Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MOLGEN > Chapter 17 - Prokaryotic Transcription > Flashcards

Chapter 17 - Prokaryotic Transcription Flashcards

1
Q

Transcription proceeds in a … direction down a template strand that is oriented …

A

5’ to 3’
3’ to 5’

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

RNA polymerase

A

An enzyme that synthesizes a complementary RNA using a DNA template

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

Transcription unit

A

Stretch of DNA that codes for an RNA molecule and any sequences needed for transcription

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

RNA polymerase separates the two strands of DNA in a

A

transient transcription bubble

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

Bacterial RNA polymerase transcribes how many nucleotides per second

A

40-50

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

a single type of RNA polymerase produces what in bacteria

A

all RNA

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

holoenzyme

A

The form of RNA polymerase that is used to initiate transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

holoenzyme contents

A

five subunits of the core polymerase and the sigma factor

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

RNA polymerase catalysis is derived from

A

the beta and beta prime subunits

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

the c-terminal domain in RNA polymerase

A

has the alpha subunits
is involved in stimulating transcription in prokaryotes

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

RNA polymerase has a general affinity for DNA because of

A

electrostatic interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

The core polymerase can synthesize RNA, but cannot recognize

A

promotors

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

The sigma factor is used to initiate transcription at

A

specific sites

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

promotor strength

A

Efficiency of individual promoters in initiating transcription
Frequency of initiation varies from 1/sec to 1/30 minutes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

first way RNAP finds promotors

A

Random diffusion and nonspecific binding to short sequences
Rapid dissociation of enzyme and repositioning
Very, very inefficient mechanism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

second way RNAP finds promotors

A

Nonspecific binding to genome and then movement along genome to specific promoter(s)
Sliding
Intersegment transfer
Intradomain association and dissociation (hopping)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

holoenzyme structure - initiation

A
  1. When the holoenzyme slides into a promoter it transitions to a closed binary complex
  2. If the sigma factor interacts strongly with the promoter, the holoenzyme transitions to an unstable open complex
  3. Several rNTPs are incorporated into the transcript, forming the ternary complex
  4. The RNAP transitions into a ternary elongation complex
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

a closed binary complex is

A

reversible

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

open complex

A

DNA duplex is bent 90° in order to place it into the active site
Promoter is denatured from -11 to +3 with assistance from sigma
Transcription bubble increases to 22-24 nt in length
Jaws close around downstream sequence
Transition to open state is irreversible

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

ternary complex

A

Additional rNTPs are added to the transcript while the RNAP remains tightly bound to the promoter
RNAP is not able to move down the template
RNAP pulls upstream DNA into the active site via a “scrunching” mechanism
Scrunching creates considerable stress that results in release of these short transcripts
Abortive initiation transcripts of 15-20 nucleotides
Energy of successive abortive initiation events is used to eventually break RNAP free from the promoter and transition to elongation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

ternary elongation complex

A

Sigma factor is released
Bubble returns to 10-12 nt in length
RNAP coverts into the core enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

promoters are

A

cis-acting control elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

In a typical bacterial genome, a … bp sequence would be the minimum length required to have a unique recognition site

A

12

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

the sequence of the promotor does not need to be

A

contiguous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

important conservation is localized in

A

short consensus sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

promoter structure

A
  1. purine at transcription start site
  2. -10 element
  3. -35 element
  4. Space between the -10 and -35 elements
  5. base pairs between -10 and +1
  6. Extended -10 element
  7. UP element
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

the space between -10 and -35 elements

A

Is 16-18 bp in 90% of promoters
Sequence is unimportant
Determines the separation between interacting regions of RNA polymerase
Also determines the geometric orientation of DNA helix with respect to interactions with RNAP holoenzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

base pairs between -10 and +1

A

Discriminator sequence
Base pairs downstream of -10 on the nontemplate strand
Interactions between these base pairs and 2 are important for stability of the open complex

29
Q

extended -10 element

A

Upstream of the -10 element
TGN sequence at this position can compensate for a -35 element that does not closely match the -35 consensus sequence

30
Q

UP element

A

20 bp region upstream of the -35 element
Interacts with the CTD
When the UP closely matches the consensus, transcription is greatly increased

31
Q

down mutations

A

Usually reduce conformance to the consensus sequences
Decrease promoter efficiency

32
Q

up mutations

A

increase conformance to the consensus sequence
increase promoter effiency

33
Q

Mutations in the -35 sequence can affect

A

initial binding of RNA polymerase

34
Q

Mutations in the -10 sequence can affect

A

Binding of RNA polymerase
The efficiency of the melting reaction that converts closed to open complex

35
Q

Some promoters lack recognizable -10 and -35 elements and Require

A

ancillary activator proteins to recruit RNA polymerase and initiate transcription

36
Q

Different sigma factors bind to the core polymerase in a similar way Even though

A

different sigma factors have different amino acid sequences

37
Q

sigma 70

A

associated with basal gene expression

38
Q

alpha helical domains of sigma 70 associate with

A

the promoter

39
Q

N-terminal domain of sigma is

A

autoinhibitory

40
Q

N-terminal domain of sigma functions

A

Normally masks the DNA binding domain of sigma
Prevents sigma from nonspecifically binding to and blocking promoters
Swings out of the way once sigma binds to the core RNAP
N-terminal domain also blocks the DNA-binding domain of the holoenzyme until an open complex is formed

41
Q

The consensus sequences at -35 and -10 provide most of

A

the contact points for RNA polymerase in the promoter

42
Q

a nonspecific interaction

A

occurs between sigma2 and only the phosphodiester backbone in the closed binary RNAP complex

43
Q

a specific interaction

A

between sigma 2 and base pairs of the -10 and discriminator facilitates the melting that leads to the irreversible transition to the open RNAP complex

44
Q

A portion of sigma must be displaced to accommodate RNA synthesis

A

The sigma3-sigma4 linker mimics RNA
Lies in the middle of the RNA exit channel
Must be ejected in order to produce a transcript > 20 nt in length
Loss of interaction between sigma3-sigma4 and RNAP is often associated with release of entire sigma and transition to core RNAP and elongation

45
Q

The DNA unwound during scrunching is rewound

A

Energy of DNA rewinding is used to break -core RNAP and promoter-RNAP interactions
Scrunching allows for storage and use of energy needed to transition to elongation

46
Q

All RNA polymerases share

A

similar structures and mechanisms

47
Q

shared RNA polymerase structures and mechanisms

A

DNA-binding primary channel lined with positive charges
active site with Mg2+
ssDNA is bent at 90 degree angle

48
Q

RNA polymerase moves forward using a

A

Brownian ratchet mechanism

49
Q

Brownian motion leads to

A

random fluctuations of structures in the active site

50
Q

Binding of the correct rNTP will stabilize the

A

active site structure in the active conformation

51
Q

A “trigger loop” becomes … when a correct rNTP enters the active site

A

folded

52
Q

Any event that displaces the 3’-OH of the RNA transcript from the active site will interrupt

A

core polymerase action

53
Q

The core polymerase has an … function that is able to remove mispaired nucleotides in order to restore correct RNA placement and activity

A

exonuclease

54
Q

The exonuclease function is stimulated by accessory factors

A

Accessory factors insert a narrow domain into the RNA polymerase
Domain closely approaches the active site
Allows a second Mg2+ to enter the active site
Converts active site from polymerase function to exonuclease function

55
Q

The core RNA polymerase does not move at a constant rate

A

Can pause or backtrack
Movement determined by context of template strand sequence

56
Q

at a true terminator

A

Extended pause
All hydrogen bonds of RNA-DNA hybrid are broken
DNA duplex reforms

57
Q

extrinsic terminators

A

require Rho

58
Q

Intrinsic terminators have two sequence features

A

G+C rich hairpin loop formation in RNA transcript
Up to seven uracil nucleotides in the RNA transcript following the hairpin region

59
Q

the hairpin induces

A

a change in RNA polymerase activity that leads to a disruption in the active site and dissociation of U-A base pairs

60
Q

readthrough transcripts

A

Transcripts that are not stopped by the terminator
Can be facilitated by factors that interact with RNA polymerase and/or the RNA transcript
Antitermination

61
Q

Mutational studies have shown the importance of the

A

G-C base pairs of the hairpin and U-rich downstream region

62
Q

Other upstream and downstream sequences also influence the

A

effiecency of termination

63
Q

extrinsic termination

A
  1. Rho binds to rut sites in the RNA transcript upstream of the termination site
  2. Rho moves downstream along the RNA transcript
  3. The RNA polymerase will pause
  4. Rho invades the active site and uses its intrinsic helicase function to break the RNA-DNA hybrid
64
Q

Rho

A

Hexameric ATP-dependent helicase

65
Q

How does Rho work

A

RNA is wound from the 3’ end around the N-terminal RNA binding domains
5’ end of RNA pushed through interior of ring to ATP binding domains
ATP hydrolysis used to translocate Rho in a 3’ direction down RNA

66
Q

heat shock response

A

is a conserved pathway that protects cells from temperature stress
Increased denaturing of proteins

67
Q

products of heat shock response

A

Chaperones that refold proteins
Proteases that degrade denatured proteins

68
Q

sigma factor for heat shock

A

sigma 32

69
Q

Unfolded protein levels decrease after a heat shock response has activated

A

Concentration of unoccupied proteases and chaperones increases
Proteases degrade free sigma32 at a greater rate
Relative concentration of sigma32 decreases
Relative concentration of sigma70 increases
RNA polymerases are less likely to complex with sigma32

MOLGEN (28 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions