Lecture 10: Mutability and DNA Repair

Question 1

Transition (base substitution)

Answer 1

Replace base with one having the same chemical properties (purine to purine or pyrimidine to pyrimidine)

Question 2

Transversion (base substitution)

Answer 2

Replace base with one having different chemical properties (purine to pyrimidine or vice versa)

Question 3

Purines

Answer 3

A and G

Question 4

Pyrimidines

Answer 4

C and T

Question 5

What are indels?

Answer 5

Base addition/insertions: one or more nucleotides added

Base deletion: one or more nucleotides deleted

Question 6

What kind of mutations to indels cause?

Answer 6

Frameshift mutations

Question 7

Silent mutation

Answer 7

Nucleotides sequence changes but polypeptide sequence does not

Question 8

Missense mutation

Answer 8

Change in nucleotide sequence causes change in AA sequence

Question 9

Nonsense mutation

Answer 9

Premature stop codon (TAA, TAG, TGA)

Question 10

What is a conservative missense mutation?

Answer 10

Altered AA is in same group as the one it replaced (e.g., lysine to arginine; both are basic)

Question 11

What is a non-conservative missense mutation?

Answer 11

Altered AA is in a different group than the one it replaced (e.g., Phe to Ser is nonpolar to polar)

Question 12

4 causes of spontaneous cleavage of chemical bonds in DNA

Answer 12

(1) Genotoxic chemicals in environment
(2) Chemical byproducts of normal cellular metabolism
(3) Environmental agents like UV light and ionizing radiation
(4) Copying errors by DNA polymerase during replication

Question 13

What happens in deamination of 5-methyl cytosine?

Answer 13

Amino group is replaced with O, and molecule becomes thymine

Question 14

What happens in deamination of cytosine?

Answer 14

Amino group replaced with O, and molecule becomes uracil (bad bc DNA doesn’t have uracil)

Question 15

Which base is exempt from deamination?

Answer 15

Thymine

Question 16

What happens in depurination?

Answer 16

Guanine or adenine are released from the DNA strand

Question 17

Base substitution (and types)

Answer 17

Change of one base to another: transitions and transversions

Question 18

Possible effect of depurination

Answer 18

Deletion mutation

Question 19

Cause and effect of thymine dimers

Answer 19

Caused by UV light, effect is that DNA assumes rigid structure (interfering with DNA replication and RNA transcription)

Question 20

Basis of Ames Test

Answer 20

When His-/- cells added to dish with mutagen, it makes them His+/+ and allows them to grow

Question 21

What are base analogs and what do they do? Give one example.

Answer 21

Similar in structure to bases, but cause mutation if they pair with actual base (e.g., 5-bromouracil is similar to cytosine so will pair with guanine)

Question 22

What do intercalating agents do?

Answer 22

Get into DNA structure and destroy it

Question 23

3 examples of intercalating agents

Answer 23

ethidium, proflavin, acridine orange

Question 24

What ability allows some DNA polymerases to proofread?

Answer 24

3’ to 5’ exonuclease activity (they have an exonuclease site, distinct from the polymerase site)

Question 25

What does E. coli Dam methylase do?

Answer 25

Methylates A residues of GATC sequence, only on template strands (if mistake is made, cell knows to remove newly synthesized strand since the old one is correct and methylated)

Question 26

Basis of translesion DNA synthesis

Answer 26

When replicative DNA pol finds mistake, translesion DNA pol replaces it (lacks proofreading ability), continues synthesis, and then replicative pol comes back

Question 27

What happens in photoreactivation?

Answer 27

DNA photolyase (activated by UV light) breaks thymine dimers

Question 28

What does methyl transferase do (with regards to DNA repair)?

Answer 28

Removes unwanted methyl groups between base pair

Question 29

Basis of base excision repair

Answer 29

Glycosylates remove damaged bases (one nucleotide only)

Question 30

Which enzymes remove the sugar phosphate in base excision repair in prokaryotes?

Answer 30

AP endonuclease and phosphodiesterase

Question 31

What common mismatch is almost always caused by deamination of 5-methyl cytosine?

Answer 31

G-T (the T is the wrong one, should be C instead)

Question 32

What enzymes cut/remove the DNA backbone during base excision repair in eukaryotes?

Answer 32

APEI cuts 5' end, then AP lyase removes deoxyribose phosphate

Question 33

Nucleotide excision repair: order of proteins recruited

Answer 33

XP-C and 23B, TFIIH, XP-G and RPA, XP-F, DNA polymerase delta/epsilon, DNA lipases

Question 34

Nucleotide excision repair: which protein cuts 3' end and which one cuts 5' end?

Answer 34

XP-F cuts 5' and XP-G cuts 3'

Question 35

Function of RAD51 in homologous recombination

Answer 35

Forms nucleoprotein filaments on exposed 3' ends of damaged strands, which search for homologous sequences in sister chromatids

Question 36

Homologous recombination: order of molecules recruited

Answer 36

ATM kinase (activated by break), BRCA1 and BRCA2, RAD51, RAD54 and RAD52, DNA polymerase, DNA ligation

Question 37

NHEJ: order of molecules used

Answer 37

Ku70/80, DNA protein kinase, Artemis (exonuclease), DNA ligase