Module 2:6 DNA Mutation and Repair

Question 1

Replication has high _____

Answer 1

Fidelity (high proofreading ability)

Question 2

Somatic mutations

Answer 2

mutations that only occur in non-reproductive cells; do not pass to next generation. only some cells will have it

Question 3

Germ-line mutation

Answer 3

A mutation occurring in gametes; passed on to offspring, all next generation cells will have it

Question 4

Gene mutation

Answer 4

A mutationthat affects a single gene

Question 5

Chromosomal mutation

Answer 5

A large-scale, chromosomal rearrangement - change in the number of chromosomes (ex downs syndrome)

Question 6

Gene mutation: substitution

Answer 6

One base converts to another

Question 7

Gene mutation: transition

Answer 7

Purine to purine or pyrimidine to pyrimidine substitution

Question 8

Gene mutation: transversion

Answer 8

A purine to pyridine or pyridine to purine

Question 9

Gene mutation: indel

Answer 9

A mutation in which one or two nucleotides is either inserted ordeleted from a gene, aka a frame shift

Question 10

Gene mutation: expanding nucleotide repeats

Answer 10

Process:
1. A hairpin forms on the newly synthesized strand between complimentary bases.
2. This causes the sequence that was bound in the hairpin to be replicated a second time
3. This new strand is then used as a template for replication.

Variations:
-In coding regions- increase in a certain amino acid can lead to “toxic” proteins
-In non-coding regions this can affect gene expression (can lead to DNA methylation and gene silencing)

Often a CNG repeat causes this.
The Trinucleotide can increase from a few before the hairpin and replication to over a thousand afte

Question 11

Gene mutation: missense mutation

Answer 11

The new codon encodes a different amino acid; there is a change in amino acid sequence (the codon usually has an error in the middle or first nucleotide).

If the mutated coded-for amino acid has different properties (polarity, bonding abilities) than the wild type, the protein will be different. If not, the protein may have similar function to wild type.

Question 12

Gene mutation: nonsense mutation

Answer 12

The new codon is a stop codon; there is a premature termination of translation.

Question 13

Stop codons

Answer 13

UAA, UAG, UGA (and T in place of U on DNA)

Question 14

Gene mutation:silent mutation

Answer 14

The new codon encodes the same amino acid; there is no change in the amino acid sequence. Wobble pairing can lead to this.

Question 15

Mutation class: loss-of-function

Answer 15

A protein is not expressed when it usually is. Can be beneficial or not.

Question 16

Mutation class: gain-of function

Answer 16

Protein is expressed when it usually is not. Can be beneficial or not

Question 17

mutation class: conditional

Answer 17

Mutation is always present, but only expressedunder certain conditions

Question 18

mutation class: lethal

Answer 18

Mutation always present, but when expressed the organism will die. Hard to catch in individuals because often embryo mutations

Question 19

mutation class: forward

Answer 19

Causes change in the phenotype

Question 20

mutation class: reverse/suppressor

Answer 20

Both revert the change in phenotype to wild type

True reverse: the sequence is reverted to its original

Suppressor: the mutated gene is not reversed, but a 2nd mutation causes the phenotype to revert

Question 21

supressor mutations: intragenic

Answer 21

Occurs when the suppressor mutation occurs within the same gene as the original mutation

Question 22

suppressor mutations: intergenic

Answer 22

Occurs when the suppressor mutation occurs in a secondary site

Question 23

rate of mutation

Answer 23

The frequency with which a wild type allele changes to a mutant allele - can be applied to a single gene or whole genome

Question 24

rate of mutation _____ when mutation is repaired

Answer 24

Decreases

Question 25

rate of mutation _____ when the orgainism is exposed to mutagen

Answer 25

Increases

Question 26

rate of mutation: actual vs observed

Answer 26

Actual: can only be detected through gene sequencing Observed: is detected through phenotype changes

Question 27

mutational hotspots

Answer 27

Areas within genome where mutations are more common than in other areas

Question 28

causes of mutations: spontaneous

Answer 28

Mutations that arise under normal conditions in the cell

Question 29

spontaneous mutation: strand slippage

Answer 29

Slipping of the template and newly synthesized strands in replication in which one of the strands loops out from the other and nucleotides are inserted or deleted on the newly synthesized strand - if the newly synthesized strand loops out it results in the addition of one extra nucleotide on the strand - if the template strand loops out it results in the omission of one nucleotide on the new strand

Question 30

spontaneous mutations: replicated errors

Answer 30

Unusual wobble pairings that leads to misincorporations of a nucleotide (mismatched base); when the replicated mutation is incorporated into the next round of replicons, it becomes a permanent mutation - After replicated error is bonded with its complimentary base pairing the replication is technically correct, so there is mechanism to detect error

Question 31

spontaneous mutations: incorporated errors

Answer 31

Unusual wobble pairings that leads to misincorporations of a nucleotide (mismatched base); incorrect base pairings on the newly synthesized strands have not gone though a second round of replication yet. The mutation is not permanent - The cell has mechanisms to recognize incorrect base pairings, so before the mutation is replicated, it can still be repaired

Question 32

spontaneous mutation: cross over indels

Answer 32

A mutation that occurs when homologous chromosomes misalign during crossing over One crossover product will contain an insertion while the other will have a deletion

Question 33

spontaneous mutation: depurination

Answer 33

A chemical mutation to the DNA in which spontaneous cleavage of a purine base from the 1’ carbon on either strand occurs ( typically replaced by A, regardless of whether A or G was cleaved) Happens frequently

Question 34

spontaneous mutation: deamination

Answer 34

Removal of an amino group from G, C, or A, resulting in the formation of other bases If error replicated, can produce a C:G to T:A transition

Question 35

causes of mutation: induced

Answer 35

Mutations brought about by some agent

Question 36

induced mutation: oxidizers

Answer 36

Causes mispairing of bases by the additionof an oxygen to the nitrogenous base, typically transversion

Question 37

induced mutation: intercalating agents

Answer 37

An indel mutation caused by the distortion of the DNA due to a substance inserting itself into and binding with the structure of the DNA

Question 38

induced mutation: radiation

Answer 38

UV: formation of thymine dimer-covalent bonds between 2 thymines, cannot fit into double helix; this causes molecular distortion and replication and transcription stalls In bacteria the dimers prevent replication and kill the bacteria. Bacteria have an SOS system to bypass lesions (kinks)- not very efficiend X-Ray and gamma rays: cause ionizing radiation (generate reactive ions and free redicals, modify bases, and cause breakage in the DNA)

Question 39

ames test

Answer 39

A test to determine the mutagenic activity of chemicals by observing whether they cause mutations in sample bacteria

Question 40

DNA repair mechanisms: mismatch repair

Answer 40

When mismatched nucleotides are incorporated, kinks are produced in the DNA. The mismatch repair enzyme recognizes the kink and causes exonucleases to remove nucleotides on the new strand and DNA polymerase replaces them. In E. coli the new and old strands are differentiated for removal of nucleotides by methylation on the old strand.

Question 41

DNA repair mechanisms: direct repair

Answer 41

The nucleotide is repaired enzymes convert alerted nucleotides back to the original photolyase cleaves pyrimidine dimers (UV radiation) Methylthansferase demethylates methyl-guanosine (deamination)

Question 42

DNA repair mechanisms: base excision repair

Answer 42

The nucleotide is removed/replaced The enzyme uridine glycosylase removes damages bases from the nucleotide. This leads to removal of the sugar and phosphate by AP endonuclease, filling in why polymerase and sealing by ligase.

Question 43

DNA repair mechanisms: necleotide-excision repair

Answer 43

DNA segment is removed/replaced Repair enzymes recognize damage in the DNA by distortions (kinks) and separate the strands, and cleave damages strand; (replication machinery fills in)

Question 44

DNA repair mechanisms: double-stranded breaks

Answer 44

Aims to repair damage caused during homologous recombination (cross-over indels), but it is error-prone

Question 45

DNA repair mechanisms: translesion DNA polymerases

Answer 45

specialized DNA polymerases that are able to replicate through distorted structures and bulky lesions that halt other DNA polymerases. They often make more errors during DNA synthesis than other DNA polymerases

Question 46

Transposons

Answer 46

segments of DNA that can move from one region of DNA to another