Chapter 19: Gene Mutation and DNA Repair

Double-strand breaks (DSBs) are repaired with homologous recombination repair (HRR) and nonhomologous end joining (NHEJ).

- HRR uses DNA sequence from a sister chromatid, restoring the original sequence - NHEJ connects the broken ends of DNA without replacing the original sequence, and is therefore a cause of deletions in chromosomes - NHEJ is quicker but error-prone, while HRR is limited to parts of the cell cycle when sister chromatids are present (The S and G2 phases of cell cycle).

Mismatch repair removes the mismatched segment from the newly made daughter strand.

- In E.coli this involves the use of the MutH, MutL, and MutS proteins - Since daughter strands are not methylated immediately, this can be used as a chemical indicator of which strand is the daughter strand, and thus contains the mismatch.

Direct repair of damaged bases is achieved by certain enzymes

- Photolyase in yeast can repair thymine dimmers - Alkyltransferase can remove ethyl or methyl groups resulting from the action of nitrogen mustards or EMS

position effect

- The gene may be moved next to new regulatory sequences. - The rearrangement may move the gene from euchromatin to heterochromatin.

DNA repair mechanisms are protein based, and usually involve several steps.

- The mutation must be recognized. - The mutation must be removed. - New DNA must be synthesized.

Translesion DNA polymerases assist replicative DNA polymerases to bypass damaged DNA.

- The replicative DNA polymerase stalls when it encounters a damaged base in the template DNA. - A translesion DNA polymerase instead insert available nucleotides over the damaged base, switching back to the replicative DNA polymerase. - Translesion DNA polymerases have a much lower fidelity, and are more likely to introduce incorrect bases into the DNA.

Base excision repair (BER) uses a category of enzymes called DNA-N-glycosylases.

- These enzymes recognize abnormal bases and cleave the bond between it and the sugar in the DNA backbone - A cut in the DNA is made by AP-endonuclease - In E. coli, DNA polymerase I replaces the abnormal region with normal nucleotides - In humans, either polymerase beta or polymerase / synthesizes the correct nucleotides, and Flap endonuclease removed the abnormal region for polymerase /

Mutation rate

- likelihood that a gene will be altered by a new mutation. - It is expressed as the number of new mutations in a given gene per generation.

(Comprehension Q) Which of the following does NOT cause a frameshift mutation? 5'-ATTTCGGGTTAA-3' TO 5'-ATTTCTAA-3' 5'-ATTTCGGGTAA-3' TO 5'-ATTTTTCGGGTAA-3' 5'-ATTTCGGGTTAA-3' TO 5'-ATTTGGTTAA-3' 5'-ATTTCGGGTTAA-3' TO 5'-ATTTAA-3'

5'-ATTTCGGGTTAA-3' TO 5'-ATTTAA-3'

A mutagen that is a base analog is

5-bromouracil

Which of the following is NOT due to a position effect? -A change in gene expression due to a down promoter mutation -Variegated eye color in a fruit fly -A change in gene expression due to an inversion -Inhibited gene expression due to translocation

A change in gene expression due to a down promoter mutation

Which of the following is NOT an example of a spontaneous mutation? A mutation caused by deamination A mutation caused by an error in DNA replication A mutation caused by depurination A mutation caused by UV light

A mutation caused by UV light

Which of the following is NOT an example of a spontaneous mutation? A mutation caused by depurination A mutation caused by deamination A mutation caused by an error in DNA replication A mutation caused by UV light

A mutation caused by UV light

Which of the following is NOT an example of an induced mutation? A mutation caused by UV light A mutation caused by an error in DNA replication A mutation caused by X-rays A mutation caused by a chemical agent in cigarette smoke

A mutation caused by an error in DNA replication

Which of the following is an example of a germline mutation? A mutation in an embryonic muscule cell A mutation in an egg cell A mutation in an adult liver cell A mutation in an adult skin cell

A mutation in an egg cell

up mutation

A mutation in the promoter sequence that increases the rate of mutation

(Comprehension Q) Depurination creates an apurinic (AP) site. If not repaired, it can cause a base substitution during DNA replication (see Fig. 19.7). Which of the following may repair AP sites prior to DNA replication? Non-homologous end joining photolyase Mismatch repair Base excision repair

Base excision repair

(Comprehension Q) Methylated cytosine bases tend to produce hotspots for spontaneous mutations. Which of the following mutations is typically observed at a C:G base pair in which the cytosine is methylated?

C:G > T:A

(Comprehension Q) For an Ames test, two different His- strains are available; one detects base substitutions (His-A) and the other frameshift mutations (His-B). After culturing these strains with ethyl methanesulfonate (EMS) separately, we plated cells on media lacking histidine. Which of the following correctly predicts the results from this experiment?

Compared to untreated control groups, the number of revertant colonies should be increased for His-A strain (base substitutions) but not for His-B strain (frameshift mutations).

What is the mechanism by which UV-rays induce mutations?

Creating thymine dimers

Which of the following enzymes recognizes abnormal base structures during base excision repair? the UvrA/UvrB complex photolyase MutS DNA N-glycosylases

DNA N-glycosylases

Which of the following enzyme is involved in the step that synthesizes a new DNA strand in base excision repair in bacteria? DNA polymerase I DNA polymerase beta DNA polymerase III DNA polymerase delta

DNA polymerase I

Which of the following enzyme is involved in the step that synthesizes a new DNA strand in base excision repair in bacteria? DNA polymerase I DNA polymerase beta DNA polymerase III DNA polymerase delta

DNA polymerase I

Which of the following enzymes works together with flap endonuclease in the step that synthesizes normal DNA during base excision repair in eukaryotes? DNA polymerase beta DNA polymerase I DNA polymerase III DNA polymerase delta

DNA polymerase delta

Base excision repair (BER) uses a category of enzymes called

DNA-N-glycosylases

Silent mutations

Have no effect on the amino acid sequence of the polypeptide

Nucleotide excision repair (NER) can repair thymine dimmers, chemically modified bases, missing bases, and some cross-links

In E. coli, the system utilizes four important proteins, UvrA, UvrB, UvrC, and UvrD. - In humans, several genetic diseases are the result of mutations in the NER system.Xeroderma pigmentosum, Cockayne syndrome.

Ames test

Indicates whether a compound is a mutagen. - This test examines the increase in mutations in the bacteria Salmonella typhimurium. - The test examines the rate of reversion of this mutation to wild-type by a suspected mutagen

Which of the following statements is incorrect about nonhomologous end joining (NHEJ)? Many bacteria lack or rarely use NHEJ to repair DNA double strand breaks. It is a highly accurate process, because two broken DNA ends are simply pieced back together.

It is a highly accurate process, because two broken DNA ends are simply pieced back together.

Which of the following statements is correct about homologous recombination repair (HRR)? - It primarily uses a homologous chromosome as a template to repair a DNA double strand break in the other homologous chromosome during the G1 phase of the cell cycle. - It primarily uses a homologous chromosome as a template to repair a DNA double strand break in the other homologous chromosome during the S and G2 phases of the cell cycle. - It primarily uses a sister chromatid as a template to repair a DNA double strand break in the other sister chromatid during the G1 phase of the cell cycle. - It primarily uses a sister chromatid as a template to repair a DNA double strand break in the other sister chromatid during the S and G2 phases of the cell cycle.

It primarily uses a sister chromatid as a template to repair a DNA double strand break in the other sister chromatid during the S and G2 phases of the cell cycle.

In DNA repair by nucleotide excision repair, which of the following is NOT one of the steps that occurs? Removing the strand that containing a lesion Joining two broken double strand DNA ends Sensing a DNA lesion Use of the opposite strand (without a lesion) as a template strand to synthesize a new DNA

Joining two broken double strand DNA ends

Which of the following DNA repair mechanisms primarily works after DNA replication? Nucleotide exicison repair Base excision repair Mismatch repair Non-homologous end joining

Mismatch repair

Which of the following enzymes recognizes base mismatches during mismatch repair? The UvrA/UvrB complex DNA N-glycosylases MutS MutH

MutS

DNA double-strand breaks are repaired by Photolyase NHEJ and HRR Nucleotide exicison repair Base excision repair

NHEJ and HRR

(Comprehension Q) Benzo[α]pyrene (BaP) is a major carcinogen (mutagen) in cigarette smoke. It creates a bulky guanine adduct. Which of the following DNA repair systems is likely to repair this type of DNA damage caused by Benzo[α]pyrene (BaP)? Nucleotide excision repair Mismatch repair photolyase Non-homologous end joining

Nucleotide excision repair

Which of the following enzymes recognizes thymine dimers during nucleotide excision repair? MutS The UvrA/UvrB complex DNA N-glycosylase Alkyltransferase

The UvrA/UvrB complex

Which of the following enzymes recognizes thymine dimers during nucleotide excision repair? The UvrA/UvrB complex DNA N-glycosylase MutS Alkyltransferase

The UvrA/UvrB complex

When human individuals are deficient for nucleotide excision repair, which of the following would best describe the symptoms of these individuals? Their cells are unable to repair thymine dimers induced by the sunlight, and many of them die with skin cancer before 40 years of age. Their cells are unable to repair base mismatches, so they are at a high risk of developing colon cancer due to high rates of spontaneous mutations. Their cells are unable to repair DNA double strand breaks, so females have high risks of developing breast cancer.

Their cells are unable to repair thymine dimers induced by the sunlight, and many of them die with skin cancer before 40 years of age.

When E. coli cells are defective in mismatch repair, which of the following most likely happens? They would have more mutations after exposure to UV-rays (relative to wild-type cells), because they are unable to repair thymine dimers. They would die more easily after X-ray exposure (relative to wild-type cells), because they are unable to repair DNA double strand breaks. They would have more mutations after exposure to EMS, because they are unable to repair alkylated bases. They would have high rates of spontaneous mutations, because they are unable to repair base mismatches.

They would have high rates of spontaneous mutations, because they are unable to repair base mismatches.

(Comprehension Q) In E. coli, a methyltransferase enzyme encoded by the dam gene recognizes the sequence of 5'-GATC-3' and attaches a methyl group to the nitrogen at position 6 of adenine. E. coli strains that are missing the dam gene are known to have higher rates of spontaneous mutations than wild-type strains. Why? This is because these strains are unable to recognize the daughter strand as a repair template to remove incorrect bases in the parental strand during mismatch repair. This is because MutS is unable to recognize the parental strand. This is because these strains are unable to recognize the parental strand as a repair template to remove incorrect bases in the daughter strand during mismatch repair. This is because MutS is unable to recognize the daughter strand.

This is because these strains are unable to recognize the parental strand as a repair template to remove incorrect bases in the daughter strand during mismatch repair.

Conditional mutations

affect the phenotype only under a defined set of conditions. An example is a temperature-sensitive (ts) mutation.

Somatic mutation

affects only those cells that arise from the mutated cell.Genetic mosaics are individuals with somatic regions that are genotypically different.

The function of alkyltransferase is to repair base mismatches thymine dimers alkylated guanines double strand breaks

alkylated guanines

EMS (ethyl methanesulfonate ) causes base substitutions by ( ) bases. removing oxidizing alkylating deaminating

alkylating

EMS (ethyl methanesulfonate) causes base substitutions by _______ bases.

alkylating

neutral mutations

alter the amino acid sequence, but not protein function.

Translesion DNA polymerases

assist replicative DNA polymerases to bypass damaged DNA.

Nucleotide excision repair (NER)

can repair thymine dimmers, chemically modified bases, missing bases, and some cross-links

Lethal mutations

cause death, often before birth

Intercalating agents

cause single-nucleotide additions and/or deletions during replication.

Nonionizing radiation (UV light)

causes the formation of thymine dimmers.o Mutation rate and mutation frequency

Nonsense mutations

change a normal codon to a termination codon.

Point mutations

change a single base within the DNA (base substitution).

Transversions

change from a pyrimidine to a purine, or vice-versa.

Transitions

change from a pyrimidine to another pyrimidine (C to T) or a purine to another purine (A to G).

Missense mutations

change the amino acid sequence of the polypeptide.

Spontaneous mutation

changes in DNA structure that result in abnormalities from biological processes.

Base modifiers such as nitrous acid and alkylating agents:

covalently modify the structure of DNA, causing base substitutions.

After DNA replication, mismatch repair systems recognize incorrect bases in the ( ) strand, which is ( ). daughter, methylated parental, methylated daughter, nonmethylated parental, nonmethylated

daughter, nonmethylated

Nitrous acid replaces amino acid groups with keto groups via a process called

deamination

Deleterious mutations

decrease the chances of survival.

Beneficial mutations

enhance the survival or reproductive success of an organism

Induced mutations are caused by

environmental agents.

A mutation that adds one base pair to the coding sequence of a gene would cause a

frameshift mutation

Which of the following is NOT an example of a point mutation? a transversion a transition a base substitution frameshift mutation

frameshift mutation

Mutations may also involve

he addition or deletion of short sequences of DNA

Double-strand breaks (DSBs) are repaired with

homologous recombination repair (HRR) and nonhomologous end joining (NHEJ).

Base analogs

incorporated into the DNA strands during replication, causing base substitutions

Proflavin ______ , creating frameshift mutations.

intercalates within DNA helix

Frameshift mutations

involve the addition or deletion of a number of nucleotides that are not divisible by three. This produces a completely new amino acid sequence downstream of the mutation.

Mutations in germ cells (eggs and sperm)

may be passed from parent to offspring

Chromosomal rearrangements (translocations, inversions)

may influence the phenotype when the rearrangement moves the gene to a new location. This is called the position effect.

A mutation that changes a codon that specifies glycine into a codon that specifies glutamic acid is a

missence mutation

An up promoter mutation causes the promoter of a gene to be ( ) like the consensus sequence and ( ) transcription.

more, stimulates

down mutation

mutation that decreases the rate of transcription

A mutation is called a ( ) mutation, when a change in a single amino acid does not have a noticeable effect on the polypeptide.

neutral

A mutation that changes an alanine codon into a stop codon is a nonsense mutation. silent mutation. missence mutation. frameshift mutation.

nonsense mutation

Human individuals with xeroderma pigmentosum (XP) carry germline mutations in one of the ( ) genes. XP patients are at a high risk of developing ( ), because their cells are unable to repair ( ) Alkyltransferase, brain cancer, alkylated bases nucleotide exicison repair, skin cancer, thymin dimers base excision repair, skin cancer, AP sites mismatch repair, colon cancer, thymine dimers

nucleotide exicison repair, skin cancer, thymin dimers

Mutation frequency

number of mutant genes divided by the total number of genes within a given population.

Deamination

occurs primarily with cytosine and involves the removal of an amino group from the cytosine base.

An advantage of translesion-replicating polymerases is that they can replicate ( ), but a disadvantage is that they ( ). very quickly, have low fidelity over damaged DNA, have high fidelity over damaged DNA, have low fidelity very quickly, have high fidelity

over damaged DNA, have low fidelity

Physical agents (such as ionizing radiation)

reate free radicals that can cause base deletions, single nicks in DNA strands, and chromosomal breaks.

MutH

recognizes a hemimethylated sequence.

AP endonuclease

recognizes a missing base.

Depurination

removes a purine (G or A) from the DNA.

DNA polymerase I

removes the damaged region and then fills in the region with normal DNA.

Mismatch repair

removes the mismatched segment from the newly made daughter strand.

A ( ) mutation changes a mutant allele back to a wild-type allele. nonsence neutral reverse missence

reverse

A ______ mutation changes a mutant allele back to a wild-type allele.

reverse

reverse mutations (reversions)

second mutation can change a mutant allele back to a common, wild-type sequence

In an Ames test, a _____ number of colonies is observed if a substance _____ a mutagen, compared with the number of colonies for a control sample that is not exposed to the suspected mutagen.

significantly higher, is

A mutation that changes the base sequence without a subsequent change in the amino acid is a

silent mutation

The function of photolyase is to repair DNA double strand breaks base mismatches thymine dimers apurinic sites

thymine dimers

Mutagens

usually classified as chemical or physical mutagens