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MOLGEN > Exam 3 study guide break down > Flashcards

Exam 3 study guide break down Flashcards

1
Q

3 primary mechanisms to find bacterial RNAP promoter

A

sliding
intersegment transfer
intradomain association association and disassociation (hopping)

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2
Q

when is holoenzyme in a closed complex

A

when it slides onto a promoter

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3
Q

when is holoenzyme in open complex

A

when sigma factor binds strongly

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4
Q

what happens when holoenzyme is in an open complex

A

DNA duplex is bent
promoter is denatured
transcription bubble gets bigger
jaws close around downstream sequence

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5
Q

what is abortivive initiation transcripts

A

RNAP pulls in DNA via a scrunching motion and the stress of that causes short abortive transcripts to come out

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6
Q

what happens from successive abortive initiation events

A

RNAP breaks away from promoter to transition to elongation

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7
Q

nonspecific interaction by sigma and DNA duplex

A

is when sigma interacts with the phosphodiester backbone in the closed binary RNAP complex

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8
Q

specific interaction between sigma and DNA duplex

A

sigma base pairs to -10 and discriminator facilitates the melting that leads to irreversible transition to open RNAP complex

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9
Q

positioning factors with TBP

A

TFIIIB
SL1
TFIID

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10
Q

where does TBP bind

A

minor groove in DNA

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11
Q

what happens when TBP binds

A

DNA bends 80 degrees
brings transcription factors bound upstream in close proximity with RNAP bound downstream

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12
Q

TATA containing initiation mechanism

A

TBP in TFIID directs TFs to TATA box
B binds
F binds
RNAPII binds
B binds to RNAP to assist D
H binds and phosphorylates CTD
E binds
complex formed

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13
Q

TATA less differences

A

TFIID binds to Inr via interactions with TAFs
some lack unique transcription start sites

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14
Q

what modification happens on the CTD of RNAPII

A

phosphorylation by TFIIH and cdk9

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15
Q

what happens when CTD is modified

A

promoter and transcription factor release
RNAP conformational change
disengages from general TF
tightens interactions with DNA
acquired new proteins to increase RNAPII processivity
recognition site for capping, tailing and splicing

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16
Q

how do elongation factors facilitate continued transcription

A
  1. recruit chromatin remodeling complexes to release chromatin that is blocking movement
  2. interacts with RNAP via a coactivator to unpause enzyme
  3. act as or recruit elongation factors
  4. decrease the likelihood RNAP will dissociate
  5. help RNAP move through nucleosomes
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17
Q

intron definition

A

5’ and 3’ splice sites are simultaneously recognized by components of the E complex.
U1 and then U2Af
used for small single intron genes in unicellular eukaryotes

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18
Q

exon definition

A

U2Af binds to 3’ splice site (end of first exon)
U1 binds to 5’ splice site (start of second exon)
complexes are switches to link across
used when introns are long and exons are short

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19
Q

U246 in splicesome interaction

A

U2 binds to branch point
U5 and U4/U6 bind
U1 and U4 are released
U6 binds to U2
U6 binding to U2 brings 5’ splice site close to branch point

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20
Q

RNAP termination allosteric changes

A

binding of cleavage factors and subsequent RNA cleavage leads to conformational change
makes enzyme more likely to dissociate

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21
Q

exonuclease tornado

A

RNA cleavage products produces an uncapped 5’ end which is bound by an exonuclease
exonuclease moves up and destroys DNA-RNA hybrid
RNAP dissociates

22
Q

RNAP termination and tail formation

A

cleavage factors cleave the RNA via an endonucleolytic cut and then the tail is added

23
Q

5’ to 3’ decay pathway

A

digest polyA tail to 10-12 nucleotides
Lsm1-7 decapping enhancer binds to short tail
Lsm1-7 activates decapping on 5’ end
removal of cap produces a 5’ monophosphorylated RNA
5’ to 3’ Xrn1 exonuclease goes to town

24
Q

3’ to 5’ decay pathway

A

digestion of poly A tail to 10-12 nucleotides triggers exosome action
exosome has 3’to 5’ exonuclease
exome goes to town from 3’ end

25
Q

tRNA charging by aminoacyl-tRNA synthetase

A
  1. Amino acids react with ATP to form aminoacyl adenylate intermediate
  2. 2’OH or 3’OH of the terminal 3’ nucleotide in the tRNA attacks the carbonyl carbon of the adenylate
  3. aminoacyl-tRNA and AMP are made
26
Q

detecting tRNA differences

A

changes in nucleotide sequences
subtle differences in shape
direct (nucleotides)
indirect(phosphodiester)
common - anticodon loop and amino acid acceptor arm

27
Q

detecting amino acid differences

A

shape of amino acids
different binding efficiencies and free energies

28
Q

kinetic proofreading

A

tRNAs that match the specific nucleotide sequence combination for the synthetase properly align the amino acid acceptor stem with ATP and amino acid in active site
triggers aminoacetylation reaction

29
Q

chemical proofreading

A

pretransfer editing
posttransfer editing

30
Q

pretransfer editing

A

incorrect amino-acylAMP is hydrolized after tRNA binding but before charging

31
Q

posttransfer editing

A

amino acid is hydrolized from aminoacyl-tRNA after charging by using an editing active site

32
Q

1st sieve

A

amino acids larger than correct amino acid will be excluded from synthetic site and loading will not occur

33
Q

2nd sieve

A

amino acids smaller than the correct amino acid will fit into the editing site and will be hydrolyzed and removed

34
Q

IF3

A

helps stabilize 30S subunit and helps it bind to the initiation site on mRNA

35
Q

IF2

A

aids in binding the initiator tRNA to complex

36
Q

IF1

A

binds to 30s subunit at the A site and prevents tRNAs from binding prematurely

37
Q

scanning model

A

small subunit binds to 5’ cap and moves 5’to 3’ done the mRNA
melts some secondary structures
stops when it recognizes the start codon and flanking sequences -4 and +1 (Kozak)

38
Q

steps of elongation

A

EF-Tu-GTP binds to aminoacyl-tRNA
anticodon end moves to A site
EF-Tu-GTP end binds to factor binding center
EF-Tu-GTP hydrolysis
aminoacyl end moves to face the P site tRNA
EF-Tu-GDP released
EF-Ts regenerates EF-Tu-GTP
peptidyl transferase creates peptide bond
hybrid state
EF-G-GTP binds
EF-G-GTP hydrolysis by factor binding site
EF-G-GDP unlocks ribosome and opens gates
EF-G-GDP binds to A site
A site anticodon pushed to P site
P site anticodon pushed to E site
small subunits rotates and loses affinity for EF-G-GDP
EF-G-GDP dissociates
EF-G released GDP and picks up GTP
repeat

39
Q

proofreading of EF-Tu

A

EF-Tu-GTP only interacts with factor binding center if aminoacyl-tRNA fully enters the A site
incorrect tRNA will dissociate before GTP hydrolysis

40
Q

23S rRNA

A

positions aminoacyl end of aminoacyl-tRNA near the end of the peptidyl-tRNA
places amino group on A-tRNA in close proximity to the carbonyl group on P-tRNA

41
Q

hybrid state

A

the anticodons of the tRNAs remain in their pre-peptidyl transfer positions
3’end of A-site tRNA is now bound to polypeptide and prefers the P site
3’end of P site tRNA is deacetylated and prefers the E site
EF-G-GDP is needed to open gates

42
Q

termination via release factors

A

termination codons recognized by RF1 and 2
RF3-GDP binds to ribosome
polypeptide released
RF3-GDP turns to RF3-GTP
RF 1 and 2 dissociate
RF3-GTP hydrolyzed by factor binding center
RF3-GDP released
RRF binds to A site and recruits EF-G-GTP
EF-G-GTP hydrolyzed
unloaded tRNAs are released
EF-G-GDP, RRF, and mRNA dissociate
IF3 binds to dissociate ribosome subunits

43
Q

lacOc

A

constitutive cis-acting mutation
repressor cannot bind to mutant operator
always on

44
Q

lacI-

A

constitutive trans-acting mutation
defective repressor cannot bind
always on

45
Q

LacIs

A

uninducible trans-acting mutation
super repressor
always off

46
Q

lacI-d

A

dominant negative trans-mutation
one mutant subunit makes repressor nonfunctional

47
Q

how does the repressor bind to the operator

A

inverted repeats in the operator, in major groove of DNA

48
Q

when repressor binds to two operators

A

it induces a loop into the DNA between the two binding sites

49
Q

what does repressor binding do to RNAP

A

repressor binding enhances RNAP binding to promoter

50
Q

how often does active repressor bind to operator

A

96% of the time

51
Q

how often does inactive repressor bind to operator

A

3% of the time

52
Q

active repressor has a … affinity for random DNA

A

low

MOLGEN (28 decks)

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