxisomes consume oxygen in various metabolic functions

The proxisome is a specialized metabolic compartment bounded by a single membrane.

Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen,
producing hydrogen peroxide (H202) as a by-product, from which the organelle derives its
name. These reactions may have many different functions. Some peroxisomes use
oxygen to break fatty acids down into smaller molecules that can then be transported to
mitochondria as fuel for cellular respiration. Peroxisomes in the liver detoxify alcohol
and other harmful compounds by transferring hydrogen from poisons to oxygen. The
H202 formed by peroxisome metabolism is itself toxic, but the organelle contains an
enzyme that converts H202 to water. Packaging the enzymes that produce hydrogen
peroxide in an enclosure where an enzyme that disposes of this by-product is also
concentrated is another example of how the cell’s compartmental structure is crucial to its
functions.

Specialized peroxisomes called glyoxysomes are found in the far-storing tissues of the
germinating seeds of plants. These organelles contain enzymes that initiate the
conversion of fatty acids to sugar, a process that makes the energy stored in the oils of the
seed available until the seedling is able to produce its own sugar by photosynthesis.

Unlike lysosomes, peroxisomes are not budded from the endomembrane system. They
grow by incorporating proteins and lipids produced in the cytosol, and increase in number
by splitting in two when they reach a certain size.
Mitochondria and chloroplasts are the main energy transformer of cells

One of this book’s themes is that organisms are open systems that transform energy they
acquire from their surroundings. In eukaryotic cells, mitochondria and chloroplasts are
the organelles that convert energy to forms that cells can use for work. Mitochondria
(singular, mitochondrion) are the sites of cellular respiration, the catabolic process that
generates ATP by extracting energy from sugars, fats, and other fuels with the help of
oxygen. Chloroplasts, found only in plants and eukaryotic algae (kingdom Protista), are
the sites of photosynthesis. They convert solar energy to chemical energy by absorbing
sunlight and using it to drive the synthesis of organic compounds from carbon dioxide
and water.

Although mitochondria and chloroplasts are enclosed membranes, they are not
considered part of the endomembrane system. Their membrane proteins are made not by
the ER, but by free ribosomes in the cytosol and by ribosomes contained within the
mitochondria and chloroplasts themselves. Not only do these organelles have ribosomes,
but they also contain a small amount of DNA that programs the synthesis of some of their
own proteins (although most proteins in these organelles are made in the cytosol,
programmed by messenger RNA sent by the nuclear genes). Mitochondria and
chloroplasts are semiautonomous organelles that grow and reproduce within the cell. In
chapters 9 and 10, we will focus on how mitochondria and chloroplasts function. We will
consider the evolution of these organelles in Chapter 26. Here, we are concerned mainly
with the structure of these energy transformers.

Mitochondria
Mitochondria are found in nearly all eukaryotic cells. In some cases, there is a single
large mitochondrion, but more often, a cell has hundreds or even thousands of
mitochondria; the number is correlated with the cell’s level of metabolic activity.
Mitochondria are about 1 to 10 µm long. Time-lapse films of living cells reveal
mitochondria moving around, changing their shapes, and dividing in two, unlike the static
cylinders seen in electron micrographs of dead cells.

The mitochondrion is enclosed in

an envelope of two membranes,
each a phospholipid bilayer with a
unique collection of embedded
proteins. The outer membrane is
smooth, but the inner layer is
convoluted, with infoldings called
cristae. The membranes divide the
mitochondrion into two internal
compartments. The first is the
intermembrane space, the narrow
region between the inner and outer membranes. The second compartment, the
mitochondrial matrix, is enclosed by the inner membrane. Some of the metabolic steps
of cellular respiration occur in the matrix, where many different enzymes are
concentrated. Other proteins that function in respiration, including the enzyme that makes
ATP, are built into the inner membrane. The cristae give the inner mitochondrial
membrane a large surface area that enhances the productivity of cellular respiration,
another example of the correlation between structure and function.

FIGURE 7.18
The mitochondrion, site of cellular respiration. The double membrane of the mitochondrion is evident in the
drawing and the micrograph (TEM). The cristae are infoldings of the inner membrane. The cutaway drawing
emphasizes the relationships between the two membranes and the compartments they bound: the intermembrane space
and the mitochondrial matrix.

Chloroplasts
The chloroplasts is a specialized member of a family of closely related plant organelles
called plastids. Amyloplasts are colorless plastids that store starch (amylose), particularly
in roots and tubers. Chromoplasts are enriched in pigments that give fruits and flowers
their orange and yellow hues. Chloroplasts contain the green pigment chlorophyll along
with enzymes and other molecules that function in the photosynthetic production of food.
These lens-shaped organelles, measuring about 2 µm by 5 µm, are found in leaves and
other green organs of plants and in eukaryotic algae.
FIGURE 7.19
The chloroplast, site of photosynthesis. Chloroplasts, like mitochondria, are enclosed by two membranes separated by a narrow
intermembrane space. The inner membrane encloses fluid called stroma. The stroma surrounds a third compartment, delineated by its
own membrane, the thylakoid membrane. Throughout the chloroplast, thylakoid sacs are stacked to form structures called grana.
Individual thylakoids of one granum are continuous with other grana through extensions that traverse the stroma (TEM).

The contents of a chloroplast are partitioned from the cytosol by an envelope consisting
of two membranes separated by a very narrow intermembrane space. Inside the
chloroplast is another membranous system, arranged into flattened sacs called
thylakoids. In some regions, thylakoids are stacked like poker chips forming structure
called grana (singular, granum). The fluid outside the thylakoids is called the stroma.
Thus, the thylakoid membrane divides the interior of the chloroplast into two
compartments: the thylakoid space and the stroma. In Chapter 10, you will learn how this
compartmental organization enables the chloroplast to convert light energy to chemical
energy during photosynthesis.

As with mitochondria, the static and rigid appearance of chloroplasts in electron

micrographs do not true to their dynamic behavior in the living cell. Their shapes are
plastic, and they occasionally pinch in two. They are mobile and move around the cell
with mitochondria and other organelles along tracks of the cytoskeleton, the next stop on
our tour of the cell.

The cytoskeleton provides structural support and functions in cell motility

In the early days of electron microscopy, the cell seemed to consist of a variety of
organelles suspended or floating in a formless, jellylike cytosol. But improvements in
both light microscopy and electron microscopy have revealed a network of fibers
throughout the cytoplasm. This mesh is called the cytoskeleton.
One function of the cytoskeleton is to give mechanical support to the cell and help
maintain its shape. This is especially important for animal cells, which lack walls.
Organelles and even cytoplasmic enzymes may be held in place by anchoring to the
cytoskeleton. The cytoskeleton also enables a cell to change its shape; like a scaffold, the
cytoskeleton can be dismantled in one part of the cell and reassembled in a new location.
The cytoskeleton also functions in cell motility by interacting with specialized proteins
called motor molecules. This motility includes movement of the entire cell or movement
of organelles within the cell. Components of the cytoskeleton wiggle cilia and flagella
and enable muscle cells to contract. The cytoskeleton extends the pseudopodia of
Amoeba and also functions in the streaming of cytoplasm that circulates materials within
many large plant cells. Vesicles may travel to their destination in the cell along
“monorails” provided by the cytoskeleton, and contractile components of the
cytoskeleton manipulate the plasma membrane to form food vacuoles during
phagocytosis.

The cytoskeleton is constructed from at least three types of fibers. Microtubules are the
thickest of the three types; microfilaments (also called actin filaments) are the thinnest.
Intermediate filaments are collections of fibers whose diameters fall in a middle range.

Microtubules
Microtubules are found in the cytoplasm of all eukaryotic cells. They are straight, hollow
rods measuring about 25 nm in diameter and from 200 nm to 25 µm in length. The wall
of the hollow tube is constructed from globular proteins called tubulins, of which there
are two closely related kinds, α-tubulin and β-tubulin. A microtubule elongates by adding
tubulin molecules to its ends. Microtubules can be disassembled and their tubulin used to
build microtubules elsewhere in the cell.

Microtubules shape and support the cell and also serve as tracks along which organelles
equipped with motor molecules can move. For example, microtubules probably help
guide secretory vesicles from the Golgi apparatus to the plasma membrane. Microtubules
are also involved in the separation of chromosomes during cell division, discussed in
Chapter 11.

In many cells, microtubules radiate from a centrosome, a region located near the nucleus.
These microtubules function as girders that support the cell. Within the centrosome of an
animal cell are a pair of centrioles. Each centriole is composed of nine sets of triplet
microtubules arranged in a ring. When a cell divides, the centrioles replicate. Although
centrioles may help organize microtubule assembly, they are not mandatory for this
function in all eukaryotes; centrosomes of plant cells lack centrioles altogether.

Cilia and Flagella. In eukaryotes, a specialized arrangement of microtubules is

responsible for the beating of flagella and cilia, locomotive appendages that protrude
from some cells. Many unicellular organisms (kingdom Protista) are propelled through
water by cilia and flagella, and the sperm of animals, algae, and some plants are
flagellated. If cilia or flagella extend from cells that are held in place as part of a tissue
layer, then they function to draw fluid over the surface of the tissue. For example, the
ciliated lining of the windpipe sweeps mucus with trapped debris out of the lungs.

Cilia usually occur in large numbers on the cell surface. They are about 0.25 µm in
diameter and about 2 to 20 µm in length. Flagella are the same diameter but longer than
cilia, measuring 10 to 200 µm in length. Also, flagella are usually limited to just one or a
few per cell.

Flagella and cilia also differ in their patterns of beating. A flagellum has an undulating
motion that generates force in the same direction as the flagellum’s axis. In contras, cilia
work more like oars, with alternating power and recovery strokes generating force in a
direction perpendicular to the cilium’s axis.

Though different in length, number per cell, and beating pattern, cilia and flagella
actually share a common ultrastructure. A cilium or flagellum has a core of microtubules
ensheathed in an extension of the plasma membrane. Nine doublets of microtubules, the
members of each pair sharing part of their walls, are arranged in a ring. In the center of
the ring are two single microtubules. This arrangement, referred to as the “9 + 2” pattern,
is found in nearly all eukaryotic flagella and cilia. (The flagella of motile prokaryotes are
entirely different.) The doublets of the outer ring are connected to the center of the cilium
or flagellum by radial spokes that terminate near the central pair of microtubules. Each
doublet of the outer ring also has pairs of arms evenly spaced along its length and
reaching toward the neighboring doublet of microtubules. The microtubule assembly of a
cilium or flagellum is anchored in the cell by a basal body, which is structurally identical
to a centriole.

The arms extending from each microtubule doublet to the next are the motors responsible
for the bending movements of cilia and flagella. The motor molecule that makes up these
arms is a very large protein called dynein. A dynein arm performs a complex cycle of
movements caused by changes in the conformation (shape) of the protein, with ATP
providing the energy for these changes. The mechanics of dynein “walking” are
reminiscent of a cat climbing a tree by attaching its claws, moving its legs, releasing its
claws, and grabbing again farther up the tree. Similarly, the dynein arms of one doublet
attach to an adjacent doublet and pull so that the doublets slide past each other in opposite
directions. The arms then release from the other doublet and reattach a little farther along
its length. Without any restraints on this movement, one doublet would continue to
“walk” along the surface of the other, elongating the cilium rather than bending it. For
lateral movement of a cilium, the dynein “walking” must be restrained’ that is, it must
have something to pull against, as when the muscles in your leg pull against your bones
to move your knee. In cilia and flagella, the microtubule doublets are held in place
perhaps by the radial spokes or other structural elements. Thus neighboring doublets
cannot slide past each other very far. Instead, the forces exerted by the dynein arms cause
the doublets to curve, bending the cilium or flagellum. In the beating mechanism of cilia
and flagella, we see once again that structure fits function.
Microfilaments (Actin Filaments)
Microfilaments are solid rods about 7 nm in diameter. They are also called actin
filaments because they are built from molecules of actin, a globular protein. The actin
molecules are linked into chains; two of these chains twisted about each other in a helix
form the microfilament.

Microfilaments are part of the contractile apparatus in muscle cells. Thousands of actin
filaments are arranged parallel to one another along the length of a muscle cell,
interdigitated with thicker filaments made of a protein called myosin. Contraction of the
cell results from the actin myosin filaments sliding past one another, which shortens the
cell. Extending from the myosin filaments to the actin filaments are movable arms,
regions of the myosin proteins that function as motor molecules. Powered by ATP, the
conformational changes of these arms slide the adjacent actin filaments.

Although microfilaments are especially concentrated and well ordered in muscle cells,
they seem to be present to some extent in all eukaryotic cells. Along with the rest of the
cytoskeleton, microfilaments function in support. For example, bundles of microfilaments
make up the core of microvilli, delicate projections that increase the surface area of cells
specialized for the transport of material across the plasma membrane.

In some parts of the cell, actin filaments are associated with myosin in miniature versions
of the arrangement found in muscle cells. These actin-myosin aggregates are responsible
for localized contractions of cells. For example, when an animal cell divides, it is pinched
in two by a contracting belt of microfilaments. In addition, microfilaments function in
ameboid movement, in which a cell moves along a surface by extending and flowing into
cellular extensions called pseudopodia (Gr. pseudes, “false,” and pod, “foot”).
Microfilaments in plant cells function in cytoplasmic streaming, a circular flow of
cytoplasm within cells. This movement, which is especially common in large plant cells,
speeds the distribution of material within the cell.

Intermediate Filaments
Intermediate filaments are named for their diameter, which at 8 to 12 nm, is a larger than
the diameter of microfilaments but smaller than that of microtubules. Intermediate
filaments actually include a diverse class of cytoskeletal elements. Each type is
constructed from a different molecular subunit belonging to a diverse family of proteins
called keratins. Microtubules and microfilaments, in contrast, are consistent in diameter
and composition in all eukaryotic cells.

Intermediate filaments are also more permanent fixtures of cell’s than are microfilaments
and microtubules, which are often disassembled and reassembled in various parts of a
cell. Chemical treatments that remove microfilaments and microtubules from the
cytoplasm leave a web of intermediate filaments that retains its original shape. Such
experiments suggest that intermediate filaments are especially important in reinforcing
the shape of a cell and fixing the position of certain organelles. For example, the nucleus
commonly sits within a cage made of intermediate filaments, fixed in location by
branches of the filaments that extend into the cytoplasm. Other intermediate filaments
make up the nuclear lamina that lines the interior of the nuclear envelope. In cases where
the shape of the entire cell is correlated with function, intermediate filaments support that
shape. For instance, the long extension (axions) of nerve cells that transmit impulses are
strengthened by one class of intermediate filament. Specialized for bearing tension, the
various kinds of intermediate filaments may function as the framework of the entire
cytoskeleton.

Having criss-crossed the interior of the cell to explore various organelles, we complete
our tour of the cell by returning to the surface of this microscopic world, where there are
additional structures with important functions. Although the plasma membrane is usually
regarded as the boundary of the living cell, most cells synthesize and secrete coats of one
kind or another that are external to the plasma membrane.

Plant cells are encased by cell walls

The cell wall is one of the features of plant cells that distinguishes them from animal
cells. The wall protects the plant cell, maintains its shape, and prevents excessive uptake
of water. On the level of the whole plant, the strong walls of specialized cells hold the
plant up, against the force of gravity. Prokaryotes, fungi, and some protists also have cell
walls, but we will postpone discussion of them until Unit Five.

Plant cell walls are much thicker than the plasma membrane, ranging from 0.1 to several
µm. the exact chemical composition of the wall varies from species to species and from
one cell type to another in the same plant, but the basic design of the wall is consistent.
Microfibrils made of the polysaccharide cellulose are embedded in a matrix of other
polysaccharide and protein. This combination of materials, strong fibers in a “ground
substance” (matrix), is the basic architectural design found in steel-reinforced concrete
and in fiberglass.

A young plant cell first secretes a relatively thin and flexible wall called the primary cell
wall. Between primary wall of adjacent cell is the middle lamella, a thin layer rich in
sticky polysaccharides called pectins. The middle lamella glues the cells together (pectin
is used as a thickening agent in jams and jellies). When the cell matures and stops
growing, it strengthens its wall. Some cells do this by secreting hardening substances into
the primary wall. Other plant cells add a secondary cell wall between the plasma
membrane and the primary wall. The secondary wall, often deposited in several
laminated layers, has a strong durable matrix that affords the cell protection and support.
Wood, for example, consists mainly of secondary walls.
The extracellular matrix (ECM) of animal cells
functions in support, adhesion, movement and development

Although animal cells lack walls akin to those of plant cells, they do have an elaborate
extracellular matrix (ECM). The main ingredients of the ECM are glycoproteins
secreted by the cells. (Recall that glycoproteins are proteins covalently bonded to
carbohydrate.) The most abundant glycoprotein in the ECM of most animal cells is
collagen, which forms strong fibers outside the cells. In fact, collagen accounts for about
half of the total protein in the human body. The collagen fibers are embedded in a
network woven from another class of glycoproteins called proteoglycans. These
molecules are especially rich in carbohydrate—up to 95%. Some cells are attached to the
ECM by still another class of glycoproteins, most commonly fibronectins. Fibronetins
bind to receptor proteins called integrins that are built into the plasma membrane.
Integrins span the membrane and bind on their cytoplasmic side to microfilaments of the
cytoskeleton. Thus, integrins integrate responses of the cytoskeleton to changes in the
ECM, and vice versa.

In addition to providing support and anchorage for cells, the ECM functions in a cell’s
dynamic behavior. For example, some cells in a developing embryo migrate along
specific pathways by matching the orientation of their microfilaments to the “grain” of
fibers in the extracellular matrix. Researchers are also learning that a cell’s contacts with
its ECM help control the activity of genes in the nucleus—that is, the production of
messenger RNA by specific genes. Perhaps integrins transmit mechanical stimuli from
the ECM to the cytoskeleton, which in turn triggers production of chemical signals within
the cell that relay the information into the nucleus. Biologists are just beginning to
understand the important functions of the extracellular matrix in the lives of cells.

Intercellular junctions integrate cells into

higher levels of structure and function

The many cells of an animal or plant are integrated into one functional organism.
Neighboring cells often adhere, interact, and communicate to special patches of direct
physical contact.

It might seem that the nonliving cell walls of plants would isolate cells from one another.
In fact, the walls are perforated with channels called plasmodesmata (sigular,
plasmodesma; Gr. desmos, “to bind”). Strands of cytoplasm pass through the
plasmodesmata and connect the living contents of adjacent cells. This unifies most of the
plant into one living continuum. The plasma membranes of adjacent cells are continuous
through a plasmodesma; the membrane lines the channel. Water and small solutes can
pass freely from cell to cell, a transport that is enhanced by cytoplasmic streaming.
In animals, there are three main types of intracellular junctions: tight junctions,
desmosomes, and gap junctions.

The cell is a living unit greater than the sum of its parts

From our panoramic view of the cell’s overall compartmental organization to our closeup
inspection of each organelle’s architecture, this tour of the cell has provided many
opportunities to correlate structure with function. But even as we dissect the cell,
remember that none of its organelles works alone. As an example of cellular integration,
consider the microscopic scene in FIGURE 7.31. The large cell is a macrophage. It helps
defend the body against infections by
ingesting bacteria (the smaller green cells).
The macrophage creeps along a surface and
reaches out with cellular extensions that help
it catch the bacteria. Actin filaments interact
with other elements of the cytoskeleton in
these movements. After the macrophage
engulfs the bacteria, they are destroyed by
lysosomes. The elaborate endomembrane
system, ehich inclydes the ER and the Golgi
apparatus, produces the lysosomes. The
digestive enzymes of the lysosomes and the
FIGURE 7.31 proteins of the cytoskeleton are all made on
The emergence of cellular functions from the
cooperation of many organelles. The ability of
ribosomes. And the synthesis of these
this macrophage (orange) to recognize, proteins is programmed by genetic messages
apprehend, and destroy bacteria (green) is a dispatched from the DNA in the nucleus. All
coordinated activity of the whole cell. The
cytoskeleton, lysosomes, and plasma membrane
these processes require energy, which
are among the components that function in mitochondria supply in the form of ATP.
phagocytosis. Other cellular functions are also Cellular functions arise from cellular order:
emergent properties that depend on interaction of
the cell parts. (Colorized SEM).
the cell is a living unit greater that the sum of
its parts.

REVIEW OF KEY CONCEPTS

 Microscopes provide windows to the world of the cell

 Electron microscopes and improvements in light microscopes have catalyzed the progress in the
study of the cell structure.

 Cell biologists can isolate organelles to study their function.

 After homogenizing cells, researchers use ultracentrifuge to fractionate the cells into pellts
enriched in specific organelles.
 A panoramic view of the cell
 Prokaryotic cells lack nuclei and membrane-enclosed organelles; bacteria are prokaryotes. All
other organisms are made up of eukaryotic cells with membrane-enclosed nuclei surrounded by
cytoplasm, in which are suspended specialized organelles not found in prokaryotic cells.
 The requirement for a favorable ratio of membrane surface to cell volume sets upper limits on cell
size.
 Eukaryotic cells are surrounded by a plasma membrane and are partitioned into various
compartments by internal membranes. These internal membranes provide local environments for
specific metabolic processes.
 All membranes consist of phospholipids and proteins. The diversity of membrane function reflects
the variation in a membrane’s specific molecular composition.

 The nucleus contains a cell’s genetic library.

 The trademark of a eukaryotic cell is its distinctive nucleus, enclosed in the nuclear envelope.
Pores in the envelope allow for exchange of macromolecules between the nucleus and the
cytoplasm.
 The nucleus contains the genetic material, DNA, organized with proteins in a characteristic
number of chromosomes in each eukaryotic species.
 The nucleolus is the nuclear site where the parts of ribosomes are produced.

 Ribosomes build a cell’s proteins

 Ribosomes carry out protein synthesis in the cytosol (free ribosomes) or attached to the outside the
membranous endoplasmic reticulum (bound ribosomes)

 Many organelles are related through the endomembrane system.

 Many membranes of a eukaryotic cell are interrelated directly through physical continuity or
indirectly through transport vesicles, pinched-off portion of membrane in transit from one
membrane site to another.

 The endoplasmic reticulum manufactures membranes and performs many other biosynthetic
functions.
 The endoplasmic reticulum (ER) is a network of membrane-enclosed compartments called
cisternae. Smooth ER, so named because it lacks ribosomes, synthesizes seteroids, metabolizes
carbohydrates, stores calcium in muscle cells, and detoxifies poisons in liver cells.
 Rough ER, that potion of the ER with bound ribosomes, is continuous with the nuclear envelope
and function in producing cell membrane and manufacturing proteins for secretion. Membrane and
secretory proteins can be transferred to other location in the cell by the budding of the transport
vesicles from ER.

 The Golgi apparatus finishes, sorts, and ships many products of the cell.
 The Golgi apparatus consists of stacks of membranous sacs that synthesize various
macromolecules and also modify, store, sort, and export products of the ER.
 One side of a Golgi stack, the cis face, receives secretory proteins from the ER through transport
vesicles. Once inside, these proteins can be chemically modified and sorted before release from
the trans face of the Golgi in vesicles.

 Lysosomes are digestive compartments

 A lysosome is a membrane-enclosed sac of hydrolytic enzymes. Its acidic microenvironment is
optimal for the functioning of its enzymes in recycling monomer from cell macromolecules and in
digesting substances ingested by phagocytosis.

 Vacuoles have diverse function in cell maintenance.

  The central vacuole of plant cells function in storage, waste disposal, cell elongation, and
protection. The vacuole’s membrane is called the tonoplast.
 Food vacuoles of animal cells and contractile vacuoles of freshwater protists are other examples of
vacuoles

 Peroxisomes consume oxygen in various metabolic functions.

 Peroxisomes function in a variety of metabolic processes that produce hydrogen peroxide as a
waste product. An enzyme in the peroxisome then converts the peroxide to water.

 Mitochondria and chloroplasts are the main energy transformers of cells.

 Mitochondria are sites of cellular respiration in eukaryotic cells. Energy is released, with the help
of oxygen, from chemical fuels such as sugars and fats and is used to restock the cellular supply of
ATP.
 Mitochondria are compartmentalized by an outer membrane and an inner membrane folded into
convolutions called cristae. Some of the metabolic reactions of respiration take place in the space
enclosed by the inner membrane, the mitochondrial matrix. Enzymes built into the inner
membrane also function in respiration
 Chloroplasts, specialized members of a family of plan organelles called plastids, contain
chlorophyll and other pigments, which function in photosynthesis. Chloroplasts are enclosed by
two membranes surrounding the fluid called stroma, in which are embedded the membranous
thylakoids. These flattened sacs are stacked in some regions forming grana.

 The cytoskeleton provides structural support and functions in cell motility.

 The cytoskeleton is constructed from microtubules, microfilaments, and intermediate filaments.
 Microtubules are hollow cylinders. In many cells, microtubules radiate out from the centrosome,
an area near the nucleus that surrounds the centrioles in animal cells. Microtubules shape and
support the cell, guide the movement of organelles, and participate in chromosome separation
during cell division.
 Cilia and flagella are motile cellular appendages consisting of a “9 + 2” arrangement of
microtubules. Movement of cilia and flagella occurs when arms consisting of the protein dynein
move the microtubule doublets past each other.
 Microfilaments, thinner than microtubules, are solid rods built from the protein actin.
Microfilaments in muscle cells interact with the protein myosin to cause contraction. They also
function in ameboid movement, cytoplasmic streaming, and support for cellular projections, such
as microvilli.
 In addition to microtubules and microfilaments, most cells have a variety of intermediate filaments
that are important in supporting cell shape and fixing various organelles in place.

 Plant cells are encased by cell walls.

 The cells of plants, prokaryotes, fungi, and some protists are reinforced by cell walls external to
the plasma membrane. Plant cell walls are composed of cellulose fibers embedded in other
polysaccharides and protein.

 The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and
development.
 Plants have plasmodesmata, cytoplasmic channels that pass through adjoining cell walls.
 Cell-to-cell contact in animals is provided by tight junctions, desmosomes, and gap junctions.

 Intracellular junctions integrate cells into higher levels of structure and function.
 Organelles do not function in isolation; they cooperate with other organelles. At the cellular level,
life emerges from these complex interactions of a cell’s parts.