transcriptional regulation

Question 1

what do contemporary techniques rely on?

Answer 1

dNTPs which emit light (when exited) upon incorporation into DNA.

Question 2

contemporary techniques can be scaled up to sequence a __________ bases

Answer 2

whole human genome of 3 x 10^10

Question 3

in massive parallel sequencing, all DNA clusters are sequenced in _____

Answer 3

parallel

Question 4

in RNA sequencing, RNA is ____ from a sample and converted to ____ by the use of a ______.

Answer 4

isolated, DNA, specific primer

Question 5

chromatin immunoprecipitation (ChIP) is a ______ technique that detects the _____ of a specific ________ to a specific _________. is this in vivo or in vitro?

Answer 5

multi-step, binding, protein, DNA element.
In vivo

Question 6

gel-mobility shift is a _____ technique that detects the _____ of a specific _____ to a specific _______. Is this in vivo or in vitro?

Answer 6

simple, binding, protein, DNA element.
in vitro

Question 7

in the pre initiation complex the helices activity of _____ locally “___” DNA at the ______ site

Answer 7

TFIIH, melts, initiation

Question 8

what is Ssl2?

Answer 8

component of the TFIIH that opens initiation transcription

Question 9

what have mutations in subunits of TFIIH been identified as?

Answer 9

cause of a specific skin cancer: Xeroderma pigmenostum

Question 10

what does the mutation of TFIIH inhibit?

Answer 10

DNA repair caused by such things as exposure to light

Question 11

HIV has a mechanism to suppress _____ activity by a virally encoded protein called ____. this _____ RNA polymerase II at its ______. Upon ______, TAT _______ CDK9/CycT and the polymerase ________ the virus.

Answer 11

CDK9/CycT, TAT. pauses, promoter. stress, releases, transcribes.

Question 12

NELF and DSIF cause the ____ of the polymerase _____ initiation. further _____ of CTD by CDK9/CycT _______ the polymerase: _______ begins

Answer 12

pausing, after. phosphorylation, release. elongation.

Question 13

how is expression of eukaryotic protein coding genes regulated?

Answer 13

through protein binding transcription control regions at various distances from the transcription start site

Question 14

what do promoters direct, determine and influence?

Answer 14

-direct the binding of RNA pol II to DNA
-determine the site of transcription initiation
- influence the frequency of transcription initiation

Question 15

true or false. promoter-proximal elements and enhancers are cell type non-specific.

Answer 15

false
cell type specific

Question 16

do promoters function within a short or long distance? what distance exactly?

Answer 16

short distance
several hundred bps from transcription initiation site

Question 17

do enhancers function within a short or long distance? what distance exactly?

Answer 17

long distance
over tens of kbps from transcription initiation site

Question 18

are promoters upstream or downstream from the initiation site? or within introns?

Answer 18

upstream of the initiation site

Question 19

are enhancers upstream or downstream from the initiation site? or within introns?

Answer 19

can be upstream
downstream from the start or within introns

Question 20

are promoters position dependent or position independent? if moved are they non-functional or functional?

Answer 20

dependent
non-functional

Question 21

are enhancers position dependent or position independent? if moved are they non-functional or functional?

Answer 21

independent
functional

Question 22

are promoters orientation dependent or orientation independent? uni or bi directional

Answer 22

orientation dependent
drive transcription in only one direction

Question 23

are enhancers orientation dependent or orientation independent? uni or bi directional

Answer 23

orientation independent
function in either normal or the inverted orientation

Question 24

how do enhancers communicate with promoters?

Answer 24

via bending DNA

Question 25

in the communication between enhancers and promoters, when do nucleosomes move away and come back in?

Answer 25

moved away when pol II initiates
moves back when pol II passes

Question 26

what is the function of a helix loop helix

Answer 26

forms single functioning enhancer