prokaryotic transcription and gene regulation

Question 1

transcription

Answer 1

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

Question 2

messenger RNA (mRNA)

Answer 2

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

Question 3

transfer RNA (tRNA)

Answer 3

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

Question 4

ribosomal RNAs (rRNA)

Answer 4

structural components of a ribosome, the enzyme that catalyzes translation

Question 5

_____ 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’

Answer 5

RNA

Question 6

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

Answer 6

G-U

Question 7

internal base pairing within an RNA strand yields…

Answer 7

complex secondary and tertiary structures

Question 8

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

Answer 8

template

Question 9

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

Answer 9

reverse complement

Question 10

the RNA transcript resembles…

Answer 10

the coding strand

Question 11

trans-acting factors

Answer 11

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

Question 12

cis-acting elements

Answer 12

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

Question 13

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

Answer 13

promoter; terminator; primary transcript

Question 14

a gene includes the ….

Answer 14

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

Question 15

in bacteria, a primary transcript is used as…

Answer 15

an mRNA for translation without further modification

Question 16

open reading frame (ORF)

Answer 16

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

Question 17

operons

Answer 17

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

Question 18

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

Answer 18

promotor; RNA polymerase

Question 19

the bacterial consensus promoter

Answer 19

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

Question 20

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

Answer 20

transcription initiation

Question 21

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

Answer 21

constitutive promoter (always available/on)

Question 22

strong promoters

Answer 22

have very high sequence identity with the promoter consensus sequence

Question 23

weak promoters

Answer 23

have several base differences

Question 24

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

Answer 24

decreases the rate of transcription initiation

Question 25

E.coli has only one ...

Answer 25

RNA polymerase

Question 26

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

Answer 26

RNA polymerase holoenzyme

Question 27

holoenzyme consists of the ____________ subunits

Answer 27

a2BB'wsigma

Question 28

subunit sigma

Answer 28

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

Question 29

subunits a2

Answer 29

essential for enzyme assembly and interact with activators

Question 30

subunits B and B'

Answer 30

form the catalytic core

Question 31

subunit w

Answer 31

provides structural stability

Question 32

RNA polyermase core enzyme (a2BB'w)

Answer 32

carries out transcription elongation

Question 33

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.

Answer 33

de novo (without a primer)

Question 34

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

Answer 34

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

Question 35

NTP

Answer 35

ribonucleoside 5'triphosphates

Question 36

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

Answer 36

closed complex; sigma70

Question 37

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

Answer 37

open complex

Question 38

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

Answer 38

holoenzyme

Question 39

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

Answer 39

promoter clearance

Question 40

__________________ 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

Answer 40

transcription elongation; topoisomerases

Question 41

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

Answer 41

transcription termination

Question 42

rho-independent termination

Answer 42

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

Question 43

rho-dependent termination

Answer 43

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

Question 44

inducible promotors can be _________________

Answer 44

turned off and on

Question 45

repressors

Answer 45

transcription factors that decrease the rate of transcription from a promoter

Question 46

activators

Answer 46

transcription factors that increase the rate of transcription from a promoter

Question 47

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

Answer 47

helix-turn-helix

Question 48

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

Answer 48

transcription factors

Question 49

transcription factors bind to ___________ and ____________

Answer 49

major and minor grooves

Question 50

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

Answer 50

a-helix; major

Question 51

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

Answer 51

recognition helix

Question 52

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

Answer 52

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

Question 53

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

Answer 53

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

Question 54

protein motifs

Answer 54

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

Question 55

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

Answer 55

major groove

Question 56

CG and AT pairs can be distinguished in the __________

Answer 56

minor groove

Question 57

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

Answer 57

AT and TA

Question 58

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

Answer 58

4;3

Question 59

helix-turn-helix motif

Answer 59

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

Question 60

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

Answer 60

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

Question 61

________ 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

Answer 61

homodimeric; palindromic sequence

Question 62

why dimers and oligomers?

Answer 62

improved specificity and improved stability (more interactions)

Question 63

____________ 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.

Answer 63

repressors; RNA polymerase; ligands; repressors

Question 64

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

Answer 64

repressor; inducible promoter

Question 65

a repressor bound downstream inhibits...

Answer 65

promoter clearance by RNA polymerase

Question 66

a repressor bound to the promoter sequence blocks...

Answer 66

RNA polymerase from binding to the promoter

Question 67

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

Answer 67

dimer of dimers helix-turn-helix

Question 68

____ at lac promoter is the highest affinity binding site.

Answer 68

O1

Question 69

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

Answer 69

O2 and O3

Question 70

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

Answer 70

O1; O2 or O3 O1

Question 71

_________ 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

Answer 71

activators; RNA polymerase; promoter; ligands; activators

Question 72

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

Answer 72

inducible promoter

Question 73

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

Answer 73

activator; positive regulatory element

Question 74

____ 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

Answer 74

CRP; activator; cAMP; CRP; CRP-cAMP

Question 75

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

Answer 75

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

Question 76

in the absence of glucose, adenylate cyclase produces

Answer 76

cAMP

Question 77

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

Answer 77

glucose; lactose

Question 78

(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

Answer 78

lacl; lac repressor; lac repressor; allolactose; operator

Question 79

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

Answer 79

cAMP receptor protein; cAMP; CRP binding site