Genetics (chap 5-7)

5: linkage, recombination, and mapping 6:DNA replication & recombination 7:MUTATION

Term for genes with one common allele

monomorphic

genes with several common alleles in natural populations

polymorphic

What does “wild-type” allele apply to clearly?

monomorphic genes- allele found in large majority of chromosomes in population

What is “wild-type” allele not clear with?

polymorphic genes- alleles with a frequency greater than one or “common variants”

What is a mutation that changes a wild-type allele of a gene to a different allele?

A forward mutation

How do geneticists diagram forward mutations?

A+ to a- when the mutation is recessive to the wild-type allele

b+ to B- when the mutation is dominant to the wild-type allele

Can mutations cause a mutant allele to revert back to wild type?

Yes, through reverse mutation or reversion

What is it called when a base at a certain position in one strand of DNA molecule is replaced by one of the other three bases?

substitution

How can substitutions be subdivided?

into transitions

What happens during transitions?

one puring (A/G) replaces the other purine or one pyrimidine (C/T) replaces the other pyrimidine

What are transversions?

When a purine (A/G) changes to a pyrimidine (T/C)

What happens when a deletion mutation happens?

A block of one or more nucleotide pairs is lost from a DNA milecule

What happens when an insertion mutation happens?

One or more nucleotide pairs is added

What are the sizes of deletions and insertions?

Can be as small as a single base pair or as large as megabases

What are point mutations?

Transitions, transversions, small deletions, and small insertions

What do point mutations alter?

one gene

How often do spontaneous mutations occur?

At a low rate

What is the average mutation rate per gene per gamete?

2-12×10^-6

What does the variation in the mutation rate of different genes in the organism reflect about the genes?

Their different sizes as well as the susceptibility of particular genes to various mechanisms that cause mutations

Do larger or smaller genes have a higher mutation rate?

Larger genes

How are mutation rates counted for bacteria?

Mutations per gene per cell division

How are mutation rates counted for multicellular eukaryotes?

Mutations per gene per gamete

Which rate of mutations per generation is higher?

Average rate of mutation per generation in multicellular eukaryotes

What drives multicellular eukaryotes cell mutations?

The numerous cell divisions that occur between the formation of a zygote and meiosis in the gonads of the organism

What is the rate of reverse mutation range from?

0 to 2.5×10^-6 per gene per gamete

Why does it make sense that the reversion rate is significantly lower than the rate of forward mutation?

Because there are many ways to disrupt gene function but there are only a few ways to restore function once it has been disrupted

Why can’t deletions be reverted?

Because DNA information that has disappeared from the genome cannot reappear spontaneously

Which parent are mutations inherited from 3 to 4 times more than the other?

The father

Why are there more mutations in sperm than the egg?

There are more rounds of cell division that are needed to produce human sperm

What is the fluctuation test?

When Salvador Luria and Max Delbruck tested if bacteria spontaneously mutated to have resistance by mixing colonies and antibiotics

What does replica plating verify?

That mutations are arising spontaneously

What kind of events initiate DNA alterations? (2)

DNA being damaged by chemical reactions/irridiation or mistakes happening when DNA is copied during replication

How do heritable mutations occur?

When DNA repair happens slower than DNA replication

What is depurination?

The hydrolysis of a purine (A/C) causing it to be released from the deoxyribose-phosphate backbone

What is deamination?

The removal of an amino (-NH2) group which changes C (cytosine) to U (uracil) which causes a transition after DNA replication since U pairs with A not G

What do X-rays break?

The sugar-phosphate backbone

What does radiation cause?

The adjacent thymine residues to become chemically linked into thymine dimers and oxidative damage to any of the four bases

What do polymerase molecules provide along with their polymerization function?

Proofreading/editing function

What part of the polymerase molecule recognizes a mispaired base and excises it?

The nuclease portion of the polymerase molecule called the 3’ to 5’ exonuclease

What is one reason why DNA polymerase may make mistakes?

The tautomerization of bases

What is tautomerization?

The interconversion of bases between two similar forms, or tautomers

How many tautomers do each of the four bases have?

two

What are tautomers?

similar chemical forms that interconvert continually

What are the categories of diseases caused by unstable trinucleotide repeats? (2)

polyQ diseases and non-polyQ diseases

What does the Q stand for in polyQ and non-polyQ?

For the amino acid glutamine

What is the repeated triplet in poly Q diseases?

Always CAG

What is the repeated triplet in non-poly Q diseases?

CGG, CTG, GCC, or GAA

What do polyQ diseases do?

Makes an abnormal protein that causes things like Huntington diseases

What do non-polyQ diseases do?

Produce either no protein or decreased protein amounts that causes things like fragile X syndrome

What are PolyQ disease alleles called? Why?

gain-of-function mutants because they specify proteins whose functions are qualitatively different from those of the corresponding wild-type protein. Usually show dominant inheritance and affects the nature of gene product

What are non-poly Q disease alleles called? Why?

loss-of-function alleles because they typically prevent protein production. affects the amount of gene product

What are pre-mutation alleles?

a normally functioning allele of an unstable trinucleotide repeat gene with a repeat region expanded to the point where further expansion to a disease allele occurs at high frequency

What is slipped mispairing?

When, during DNA replication, DNA polymerase pauses as it replicates through repeat region and alllows one DNA strabd to slip relative to the other

What does slipped mispairing cause?

trinucleotide repeat instability

What is a mutagen?

Any physical or chemical agent that raises the frequency of mutations above the spontaneous rate

What are base analogs?

mutagens that are so similar in chemical structure to the normal nitrogenous bases in DNA that the replication mechanism can incorporate them into DNA in place of the normal bases

What are intercalators?

Flat molecules that can sandwich themselves between succesive base pairs and disrupt the machinery for replication, generates deletions or insertions of a single base pair

How do you test for potential carcinogens?

Through the Ames test

How does the Ames test work?

by seeing if a particular chemical can induce Histidine+ revertants of special Histidine- mutant strains of the bacterium Salmonella typhimurium

Which can synthesize histidine: His+ or His-?

His+

What removes mistakingly added methyl or ethyl groups from guanine?

alkyltransferase

What reverses the damage cause by thymine dimers?

photolyase

How does photolyase work?

It splits the chemical linkage between the thymines, only works in visible light

What does photolyase associate with>

chromophore

What is photolyase’s mechanism called?

light repair or photorepair

What is homology-dependent repair?

When they remove a small region from the DNA strand that contains the altered nucleotide then uses the other strand as a template to resynthesize the region removed

What is base excision repair?

Starts by cleaving an altered nitrogenous base from the sugar of its nucleotide, releasing the base and creating an apurinic or apyrimidinic site in the DNA chain. Then it makes a nick in the DNA backbone at the AP site which allows an enzyme to attack the nick and remove nucleotides from their vicinity to create a gap in the previously damaged strand. It then fills in the gap by copying the undamaged strand and seals the backbone of the newly repaied DNA strand

What is a nick?

a cleaved phosphodiester bond in one DNA strand

What does DNA glycosylases do in base excision repair?

cleaves an altered nitrogenous base from the sugar of its nucleotide, releasing the base and creating an apurinic or apyrimidinic site in the DNA chain

What does AP endo nuclease do in base excision repair?

makes a nick in the DNA backbone at the AP site

What does DNA exonucleases do in base excision repair?

attack the nick and remove nucleotides from their vicinity to create a gap in the previously damaged strand.

What does DNA polymerase do in base excision repair?

fills in the gap by copying the undamaged strand

What does DNA ligase do in base excision repair?

seals the backbone of the newly repaied DNA strand

What does Nucleotide excision repair?

Removes alterations that base excision cannot repair becaise the cell lacks a DNA glycosylase that recognizes the problematic bases

What types of enzymes does nucleotide excision repair depend on?

Enzyme complexes containing more than one protein molecule

What enzymes are used for E. Coli in nucleotide excision repair?

Two out of three possible proteins: UvrA, UrvB, and UvrC

What does UvrA + UvrB do?

patrol the DNA for irregularities, detecting lesions that disrupt Watson-Crick base pairing and thus distort the double helix, such as thymine dimers that have not been correctedc by photorepair

What does UvrB + UvrC do?

cuts the damaged strand in two places that flank the damage. This double-cutting excises a short region of the damaged strand and leaves a gap that will be filled in by DNA polymerase and sealed with DNA ligase

What can repair double-strand breaks? (2)

Homologous recombination (HR) and nonhomologous end-joining (NHEJ)

What happens when a double-strand break doesn’t repair properly?

Point mutations, large deletions, and other kinds of chromosomal rearrangements

How does homologous recombination work?

It uses complementary base pairing to repair breaks accurately with no loss or gain of nucleotides

How does nonhomologous end-joining work?

It can bring together even DNA ends that were not previously adjacent to each other, and a few base pairs can be lost or added improperly in the process

What can homologous recombination use as the template for repair?

Either a homologous chromosome or (more often) a sister chromatid

What often happens when the homologous chromosome serves as the template?

mitotic recombination

Why doesn’t mitotic recombination happen when using sister chromatids during homologous recombination?

Because the template chromatid base-pair sequences are identical

When does homologous recombination happen?

G2

When does nonhomologous end joining happen?

G1

Which end can nonhomologous end joining join together?

it can join together any DNA ends that aren’t telomeres, even if those ends were not adjacent to each other in the genome originally

What could happen when using NHEJ if the genome suffers more than one double-strand break?

NHEJ can potentially join the wrong ends together, causing chromosome rearrangements such as inversions or large deletions. It can sometimes result in small changes to the DNA sequences where the broken ends are joined together

What is the backup repair system in bacteria?

methyl-directed mismatch repair