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BIOL 200 > PL2 > Flashcards

PL2 Flashcards

1
Q

what is DNA subjected to

A

constant damage

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2
Q

name the types of damage DNA is subjected to

A

Hydrolytic depurination
cytosine deamination
guanidine oxidation
methylation

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3
Q

what can damage DNA

A

many chemical processes in cell and effects from environmental factors (chemicals and radiation)

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4
Q

what is a mutation

A

permanent and transmissible changes to genetic material of a cell or organism

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5
Q

why/when can mutations occur

A

can occur spontaneously
by transposable elements (segments of DNA that can move around in genome)
by errors during replication

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6
Q

what are mutagens

A

chemical compounds or UV radiation or ionizing radiation that increase frequency of mutations
like r rays and atomic particles

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7
Q

what happens if mutation in germline

A

can be passed to progeny

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8
Q

what happens if mutation in somatic cells

A

wont go to progeny but cause functional changes in soma

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9
Q

what are carcinogens

A

agents that cause cancer
many are mutagens
damaged somatic cells and divide uncontrollably

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10
Q

why do mechanism exist to repair damage to DNA

A

since DNA stores all info of cell
stability of DNA is very important

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11
Q

name a few diseases that are caused by defects in DNA repair systems - 5

A

hereditary nonpolyposis colorectal cancer
xeroderma pigmentosum
blooms syndrome
fanconi anemia
hereditery breast cancer - BRCA1 and BRCA2 deficiency

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12
Q

are DNA polymerases perfect

A

uhmmmno
they introduce 1 error every 10,000 incorporated nucleotides

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13
Q

what is measured rate of incorrect incorporation in cells and why

A

1 in 1,000,000,000
largely due to proofreading

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14
Q

what do DNA polymerases have

A

proofreading activity

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15
Q

which polymerases have proofreading activity

A

polymerases epsilon and delta have a 3’ to 5’ associated exonuclease (proofreading activity)

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16
Q

which DNA polymerase does not have proofreading activity

A

alpha

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17
Q

describe proofreading activity

A

Incorporation of incorrect base casues polymerase to pause
3’ end of new strand is free to move (flops around) to the 3’ to 5’ exonucleuase site and mispaired base is removed - chomps and digests it

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18
Q

what is a point mutation

A

single base change

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19
Q

what is most common point mutation

A

C to T

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20
Q

explain point mutation from C to T

A

chemical reaction - deamination that can affect either cytosine or methylated cytosine
if methyl cytosine undergoes deamination the amino group is replaced with keto group = thymine

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21
Q

how can a T-G mismatch be fixed

A

base excision repairs

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22
Q

in a mismatched base pair which base is correct and which base is wrong

A

T-G mismatches almost always result from deamination of C to U or 5mC to T
so T is wrong and should be replaced by C
*always assume T is wrong

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23
Q

what is first step in BER (base excision repair)

A

DNA glycosylase breaks bond between T and sugar phosphate backbone

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24
Q

what is second step in BER (base excision repair)

A

APEI endonucleases cuts DNA strand where it missing a base (on one side - a basic site)

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25
Q

what is third step in BER (base excision repair)

A

AP lyase (part of DNA pol beta) removes deoxyribose phosphate
want to get rid of one unit of sugar phosphate backbone so it can place a base there

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26
Q

what is a mismatch excision repair

A

fixes errors introduced during replication
including base pair mismatches and insertions or deletions of one/few nucleotides

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27
Q

in a mismatch excision repair which strand is correct and which is wrong

A

newly synthesized strand is wrong one
mechanisms can recognize which strand it is

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28
Q

when do mismatch excision repairs happen

A

after DNA replication

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29
Q

what point mutation can occur from deamination of cytosine

A

produce uracil from cytosine

30
Q

when must repair occur if a point mutation occurs

A

before replication - once it replicates there is no mismatch anymore
must recognize before

31
Q

what is fourth step in BER (base excision repair)

A

special DNA polymerase (beta) inserts C using G as template
ligase repairs sugar phosphate backbone

32
Q

how to tell which strand is correct for mismatch excision repair in e coli

A

extensive methylation of the strands is common but newly synthesized strands are not very methylated (since methylation happens after replication)

33
Q

how to tell which strand is correct for mismatch excision repair in mammalian cells

A

recognition of 3’ free end of DNA being synthesized - interacts with this - template does not have this 3’ free end

34
Q

describe step 1 of mismatch excision repair

A

MSH2 and MSH6 recognize the mismatch and distinguish the newly synthesized daughter strand

35
Q

describe step 2 of mismatch excision repair

A

MSH2 and MSH6 recognition (step 1) triggers binding and activity of MLH1 endonucleases (dimerized with PMS2)
MLH1 cuts the newly synthesized strand
DNA helicases unwind DNA
exonucleases digests seveal nucleotides of the daughter strand (always cuts a few)

36
Q

describe step 3 of mismatch excision repair

A

DNA polymerase (delta) fills in gaps (missing nts) using the other strand as template
ligase repairs the sugar phosphate backbone

37
Q

what do nucleotide excision repairs do

A

operates to fix DNA regions where chemically modified bases locally distort double helix

38
Q

give an example of a region that would be fixed by nucleotide excision repair

A

thymine-thymine dimer
caused by uv radiation
two adjacent thymine bases become chemically bonded together (covalent bond distorts shape of duplex)

39
Q

what other outside factors can locally distort double helix

A

chemicals that can bind to DNA bases including many carcinogens can also distort double helix

40
Q

what is step 1 of nucleotide excision repair

A

XP-C and 23B proteins recognize distorted double helix

41
Q

what is step 2 of nucleotide excision repair

A

TFIIH XP-G and RPA unwind the helix
makes a bubble of ~25 nucleotides.

42
Q

what is step 3 of nucleotide excision repair

A

XP-F and XP-G cut the damaged strand

43
Q

what is step 4 of nucleotide excision repair

A

DNA polymerase fills in missing nts using other strand as template
ligase repairs sugar phosphate backbone

44
Q

what do XP-n names derive from + explain

A

xeroderma pignmentosum
genetic disease that causes a high disposition to uv induced cancer
mutations that affect XP proteins can disease

45
Q

what happens if a thymine-thymine dimer is not repaired and it enters a replication fork - step 1

A

normal replicative DNA polymerases (delta and epsilon) stall when they reach a thymine-thymine dimer

46
Q

what happens if a thymine-thymine dimer is not repaired and it enters a replication fork - step 2

A

special translesion polymerase (n -eta) reads through dimer
but lacks proofreading ability

47
Q

what happens if a thymine-thymine dimer is not repaired and it enters a replication fork - step 3

A

region in vicinity of dimer will be likely to have mutations caused by replication errors
eventually pol eta will be replaced by one of the normal replicative polmerases

48
Q

what is NHEJ

A

double strand break repair end joining

49
Q

what can cause double strand breaks in DNA

A

radiation - x rays and gamma rays
anticancer drugs (ex bleomycin)

50
Q

what happens if double strand break is not repaired

A

the part of the chromosome distal to the break would be lost at next cell division
probably lethal to cells
very bad

51
Q

what does NHEJ do

A

rejoins broken chromosome ends
base pairs are usually lost at the joining point - produces a small deletion

52
Q

describe step 1 of NHEJ

A

Ku and DNA-PK bind the end of a double-strand break (DSB)

53
Q

describe step 2 of NHEJ

A

the 2 DSBs bound by the proteins (step 1 ) come together and recruit nucleases - they remove several bases (clean ups ends - single stranded loose ends)

54
Q

describe step 3 of NHEJ

A

the 2 double stranded molecules are ligated together

55
Q

why can the NHEJ mechanism produce chromosomal rearrangements

A

since mechanism does not ensure that what is ligated together comes from the adjacent parts of the same chromosome
can fuse DSBs coming from different chromosomes or far apart on the same chromosome
usually fine since cytoplasm is viscous and the breaks stay together

56
Q

describe double strand break repair by homologous recombination

A

damaged DNA sequence is replaced by copy of undamaged copy of the same sequence on the homologous chromosome in diploid organisms
involves exchange of strands between separate DNA molecules (process of recombination)

57
Q

describe BRCA1 & BRCA2 genes (double strand break repair by homologous recombination)

A

these mutations (associated with increases chances to breast cancer) encode proteins involved in homologous recombination repair

58
Q

what mechanism can repair a collapsed replication fork

A

double strand break repair by homologous recombination

59
Q

what can point mutations be repaired by

A

base excision repair
mismatch repair
nucleotide excision repair

60
Q

what can double strand breaks be repaired by

A

non homologous end joining
homologous recombination

61
Q

are DNA repair systems of all organisms the same

A

No
some organisms have highly efficient DNA repair systems and are highly resistant to radiation (tardigrades, deinococcus)

62
Q

describe step 1 of double strand break repair by homologous recombination

A

parental strands - light and dark blue
replication of light blue strand (synthesis of dark green) stops when break (in backbone) is reached
generally lethal to one daughter cell since partial chromosome loss

63
Q

describe step 2 of double strand break repair by homologous recombination

A

light green daughter strand gets ligated to segment of parental strand distal to the break to make unbroken chromosome
5’ exonuclease acts on broken end

64
Q

describe step 3 of double strand break repair by homologous recombination

A

strand invasion is key part of recombination process
newly ligated strand anneals to the dark green daughter strand whose synthesis was interrupted by break

65
Q

describe step 4 of double strand break repair by homologous recombination

A

branch migration
an increased stretch of the dark green strand denatures from light blue parental strand and anneals to light green daughter strand
allows light blue parental strand to cross over and anneal to dark blue parental strand

66
Q

describe step 5 of double strand break repair by homologous recombination

A

cut strands at crossover
no more double strand break

67
Q

describe step 6 of double strand break repair by homologous recombination

A

ligate ends
produces a similar structure to a replication fork

68
Q

describe step 7 of double strand break repair by homologous recombination

A

rebuild replication fork and continue replication
recruitment of replication fork proteins enables further extension of the leading strand, re initiation of lagging strand synthesis and continuation of replication

69
Q

a similar mechanism can…

A

repair a double-strand break in a chromosome and can also produce an exchange of segments between two double-stranded DNA molecules

70
Q

what is holliday structure

A

involves all 4 strands can be resolved in 2 alternative ways

71
Q

describe the 2 alternative ways of holliday structure

A

regenerates original chromosomes
produces 2 uniparental strands and 2 recombinant strands containing DNA from both parents

72
Q

what do diagonals represent (in drawing of homologous recombination double strand break repair)

A

only a single phosphodiester bond between single adjacent nucelotides

BIOL 200 (29 decks)

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