BIL 104 - Lecture 13

MUTATIONS: The Raw Material of Evolution

A MUTATION is defined as

the process by which a gene changes from one allele to another
the end result of that allelic change.

Major changes can take place with only a small rearrangement of base pairs on the DNA strand, either due to errors in DNA replication or from outside damage to the DNA.

Be sure you know the difference between adaptation and evolution!

Adaptation is short-term change (via gene expression) in response to environmental factors; it does not (usually) involve permanent genetic change. (Caution: recall epigenesis!)

Organic Evolution is a shift in allele frequencies in a population (microevolution) which can ultimately lead to speciation (macroevolution) under certain circumstances.

Individuals ADAPT. (They do not evolve.)
Populations EVOLVE.

Only evolution involves overall change in allele frequencies and genetic composition of the main unit of evolution: the population.

Key ideas:

mutations can occur "spontaneously" due to errors in DNA replication or other "spontaneous" DNA damage.
mutations can also be induced by outside factors.
A mutagen is an agent which increases the frequency of mutagenesis (the generation of mutations), usually by changing the DNA. (note: a carcinogen is a mutagen which causes a carcinoma--a cancer of the epithelial tissues)

Also note that there's a big difference in the consequences of

SOMATIC (body cell) mutations
and
GERMLINE (reproductive cell) mutations.

Germline Mutations:

Mutations affecting the germ (spermatogonial or oogonial) cells are the only mutations with evolutionary consequences.

Somatic mutations:

Mutations that occur in the somatic cells may disrupt the function of that particular cell, causing it to die, or causing it to become cancerous (highly proliferative and nasty!).

Fortunately for us...

The cell has biological repair mechanisms which can restore the original configuration of DNA after mutation.
We know this because abnormal cells lacking certain repair systems have a higher than normal rate of mutation actually "showing up".

MUTATIONS CAN OCCUR AT SEVERAL LEVELS IN THE GENOME At the level of the DNA.

point mutation - change in a single base pair
base pair substitution - one entire base pair (across from each other on the complementary DNA strands) is replaced by another (AT-->GC or GC --> AT)

At level of the CHROMOSOME.

A piece of a chromosome may break off one chromosome and attach to a different chromosome (TRANSLOCATION MUTATION)
A piece of a chromosome may be accidentally duplicated during DNA replication (DUPLICATION MUTATION)
A piece of a chromosome may be accidentally deleted during DNA replication (DELETION MUTATION)

At the level of the HOMOLOGOUS CHROMOSOME PAIR.

a homologous pair may be missing entirely from a cell (NULLISOMY)
a homologous pair may be missing one member (MONOSOMY)
a homolgous pair may have one or more extra members (e.g., TRISOMY, in which there are three homologs instead of two.

At the level of the ENTIRE CHROMOSOME SET.

One entire set of chromosomes may end up missing from a cell (HAPLOIDY)
Extra complete sets of chromosomes may end up in a single cell (POLYPLOIDY)

All these different types of mutations have characteristic effects on phenotype.

Mutations at the DNA or the chromosome level will affect the actual DNA sequence, causing a change in protein during gene expression.
Mutations at the level of the homologous pair or entire chromosome set will not change the form of the proteins made, but the proportions of gene products will change (as in the case of nullisomy, monosomy, trisomy, etc.)
Mutations at the level of the entire chromosome set will not affect proteins made or the proportions of each gene product, but the total amount (not the relative proportions) of entire sets of gene products may change.

Mutations that affect phenotypic expression

Forward mutations: change in phenotype from wild type to mutant
Reverse mutations (= reversion mutations): change phenotype from mutant to wild type
also known as "reversions" or "back mutations".
- SUPPRESSOR MUTATION: A mutation which occurs at one DNA site that reverses or partially reverses the effects of a mutation at a completely different site. (Suppressor mutations at separate loci are said to occur in "SUPPRESSOR GENES.")

WHAT CAUSES MUTATIONS?

Mutations can be

INDUCED - produced by mutagens (either intentionally or unintentionally)

SPONTANEOUS - arising apparently in the absence of known mutagens.

Spontaneous mutations are obviously caused by something, but they are what could also be termed "natural" mutations, which occur at a relatively constant rate in natural situations due to naturally occuring mutagenesis.

INDUCED MUTATIONS can be caused by a variety of different mutagens, and many mutagens cause specific mutations at special DNA "hot spots."
These are useful in the laboratory.

CHEMICAL MUTAGENS

Here are a few types of chemical mutagens:

Base modifying agents - change the chemical structure of the nitrogenous bases (A, T, C and G), resulting in mispairing and other problems.
Base analogs can resemble nitrogenous bases (A, T, C and G) so closely that they replace them in the DNA molecule, but do not pair normally with other bases.
Base pair analogs - some chemicals are chemically similar to an entire nucleotide pair. These can act as intercalating agents, causing the insertion or deletion of an entire base pair (and hence, DNA replication errors, since the fit is not exact).

SHORT WAVELENGTH IONIZING RADIATION ionizing electromagnetic radiation: x rays, gamma rays

ionizing rays easily pass through the plasma membrane and into the cell where they are absorbed by intracellular molecules such as water.
electrons of the absorbing molecules are boosted to such a high energy state that they spin out of their orbitals and are lost.
the remaining particle (often a proton) is a positively charged FREE RADICAL which is highly unstable and highly reactive.
free radicals react energetically with anything nearby, from enzymes to RNA to DNA. Obviously, reactions with DNA are the most long-lasting (other reactions usually being more ephemeral in their effect).
ionizing radiation events such as these can also break the DNA across both backbones, effectively snapping it in half.
- Eukaryotes can repair damage like this during synapsis, when the homologs lie in close apposition and the DNA can be re-linked by repair mechanisms.
- Is meiosis the evolutionary result of a mechanism whose original benefit was to serve as a repair mechanism?)
  Who knows? But just to be on the safe side: EAT MORE FREE RADICAL SCAVENGERS!

ULTRAVIOLET RADIATION damage: Why repeated sun tanning can kill you

pyrimidine bases are highly sensitive to UV radiation; exposure of a pyrimidine to 1 quantum of UV can boost the energy level of the electrons, making them unstable and highly reactive.

If two pyrimidines are next door neighbors on the DNA strand, their disrupted electrons may share an orbital, forming a covalent bond.

The result: a dimer ("two part" in Greek) of that pyrimidine. (Thymine is particularly prone to form these in the presence of UV)

Thymine dimers prevent proper replication. The cell either dies or begins to divide erratically, forming a malignant tumor.

Fortunately for us (but not for the dermatologists), the cell has UV repair systems. Enzymes can either:

2. remove the faulty piece and use the complementary DNA strand as a template to fix the piece.

xeroderma pigmentosum: recessive disorder in which victims lack the normal UV repair enzymes. Result: even the slightest exposure to UV results in copious skin tumors. The following images are disturbing, and you need not view them if you do not wish to see them. However, they illustrate the magnitude of phenotypic effect caused by a simple error resulting in a non-functional repair enzyme.

Image 1 - skin lesions

Image 2 - condition progressed to carcinoma (cancer)

REPAIR MECHANISMS

Damage prevention - The cell has various enzymes that de-tox potential mutagens before they can act.
Damage reversal - the pyrimidine dimers mentioned previously can be excised and replaced with a normal pair.
Excision repair - a variety of enzymes can sense distortion of the DNA strand, and cooperate to excise the mistake and replace it with a correct DNA sequence.
Mismatch repair - This is responsible for about 90% of all DNA repair, usually due to mismatching during replication.
A mismatch repair system, enzymes encoded by a series of genes, zip along behind the replication fork, removing incorrect bases, and able to distinguish between the new and old strands because only the OLD strand is methylated.
The genes encoding these enzymes are called mut genes, which is short for "mutator" genes because when these genes mutate, it results in an unusually high level of mutation in the cell (due to faulty repair!).

SOMATIC VERSUS GERMLINE MUTATIONS

In animals, only germline mutations can be passed on to future generations. Somatic mutations can result in phenotypes from differing color patches to cancer.
In plants, protists and fungi, somatic mutations *can* be passed on, since these organisms exhibit INDETERMINATE GROWTH, and have tissues that can potentially develop into germinal cell lines throughout the life cycle.
What's the deal with mutations? Judging from what we see in the lab and in the field, the vast majority of unrepaired mutations are recessive. In homozygous condition, they are often maladaptive or lethal.

Some non-lethal mutations can be dominant over the wild type allele. These changes, known as GAIN-OF-FUNCTION MUTATIONS, can produce new phenotypes that are then subject to the same natural selection as any other allele. Some of these mutations could cause a disadvantage, such as this one:

Various types of mutation can be studies because of their effect on

Morphology (morphological mutations)
Viability (lethal mutations)
Biochemical pathways (biochemical mutations)
- Wild type bacteria are able to make their own leucine and adenine to use in constructing other substances.
- Mutation of the DNA locus controlling one enzyme in the leucine pathway will cause bacteria to fail to make leucine
- Mutation of the DNA locus controlling one enzyme in the adenine pathway will cause bacteria to fail to make adenine
- Bacterial strains exist that have one or both of these mutations.
- The scientist can isolate these strains by growing spots of bacteria ("lawns") on agar (a nutrient gel) with various additives, as explained in lecture.
Phenotype in combination with environmental conditions (conditional mutations)