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Molecular Biology > Exam 2 > Flashcards

Exam 2 Flashcards

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1
Q

what is a conservative mutation

A

a missense mutation (point mutation) that switches one AA to another AA with similar chemical properties

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2
Q

what are the functions of the phosphorylation of the CTD during transcription by RNA Pol II in eukaryotes

A
  • promoter clearance/start of elongation
  • recruitment of capping factors
  • attachment of cap binding complex
  • recruitment of splicing proteins
  • recruitment of polyA complex
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3
Q

which strand is the template strand

A

the 3’ –> 5’ strand in the direction of transcription

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4
Q

where does transcription start

A

+1 is the first nucleotide

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5
Q

which pathway repairs an incorrect nucleotide incorporated by DNA pol

A

mismatch repair

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6
Q

which pathway repairs a crosslink generated by UV light

A

nucleotide excision repair

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7
Q

which pathway repairs an oxidation of guanines by a reactive oxygen species

A

base excision repair (can just remove the base)

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8
Q

which pathway repairs a damage base started to get repaired during replication, leading to conversion of a single strand break to a double strand break

A

homologous recombination

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9
Q

what genes are transcribed by pol I

A

rRNA

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10
Q

what genes are transcribed by pol II

A

mRNA

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11
Q

what genes are transcribed by pol III

A

other small RNAs

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12
Q

which pol transcribes the largest variety of genes

A

pol II

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13
Q

which pol transcribes the largest total amount of genes

A

pol I

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14
Q

where does synthesis of pol I occur

A

nucleolus

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15
Q

where does synthesis of pol II occur

A

nucleoplasm

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16
Q

where does synthesis of pol III occur

A

nucleoplasm

17
Q

what are the steps of transcription initiation in bacteria

A
  1. sigma bound pol binds to promoter, sigma factor blocks active site to create closed complex state
  2. sigma factor moves away from active site, DNA enters active site, pin promotes opening of DNA (open state)
  3. the polymerase needs to hold the first nucleotides together (unstable) which leads to several cycles of abortive initiation until RNA chain is ~10nt
  4. structural transition at 10nt, sigma factor is cleared from RNA exit channel and falls off (called promoter clearance)
18
Q

what is the function of primase

A

synthesizes RNA primers for replication

19
Q

what are the functions of chromodomain and bromodomain proteins

A

binds methylated histone tails to maintain open/closed chromatin

20
Q

what is the function of the mediator complex

A

binds to enhancer-bound transcription factors to promote transcription in eukaryotes

21
Q

what is the function of guanylyltransferase

A

adds 5’ cap to mRNA in eukaryotes

22
Q

what is the function of cas9

A

creat ds break

23
Q

what kind of enzyme is cas9

A

bacterial enzyme

24
Q

what is the function of gRNA in crispr/cas

A

bring cas9 to target on DNA (needs break on DNA not RNA)

25
Q

what pathway will most likely repair the lesion in crispr/cas

A

NHEJ

26
Q

if there is a gene knocked out during crispr/cas, what mutation will there be

A

indels

27
Q

what is a knock in gene repaired by

A

HR

28
Q

does a knock in or knock out need a donor sequence

A

knock in

29
Q

is sigma70 or sigma34 spontaneous

A

sigma70

30
Q

what is the role of a sigma factor in bacteria

A

brings RNA pol to a specific set of promoters

31
Q

when splicing, what exons need to be included

A

first and last

32
Q

what is the mechanism by which different mature mRNAs can be made from same pre mRNA

A

alternative splicing

33
Q

what end is the cap added to

A

5’

34
Q

what is the cap made of

A

7-methyl guanosine (7-MeG)

35
Q

is 5’ cap attached at beginning or end of transcription

A

beginning

36
Q

where is the capped mRNA attached to RNA pol II

A

c terminal domain

37
Q

what are functions of the 5’ cap

A

inhibits 5’->3’ exonuclease
attaches to pol II
recruits ribosomes

38
Q

what are the two different mechanisms of transcription termination in bacteria

A

rho-independent: without a protein

rho-dependent: uses protein

39
Q

what is the order of splicing events

A
  1. U1 binds to 5’ splice site and U2 binds to branch point
  2. U1 brings the 5’ splice site and the A of branch point together
  3. binding of U4, U5, U6
  4. 2’ OH of A branch point serves as nu and attacks phosphodiester bond at 5’ exon
  5. formation of lariat on intron
  6. U5 base pairs w/ exons 1 and 2, maintaining them together
  7. 3’ OH of exon 1 serves as nu and attacks phosphodiester bond at 3’ splice site
  8. release of exon as lariat

Molecular Biology (4 decks)

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