CBG Lecture 8: Mutation and Repair

Question 1

how are mutations in DNA introduced

Answer 1

spontaneous

introduced by mutagens: virus/UV/chemicals

Question 2

name some mutagens

Answer 2

virus
uv
chemical

Question 3

per how many bases does polymerisation make a mistake 1

Answer 3

10^4 or 10^5

Question 4

of the bases that polymerisation makes a mistake on, how many does exonuclease proofreading fail to correct

Answer 4

1 in 100 of 10^4 mistakes

Question 5

what is the overall error rate of polymerisation

Answer 5

10^-9 per nucleotide

Question 6

give some examples of where mutations can arise

Answer 6

tautomery during replication/transcription
mispairing of aa to tRNA by aaRS
mutations in DNA by mutagens
damage to mRNA eg. truncation
misfolding of proteins by prions

Question 7

how is /dna prone to mutations

Answer 7

oxidative deamination by free radicals
depurination - spontaneous hydrolysis
thymine dimerisation by UV light

Question 8

how does thymine dimerisation occur

what does it make

Answer 8

by UV light

cyclobutane dimer

Question 9

what happens to cytosine in oxidative deamination

how does it happen

Answer 9

cytosine + free radicals -> uracil

Question 10

what happpens to a depurinated adenine

Answer 10

adenine + spontaneous hydrolysis -> hole

Question 11

how is hole made

Answer 11

by spontaneous hydrolysis and depurination of adenine

Question 12

how is thymine dimerised

what does it make

Answer 12

thymine is dimerised by UV light and makes a cyclobutane dimer

Question 13

what do uncorrected lesions lead to

Answer 13

mutation

Question 14

name a potent mutagen

Answer 14

5-bromouracil

Question 15

in what way can smaller lesions be repaired

Answer 15

base excision by a glycosylase, endonuclease, polymerase, ligase

Question 16

in what way can large lesions be repaired

Answer 16

nucleotide excisions

Question 17

name subtypes for a mutation with point change in a single base

Answer 17

missense
nonsense
silent

Question 18

what is a missense mutation

Answer 18

change in codon (normally second base) leads to change in aa

Question 19

give an example of a missense mutation disease

Answer 19

glu -> vale
(GAG->GUG)
sickle cell anaemia (Hb)

Question 20

give an example of a nonsense mutation

Answer 20

GGA -> UGA
gly -> STOP
chloride channel : cystic fibrosis

Question 21

what is a nonsense mutation

Answer 21

change in codon, making it a STOP codon

Question 22

what is a silent mutation

Answer 22

change in base, no change in aa

Question 23

what is an indel mutation

Answer 23

insertion or deletion of base

Question 24

what is a frameshift mutation

Answer 24

when an INDEL occurs causing the reading of the bases to no longer be read the same

Question 25

what does a frameshift mutation often cause

Answer 25

protein truncation as 3/64 triplets will be STOP codons

Question 26

why is it that many lesions are easily repaired

Answer 26

because DNA is double stranded

Question 27

what does DNA glycosylase do? how?

Answer 27

flips out and breaks the glycosidic bond between DNA and uracil in a U:G lesion

Question 28

what process is repair often coupled with? why

Answer 28

repair is often coupled to transcription, ensuring that the most used genes (those actively transcribed) are given the most attention by repair enzymes

Question 29

why is it that daughter DNA strands are often distinguishable from the parente strand for a while after replication

Answer 29

because of the lag in post-replicative modification of the DNA eg. by methylation so the daughter strand (which is more likely to contain the error) will be more likely to be targeted for correction

Question 30

what do prokaryotes use to deal with mistranscribed, truncated mRNA

Answer 30

tmRNA - transfer messenger RNA

Question 31

what does tmRNA encode

Answer 31

has an mRNA like domain encoding the degradation tag ANDENYALAA

Question 32

name some functions of tmRNA

Answer 32

deals with mistranscribed truncated mRNA recycles the stalled ribopsome adds a proteolysis inducing tag to the unfinished pp facilitates the degradation of aberrant mRNA

Question 33

at which two points in translation does fidelity need to be maintained

Answer 33

1. ribosome decoding of codon to anticodon | 2. tRNA aminoacylation of tRNA to amino acid

Question 34

what is the effect of streptomycin

Answer 34

causes pyrimidines to be misread during translation

Question 35

what is the effect of mupirocin

Answer 35

new antibiotic that inhibits IleRS in MRSA: inhibits aminoacyl synthetases

Question 36

describe tRNAs

Answer 36

large and easily distinguished by aaRS | readily distinguishable by their anticodons

Question 37

what are aaRS

Answer 37

alanyl-tRNA synthetase helps attach the aa to the tRNA have proofreading esterase

Question 38

what is the error rate of tRNA

Answer 38

10^-4 per tRNA

Question 39

what AS's do aaRS's have

Answer 39

aminoacylation active site - large enough to accommodate aa | esterase proofreading active site smaller

Question 40

in what way is genetic code robust

Answer 40

the mutations that do make a difference to the encoded mutations very rarely replace a hydrophobic amino acid with a very polar one or vv

Question 41

in what way is the genetic code redundant

Answer 41

several codons code for the same amino acid because the third base of the codon is usually irrelevant

Question 42

what is the difference in binding eneryies between valine and isoleucine

Answer 42

difference in one CH2 | difference in binding energy is 12kJmol-1

Question 43

name 2 enzymes that have separate active sites for the process and and for proofreadin

Answer 43

DNAP | aaRS

Question 44

why is it good for an enzyme to have proofreading performed by a separate active site

Answer 44

ensures the two processes are independent and that the probability of error is minimised since it will make the probability the product of two independent processes

Question 45

name some confusing amino acid pairs

Answer 45

valine : isoleucine:leucine alanine + glycine aspartamine + glycine serine and lysine

Question 46

what happens to errors that do slip through

Answer 46

degradation mechanisms to fix or remove them

Question 47

what do aaRSs do

Answer 47

catalyse the esterification of a specific amino acid to its compatible cognate tRNA

Question 48

in which number base of a codon does a mutation make little difference to codon

Answer 48

first base