A Basic Introduction to the Science Underlying
WHAT IS A GENOME?
Life is specified by genomes. Every organism, including
humans, has a genome that contains all of the biological information
needed to build and maintain a living example of that organism.
The biological information contained in a genome is encoded in its
deoxyribonucleic acid (DNA) and is divided into discrete
units called genes. Genes code for proteins that attach to
the genome at the appropriate positions and switch on a series of
reactions called gene expression.
|In 1909, Danish botanist
Wilhelm Johanssen coined the word gene for the hereditary
unit found on a chromosome. Nearly 50 years earlier, Gregor
Mendel had characterized hereditary units as factors—
observable differences that were passed from parent to offspring.
Today we know that a single gene consists of a unique sequence of
DNA that provides the complete instructions to make a functional
product, called a protein. Genes instruct each cell type—
such as skin, brain, and liver—to make discrete sets of
proteins at just the right times, and it is through this specificity
that unique organisms arise.
The Physical Structure of the Human Genome
Inside each of our cells lies a nucleus, a membrane-bounded
region that provides a sanctuary for genetic information. The nucleus
contains long strands of DNA that encode this genetic information.
A DNA chain is made up of four chemical bases: adenine
(A) and guanine (G), which are called purines, and cytosine (C)
and thymine (T), referred to as pyrimidines. Each base has a slightly
different composition, or combination of oxygen, carbon, nitrogen,
and hydrogen. In a DNA chain, every base is attached to a sugar
molecule (deoxyribose) and a phosphate molecule, resulting in a
nucleic acid or nucleotide. Individual nucleotides are linked
through the phosphate group, and it is the precise order, or sequence,
of nucleotides that determines the product made from that gene.
Figure 1. The four DNA bases.
Each DNA base is made up of the sugar
2'-deoxyribose linked to a phosphate group and one of the
four bases depicted above: adenine (top left), cytosine (top right),
guanine (bottom left), and thymine (bottom right).
|A DNA chain, also called
a strand, has a sense of direction, in which one end is chemically
different than the other. The so-called 5' end terminates
in a 5' phosphate group (-PO4); the 3' end terminates in a 3'
hydroxyl group (-OH). This is important because DNA strands
are always synthesized in the 5' to 3' direction.
The DNA that constitutes a gene is a double-stranded molecule consisting
of two chains running in opposite directions. The chemical nature
of the bases in double-stranded DNA creates a slight twisting force
that gives DNA its characteristic gently coiled structure, known as
the double helix. The two strands are connected to each
other by chemical pairing of each base on one strand to a specific
partner on the other strand. Adenine (A) pairs with thymine (T),
and guanine (G) pairs with cytosine (C). Thus, A-T and G-C base
pairs are said to be complementary. This complementary base
pairing is what makes DNA a suitable molecule for carrying our genetic
information—one strand of DNA can act as a template to direct
the synthesis of a complementary strand. In this way, the information
in a DNA sequence is readily copied and passed on to the next generation
Not all genetic information is found in nuclear DNA. Both plants
and animals have an organelle—a "little organ" within the cell—
called the mitochondrion. Each mitochondrion has its own set of genes.
Plants also have a second organelle, the chloroplast, which also has
its own DNA. Cells often have multiple mitochondria, particularly
cells requiring lots of energy, such as active muscle cells. This
is because mitochondria are responsible for converting the energy
stored in macromolecules into a form usable by the cell, namely,
the adenosine triphosphate (ATP) molecule. Thus, they are
often referred to as the power generators of the cell.
Unlike nuclear DNA (the DNA found within the nucleus of
a cell), half of which comes from our mother and half from our
father, mitochondrial DNA is only inherited from our mother. This
is because mitochondria are only found in the female gametes or
"eggs" of sexually reproducing animals, not in the male gamete,
or sperm. Mitochondrial DNA also does not recombine; there is no
shuffling of genes from one generation to the other, as there is
with nuclear genes.
|Large numbers of mitochondria
are found in the tail of sperm, providing them with an engine
that generates the energy needed for swimming toward the egg.
However, when the sperm enters the egg during fertilization,
the tail falls off, taking away the father's mitochondria.
Why Is There a Separate Mitochondrial Genome?
The energy-conversion process that takes place in the mitochondria
takes place aerobically, in the presence of oxygen. Other
energy conversion processes in the cell take place anaerobically,
or without oxygen. The independent aerobic function of these organelles
is thought to have evolved from bacteria that lived inside of other
simple organisms in a mutually beneficial, or symbiotic,
relationship, providing them with aerobic capacity. Through the
process of evolution, these tiny organisms became incorporated into
the cell, and their genetic systems and cellular functions became
integrated to form a single functioning cellular unit. Because
mitochondria have their own DNA, RNA, and ribosomes, this scenario
is quite possible. This theory is also supported by the existence of
a eukaryotic organism, called the amoeba, which lacks mitochondria.
Therefore, amoeba must always have a symbiotic relationship
with an aerobic bacterium.
Why Study Mitochondria?
There are many diseases caused by mutations in mitochondrial
DNA (mtDNA). Because the mitochondria produce energy in cells,
symptoms of mitochondrial diseases often involve degeneration or
functional failure of tissue. For example, mtDNA mutations have
been identified in some forms of diabetes, deafness, and certain
inherited heart diseases. In addition, mutations in mtDNA are able
to accumulate throughout an individual's lifetime. This is different
from mutations in nuclear DNA, which has sophisticated repair
mechanisms to limit the accumulation of mutations. Mitochondrial DNA
mutations can also concentrate in the mitochondria of specific tissues.
A variety of deadly diseases are attributable to a large number of accumulated
mutations in mitochondria. There is even a theory, the Mitochondrial
Theory of Aging, that suggests that accumulation of mutations
in mitochondria contributes to, or drives, the aging process. These
defects are associated with Parkinson's and Alzheimer's disease,
although it is not known whether the defects actually cause or are
a direct result of the diseases. However, evidence suggests that
the mutations contribute to the progression of both diseases.
In addition to the critical cellular energy-related functions,
mitochondrial genes are useful to evolutionary biologists because
of their maternal inheritance and high rate of mutation. By studying
patterns of mutations, scientists are able to reconstruct patterns
of migration and evolution within and between species. For example,
mtDNA analysis has been used to trace the migration of people from
Asia across the Bering Strait to North and South America. It has
also been used to identify an ancient maternal lineage from which
modern man evolved.
|In addition to mRNA,
DNA codes for other forms of RNA, including ribosomal
RNAs (rRNAs), transfer RNAs (tRNAs), and small nuclear
RNAs (snRNAs). rRNAs and tRNAs participate in protein
assembly whereas snRNAs aid in a process called splicing
—the process of editing of mRNA before it can be used as
a template for protein synthesis.
Just like DNA, ribonucleic acid (RNA) is a chain, or polymer,
of nucleotides with the same 5' to 3' direction of its strands.
However, the ribose sugar component of RNA is slightly different
chemically than that of DNA. RNA has a 2' oxygen atom
that is not present in DNA. Other fundamental
structural differences exist. For example, uracil takes the place
of the thymine nucleotide found in DNA, and RNA is, for the most part,
a single-stranded molecule. DNA directs the synthesis of a variety of
RNA molecules, each with a unique role in cellular function. For example,
all genes that code for proteins are first made into an RNA strand in the
nucleus called a messenger RNA (mRNA). The mRNA carries the
information encoded in DNA out of the nucleus to the protein assembly
machinery, called the ribosome, in the cytoplasm. The ribosome
complex uses mRNA as a template to synthesize the exact protein
coded for by the gene.
|"DNA makes RNA,
RNA makes protein, and proteins make us."
Although DNA is the carrier of genetic information in a cell, proteins
do the bulk of the work. Proteins are long chains containing as
many as 20 different kinds of amino acids. Each cell contains thousands
of different proteins: enzymes that make new molecules and catalyze
nearly all chemical processes in cells; structural components that
give cells their shape and help them move; hormones that transmit
signals throughout the body; antibodies that recognize foreign molecules;
and transport molecules that carry oxygen. The genetic code carried
by DNA is what specifies the order and number of amino acids and,
therefore, the shape and function of the protein.
The "Central Dogma"—a fundamental principle of
molecular biology—states that genetic information flows from DNA
to RNA to protein. Ultimately, however, the genetic code resides
in DNA because only DNA is passed from generation to generation. Yet,
in the process of making a protein, the encoded information must
be faithfully transmitted first to RNA then to protein. Transferring
the code from DNA to RNA is a fairly straightforward process called
transcription. Deciphering the code in the resulting mRNA
is a little more complex. It first requires that the mRNA leave
the nucleus and associate with a large complex of specialized RNAs
and proteins that, collectively, are called the ribosome. Here
the mRNA is translated into protein by decoding the mRNA sequence in blocks
of three RNA bases, called codons, where each codon specifies
a particular amino acid. In this way, the ribosomal complex
builds a protein one amino acid at a time, with the order of amino
acids determined precisely by the order of the codons in the mRNA.
|In 1961, Marshall Nirenberg
and Heinrich Matthaei correlated the first codon (UUU)
with the amino acid phenylalanine. After that, it was
not long before the genetic code for all 20 amino acids
A given amino acid can have more than one codon. These redundant
codons usually differ at the third position. For example, the amino
acid serine is encoded by UCU, UCC, UCA, and/or UCG. This redundancy
is key to accommodating mutations that occur naturally as DNA is
replicated and new cells are produced. By allowing some of the random
changes in DNA to have no effect on the ultimate protein sequence,
a sort of genetic safety net is created. Some codons do not code
for an amino acid at all but instruct the ribosome when to stop
adding new amino acids.
Table 1. RNA triplet codons and their corresponding amino
| AAU Asparagine
| AGU Serine
A translation chart of the 64 RNA codons.
The Core Gene Sequence: Introns and Exons
Genes make up about 1 percent of the total DNA in our genome.
In the human genome, the coding portions of a gene, called exons,
are interrupted by intervening sequences, called introns.
In addition, a eukaryotic gene does not code for a protein in one continuous
stretch of DNA. Both exons and introns are "transcribed"
into mRNA, but before it is transported to the ribosome, the primary
mRNA transcript is edited. This editing process removes the introns,
joins the exons together, and adds unique features to each end of the
transcript to make a "mature" mRNA. One might then ask what
the purpose of an intron is if it is spliced out after it is transcribed? It
is still unclear what all the functions of introns are, but scientists
believe that some serve as the site for recombination, the
process by which progeny derive a combination of genes different
from that of either parent, resulting in novel genes with new combinations
of exons, the key to evolution.
Figure 2. Recombination.
Recombination involves pairing between complementary
strands of two parental duplex DNAs (top and middle panel). This process
creates a stretch of hybrid DNA (bottom panel) in which the single strand of one
duplex is paired with its complement from the other duplex.
Gene Prediction Using Computers
When the complete mRNA sequence for a gene is known,
computer programs are used to align the mRNA sequence with the appropriate
region of the genomic DNA sequence. This provides a reliable indication
of the beginning and end of the coding region for that gene. In
the absence of a complete mRNA sequence, the boundaries can be estimated
by ever-improving, but still inexact, gene prediction software.
The problem is the lack of a single sequence pattern that indicates
the beginning or end of a eukaryotic gene. Fortunately, the middle
of a gene, referred to as the core gene sequence--has enough
consistent features to allow more reliable predictions.
From Genes to Proteins: Start to Finish
We just discussed that the journey from DNA to mRNA to protein
requires that a cell identify where a gene begins and ends. This must
be done both during the transcription and the translation process.
Transcription, the synthesis of an RNA copy from a sequence
of DNA, is carried out by an enzyme called RNA polymerase.
This molecule has the job of recognizing the DNA sequence where
transcription is initiated, called the promoter site. In general,
there are two "promoter" sequences upstream from the beginning
of every gene. The location and base sequence of each promoter site
vary for prokaryotes (bacteria) and eukaryotes
(higher organisms), but they are both recognized by RNA polymerase, which
can then grab hold of the sequence and drive the production of an mRNA.
Eukaryotic cells have three different RNA polymerases, each
recognizing three classes of genes. RNA polymerase II is
responsible for synthesis of mRNAs from protein-coding genes. This
polymerase requires a sequence resembling TATAA, commonly referred
to as the TATA box, which is found 25-30 nucleotides upstream
of the beginning of the gene, referred to as the initiator sequence.
Transcription terminates when the polymerase stumbles upon
a termination, or stop signal. In eukaryotes, this process is not
fully understood. Prokaryotes, however, tend to have a short region
composed of G's and C's that is able to fold in on itself and form
complementary base pairs, creating a stem in the new mRNA. This
stem then causes the polymerase to trip and release the nascent,
or newly formed, mRNA.
The beginning of translation, the process in which
the genetic code carried by mRNA directs the synthesis of proteins
from amino acids, differs slightly for prokaryotes and eukaryotes,
although both processes always initiate at a codon for methionine.
For prokaryotes, the ribosome recognizes and attaches at the sequence
AGGAGGU on the mRNA, called the Shine-Delgarno sequence, that
appears just upstream from the methionine (AUG) codon. Curiously,
eukaryotes lack this recognition sequence and simply initiate translation
at the amino acid methionine, usually coded for by the bases AUG,
but sometimes GUG. Translation is terminated for both prokaryotes
and eukaryotes when the ribosome reaches one of the three stop codons.
Structural Genes, Junk DNA, and Regulatory Sequences
|Over 98 percent of
the genome is of unknown function. Although often referred
to as "junk" DNA, scientists are beginning to
uncover the function of many of these intergenic sequences—the
DNA found between genes.
Sequences that code for proteins are called structural
genes. Although it is true that proteins are the major components
of structural elements in a cell, proteins are also the real workhorses
of the cell. They perform such functions as transporting nutrients
into the cell; synthesizing new DNA, RNA, and protein molecules;
and transmitting chemical signals from outside to inside the cell,
as well as throughout the cell—both critical to the process of
A class of sequences called regulatory sequences makes
up a numerically insignificant fraction of the genome but provides
critical functions. For example, certain sequences indicate the
beginning and end of genes, sites for initiating replication and
recombination, or provide landing sites for proteins that turn genes
on and off. Like structural genes, regulatory sequences are inherited;
however, they are not commonly referred to as genes.
Other DNA Regions
Forty to forty-five percent of our genome is made up of short sequences
that are repeated, sometimes hundreds of times. There are numerous
forms of this "repetitive DNA", and a few have known
functions, such as stabilizing the chromosome structure or inactivating
one of the two X chromosomes in developing females, a process called
X-inactivation. The most highly repeated sequences found
so far in mammals are called "satellite DNA" because
their unusual composition allows them to be easily separated from
other DNA. These sequences are associated with chromosome structure
and are found at the centromeres (or centers) and telomeres (ends)
of chromosomes. Although they do not play a role in the coding
of proteins, they do play a significant role in chromosome structure,
duplication, and cell division. The highly variable nature of these
sequences makes them an excellent "marker" by which
individuals can be identified based on their unique pattern of their satellite DNA.
Figure 3. A chromosome.
A chromosome is composed of a very
long molecule of DNA and associated proteins that carry hereditary
information. The centromere, shown at the center of this chromosome,
is a specialized structure that appears during cell division and ensures
the correct distribution of duplicated chromosomes to daughter cells.
Telomeres are the structures that seal the end of a chromosome.
Telomeres play a critical role in chromosome replication and maintenance
by counteracting the tendency of the chromosome to otherwise shorten
with each round of replication.
Another class of non-coding DNA is the "pseudogene",
so named because it is believed to be a remnant of a real gene that
has suffered mutations and is no longer functional. Pseudogenes
may have arisen through the duplication of a functional gene, followed
by inactivation of one of the copies. Comparing the presence or
absence of pseudogenes is one method used by evolutionary geneticists to
group species and to determine relatedness. Thus, these sequences are
thought to carry a record of our evolutionary history.
How Many Genes Do Humans Have?
In February 2001, two largely independent draft versions
of the human genome were published. Both studies estimated that
there are 30,000 to 40,000 genes in the human genome, roughly one-third
the number of previous estimates. More recently scientists estimated that
there are less than 30,000 human genes. However, we still have to
make guesses at the actual number of genes, because not all of the human
genome sequence is annotated and not all of the known sequence has
been assigned a particular position in the genome.
So, how do scientists estimate the number of genes in a genome?
For the most part, they look for tell-tale signs of genes in a DNA
sequence. These include: open reading frames, stretches of
DNA, usually greater than 100 bases, that are not interrupted by
a stop codon such as TAA, TAG or TGA; start codons
such as ATG; specific sequences found at splice junctions, a
location in the DNA sequence where RNA removes the non-coding areas
to form a continuous gene transcript for translation into a protein;
and gene regulatory sequences. This process is dependent
on computer programs that search for these patterns in various sequence
databases and then make predictions about the existence of a gene.
From One Gene–One Protein to a More Global Perspective
Only a small percentage of the 3 billion bases in the human genome
becomes an expressed gene product. However, of the approximately
1 percent of our genome that is expressed, 40 percent is alternatively
spliced to produce multiple proteins from a single gene. Alternative
splicing refers to the cutting and pasting of the primary mRNA
transcript into various combinations of mature mRNA. Therefore the one
gene–one protein theory, originally framed as "one gene–one enzyme",
does not precisely hold.
With so much DNA in the genome, why restrict transcription to a
tiny portion, and why make that tiny portion work overtime to produce
many alternate transcripts? This process may have evolved as a way
to limit the deleterious effects of mutations. Genetic mutations
occur randomly, and the effect of a small number of mutations on
a single gene may be minimal. However, an individual having many
genes each with small changes could weaken the individual, and thus
the species. On the other hand, if a single mutation affects several
alternate transcripts at once, it is more likely that the effect
will be devastating—the individual may not survive to contribute
to the next generation. Thus, alternate transcripts from a single
gene could reduce the chances that a mutated gene is transmitted.
Gene Switching: Turning Genes On and Off
The estimated number of genes for humans, less than 30,000,
is not so different from the 25,300 known genes of Arabidopsis
thaliana, commonly called mustard grass. Yet, we appear, at
least at first glance, to be a far more complex organism. A person
may wonder how this increased complexity is achieved. One answer
lies in the regulatory system that turns genes on and off. This
system also precisely controls the amount of a gene product that
is produced and can further modify the product after it is made.
This exquisite control requires multiple regulatory input points.
One very efficient point occurs at transcription, such that an mRNA
is produced only when a gene product is needed. Cells also regulate
gene expression by post-transcriptional modification; by allowing
only a subset of the mRNAs to go on to translation; or by restricting
translation of specific mRNAs to only when the product is needed.
At other levels, cells regulate gene expression through DNA folding,
chemical modification of the nucleotide bases, and intricate
"feedback mechanisms" in which some of the gene's own
protein product directs the cell to cease further protein production.
Promoters and Regulatory Sequences
Transcription is the process whereby RNA is made from DNA. It is
initiated when an enzyme, RNA polymerase, binds to a site on
the DNA called a promoter sequence. In most cases, the
polymerase is aided by a group of proteins called "transcription
factors" that perform specialized functions, such as DNA sequence
recognition and regulation of the polymerase's enzyme activity. Other
regulatory sequences include activators, repressors, and
enhancers. These sequences can be cis-acting (affecting
genes that are adjacent to the sequence) or trans-acting
(affecting expression of the gene from a distant site), even on another chromosome.
Globin Genes: An Example of Transcriptional Regulation
An example of transcriptional control occurs in the family
of genes responsible for the production of globin. Globin
is the protein that complexes with the iron-containing heme
molecule to make hemoglobin. Hemoglobin transports oxygen
to our tissues via red blood cells. In the adult, red blood
cells do not contain DNA for making new globin; they are ready-made
with all of the hemoglobin they will need.
During the first few weeks of life, embryonic globin
is expressed in the yolk sac of the egg. By week five of gestation,
globin is expressed in early liver cells. By birth, red blood
cells are being produced, and globin is expressed in the bone
marrow. Yet, the globin found in the yolk is not produced from
the same gene as is the globin found in the liver or bone marrow
stem cells. In fact, at each stage of development, different
globin genes are turned on and off through a process of transcriptional
regulation called "switching".
To further complicate matters, globin is made from two
different protein chains: an alpha-like chain coded for on chromosome
16; and a beta-like chain coded for on chromosome 11. Each chromosome
has the embryonic, fetal, and adult form lined up on the chromosome
in a sequential order for developmental expression. The developmentally
regulated transcription of globin is controlled by a number
of cis-acting DNA sequences, and although there remains a lot
to be learned about the interaction of these sequences, one
known control sequence is an enhancer called the Locus Control
Region (LCR). The LCR sits far upstream on the sequence
and controls the alpha genes on chromosome 16. It may also interact
with other factors to determine which alpha gene is turned on.
Thalassemias are a group of diseases characterized
by the absence or decreased production of normal globin, and
thus hemoglobin, leading to decreased oxygen in the system.
There are alpha and beta thalassemias, defined by the defective
gene, and there are variations of each of these, depending on
whether the embryonic, fetal, or adult forms are affected and/or
expressed. Although there is no known cure for the thalassemias,
there are medical treatments that have been developed based
on our current understanding of both gene regulation and cell
differentiation. Treatments include blood transfusions, iron
chelators, and bone marrow transplants. With continuing research
in the areas of gene regulation and cell differentiation, new
and more effective treatments may soon be on the horizon, such
as the advent of gene transfer therapies.
The Influence of DNA Structure and Binding Domains
Sequences that are important in regulating transcription do not
necessarily code for transcription factors or other proteins. Transcription
can also be regulated by subtle variations in DNA structure and by chemical
changes in the bases to which transcription factors bind. As stated
previously, the chemical properties of the four DNA bases differ
slightly, providing each base with unique opportunities to chemically
react with other molecules. One chemical modification of DNA, called
methylation, involves the addition of a methyl group (-CH3).
Methylation frequently occurs at cytosine residues that are preceded
by guanine bases, oftentimes in the vicinity of promoter sequences.
The methylation status of DNA often correlates with its functional
activity, where inactive genes tend to be more heavily methylated.
This is because the methyl group serves to inhibit transcription
by attracting a protein that binds specifically to methylated DNA,
thereby interfering with polymerase binding. Methylation also plays
an important role in genomic imprinting, which occurs when
both maternal and paternal alleles are present but only one allele
is expressed while the other remains inactive. Another way to think
of genomic imprinting is as "parent of origin differences"
in the expression of inherited traits. Considerable intrigue surrounds
the effects of DNA methylation, and many researchers are working
to unlock the mystery behind this concept.
Translation is the process whereby the genetic code carried
by an mRNA directs the synthesis of proteins. Translational regulation
occurs through the binding of specific molecules, called repressor
proteins, to a sequence found on an RNA molecule. Repressor proteins
prevent a gene from being expressed. As we have just discussed, the default
state for a gene is that of being expressed via the recognition of its promoter by
RNA polymerase. Close to the promoter region is another cis-acting
site called the operator, the target for the repressor protein.
When the repressor protein binds to the operator, RNA polymerase
is prevented from initiating transcription, and gene expression is
Translational control plays a significant role in the process
of embryonic development and cell differentiation. Upon fertilization,
an egg cell begins to multiply to produce a ball of cells that are
all the same. At some point, however, these cells begin to differentiate,
or change into specific cell types. Some will become blood cells
or kidney cells, whereas others may become nerve or brain cells. When
all of the cells formed are alike, the same genes are turned on.
However, once differentiation begins, various genes in different
cells must become active to meet the needs of that cell type. In
some organisms, the egg houses store immature mRNAs that become
translationally active only after fertilization. Fertilization then
serves to trigger mechanisms that initiate the efficient translation
of mRNA into proteins. Similar mechanisms serve to activate mRNAs
at other stages of development and differentiation, such as when
specific protein products are needed.
Mechanisms of Genetic Variation and Heredity
Does Everyone Have the Same Genes?
When you look at the human species, you see evidence of a process
called genetic variation, that is, there are immediately
recognizable differences in human traits, such as hair and eye color,
skin pigment, and height. Then there are the not so obvious genetic
variations, such as blood type. These expressed, or phenotypic,
traits are attributable to genotypic variation in a person's
DNA sequence. When two individuals display different phenotypes of the
same trait, they are said to have two different alleles for the
same gene. This means that the gene's sequence is slightly different
in the two individuals, and the gene is said to be polymorphic,
"poly" meaning many and "morph" meaning
shape or form. Therefore, although people generally have the same genes,
the genes do not have exactly the same DNA sequence. These polymorphic sites
influence gene expression and also serve as markers for genomic research
|The cell cycle is the
process that a cell undergoes to replicate.
Most genetic variation occurs during the phases of the
cell cycle when DNA is duplicated. Mutations in the new DNA strand
can manifest as base substitutions, such as when a single
base gets replaced with another; deletions, where one or
more bases are left out; or insertions, where one or more
bases are added. Mutations can either be synonymous, in which the
variation still results in a codon for the same amino acid or non-synonymous,
in which the variation results in a codon for a different amino acid. Mutations
can also cause a frame shift, which occurs when the variation
bumps the reference point for reading the genetic code down a base
or two and results in loss of part, or sometimes all, of that gene
product. DNA mutations can also be introduced by toxic chemicals
and, particularly in skin cells, exposure to ultraviolet radiation.
|The manner in which a cell replicates
differs with the various classes of life forms, as well as with
the end purpose of the cell replication. Cells that compose
tissues in multicellular organisms typically replicate by organized
duplication and spatial separation of their cellular genetic
material, a process called mitosis. Meiosis is
the mode of cell replication for the formation of sperm and
egg cells in plants, animals, and many other multicellular life
forms. Meiosis differs significantly from mitosis in that the
cellular progeny have their complement of genetic material reduced
to half that of the parent cell.
|Mutations that occur in somatic cells—any cell in
the body except gametes and their precursors—will not be passed on
to the next generation. This does not mean, however, that somatic
cell mutations, sometimes called acquired mutations, are benign.
For example, as your skin cells prepare to divide and produce new
skin cells, errors may be inadvertently introduced when the DNA is
duplicated, resulting in a daughter cell that contains the error.
Although most defective cells die quickly, some can persist and may
even become cancerous if the mutation affects the ability to regulate
Mutations and the Next Generation
There are two places where mutations can be introduced and carried
into the next generation. In the first stages of development, a
sperm cell and egg cell fuse. They then begin to divide, giving
rise to cells that differentiate into tissue-specific cell types.
One early type of differentiated cell is the germ line cell, which
may ultimately develop into mature gametes. If a mutation occurs
in the developing germ line cell, it may persist until that individual
reaches reproductive age. Now the mutation has the potential to
be passed on to the next generation.
Mutations may also be introduced during meiosis, the mode of
cell replication for the formation of sperm and egg cells. In this case,
the germ line cell is healthy, and the mutation is introduced during
the actual process of gamete replication. Once again, the
sperm or egg will contain the mutation, and during the reproductive
process, this mutation may then be passed on to the offspring.
One should bear in mind that not all mutations are bad.
Mutations also provide a species with the opportunity to adapt to
new environments, as well as to protect a species from new pathogens.
Mutations are what lie behind the popular saying of "survival
of the fittest", the basic theory of evolution proposed
by Charles Darwin in 1859. This theory proposes that as new environments
arise, individuals carrying certain mutations that enable an evolutionary
advantage will survive to pass this mutation on to its offspring.
It does not suggest that a mutation is derived from the environment,
but that survival in that environment is enhanced by a particular
mutation. Some genes, and even some organisms, have evolved to tolerate
mutations better than others. For example, some viral genes are
known to have high mutation rates. Mutations serve the virus well
by enabling adaptive traits, such as changes in the outer protein coat
so that it can escape detection and thereby destruction by the host's
immune system. Viruses also produce certain enzymes that are necessary
for infection of a host cell. A mutation within such an enzyme may
result in a new form that still allows the virus to infect its host
but that is no longer blocked by an anti-viral drug. This will allow
the virus to propagate freely in its environment.
Mendel's Laws—How We Inherit Our Genes
In 1866, Gregor Mendel studied the transmission
of seven different pea traits by carefully test-crossing many
distinct varieties of peas. Studying garden peas might seem trivial
to those of us who live in a modern world of cloned sheep and
gene transfer, but Mendel's simple approach led to fundamental insights
into genetic inheritance, known today as Mendel's Laws. Mendel
did not actually know or understand the cellular mechanisms that
produced the results he observed. Nonetheless, he correctly surmised
the behavior of traits and the mathematical predictions of their
transmission, the independent segregation of alleles during gamete
production, and the independent assortment of genes. Perhaps as
amazing as Mendel's discoveries was the fact that his work was largely
ignored by the scientific community for over 30 years!
Principles of Genetic Inheritance
Law of Segregation: Each of the two inherited
factors (alleles) possessed by the parent will segregate and
pass into separate gametes (eggs or sperm) during meiosis, which
will each carry only one of the factors.
Law of Independent Assortment: In the gametes,
alleles of one gene separate independently of those of another
gene, and thus all possible combinations of alleles are equally
Law of Dominance: Each trait is determined by
two factors (alleles), inherited one from each parent. These
factors each exhibit a characteristic dominant, co-dominant,
or recessive expression, and those that are dominant will mask
the expression of those that are recessive.
How Does Inheritance Work?
Our discussion here is restricted to sexually reproducing organisms
where each gene in an individual is represented by two copies, called
alleles—one on each chromosome pair. There may be more than
two alleles, or variants, for a given gene in a population,
but only two alleles can be found in an individual. Therefore, the
probability that a particular allele will be inherited is 50:50,
that is, alleles randomly and independently segregate into daughter
cells, although there are some exceptions to this rule.
The term diploid describes a state in which a cell has two
sets of homologous chromosomes, or two chromosomes that are the
same. The maturation of germ line stem cells into gametes requires
the diploid number of each chromosome be reduced by half. Hence,
gametes are said to be haploid—having only a single set
of homologous chromosomes. This reduction is accomplished through
a process called meiosis, where one chromosome in a diploid pair
is sent to each daughter gamete. Human gametes, therefore, contain
23 chromosomes, half the number of somatic cells—all the other
cells of the body.
Because the chromosome in one pair separates independently of all
other chromosomes, each new gamete has the potential for a totally
new combination of chromosomes. In humans, the independent segregation
of the 23 chromosomes can lead to as many as 16 to 17 million different
combinations in one individual's gametes. Only one of these gametes
will combine with one of the nearly 17 million possible combinations
from the other parent, generating a staggering potential for individual
variation. Yet, this is just the beginning. Even more variation
is possible when you consider the recombination between sections
of chromosomes during meiosis as well as the random mutation that
can occur during DNA replication. With such a range of possibilities,
it is amazing that siblings look so much alike!
Expression of Inherited Genes
Gene expression, as reflected in an organism's phenotype, is based
on conditions specific for each copy of a gene. As we just discussed,
for every human gene there are two copies, and for every gene there
can be several variants or alleles. If both alleles are the same,
the gene is said to be homozygous. If the alleles are different,
they are said to be heterozygous. For some alleles, their
influence on phenotype takes precedence over all other alleles.
For others, expression depends on whether the gene appears in the
homozygous or heterozygous state. Still other phenotypic traits
are a combination of several alleles from several different genes.
Determining the allelic condition used to be accomplished solely
through the analysis of pedigrees, much the way Mendel carried out
his experiments on peas. However, this method can leave many questions
unanswered, particularly for traits that are a result of the interaction
between several different genes. Today, molecular genetic techniques
exist that can assist researchers in tracking the transmission of
traits by pinpointing the location of individual genes, identifying
allelic variants, and identifying those traits that are caused by
Nature of Alleles
A dominant allele is an allele that is almost
always expressed, even if only one copy is present. Dominant
alleles express their phenotype even when paired with a different
allele, that is, when heterozygous. In this case, the phenotype
appears the same in both the heterozygous and homozygous states.
Just how the dominant allele overshadows the other allele depends
on the gene, but in some cases the dominant gene produces a
gene product that the other allele does not. Well-known dominant
alleles occur in the human genes for Huntington disease, a form
of dwarfism called achondroplasia, and polydactylism (extra
fingers and toes).
On the other hand, a recessive allele will be
expressed only if there are two identical copies of that allele,
or for a male, if one copy is present on the X chromosome. The
phenotype of a recessive allele is only seen when both alleles
are the same. When an individual has one dominant allele and
one recessive allele, the trait is not expressed because it
is overshadowed by the dominant allele. The individual is said
to be a carrier for that trait. Examples of recessive disorders
in humans include sickle cell anemia, Tay-Sachs disease, and
A particularly important category of genetic linkage
has to do with the X and Y sex chromosomes. These chromosomes
not only carry the genes that determine male and female traits,
but also those for some other characteristics as well. Genes
that are carried by either sex chromosome are said to be sex
linked. Men normally have an X and a Y combination of sex chromosomes,
whereas women have two X's. Because only men inherit Y chromosomes,
they are the only ones to inherit Y-linked traits. Both
men and women can have X-linked traits because both inherit
X-linked traits not related to feminine body
characteristics are primarily expressed in the phenotype of
men. This is because men have only one X chromosome.
Subsequently, genes on that chromosome that do not code for
gender are expressed in the male phenotype, even if they are
recessive. In women, a recessive allele on one X chromosome
is often masked in their phenotype by a dominant normal allele
on the other. This explains why women are frequently carriers
of X-linked traits but more rarely have them expressed in their
own phenotypes. In humans, at least 320 genes are X-linked.
These include the genes for hemophilia, red–green
color blindness, and congenital night blindness.
There are at least a dozen Y-linked genes, in addition to those
that code for masculine physical traits.
|It is now known that one of the
X chromosomes in the cells of human females is completely,
or mostly, inactivated early in embryonic life. This is
a normal self-preservation action to prevent a potentially
harmful double dose of genes. Recent research points to
the "Xist" gene on the X chromosome as being responsible
for a sequence of events that silences one of the X chromosomes
in women. The inactivated X chromosomes become highly
compacted structures known as Barr bodies. The
presence of Barr bodies has been used at international
sport competitions as a test to determine whether an athlete
is a male or a female.
Exceptions to Mendel's Laws
There are many examples of inheritance that appear to be exceptions
to Mendel's laws. Usually, they turn out to represent complex interactions
among various allelic conditions. For example, co-dominant alleles
both contribute to a phenotype. Neither is dominant over the other.
Control of the human blood group system provides a good example
of co-dominant alleles.
Four Basic Blood Types
There are four basic blood types, and they
are O, A, B, and AB. We know that our blood type is determined
by the "alleles" that we inherit from our parents. For the blood
type gene, there are three basic blood type alleles: A, B, and
O. We all have two alleles, one inherited from each parent.
The possible combinations of the three alleles are OO, AO,
BO, AB, AA, and BB. Blood types A and B are "co-dominant" alleles,
whereas O is "recessive". A codominant allele is apparent
even if only one is present; a recessive allele is apparent
only if two recessive alleles are present. Because blood type
O is recessive, it is not apparent if the person inherits an
A or B allele along with it. So, the possible allele combinations
result in a particular blood type in this way:
OO = blood type O
AO = blood type A
BO = blood type B
AB = blood type AB
AA = blood type A
BB = blood type B
You can see that a person with blood type
B may have a B and an O allele, or they may have two B alleles.
If both parents are blood type B and both have a B and a recessive
O, then their children will either be BB, BO, or OO. If the
child is BB or BO, they have blood type B. If the child is OO,
he or she will have blood type O.
Pleiotropism, or pleotrophy, refers to the phenomenon
in which a single gene is responsible for producing multiple, distinct,
and apparently unrelated phenotypic traits, that is, an individual
can exhibit many different phenotypic outcomes. This is because
the gene product is active in many places in the body. An example
is Marfan's syndrome, where there is a defect in the gene coding
for a connective tissue protein. Individuals with Marfan's syndrome
exhibit abnormalities in their eyes, skeletal system, and cardiovascular
Some genes mask the expression of other genes just as a fully
dominant allele masks the expression of its recessive counterpart.
A gene that masks the phenotypic effect of another gene is called
an epistatic gene; the gene it subordinates is the hypostatic
gene. The gene for albinism in humans is an epistatic
gene. It is not part of the interacting skin-color genes. Rather,
its dominant allele is necessary for the development of any skin
pigment, and its recessive homozygous state results in the albino
condition, regardless of how many other pigment genes may be present.
Because of the effects of an epistatic gene, some individuals who
inherit the dominant, disease-causing gene show only partial symptoms
of the disease. Some, in fact, may show no expression of the disease-causing
gene, a condition referred to as nonpenetrance. The individual
in whom such a nonpenetrant mutant gene exists will be phenotypically
normal but still capable of passing the deleterious gene on to offspring,
who may exhibit the full-blown disease.
Then we have traits that are multigenic, that is, they
result from the expression of several different genes. This is true
for human eye color, in which at least three different genes are
responsible for determining eye color. A brown/blue gene and a central
brown gene are both found on chromosome 15, whereas a green/blue gene
is found on chromosome 19. The interaction between these genes is
not well understood. It is speculated that there may be other genes
that control other factors, such as the amount of pigment deposited
in the iris. This multigenic system explains why two blue-eyed individuals
can have a brown-eyed child.
Speaking of eye color, have you ever seen someone with one
green eye and one brown eye? In this case, somatic mosaicism
may be the culprit. This is probably easier to describe than explain.
In multicellular organisms, every cell in the adult is ultimately
derived from the single-cell fertilized egg. Therefore, every cell
in the adult normally carries the same genetic information. However,
what would happen if a mutation occurred in only one cell at the
two-cell stage of development? Then the adult would be composed
of two types of cells: cells with the mutation and cells without.
If a mutation affecting melanin production occurred in one of the
cells in the cell lineage of one eye but not the other, then the
eyes would have different genetic potential for melanin synthesis.
This could produce eyes of two different colors.
Penetrance refers to the degree to which a particular
allele is expressed in a population phenotype. If every individual
carrying a dominant mutant gene demonstrates the mutant phenotype,
the gene is said to show complete penetrance.
Molecular Genetics: The Study of Heredity, Genes, and DNA
As we have just learned, DNA provides a blueprint that directs
all cellular activities and specifies the developmental plan of
multicellular organisms. Therefore, an understanding of DNA, gene
structure, and function is fundamental for an appreciation of the
molecular biology of the cell. Yet, it is important to recognize
that progress in any scientific field depends on the availability
of experimental tools that allow researchers to make new scientific
observations and conduct novel experiments. The last
section of the genetic primer concludes with a discussion of
some of the laboratory tools and technologies that allow researchers
to study cells and their DNA.
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| Revised: March 31, 2004.