PHILLIPS CH9

Question 1

activators

Answer 1

regulatory proteins that increase transcription

Question 2

repressors

Answer 2

regulatory proteins that decrease transcription

Question 3

helix-turn-helix motif

Answer 3

motif on transcriptional regulators, one helix fits into major groove, sequence specific contacts with DNA bases, often found as a dimer

Question 4

zinc finger motif

Answer 4

central zinc ion coordinated by 2 cysteines and 2 histidines

Question 5

coiled-coils

Answer 5

2 alpha helices wind around eachother

Question 6

basic region-leucine zipper (bZIP)

Answer 6

2 long alpha helix monomers, N terminal ends splay out and sit in the DNA major groove

Question 7

basic region-helix-loop-helix (bHLH)

Answer 7

each monomer consists of 2 helices joined by a loop, monomers interact with DNA and one another

Question 8

beta sheets

Answer 8

DNA binding motif, can mediate DNA recognition

Question 9

operator sites

Answer 9

sequences recognized by regulators

Question 10

architectural DNA binding proteins

Answer 10

can loop DNA when regulatory sequences are several hundred bp away

Question 11

allosteric effectors

Answer 11

small molecules that can bind directly to the regulatory proteins and change their conformation (e.g. estrogen)

Question 12

operon

Answer 12

cluster of genes that are regulated and transcribed together, usually involved in the same process (Trp operon genes transcribed when tryptophan is low)

Question 13

catabolite activator protein (CAP)

Answer 13

activates more than 100 E Coli genes by enhancing RNA polymerase affinity to promoters
binds when glucose is low

Question 14

CAP activation process

Answer 14

glucose depletion > cAMP increase > cAMP binds to CAP > CAP increases affinity to bind to DNA

Question 15

lac operon

Answer 15

responsive to glucose and lactose (expressed if glucose low & lactose present > metabolize lactose as an alternative energy source)

Question 16

lac repressor

Answer 16

binds in the absence of lactose to prevent transcription of lac operon (prevent metabolizing lactose)

Question 17

allolactose

Answer 17

metabolite of lactose, allosteric regulator for the lac repressor, lac repressor is not used

Question 18

MerR protein

Answer 18

allows RNA pol to bind more efficiently, enhancing transcription

can bind to and bend the DNA to effectively change the spacing (of -10 and -35 elements), readjust orientation of promoter elements

Question 19

bacterial transcriptional regulation - two component signal transduction pathway

Answer 19

sensor kinase detects amount of a specific molecule in the environment by becoming autophosphorylated. phosphate passed to a response regulator protein which acts as a transcriptional activator or repressor

Question 20

attenuation

Answer 20

regulation of transcription by competition between ribosome binding and formation of stem-loop structures in the transcript
low trp > ribosome stalls, stem loop forms, anti-terminator
high trp > ribosome proceeds, attenuator forms - terminator stem loop

Question 21

riboswitches

Answer 21

RNA segment of an mRNA that bind a small molecule, regulate production of protein encoded by that mRNA

Question 22

aptamer

Answer 22

region of riboswitch that binds to small molecule

Question 23

expression platform

Answer 23

region of riboswitch which controls the output (ex. transcription)

Question 24

transcriptional termination by riboswitches

Answer 24

low adenine > anti-terminator, transcription proceeds
high adenine > adenine binds the aptamer to form a terminator

Question 25

enhancers

Answer 25

regulatory sequences for eukaryotic genes

Question 26

DNA binding proteins

Answer 26

do not regulate transcription directly, recruit other proteins such as co-activators and co-repressors (which cannot bind on their own), often modular

Question 27

hyperacetylated chromatin

Answer 27

tends to be actively transcribed (low transcription in hypoacetylated chromatin)

Question 28

eukaryotic transcriptional regulation in response to galactose

Answer 28

Gal4 binds to DNA upstream of genes for galactose metabolism
Gal4 activity regulated by Gal80 - binds to Gal4 and blocks recruitment of co-activators
Gal3 can bind Gal80 when galactose is bound to Gal3 (prevents Gal80 + Gal4 binding)
Gal4 recruits co-activators Mediator and SAGA

Question 29

eukaryotic transcriptional regulation by histone modification and Ume6

Answer 29

can activate and repress transcription in response to nutritional cues

adequate nitrogen & glucose > binds DNA, recruit histone deacetylase and nucleosome remodeler > pack chromatin, prevent transcription

Ume6 phosphorylated in absence of nitrogen & glucose, histone acetyltransferase recruited, opens up chromatin, promotes transcription

Question 30

eukaryotic transcriptional regulation at elongation

Answer 30

transcription pauses 30-50 bp downstream of start site due to insufficient phosphorylation

elongation can be regulated by restarting paused polymerases through heat shock > heat shock factors (Hsf) conformational change > binds to heat shock elements (HSEs) > Hsf interacts with Mediator and kinase > phosphorylates CTD > transcription resumes

Question 31

nuclear receptor proteins

Answer 31

ligand regulated transcription factors - have a DNA binding domain and a ligand binding domain

ligand binding induces conf change to recruit co-activators/co-repressors, can be competitive with drugs