Mutations are changes in DNA that can occur for various reasons and have different effects. A single mutation can range from having no observable effect to causing serious genetic disorders. The document examines mutations at the molecular, cellular, organismal, and evolutionary levels through examples like sickle cell anemia. It describes the random nature of mutations and how an experiment by Esther and Joshua Lederberg provided evidence that antibiotic resistance arises from pre-existing mutations rather than being induced by antibiotic exposure.

1. DNA: The molecular basis of mutations
Since mutations are simply changes in DNA, in order to understand how mutations work, you
need to understand how DNA does its job. Your DNA contains a set of instructions for
"building" a human. These instructions are inscribed in the structure of the DNA molecule
through a genetic code. It works like this:
DNA is made of a long sequence of smaller units strung
together. There are four basic types of unit: A, T, G, and C.
These letters represents the type of base each unit carries:
adenine, thymine, guanine, and cytosine.
The sequence of these bases encodes instructions. Some parts
of your DNA are control centers for turning genes on and off,
some parts have no function, and some parts have a function
that we don't understand yet. Other parts of your DNA are
genes that carry the instructions for making proteins — which
are long chains of amino acids. These proteins help build an
organism.
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2. Protein-coding DNA can be divided into codons — sets of three
bases that specify an amino acid or signal the end of the protein.
Codons are identified by the bases that make them up — in the
example at right, GCA, for guanine, cytosine, and adenine. The
cellular machinery uses these instructions to assemble a string of
corresponding amino acids (one amino acid for each three bases)
that form a protein. The amino acid that corresponds to "GCA" is
called alanine; there are twenty different amino acids synthesized
this way in humans. "Stop" codons signify the end of the newly
built protein.
After the protein is built based on the sequence of bases in the gene, the completed protein is
released to do its job in the cell.
Types of mutations
There are many different ways that DNA can be changed, resulting in different types of
mutation. Here is a quick summary of a few of these:
Substitution
A substitution is a mutation that exchanges one base for another (i.e., a
change in a single "chemical letter" such as switching an A to a G).
Such a substitution could:
1. change a codon to one that encodes a different amino acid and
cause a small change in the protein produced. For
example, sickle cell anemia is caused by a substitution in the
beta-hemoglobin gene, which alters a single amino acid in the
protein produced.
2. change a codon to one that encodes the same amino acid and
causes no change in the protein produced. These are called silent
mutations.
3. change an amino-acid-coding codon to a single "stop" codon and
cause an incomplete protein. This can have serious effects since
the incomplete protein probably won't function.
Insertion
Insertions are mutations in which extra base pairs are inserted into a
new place in the DNA.
Deletion
Deletions are mutations in which a section of DNA is lost, or deleted.
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3. Frameshift
Since protein-coding DNA is divided into codons three bases long,
insertions and deletions can alter a gene so that its message is no longer
correctly parsed. These changes are called frameshifts.
For example, consider the sentence, "The fat cat sat." Each word
represents a codon. If we delete the first letter and parse the sentence in
the same way, it doesn't make sense.
In frameshifts, a similar error occurs at the DNA level, causing the
codons to be parsed incorrectly. This usually generates truncated
proteins that are as useless as "hef atc ats at" is uninformative.
There are other types of mutations as well, but this short list should give
you an idea of the possibilities.
The causes of mutations
Mutations happen for several reasons.
1. DNA fails to copy accurately
Most of the mutations that we think matter to evolution are "naturally-occurring." For example,
when a cell divides, it makes a copy of its DNA — and sometimes the copy is not quite perfect.
That small difference from the original DNA sequence is a mutation.
2. External influences can create mutations
Mutations can also be caused by exposure to specific chemicals or
radiation. These agents cause the DNA to break down. This is not
necessarily unnatural — even in the most isolated and pristine
environments, DNA breaks down. Nevertheless, when the cell repairs
the DNA, it might not do a perfect job of the repair. So the cell would
end up with DNA slightly different than the original DNA and hence,
a mutation.
The effects of mutations
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4. Since all cells in our body contain DNA, there are lots of places for
mutations to occur; however, some mutations cannot be passed on to
offspring and do not matter for evolution. Somatic mutations occur in non-
reproductive cells and won't be passed onto offspring. For example, the
golden color on half of this Red Delicious apple was caused by a somatic
mutation. Its seeds will not carry the mutation.
The only mutations that matter to large-scale evolution are those that can be passed on to
offspring. These occur in reproductive cells like eggs and sperm and are called germ line
mutations.
Effects of germ line mutations
A single germ line mutation can have a range of effects:
1. No change occurs in phenotype.
Some mutations don't have any noticeable effect on the
phenotype of an organism. This can happen in many situations:
perhaps the mutation occurs in a stretch of DNA with no
function, or perhaps the mutation occurs in a protein-coding
region, but ends up not affecting the amino acid sequence of
the protein.
2. Small change occurs in phenotype.
A single mutation caused this cat's ears to curl backwards
slightly.
3. Big change occurs in phenotype.
Some really important phenotypic changes, like DDT resistance
in insects are sometimes caused by single mutations. A single
mutation can also have strong negative effects for the organism.
Mutations that cause the death of an organism are called lethals
— and it doesn't get more negative than that.
Little mutations with big effects: Mutations to control genes
Mutations are often the victims of bad press — unfairly stereotyped as unimportant or as a cause
of genetic disease. While many mutations do indeed have small or negative effects, another sort
of mutation gets less airtime. Mutations to control genes can have major (and sometimes
positive) effects.
Some regions of DNA control other genes, determining when and where other genes are turned
"on". Mutations in these parts of the genome can substantially change the way the organism is
built. The difference between a mutation to a control gene and a mutation to a less powerful gene
is a bit like the difference between whispering an instruction to the trumpet player in an orchestra
versus whispering it to the orchestra's conductor. The impact of changing the conductor's
behavior is much bigger and more coordinated than changing the behavior of an individual
orchestra member. Similarly, a mutation in a gene "conductor" can cause a cascade of effects in
the behavior of genes under its control.
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5. Many organisms have powerful control genes that determine how the body is laid out. For
example, Hox genes are found in many animals (including flies and humans) and designate
where the head goes and which regions of the body grow appendages. Such master control genes
help direct the building of body "units," such as segments, limbs, and eyes. So evolving a major
change in basic body layout may not be so unlikely; it may simply require a change in a Hox
gene and the favor of natural selection.
Mutations to control genes can transform one body part into another. Scientists
have studied flies carrying Hox mutations that sprout legs on their foreheads
instead of antennae!
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6. A case study of the effects of mutation: Sickle cell anemia
Sickle cell anemia is a genetic disease with severe symptoms, including pain and anemia. The
disease is caused by a mutated version of the gene that helps make hemoglobin — a protein that
carries oxygen in red blood cells. People with two copies of the sickle cell gene have the disease.
People who carry only one copy of the sickle cell gene do not have the disease, but may pass the
gene on to their children.
The mutations that cause sickle cell anemia have been extensively studied and demonstrate how
the effects of mutations can be traced from the DNA level up to the level of the whole organism.
Consider someone carrying only one copy of the gene. She does not have the disease, but the
gene that she carries still affects her, her cells, and her proteins:
1. There are effects at the DNA level
2. There are effects at the protein level
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7. Normal hemoglobin (left) and hemoglobin in sickled red blood cells (right) look
different; the mutation in the DNA slightly changes the shape of the hemoglobin
molecule, allowing it to clump together.
3.
4. There are effects at the cellular level
When red blood cells carrying mutant hemoglobin are
deprived of oxygen, they become "sickle-shaped" instead
of the usual round shape (see picture). This shape can
sometimes interrupt blood flow.
5. There are negative effects at the whole organism level
Under conditions such as high elevation and intense
exercise, a carrier of the sickle cell allele may occasionally
show symptoms such as pain and fatigue.
6. There are positive effects at the whole organism level
Carriers of the sickle cell allele are resistant to malaria,
because the parasites that cause this disease are killed
inside sickle-shaped blood cells. Normal red blood
cells (top) and
This is a chain of causation. What happens at the DNA level sickle cells
propagates up to the level of the complete organism. This example (bottom)
illustrates how a single mutation can have a large effect, in this
case, both a positive and a negative one. But in many cases, evolutionary change is based on the
accumulation of many mutations, each having a small effect. Whether the mutations are large or
small, however, the same chain of causation applies: changes at the DNA level propagate up to
the phenotype.
Mutations are random
Mutations can be beneficial, neutral, or harmful for the organism, but mutations do not "try" to
supply what the organism "needs." Factors in the environment may influence the rate of mutation
but are not generally thought to influence the direction of mutation. For example, exposure to
harmful chemicals may increase the mutation rate, but will not cause more mutations that make
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8. the organism resistant to those chemicals. In this respect, mutations are random — whether a
particular mutation happens or not is unrelated to how useful that mutation would be.
For example, in the U.S. where people have access to shampoos with chemicals that kill lice, we
have a lot of lice that are resistant to those chemicals. There are two possible explanations for
this:
Hypothesis A: Hypothesis B:
Resistant strains of lice were Exposure to lice shampoo
always there — and are just actually caused mutations for
more frequent now because all resistance to the shampoo.
the non-resistant lice died a
sudsy death.
Scientists generally think that the first explanation is the right one and that directed mutations,
the second possible explanation relying on non-random mutation, is not correct.
Researchers have performed many experiments in this area. Though results can be interpreted in
several ways, none unambiguously support directed mutation. Nevertheless, scientists are still
doing research that provides evidence relevant to this issue.
In addition, experiments have made it clear that many mutations are in fact random, and did not
occur because the organism was placed in a situation where the mutation would be useful. For
example, if you expose bacteria to an antibiotic, you will likely observe an increased prevalence
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9. of antibiotic resistance. Esther and Joshua Lederberg determined that many of these mutations
for antibiotic resistance existed in the population even before the population was exposed to the
antibiotic — and that exposure to the antibiotic did not cause those new resistant mutants to
appear.
The Lederberg experiment
In 1952, Esther and Joshua Lederberg performed an experiment that helped show that many
mutations are random, not directed. In this experiment, they capitalized on the ease with which
bacteria can be grown and maintained. Bacteria grow into isolated colonies on plates. These
colonies can be reproduced from an original plate to new plates by "stamping" the original plate
with a cloth and then stamping empty plates with the same cloth. Bacteria from each colony are
picked up on the cloth and then deposited on the new plates by the cloth.
Esther and Joshua hypothesized that antibiotic resistant strains of bacteria surviving an
application of antibiotics had the resistance before their exposure to the antibiotics, not as a result
of the exposure. Their experimental set-up is summarized below:
1. Bacteria are spread out on a plate, called the "original plate."
2. They are allowed to grow into several different colonies.
3. This layout of colonies is stamped from the original plate onto a new plate
that contains the antibiotic penicillin.
4. Colonies X and Y on the stamped plate survive. They must carry a mutation
for penicillin resistance.
5. The Lederbergs set out to answer the question, "did the colonies on the new
plate evolve antibiotic resistance because they were exposed to penicillin?"
The answer is no:
When the original plate is washed with penicillin, the same colonies (those in
position X and Y) live — even though these colonies on the original plate have
never encountered penicillin before.
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10. So the penicillin-resistant bacteria were there in the population before they encountered
penicillin. They did not evolve resistance in response to exposure to the antibiotic.
By Umerfarooq Dogar b.s botany university of gujrat
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