Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

when is holoenzyme in a closed complex

A

when it slides onto a promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

when is holoenzyme in open complex

A

when sigma factor binds strongly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what happens from successive abortive initiation events

A

RNAP breaks away from promoter to transition to elongation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

nonspecific interaction by sigma and DNA duplex

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

positioning factors with TBP

A

TFIIIB
SL1
TFIID

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

where does TBP bind

A

minor groove in DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what happens when TBP binds

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

TATA less differences

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what modification happens on the CTD of RNAPII

A

phosphorylation by TFIIH and cdk9

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
tRNA charging by aminoacyl-tRNA synthetase
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
detecting tRNA differences
changes in nucleotide sequences subtle differences in shape direct (nucleotides) indirect(phosphodiester) common - anticodon loop and amino acid acceptor arm
27
detecting amino acid differences
shape of amino acids different binding efficiencies and free energies
28
kinetic proofreading
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
chemical proofreading
pretransfer editing posttransfer editing
30
pretransfer editing
incorrect amino-acylAMP is hydrolized after tRNA binding but before charging
31
posttransfer editing
amino acid is hydrolized from aminoacyl-tRNA after charging by using an editing active site
32
1st sieve
amino acids larger than correct amino acid will be excluded from synthetic site and loading will not occur
33
2nd sieve
amino acids smaller than the correct amino acid will fit into the editing site and will be hydrolyzed and removed
34
IF3
helps stabilize 30S subunit and helps it bind to the initiation site on mRNA
35
IF2
aids in binding the initiator tRNA to complex
36
IF1
binds to 30s subunit at the A site and prevents tRNAs from binding prematurely
37
scanning model
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
steps of elongation
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
proofreading of EF-Tu
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
23S rRNA
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
hybrid state
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
termination via release factors
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
lacOc
constitutive cis-acting mutation repressor cannot bind to mutant operator always on
44
lacI-
constitutive trans-acting mutation defective repressor cannot bind always on
45
LacIs
uninducible trans-acting mutation super repressor always off
46
lacI-d
dominant negative trans-mutation one mutant subunit makes repressor nonfunctional
47
how does the repressor bind to the operator
inverted repeats in the operator, in major groove of DNA
48
when repressor binds to two operators
it induces a loop into the DNA between the two binding sites
49
what does repressor binding do to RNAP
repressor binding enhances RNAP binding to promoter
50
how often does active repressor bind to operator
96% of the time
51
how often does inactive repressor bind to operator
3% of the time
52
active repressor has a ... affinity for random DNA
low

MOLGEN (28 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions