Brainscape's Knowledge GenomeTM

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


See full index

biochem > prokaryotic transcription and gene regulation > Flashcards

prokaryotic transcription and gene regulation Flashcards

1
Q

transcription

A

process of DNA template-dependent RNA synthesis and is catalyzed by RNA polymerase

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

messenger RNA (mRNA)

A

houses a sequence of bases that encodes the primary amino acid sequence for a protein
- serves as a template for translation by a ribosome

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

transfer RNA (tRNA)

A

carries an amino acid into catalytic site of a ribosome. the tRNA base pairs to mRNA to ensure selection of the correct amino acid for incorporation into a nascent polypeptide chain

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

ribosomal RNAs (rRNA)

A

structural components of a ribosome, the enzyme that catalyzes translation

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

_____ is typically a linear single-stranded polynucleotide chain with:
a ribose sugar phosphate backbone
uracil in place of thymine
the sequence always read 5’->3’

A

RNA

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

________ base pairing is allowed when RNA base pairs with itself or another RNA molecule

A

G-U

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

internal base pairing within an RNA strand yields…

A

complex secondary and tertiary structures

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

RNA polymerase will use one strand of DNA as the ____________ strand when synthesizing RNA

A

template

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

the DNA template strand is said to be the ________________ of the DNA coding strand and the RNA primary transcript

A

reverse complement

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

the RNA transcript resembles…

A

the coding strand

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

trans-acting factors

A

diffusible so they can function at multiple sites in a genome; usually are DNA binding proteins; affects levels of transcription

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

cis-acting elements

A

closely tied to the gene; typically is a DNA sequence; fixed place in genome

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

transcription starts at a __________ and ends at a ____________. the finished RNA molecule is a ________________________

A

promoter; terminator; primary transcript

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

a gene includes the ….

A

DNA encoding the protein and the regulatory elements needed for its transcription

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

in bacteria, a primary transcript is used as…

A

an mRNA for translation without further modification

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

open reading frame (ORF)

A

sequence of bases that encodes the primary sequence of a protein; aka coding sequence

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

operons

A

coordinately regulated gene clusters
ORFs encoding proteins are arranged 5’->3’ in a transcription unit
use of one promoter and terminator yields a polycistronic mRNA with multiple ORFs each encoding a different protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

a _________ is a cis-acting element in the genome where ___________ binds to initiate transcription

A

promotor; RNA polymerase

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

the bacterial consensus promoter

A

TTGACA-N16-18-TATAAT-N5-9CAT

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

in bacteria, the rate of _____________________ is the major determinant of gene expression

A

transcription initiation

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

Similarly to the consensus sequence directly affects the rate of transcription initiation from a __________________

A

constitutive promoter (always available/on)

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

strong promoters

A

have very high sequence identity with the promoter consensus sequence

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

weak promoters

A

have several base differences

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

a mutation in a promoter that moves away from the consensus sequence…

A

decreases the rate of transcription initiation

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

E.coli has only one …

A

RNA polymerase

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

____________________ is responsible for transcription initiation and synthesis of 1st 10 nucleotides of RNA

A

RNA polymerase holoenzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

holoenzyme consists of the ____________ subunits

A

a2BB’wsigma

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

subunit sigma

A

recognizes a promoter; binds to most of the promoters in the E.coli genome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

subunits a2

A

essential for enzyme assembly and interact with activators

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

subunits B and B’

A

form the catalytic core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

subunit w

A

provides structural stability

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

RNA polyermase core enzyme (a2BB’w)

A

carries out transcription elongation

33
Q

RNA can start synthesizing RNA _________________. it will form a phosphodiester bond between 2 NTPs to being RNA synthesis. The 5’ end will contain 3 phosphate groups.

A

de novo (without a primer)

34
Q

RNA polymerase requires a DNA template chain but does not have ….

A

proof reading exonuclease activity meaning there will be errors ( its okay bc RNA is degraded quickly)

35
Q

NTP

A

ribonucleoside 5’triphosphates

36
Q

holoenzyme binds to a promoter forming the _______________.
- ___ identifies the promoter and makes protein-DNA interactions with -35 and -10 promoter regions (initiation)

A

closed complex; sigma70

37
Q

unwinding of DNA 12-15 bp forms a transcription bubble converting a closed complex to an _____________ (initiation)

A

open complex

38
Q

______________ initiates RNA synthesis and synthesizes about 10 nt (initiation)

A

holoenzyme

39
Q

dissociation of the sigma factor yields core enzyme allowing RNA polymerase to complete ______________

A

promoter clearance

40
Q

__________________ rate by core enzyme accelerates to ~50-90 bases/sec (not being held back by sigma anymore)
- rate of ______________ can be slowed by formation of RNA secondary structure in the transcript
- __________________ relieve supercoiling in DNA

A

transcription elongation; topoisomerases

41
Q

________________________ results in release of RNA and dissociation core enzyme from DNA

A

transcription termination

42
Q

rho-independent termination

A

termination signal resides in the nascent RNA chain sequence; no protein needed
termination occurs due to formation of a stable hairpin structure followed by a series of 7 Us (rho-independent terminator)
hairpin formation results in only a few weak U=A base pairs between transcript RNA and DNA. DNA/RNA is unstable so the RNA dissociates, termination transcription

43
Q

rho-dependent termination

A

requires Rho protein
rho is a hexameric protein that binds a nascent RNA chain at a rho utilization site (rut) within the RNA
rho is an RNA helicase that translocates along the RNA 5’->3’ using ATP hydrolysis
RNA polymerase pauses in response to formation of an RNA secondary structure
transcription terminates when rho contacts RNA polymerase

44
Q

inducible promotors can be _________________

A

turned off and on

45
Q

repressors

A

transcription factors that decrease the rate of transcription from a promoter

46
Q

activators

A

transcription factors that increase the rate of transcription from a promoter

47
Q

in bacteria, both activators and repressos have ________________ DNA binding domains

A

helix-turn-helix

48
Q

regulated gene expression is dependent on sequence-specific binding of proteins called __________________ to DNA

A

transcription factors

49
Q

transcription factors bind to ___________ and ____________

A

major and minor grooves

50
Q

an ________ of the DNA binding protein is positioned within the _________ groove

A

a-helix; major

51
Q

_______________ participates in hydrogen bonds and van der Waals interactions with the base pairs

A

recognition helix

52
Q

in prokaryotes, the predominant _____________ motif for containing a recognition helix is called the _______________

A

DNA binding domain (DBD); helix-turn-helix

53
Q

formation of a stable DNA-protein complex is dependent on …

A

additional non-covalent chemical bonds outside the recognition helix-base pair contacts

54
Q

protein motifs

A

small regions of protein 3D structure or amino acid sequence shared among different proteins

55
Q

each base pairs presents a unique set of chemical groups in the _________

A

major groove

56
Q

CG and AT pairs can be distinguished in the __________

A

minor groove

57
Q

transcription factors cannot tell the difference between _____ and _____ pairs in the minor groove

A

AT and TA

58
Q

the major groove has _____ nucleotides, while the minor groove has ____ nucleotides

A

4;3

59
Q

helix-turn-helix motif

A

two a helices; the 2nd helix is the recognition helix

60
Q

the DNA binding domain of a bacterial transcription factor consists of a _______________

A

helix-turn-helix motif
the DNA binding domain is just one small region of the transcription factor

61
Q

________ DNA binding proteins are common.
- there is a recognition helix on both subunits because both subunits contain a helix-turn-helix motif
- as a result, this protein recognizes a _______________
- the same sequence of bases is seen 5’ -> 3’ along both strands

A

homodimeric; palindromic sequence

62
Q

why dimers and oligomers?

A

improved specificity and improved stability (more interactions)

63
Q

____________ negatively regulate transcription through inhibiting transcription by ________________. _____________ from the cellular environment control the activity of _____________. Some ____________ only bind to DNA in the presence of a ligand. Some __________ only bind to DNA in the absence of a ligand.

A

repressors; RNA polymerase; ligands; repressors

64
Q

negative regulation primarily results from a __________ binding to a site proximal to an __________________

A

repressor; inducible promoter

65
Q

a repressor bound downstream inhibits…

A

promoter clearance by RNA polymerase

66
Q

a repressor bound to the promoter sequence blocks…

A

RNA polymerase from binding to the promoter

67
Q

four identical subunits: a homotetramer forms a _________________
- all four subunits have ____________ motifs for sequence-specific binding to two separate palindromic operator sites
- inducer binding pocket is located between globular domains far from the DNA binding domain

A

dimer of dimers
helix-turn-helix

68
Q

____ at lac promoter is the highest affinity binding site.

A

O1

69
Q

Both ___ and ____ are low affinity sites because of differences from consensus lac repressor recognition sequence

A

O2 and O3

70
Q

the lac repressor bind to ___ and either ___ or _____
- occupancy of the __ site is responsible for repressor activity
- a mutation destroying __ results in a loss of regulation of the lac promoter

A

O1; O2 or O3
O1

71
Q

_________ positively regulate transcription by recruiting _________________ to a ____________. __________ from the cellular environment control the activity of __________. Some only bind to DNA in the presence of a ligand while some only bind to DNA in the absence of a ligand

A

activators; RNA polymerase; promoter; ligands; activators

72
Q

some prokaryotic gene regulation results from binding of an activator to a site proximal to an _____________________

A

inducible promoter

73
Q

an __________ binds to a _______________________ located upstream of a promoter
- an activator recruits RNA polymerase to a weak promoter through protein-protein interactions with the RNA polymerase a subunit
ex. CRP activator

A

activator; positive regulatory element

74
Q

____ is an ______ and its “inducer’ _______ is present only under conditions of low glucose
- ____ is a homodimeric helix-turn-helix protein
-__________ binds 5’ to the promoter

A

CRP; activator; cAMP; CRP; CRP-cAMP

75
Q

lac promoter is weak because…
CRP recruits _____________ to the lac promoter through protein-protein interactions with the ______________________-

A

it differs from the consensus promoter
RNA polymerase
RNA polymerase a subunit

76
Q

in the absence of glucose, adenylate cyclase produces

A

cAMP

77
Q

________ is the preferred carbon source for E.coli, so it will be consumed ahead of _________

A

glucose; lactose

78
Q

(negative regulation) the _______ gene is located upstream of the lac operon and encodes the ____________
- __________ binds the operator in the absence of ___________
- the _________ site is located at the transcription start site

A

lacl; lac repressor; lac repressor; allolactose; operator

79
Q

(positive regulation) ______________________(CRP) binds DNA in the presence of its inducer, ________
- the _______________ (activator binding site) is located upstream of the lac promoter

A

cAMP receptor protein; cAMP; CRP binding site

biochem (37 decks)

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