Mutations, DNA Repair, and Recombination

Question 1

What types of mutations are transitions and transversions?

Answer 1

Substitutions

Question 2

What is a transition?

Answer 2

A base substitution where a purine changes to a purine or a pyrimidine changes for a pyrimidine.

Question 3

What is a transversion?

Answer 3

A base substitution when a purine changes to a pyrimidine or vice versa.

Question 4

What is a mutation?

Answer 4

A heritable change in DNA sequence which can either be somatic or germline.

Question 5

Which one is always larger, the forward mutation rate or the reverse mutation rate?

Answer 5

The forward mutation rate (there are many paths to mutation but only a single path to reversion).

Question 6

What is the fluctuation test?

Answer 6

A test to determine whether mutations for bacterial resistance arose in response to bacteriophages or were random (spontaneous mutations that occurred prior to exposure). Since surviving colonies had very diverse population sizes, fluctuation test determined mutations were spontaneous.

Question 7

What are the five types of naturally occurring spontaneous DNA damage?

Answer 7

Depurination, deamination, x-ray double stranded breaks, UV light producing thymine dimers, and oxidation.

Question 8

What is depurination?

Answer 8

When the hydrolysis of water causes a purine nucleotide to detach from the DNA strand, leaving the strand with an unspecified base. This causes a mutation 3/4 of the time (1/4 chance for correct base).

Question 9

What is deamination?

Answer 9

When the amine group of a pyrimidine detaches, changing its identity. Most commonly, the deamination of cytosine to uracil (C to U) results in a DNA change of CG to AT.

Question 10

How do x-rays cause double stranded breaks?

Answer 10

The X-rays break the DNA backbone, splitting it in half. These DNA fragments may be ligated back together improperly leading to a mutation.

Question 11

What are thymine dimers?

Answer 11

UV light causes adjacent Ts to form thymine dimers that lead to substitutions when DNA is replicated.

Question 12

How does oxidation result in DNA damage?

Answer 12

The oxidation of G to 8-oxodG by a an active oxygen species (free radical oxygen) causes 8-oxodG to pair with Adenine.

Question 13

What is the result of strand slippage during DNA replication?

Answer 13

Small insertions or deletions.

Question 14

If the daughter strand slips, does it result in an insertion or deletion?

Answer 14

Insertion.

Question 15

If the parent strand slips, does it result in an insertion or deletion?

Answer 15

Deletion.

Question 16

Does unequal crossing over result in a mutation?

Answer 16

Yes, one chromosome will have a duplicated section while the other will have a deleted section.

Question 17

What are transposable elements?

Answer 17

A DNA sequence which, upon being replicated, can move to other locations in the genome, resulting in a mutation.

Question 18

What are tautomers?

Answer 18

Isomers of a compound that readily interconvert.

Question 19

How does tautomerization lead to mutation?

Answer 19

Rare base tautomers do not pair correctly. For example, the rare enol form of thymine pairs with guanine. The tautomers always pair purine to pyrimidine (like A with C, not A with G).

Question 20

How did Muller prove mutagens can be used to increase mutation?

Answer 20

Crossed bar eyed females to males who had been exposed to X-rays. Some of the offspring were bar eyed females, but all of these females carried a mutated X allele from the father. When these females were crossed to normal males, all male offspring were bar eyed, indicating a single mutated X allele as lethal (recessive lethal).

Question 21

What is a mutagen?

Answer 21

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

Question 22

What are base analogs?

Answer 22

Chemicals that are similar in structure to normal nitrogenous bases, but may have tautomeric forms that lead to improper base pairing.

Question 23

Are base analogs mutagens?

Answer 23

Yes, they increase the frequency of mutations above the spontaneous rate.

Question 24

What are hydroxylating agents?

Answer 24

These agents add a hydroxyl group to bases, causing them to pair improperly.

Question 25

What are alkylating agents?

Answer 25

These agents add an alkyl group (either a methyl or ethyl), causing improper base pairing.

Question 26

What are deaminating agents?

Answer 26

These agents remove amine groups, leading to improper base pairing.

Question 27

What are intercalators / intercalating agents?

Answer 27

Flat molecules that can sandwich themselves between successive base pairs, disrupting the machinery for replication and causing deletions or insertions of a base pair.

Question 28

What is the Ames test?

Answer 28

A test used to determine whether a compound is a mutagen. Histadine negative bacteria are grown with rat liver enzymes in media without histadine. One group is exposed to a potential mutagen, the other is not. If the bacteria begin to grow in the colony exposed to the potential mutagen, it is a mutagen.

Question 29

What is direct repair of damaged bases?

Answer 29

DNA repair that eliminates damage using chemical reversion that does not require a nucleotide template, breakage of the DNA backbone, or DNA replication.

Question 30

What are alkyltransferase enzymes?

Answer 30

Enzymes that remove mistakenly added akyl groups to bases, a form of direct repair.

Question 31

What is photolyase?

Answer 31

An enzyme not present in humans that recognizes thymine dimers and reverses the damage by splitting the chemical linkage between the thymines.

Question 32

What are the 5 steps in base excision repair?

Answer 32

1. Glycosylase removes damaged base, leaving an apuryinic or apyrimidinic site (AP).
2. Endonuclease creates a nick in the backbone at the AP site.
3. Exonuclease removes nucleotides near the nick.
4. DNA polymerase synthesizes new DNA to fill in the gap.
5. DNA ligase seals the nick.

Question 33

What is the difference between nucleotide excision repair and base excision repair?

Answer 33

Nucleotide excision repair occurs in cells that lack the DNA glycosylase needed for base excision repair.

Question 34

How does nucleotide excision repair work?

Answer 34

Proteins will nick a stretch of DNA at both ends, causing the fragment to be released from the DNA. DNA polymerase and ligase fill in and seal the gap.

Question 35

How does DNA polymerase proofread?

Answer 35

As DNA polymerase synthesizes new strands of DNA, if it mistakenly adds an incorrect nucleotide at the 3’ end, exonuclease activity will remove that nucleotide, giving DNA polymerase another chance to add the correct one.

Question 36

How does mistmatch repair work in prokaryotes?

Answer 36

After DNA replication, proteins recognize mistmatched bases due to the kink in DNA they create. Using the methylated GATC sequences to identify the parent strand, another protein nicks the daughter strand before an exonuclease removes all nucleotides from the nick to a location just beyond the mismatch. DNA polymerase and ligase then resynthesize and seal the DNA. Enzymes then methylate GATC sequences of the daughter strand.

Question 37

What are two mechanisms of double-stranded DNA repair?

Answer 37

Non-homologous end joining, and homologous end joining.

Question 38

What is non-homologous end joining?

Answer 38

Following a double strand break, proteins bind to both sides of the breakage, bridging the two ends and allowing DNA ligase to join them together.

Question 39

What is SOS repair?

Answer 39

SOS repair is an emergency repair mechanism whereby error-prone DNA polymerases are attracted to replication forks that have become stalled at sides of unrepaired, damaged nucleotides. There, the error-prone polymerases add random nucleotides to the strand being synthesized opposite the damaged bases. This allows cells with damaged DNA to divide, but it is highly mutagenic (3/4 chance each added base pair).

Question 40

What process does homologous recombination mirror?

Answer 40

Meiotic recombination of homologous chromosomes.

Question 41

What are Holliday junctions?

Answer 41

X-shaped structures formed by two non-sister chromatid DNA strands overlapping during homologous recombination.

Question 42

What is a heteroduplex?

Answer 42

It forms when two non-sister chromatid DNA strands hydrogen bond to each other.