WHAT IS A CELL?

Cell Organization

Before we can discuss the various components of a cell, it is
important to know what organism the cell comes from. There are two
general categories of cells: prokaryotes and
eukaryotes.

Figure 1. History of life on earth.

Prokaryotic Organisms

It appears that life arose on earth about 4 billion years ago.
The simplest of cells, and the first types of cells to evolve, were
prokaryotic cells—organisms that lack a nuclear
membrane, the membrane that surrounds the nucleus of a cell.
Bacteria are the best known and most studied form of
prokaryotic organisms, although the recent discovery of a second
group of prokaryotes, called archaea, has provided evidence
of a third cellular domain of life and new insights into the origin
of life itself.

Prokaryotes are unicellular organisms that do not develop or
differentiate into multicellular forms. Some bacteria grow in
filaments, or masses of cells, but each cell in the colony is
identical and capable of independent existence. The cells may be
adjacent to one another because they did not separate after cell
division or because they remained enclosed in a common sheath or
slime secreted by the cells. Typically though, there is no
continuity or communication between the cells. Prokaryotes are
capable of inhabiting almost every place on the earth, from the deep
ocean, to the edges of hot springs, to just about every surface of
our bodies.

Prokaryotes are distinguished from eukaryotes on the basis of
nuclear organization, specifically their lack of a nuclear membrane.
Prokaryotes also lack any of the intracellular organelles and
structures that are characteristic of eukaryotic cells. Most of the
functions of organelles, such as mitochondria, chloroplasts, and the
Golgi apparatus, are taken over by the prokaryotic plasma membrane.
Prokaryotic cells have three architectural regions: appendages
called flagella and pili—proteins attached to the
cell surface; a cell envelope consisting of a capsule, a
cell wall, and a plasma membrane; and a cytoplasmic
region that contains the cell genome (DNA) and ribosomes
and various sorts of inclusions.

Eukaryotic Organisms

Eukaryotes include fungi, animals, and plants as well as
some unicellular organisms. Eukaryotic cells are about 10 times the
size of a prokaryote and can be as much as 1000 times greater in
volume. The major and extremely significant difference between
prokaryotes and eukaryotes is that eukaryotic cells contain
membrane-bound compartments in which specific metabolic activities
take place. Most important among these is the presence of a
nucleus, a membrane-delineated compartment that houses the
eukaryotic cell’s DNA. It is this nucleus that gives the
eukaryote—literally, true nucleus—its name.

Eukaryotic organisms also have other specialized structures,
called organelles, which are small structures within cells
that perform dedicated functions. As the name implies, you can think
of organelles as small organs. There are a dozen different types of
organelles commonly found in eukaryotic cells. In this primer, we
will focus our attention on only a handful of organelles and will
examine these organelles with an eye to their role at a molecular
level in the cell.

The origin of the eukaryotic cell was a milestone in the
evolution of life. Although eukaryotes use the same genetic code and
metabolic processes as prokaryotes, their higher level of
organizational complexity has permitted the development of truly
multicellular organisms. Without eukaryotes, the world would lack
mammals, birds, fish, invertebrates, mushrooms, plants, and complex
single-celled organisms.

This figure illustrates a typical human cell
(eukaryote) and a typical bacterium (prokaryote). The
drawing on the left highlights the internal structures of eukaryotic
cells, including the nucleus (light blue), the nucleolus
(intermediate blue), mitochondria (orange), and ribosomes
(dark blue). The drawing on the right demonstrates how bacterial
DNA is housed in a structure called the nucleoid (very light blue), as well
as other structures normally found in a prokaryotic cell, including
the cell membrane (black), the cell wall (intermediate blue), the
capsule (orange), ribosomes (dark blue), and a flagellum (also
black).

Cell Structures: The Basics

The Plasma Membrane—A Cell’s Protective Coat

The outer lining of a eukaryotic cell is called the plasma
membrane. This membrane serves to separate and protect a cell
from its surrounding environment and is made mostly from a double
layer of proteins and lipids, fat-like molecules. Embedded within
this membrane are a variety of other molecules that act as channels
and pumps, moving different molecules into and out of the cell. A
form of plasma membrane is also found in prokaryotes, but in this
organism it is usually referred to as the cell
membrane.

The Cytoskeleton—A Cell’s Scaffold

The cytoskeleton is an important, complex, and dynamic
cell component. It acts to organize and maintain the cell’s shape;
anchors organelles in place; helps during endocytosis, the
uptake of external materials by a cell; and moves parts of the cell
in processes of growth and motility. There are a great number of
proteins associated with the cytoskeleton, each controlling a cell’s
structure by directing, bundling, and aligning filaments.

The Cytoplasm—A Cell’s Inner Space

Inside the cell there is a large fluid-filled space called the
cytoplasm, sometimes called the cytosol. In
prokaryotes, this space is relatively free of compartments. In
eukaryotes, the cytosol is the “soup” within which all of the
cell’s organelles reside. It is also the home of the cytoskeleton.
The cytosol contains dissolved nutrients, helps break down waste
products, and moves material around the cell through a process
called cytoplasmic streaming. The nucleus often flows with
the cytoplasm changing its shape as it moves. The cytoplasm also
contains many salts and is an excellent conductor of electricity,
creating the perfect environment for the mechanics of the cell. The
function of the cytoplasm, and the organelles which reside in it,
are critical for a cell’s survival.

Genetic Material

Two different kinds of genetic material exist:
deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). Most organisms are made of DNA, but a few viruses have RNA as
their genetic material. The biological information contained in an
organism is encoded in its DNA or RNA sequence.

Prokaryotic genetic material is organized in a simple circular
structure that rests in the cytoplasm. Eukaryotic genetic material
is more complex and is divided into discrete units called
genes. Human genetic material is made up of two distinct
components: the nuclear genome and the mitochondrial
genome. The nuclear genome is divided into 24 linear DNA
molecules, each contained in a different chromosome. The
mitochondrial genome is a circular DNA molecule separate from
the nuclear DNA. Although the mitochondrial genome is very small, it
codes for some very important proteins.

Organelles

The human body contains many different organs, such as the heart,
lung, and kidney, with each organ performing a different function.
Cells also have a set of “little organs”, called
organelles, that are adapted and/or specialized for
carrying out one or more vital functions. Organelles are found only
in eukaryotes and are always surrounded by a protective membrane. It
is important to know some basic facts about the following
organelles.

The Nucleus—A Cell’s Center

The nucleus is the most conspicuous organelle found in a
eukaryotic cell. It houses the cell’s chromosomes and is the place
where almost all DNA replication and RNA synthesis occur. The
nucleus is spheroid in shape and separated from the cytoplasm by a
membrane called the nuclear envelope. The nuclear envelope
isolates and protects a cell’s DNA from various molecules that could
accidentally damage its structure or interfere with its processing.
During processing, DNA is transcribed, or synthesized, into a
special RNA, called mRNA. This mRNA is then transported out of the
nucleus, where it is translated into a specific protein molecule. In
prokaryotes, DNA processing takes place in the cytoplasm.

The Ribosome—The Protein Production Machine

Ribosomes are found in both prokaryotes and eukaryotes. The
ribosome is a large complex composed of many molecules,
including RNAs and proteins, and is responsible for processing the
genetic instructions carried by an mRNA. The process of converting an
mRNA’s genetic code into the exact sequence of amino acids that make
up a protein is called translation. Protein synthesis is
extremely important to all cells, and therefore a large number of
ribosomes—sometimes hundreds or even thousands—can be found
throughout a cell.

Ribosomes float freely in the cytoplasm or sometimes bind to
another organelle called the endoplasmic reticulum. Ribosomes are
composed of one large and one small subunit, each having a different
function during protein synthesis.

Mitochondria and Chloroplasts—The Power Generators

Mitochondria are self-replicating organelles that occur in
various numbers, shapes, and sizes in the cytoplasm of all
eukaryotic cells. As mentioned earlier, mitochondria contain their
own genome that is separate and distinct from the nuclear genome of
a cell. Mitochondria have two functionally distinct membrane systems
separated by a space: the outer membrane, which surrounds the whole
organelle; and the inner membrane, which is thrown into folds or
shelves that project inward. These inward folds are called
cristae. The number and shape of cristae in mitochondria
differ, depending on the tissue and organism in which they are found,
and serve to increase the surface area of the membrane.

Mitochondria play a critical role in generating energy in the
eukaryotic cell, and this process involves a number of complex
pathways. Let’s break down each of these steps so that you can better
understand how food and nutrients are turned into energy packets and
water. Some of the best energy-supplying foods that we eat contain
complex sugars. These complex sugars can be broken down into a less
chemically complex sugar molecule called glucose. Glucose can
then enter the cell through special molecules found in the membrane,
called glucose transporters. Once inside the cell, glucose
is broken down to make adenosine triphosphate (ATP), a form
of energy, via two different pathways.

The first pathway, glycolysis, requires no oxygen and is
referred to as anaerobic metabolism. Glycolysis occurs in the
cytoplasm outside the mitochondria. During glycolysis, glucose is
broken down into a molecule called pyruvate. Each reaction is
designed to produce some hydrogen ions that can then be used to make
energy packets (ATP). However, only four ATP molecules can be
made from one molecule of glucose in this pathway. In
prokaryotes, glycolysis is the only method used for converting
energy.

The second pathway, called the Kreb’s cycle, or the
citric acid cycle, occurs inside the mitochondria and is
capable of generating enough ATP to run all the cell functions. Once
again, the cycle begins with a glucose molecule, which during the
process of glycolysis is stripped of some of its hydrogen atoms,
transforming the glucose into two molecules of pyruvic acid.
Next, pyruvic acid is altered by the removal of a carbon and two
oxygens, which go on to form carbon dioxide. When the carbon
dioxide is removed, energy is given off, and a molecule called
NAD+ is converted into the higher energy form, NADH.
Another molecule, coenzyme A (CoA), then attaches to the remaining
acetyl unit, forming acetyl CoA.

Acetyl CoA enters the Kreb’s cycle by joining to a
four-carbon molecule called oxaloacetate. Once the two
molecules are joined, they make a six-carbon molecule called
citric acid. Citric acid is then broken down and modified in
a stepwise fashion. As this happens, hydrogen ions and carbon
molecules are released. The carbon molecules are used to make more
carbon dioxide. The hydrogen ions are picked up by NAD and another
molecule called flavin-adenine dinucleotide (FAD).
Eventually, the process produces the four-carbon oxaloacetate again,
ending up where it started off. All in all, the Kreb’s cycle is
capable of generating from 24 to 28 ATP molecules from one
molecule of glucose converted to pyruvate. Therefore, it is easy to
see how much more energy we can get from a molecule of glucose if our
mitochondria are working properly and if we have oxygen.

Chloroplasts are similar to mitochondria but are found
only in plants. Both organelles are surrounded by a double membrane
with an intermembrane space; both have their own DNA and are
involved in energy metabolism; and both have reticulations, or many
foldings, filling their inner spaces. Chloroplasts convert light
energy from the sun into ATP through a process called
photosynthesis.

The Endoplasmic Reticulum and the Golgi Apparatus—Macromolecule
Managers

The endoplasmic reticulum (ER) is the transport network
for molecules targeted for certain modifications and specific
destinations, as compared to molecules that will float freely in the
cytoplasm. The ER has two forms: the rough ER and the
smooth ER. The rough ER is labeled as such because it has
ribosomes adhering to its outer surface, whereas the smooth ER does
not. Translation of the mRNA for those proteins that will either
stay in the ER or be exported (moved out of the cell) occurs at
the ribosomes attached to the rough ER. The smooth ER serves as the
recipient for those proteins synthesized in the rough ER. Proteins
to be exported are passed to the Golgi apparatus, sometimes called a
Golgi body or Golgi complex, for further processing,
packaging, and transport to a variety of other cellular locations.

Lysosomes and Peroxisomes—The Cellular Digestive System

Lysosomes and peroxisomes are often referred to as
the garbage disposal system of a cell. Both organelles are somewhat
spherical, bound by a single membrane, and rich in digestive
enzymes, naturally occurring proteins that speed up
biochemical processes. For example, lysosomes can contain more than
three dozen enzymes for degrading proteins, nucleic acids, and
certain sugars called polysaccharides. All of these enzymes work best
at a low pH, reducing the risk that these enzymes will digest
their own cell should they somehow escape from the lysosome. Here we
can see the importance behind compartmentalization of the eukaryotic
cell. The cell could not house such destructive enzymes if they were
not contained in a membrane-bound system.

Peroxisomes function to rid the body of toxic substances, such
as hydrogen peroxide, or other metabolites and contain enzymes
concerned with oxygen utilization. High numbers of peroxisomes can
be found in the liver, where toxic byproducts are known to
accumulate. All of the enzymes found in a peroxisome are imported
from the cytosol. Each enzyme transferred to a peroxisime has a
special sequence at one end of the protein, called a PTS or
peroxisomal targeting signal, that allows the protein to be
taken into that organelle, where they then function to rid the cell
of toxic substances.

Peroxisomes often resemble a lysosome. However, peroxisomes are
self replicating, whereas lysosomes are formed in the Golgi complex.
Peroxisomes also have membrane proteins that are critical for
various functions, such as for importing proteins into their
interiors and to proliferate and segregate into daughter
cells.

Where Do Viruses Fit?

Viruses are not classified as cells and therefore are
neither unicellular nor multicellular organisms. Most people do not
even classify viruses as “living” because they lack a metabolic system
and are dependent on the host cells that they infect to reproduce.
Viruses have genomes that consist of either DNA or RNA, and there
are examples of viruses that are either double-stranded or
single-stranded. Importantly, their genomes code not only for the
proteins needed to package its genetic material but for those
proteins needed by the virus to reproduce during its infective
cycle.

Making New Cells and Cell Types

For most unicellular organisms, reproduction is a simple matter
of cell duplication, also known as replication. But
for multicellular organisms, cell replication and reproduction are
two separate processes. Multicellular organisms replace damaged or
worn out cells through a replication process called
mitosis, the division of a eukaryotic cell nucleus to produce
two identical daughter nuclei. To reproduce, eukaryotes must
first create special cells called gametes—eggs and
sperm—that then fuse to form the beginning of a new organism.
Gametes are but one of the many unique cell types that multicellular
organisms need to function as a complete organism.

Making New Cells

Most unicellular organisms create their next generation by
replicating all of their parts and then splitting into two cells, a
type of asexual reproduction called binary fission.
This process spawns not just two new cells, but also two new
organisms. Multicellullar organisms replicate new cells in much the
same way. For example, we produce new skin cells and liver cells by
replicating the DNA found in that cell through mitosis. Yet,
producing a whole new organism requires sexual reproduction,
at least for most multicellular organisms. In the first step,
specialized cells called gametes—eggs and sperm—are created
through a process called meiosis. Meiosis serves to reduce the
chromosome number for that particular organism by half. In the
second step, the sperm and egg join to make a single cell, which
restores the chromosome number. This joined cell then divides and
differentiates into different cell types that eventually form an
entire functioning organism.

Mitosis is the process by which the diploid
nucleus (having two sets of homologous chromosomes) of a somatic cell
divides to produce two daughter nuclei, both of which are still
diploid. The left-hand side of the drawing demonstrates how the
parent cell duplicates its chromosomes (one red and one blue),
providing the daughter cells with a complete copy of genetic
information. Next, the chromosomes align at the equatorial plate, and
the centromeres divide. The sister chromatids then separate,
becoming two diploid daughter cells, each with one red and
one blue chromosome.

Mitosis

Every time a cell divides, it must ensure that its DNA is shared
between the two daughter cells. Mitosis is the process of “divvying
up” the genome between the daughter cells. To easier
describe this process, let’s imagine a cell with only one
chromosome. Before a cell enters mitosis, we say the cell is in
interphase, the state of a eukaryotic cell when not
undergoing division. Every time a cell divides, it must first
replicate all of its DNA. Because chromosomes are simply DNA wrapped
around protein, the cell replicates its chromosomes also. These two
chromosomes, positioned side by side, are called sister
chromatids and are identical copies of one another. Before this
cell can divide, it must separate these sister chromatids from one
another. To do this, the chromosomes have to condense. This stage of
mitosis is called prophase. Next, the nuclear envelope breaks
down, and a large protein network, called the spindle,
attaches to each sister chromatid. The chromosomes are now aligned
perpendicular to the spindle in a process called metaphase.
Next, “molecular motors” pull the chromosomes away from the metaphase
plate to the spindle poles of the cell. This is called
anaphase. Once this process is completed, the cells divide,
the nuclear envelope reforms, and the chromosomes relax and
decondense during telophase. The cell can now replicate its
DNA again during interphase and go through mitosis once
more.

Meiosis, a type of nuclear division, occurs
only in reproductive cells and results in a diploid cell (having two
sets of chromosomes) giving rise to four haploid cells (having a
single set of chromosomes). Each haploid cell can subsequently fuse
with a gamete of the opposite sex during sexual reproduction. In
this illustration, two pairs of homologous chromosomes enter Meiosis
I, which results initially in two daughter nuclei, each with two
copies of each chromosome. These two cells then enter Meiosis II,
producing four daughter nuclei, each with a single copy of each
chromosome.

Meiosis

Meiosis is a specialized type of cell division that occurs
during the formation of gametes. Although meiosis may seem much more
complicated than mitosis, it is really just two cell divisions in
sequence. Each of these sequences maintains strong similarities to
mitosis.

Meiosis I refers to the first of the two divisions and is
often called the reduction division. This is because it is
here that the chromosome complement is reduced from
diploid (two copies) to haploid (one copy). Interphase in
meiosis is identical to interphase in mitosis. At this stage, there
is no way to determine what type of division the cell will undergo
when it divides. Meiotic division will only occur in cells
associated with male or female sex organs. Prophase I is
virtually identical to prophase in mitosis, involving the appearance
of the chromosomes, the development of the spindle apparatus,
and the breakdown of the nuclear membrane. Metaphase I is where the
critical difference occurs between meiosis and mitosis. In mitosis,
all of the chromosomes line up on the metaphase plate in no particular
order. In Metaphase I, the chromosome pairs are aligned on either
side of the metaphase plate. It is during this alignment that the
chromatid arms may overlap and temporarily fuse, resulting in what
is called crossovers. During Anaphase I, the spindle
fibers contract, pulling the homologous pairs away from each other
and toward each pole of the cell. In Telophase I, a cleavage
furrow typically forms, followed by cytokinesis, the changes
that occur in the cytoplasm of a cell during nuclear division; but
the nuclear membrane is usually not reformed, and the chromosomes do
not disappear. At the end of Telophase I, each daughter cell has a
single set of chromosomes, half the total number in the original
cell, that is, while the original cell was diploid; the daughter
cells are now haploid.

Meiosis II is quite simply a mitotic division of each of
the haploid cells produced in Meiosis I. There is no Interphase
between Meiosis I and Meiosis II, and the latter begins with
Prophase II. At this stage, a new set of spindle fibers forms
and the chromosomes begin to move toward the equator of the cell.
During Metaphase II, all of the chromosomes in the two cells
align with the metaphase plate. In Anaphase II, the
centromeres split, and the spindle fibers shorten, drawing the
chromosomes toward each pole of the cell. In Telophase II, a
cleavage furrow develops, followed by cytokinesis and the formation
of the nuclear membrane. The chromosomes begin to fade and are
replaced by the granular chromatin, a characteristic of interphase.
When Meiosis II is complete, there will be a total of four daughter
cells, each with half the total number of chromosomes as the
original cell. In the case of male structures, all four cells
will eventually develop into sperm cells. In the case of the
female life cycles in higher organisms, three of the cells
will typically abort, leaving a single cell to develop into an egg
cell, which is much larger than a sperm cell.

Recombination—The Physical Exchange of DNA

All organisms suffer a certain number of small mutations,
or random changes in a DNA sequence, during the process of DNA
replication. These are called spontaneous mutations and occur
at a rate characteristic for that organism. Genetic
recombination refers more to a large-scale rearrangement of a
DNA molecule. This process involves pairing between complementary
strands of two parental duplex, or double-stranded DNAs, and results
from a physical exchange of chromosome material.

The position at which a gene is located on a chromosome is called
a locus. In a given individual, one might find two different
versions of this gene at a particular locus. These alternate gene
forms are called alleles. During Meiosis I, when the
chromosomes line up along the metaphase plate, the two strands of a
chromosome pair may physically cross over one another. This may
cause the strands to break apart at the crossover point and
reconnect to the other chromosome, resulting in the exchange of part
of the chromosome.

Recombination results in a new arrangement of maternal and
paternal alleles on the same chromosome. Although the same genes
appear in the same order, the alleles are different. This process
explains why offspring from the same parents can look so different.
In this way, it is theoretically possible to have any combination of
parental alleles in an offspring, and the fact that two alleles
appear together in one offspring does not have any influence on the
statistical probability that another offspring will have the same
combination. This theory of “independent assortment” of
alleles is fundamental to genetic inheritance. However, having said
that, there is an exception that requires further discussion.

The frequency of recombination is actually not the same
for all gene combinations. This is because recombination is greatly
influenced by the proximity of one gene to another. If two genes are
located close together on a chromosome, the likelihood that a
recombination event will separate these two genes is less than if
they were farther apart. Linkage describes the tendency of
genes to be inherited together as a result of their location on the
same chromosome. Linkage disequilibrium describes a situation
in which some combinations of genes or genetic markers occur more or
less frequently in a population than would be expected from their
distances apart. Scientists apply this concept when searching for a
gene that may cause a particular disease. They do this by comparing
the occurrence of a specific DNA sequence with the appearance of a
disease. When they find a high correlation between the two, they
know they are getting closer to finding the appropriate gene
sequence.

Binary Fission—How Bacteria Reproduce

Bacteria reproduce through a fairly simple process called
binary fission, or the reproduction of a living cell by
division into two equal, or near equal, parts. As just noted, this
type of asexual reproduction theoretically results in two identical
cells. However, bacterial DNA has a relatively high mutation rate.
This rapid rate of genetic change is what makes bacteria capable of
developing resistance to antibiotics and helps them exploit invasion
into a wide range of environments.

Similar to more complex organisms, bacteria also have mechanisms for
exchanging genetic material. Although not equivalent to sexual
reproduction, the end result is that a bacterium contains a
combination of traits from two different parental cells.
Three different modes of exchange have thus far been identified in
bacteria.

Conjunction involves the direct joining of two bacteria,
which allows their circular DNAs to undergo recombination. Bacteria
can also undergo transformation by absorbing remnants of DNA
from dead bacteria and integrating these fragments into their own
DNA. Lastly, bacteria can exchange genetic material through a
process called transduction, in which genes are transported
into and out of the cell by bacterial viruses, called
bacteriophages, or by plasmids, an autonomous
self-replicating extrachromosomal circular DNA.

Viral Reproduction

Because viruses are acellular and do not use ATP, they must
utilize the machinery and metabolism of a host cell to reproduce.
For this reason, viruses are called obligate intracellular
parasites. Before a virus has entered a host cell, it is called a
virion–a package of viral genetic material.
Virions—infectious viral particles—can be passed from host
to host either through direct contact or through a vector, or
carrier. Inside the organism, the virus can enter a cell in various
ways. Bacteriophages—bacterial viruses—attach to the cell
wall surface in specific places. Once attached, enzymes make a small
hole in the cell wall, and the virus injects its DNA into the cell.
Other viruses (such as HIV) enter the host via endocytosis, the process
whereby cells take in material from the external environment. After
entering the cell, the virus’s genetic material begins the
destructive process of taking over the cell and forcing it to
produce new viruses.

This illustration depicts three types of
viruses: a bacterial virus, otherwise called a bacteriophage (left
center); an animal virus (top right); and a retrovirus
(bottom right). Viruses depend on the host cell that they infect to
reproduce. When found outside of a host cell, viruses, in their
simplest forms, consist only of genomic nucleic acid, either DNA or
RNA (depicted as blue), surrounded by a protein coat, or
capsid.

The new viruses then leave the cell either by exocytosis or by
lysis. Envelope-bound animal viruses instruct the host’s endoplasmic
reticulum to make certain proteins, called glycoproteins,
which then collect in clumps along the cell membrane. The virus is
then discharged from the cell at these exit sites, referred to as
exocytosis. On the other hand, bacteriophages must break open, or
lyse, the cell to exit. To do this, the phages have a
gene that codes for an enzyme called lysozyme. This enzyme breaks
down the cell wall, causing the cell to swell and burst. The new
viruses are released into the environment, killing the host cell in
the process.

Why Study Viruses?

Viruses are important to the study of molecular and
cellular biology because they provide simple systems that can be
used to manipulate and investigate the functions of many cell types.
We have just discussed how viral replication depends on the
metabolism of the infected cell. Therefore, the study of viruses can
provide fundamental information about aspects of cell biology and
metabolism. The rapid growth and small genome size of bacteria make
them excellent tools for experiments in biology. Bacterial viruses
have also further simplified the study of bacterial genetics and
have deepened our understanding of the basic mechanisms of molecular
genetics. Because of the complexity of an animal cell genome,
viruses have been even more important in studies of animal cells
than in studies of bacteria. Numerous studies have demonstrated the
utility of animal viruses as probes for investigating different
activities of eukaryotic cells. Other examples in which animal
viruses have provided important models for biological research of
their host cells include studies of DNA replication,
transcription, RNA processing, and protein
transport.

Deriving New Cell Types

Look closely at the human body, and it is clear that not all cells
are alike. For example, cells that make up our skin are certainly
different from cells that make up our inner organs. Yet, all of the
different cell types in our body are all derived, or arise,
from a single, fertilized egg cell through differentiation.
Differentiation is the process by which an unspecialized cell
becomes specialized into one of the many cells that make up the
body, such as a heart, liver, or muscle cell. During differentiation,
certain genes are turned on, or become activated, while other
genes are switched off, or inactivated. This process is
intricately regulated. As a result, a differentiated cell will
develop specific structures and perform certain functions.

Mammalian Cell Types

Three basic categories of cells make up the mammalian body:
germ cells, somatic cells, and stem cells. Each
of the approximately 100,000,000,000,000 cells in an adult human has
its own copy, or copies, of the genome, with the only exception being
certain cell types that lack nuclei in their fully differentiated
state, such as red blood cells. The majority of these cells are
diploid, or have two copies of each chromosome. These cells are
called somatic cells. This category of cells includes most of
the cells that make up our body, such as skin and muscle cells.
Germ line cells are any line of cells that give rise to
gametes—eggs and sperm—and are continuous through the
generations. Stem cells, on the other hand, have the ability
to divide for indefinite periods and to give rise to specialized
cells. They are best described in the context of normal human
development.

Human development begins when a sperm fertilizes an egg
and creates a single cell that has the potential to form an entire
organism. In the first hours after fertilization, this cell divides
into identical cells. Approximately 4 days after fertilization
and after several cycles of cell division, these cells begin to
specialize, forming a hollow sphere of cells, called a blastocyst.
The blastocyst has an outer layer of cells, and inside this
hollow sphere, there is a cluster of cells called the inner cell
mass. The cells of the inner cell mass will go on to form virtually all
of the tissues of the human body. Although the cells of the inner cell mass
can form virtually every type of cell found in the human body, they
cannot form an organism. Therefore, these cells are referred to as
pluripotent, that is, they can give rise to many types of
cells but not a whole organism. Pluripotent stem cells undergo
further specialization into stem cells that are committed to give
rise to cells that have a particular function. Examples include
blood stem cells that give rise to red blood cells, white blood
cells, and platelets, and skin stem cells that give rise to the
various types of skin cells. These more specialized stem cells are
called multipotent—capable of giving rise to several kinds of
cells, tissues, or structures.

The Working Cell: DNA, RNA, and Protein Synthesis

DNA Replication

DNA replication, or the process of duplicating a cell’s
genome, is required every time a cell divides. Replication, like all
cellular activities, requires specialized proteins for carrying out
the job. In the first step of replication, a special protein, called
a helicase, unwinds a portion of the parental DNA double
helix. Next, a molecule of DNA polymerase—a common name for
two categories of enzymes that influence the synthesis of DNA—
binds to one strand of the DNA. DNA polymerase begins to move along
the DNA strand in the 3′ to 5′ direction, using the single-stranded
DNA as a template. This newly synthesized strand is called the
leading strand and is necessary for forming new nucleotides
and reforming a double helix. Because DNA synthesis can only occur
in the 5′ to 3′ direction, a second DNA polymerase molecule is used
to bind to the other template strand as the double helix opens. This
molecule synthesizes discontinuous segments of polynucleotides,
called Okazaki fragments. Another enzyme, called DNA
ligase, is responsible for stitching these fragments together
into what is called the lagging strand.

Before a cell can divide, it must first
duplicate its DNA. This figure provides an overview of the DNA
replication process. In the first step, a portion of the double
helix (blue) is unwound by a helicase. Next, a molecule of DNA
polymerase (green) binds to one strand of the DNA. It moves along
the strand, using it as a template for assembling a leading strand
(red) of nucleotides and reforming a double helix. Because DNA
synthesis can only occur 5′ to 3′, a second DNA polymerase molecule
(also green) is used to bind to the other template strand as the
double helix opens. This molecule must synthesize discontinuous
segments of polynucleotides (called Okazaki Fragments). Another
enzyme, DNA Ligase (yellow), then stitches these together into the
lagging strand.

With multiple replication origin sites, one might ask, how does
the cell know which DNA has already been replicated and
which still awaits replication? To date, two replication control
mechanisms have been identified: one positive and one negative.
For DNA to be replicated, each replication origin site
must be bound by a set of proteins called the Origin Recognition
Complex. These remain attached to the DNA throughout the
replication process. Specific accessory proteins, called
licensing factors, must also be present for initiation of
replication. Destruction of these proteins after initiation of
replication prevents further replication cycles from occurring. This
is because licensing factors are only produced when the nuclear
membrane of a cell breaks down during mitosis.

DNA Transcription—Making mRNA

DNA transcription refers to the synthesis of RNA from a
DNA template. This process is very similar to DNA replication. Of
course, there are different proteins that direct transcription. The
most important enzyme is RNA polymerase, an enzyme that
influences the synthesis of RNA from a DNA template. For
transcription to be initiated, RNA polymerase must be able to
recognize the beginning sequence of a gene so that it knows where to
start synthesizing an mRNA. It is directed to this initiation site
by the ability of one of its subunits to recognize a specific DNA
sequence found at the beginning of a gene, called the promoter
sequence. The promoter sequence is a unidirectional sequence
found on one strand of the DNA that instructs the RNA polymerase in
both where to start synthesis and in which direction synthesis
should continue. The RNA polymerase then unwinds the double helix at
that point and begins synthesis of a RNA strand complementary to
one of the strands of DNA. This strand is called the
antisense or template strand, whereas the other strand
is referred to as the sense or coding strand. Synthesis can
then proceed in a unidirectional manner.

Although much is known about transcript processing, the signals
and events that instruct RNA polymerase to stop transcribing and
drop off the DNA template remain unclear. Experiments over the years
have indicated that processed eukaryotic messages contain a
poly(A) addition signal (AAUAAA) at their 3′ end, followed by
a string of adenines. This poly(A) addition, also called the
poly(A) site, contributes not only to the addition of the
poly(A) tail but also to transcription termination and the release
of RNA polymerase from the DNA template. Yet, transcription does not
stop here. Rather, it continues for another 200 to 2000 bases beyond
this site before it is aborted. It is either before or during this
termination process that the nascent transcript is cleaved,
or cut, at the poly(A) site, leading to the creation of two RNA
molecules. The upstream portion of the newly formed, or
nascent, RNA then undergoes further modifications, called
post-transcriptional modification, and becomes mRNA. The
downstream RNA becomes unstable and is rapidly degraded.

Although the importance of the poly(A) addition signal has been
established, the contribution of sequences further downstream
remains uncertain. A recent study suggests that a defined
region, called the termination region, is required for proper
transcription termination. This study also illustrated that
transcription termination takes place in two distinct steps. In the
first step, the nascent RNA is cleaved at specific subsections of
the termination region, possibly leading to its release from RNA
polymerase. In a subsequent step, RNA polymerase disengages from the
DNA. Hence, RNA polymerase continues to transcribe the DNA, at least
for a short distance.

Protein Translation—How Do Messenger RNAs Direct Protein
Synthesis?

The cellular machinery responsible for synthesizing proteins is
the ribosome. The ribosome consists of structural RNA and
about 80 different proteins. In its inactive state, it exists as two
subunits: a large subunit and a small subunit. When
the small subunit encounters an mRNA, the process of
translating an mRNA to a protein begins. In the large
subunit, there are two sites for amino acids to bind and thus be
close enough to each other to form a bond. The “A site”
accepts a new transfer RNA, or tRNA—the adaptor molecule
that acts as a translator between mRNA and protein—bearing an amino
acid. The “P site” binds the tRNA that becomes attached to
the growing chain.

As we just discussed, the adaptor molecule that acts as a
translator between mRNA and protein is a specific RNA molecule, the
tRNA. Each tRNA has a specific acceptor site that binds a
particular triplet of nucleotides, called a codon, and an
anti-codon site that binds a sequence of three unpaired
nucleotides, the anti-codon, which can then bind to the the
codon. Each tRNA also has a specific charger protein, called
an aminoacyl tRNA synthetase. This protein can only bind to
that particular tRNA and attach the correct amino acid to the
acceptor site.

The start signal for translation is the codon ATG, which
codes for methionine. Not every protein necessarily starts with
methionine, however. Oftentimes this first amino acid will be
removed in later processing of the protein. A tRNA charged with
methionine binds to the translation start signal. The large subunit
binds to the mRNA and the small subunit, and so begins
elongation, the formation of the polypeptide chain. After the
first charged tRNA appears in the A site, the ribosome shifts so
that the tRNA is now in the P site. New charged tRNAs, corresponding
the codons of the mRNA, enter the A site, and a bond is formed
between the two amino acids. The first tRNA is now released, and the
ribosome shifts again so that a tRNA carrying two amino acids is now
in the P site. A new charged tRNA then binds to the A site. This
process of elongation continues until the ribosome reaches what is
called a stop codon, a triplet of nucleotides that signals the
termination of translation. When the ribosome reaches a stop codon,
no aminoacyl tRNA binds to the empty A site. This is the ribosome
signal to break apart into its large and small subunits, releasing
the new protein and the mRNA. Yet, this isn’t always the end of the
story. A protein will often undergo further modification, called
post-translational modification. For example, it might be
cleaved by a protein-cutting enzyme, called a protease, at a
specific place or have a few of its amino acids altered.

This drawing provides a graphic overview of the
many steps involved in transcription and translation. Within the
nucleus of the cell (light blue), genes (DNA, dark blue) are
transcribed into RNA. This RNA molecule is then subject to
post-transcriptional modification and control, resulting in a mature
mRNA molecule (red) that is then transported out of the nucleus and
into the cytoplasm (peach), where it undergoes translation into a
protein. mRNA molecules are translated by ribosomes (purple) that
match the three-base codons of the mRNA molecule to the three-base
anti-codons of the appropriate tRNA molecules. These newly
synthesized proteins (black) are often further modified, such as by
binding to an effector molecule (orange), to become fully
active.

DNA Repair Mechanisms

Maintenance of the accuracy of the DNA genetic code is critical
for both the long- and short-term survival of cells and species.
Sometimes, normal cellular activities, such as duplicating DNA and
making new gametes, introduce changes or mutations in our DNA. Other
changes are caused by exposure of DNA to chemicals, radiation, or
other adverse environmental conditions. No matter the source,
genetic mutations have the potential for both positive and negative
effects on an individual as well as its species. A positive change
results in a slightly different version of a gene that might
eventually prove beneficial in the face of a new disease or changing
environmental conditions. Such beneficial changes are the
cornerstone of evolution. Other mutations are considered
deleterious, or result in damage to a cell or an individual.
For example, errors within a particular DNA sequence may end up
either preventing a vital protein from being made or encoding a
defective protein. It is often these types of errors that lead to
various disease states.

The potential for DNA damage is counteracted by a vigorous
surveillance and repair system. Within this system, there are a
number of enzymes capable of repairing damage to DNA. Some of these
enzymes are specific for a particular type of damage, whereas others
can handle a range of mutation types. These systems also differ in
the degree to which they are able to restore the normal, or
wild-type, sequence.

From Cells to Genomes

Understanding what makes up a cell and how that cell works is
fundamental to all of the biological sciences. Appreciating the
similarities and differences between cell types is particularly
important to the fields of cell and molecular biology. These
fundamental similarities and differences provide a unifying theme,
allowing the principles learned from studying one cell type to be
extrapolated and generalized to other cell types.

Perhaps the most fundamental property of all living things is
their ability to reproduce. All cells arise from pre-existing cells,
that is, their genetic material must be replicated and passed from
parent cell to progeny. Likewise, all multicellular organisms
inherit their genetic information specifying structure and function
from their parents.