4-3: Transcriptional Regulation

Question 1

What is regulation

Answer 1

Controlling the abundance/activity of gene products
How cells adapt to environment

Question 2

How is transcription initiation regulated

Answer 2

Control whether or not RNAP binds a promotor and transcribes (or the rate at which this occurs)

Question 3

What proteins largely regulates intiation

Answer 3

Transcription factors

Question 4

Most regulatory proteins are what?

Answer 4

DNA-binding proteins

Question 5

DNA-binding proteins typically contain what domain?

Answer 5

Helix-turn-helix DNA-binding domains

Question 6

What other secondary domains to DNA binding proteins contain?

Answer 6

Dimerization, interacting with other proteins, regulatory domains

Question 7

What is recognized by DNA binding proteins?

Answer 7

Consensus sequence

Question 8

How are consensus sequences typically structured?

Answer 8

Contain direct or inverted repeats that are bound by heterodimers

Question 9

What are Activators?

Answer 9

Transcription factors that promote transcription are -bind DNA at promotor & recruit RNAP

Form of positive control

Question 10

What are repressors? .

Answer 10

TF that inhibit transcription by preventing RNA pol binding or transcriptional initiation

Question 11

What is the sequence bound by the repressor called

Answer 11

Operator (after promotor region)

Question 12

How is transcription regulated allosterically

Answer 12

Molecule binds activator or repressor to activate it

Question 13

What are inducers

Answer 13

“Turn on” activator proteins (or inactivate repressors)

Question 14

What are corepressors

Answer 14

Activate repressor proteins

Question 15

What is an inducible system

Answer 15

System that is off by default, can be turned on

Question 16

What is a repressible system

Answer 16

One that is on by default, can be turned off

Question 17

What is ArgR?

Answer 17

repressor protein that controls the expression of arginine biosynthesis operon

Question 18

How does ArgR function in low and high arginine levels

Answer 18

Low = not bound by arginine, does not bind DNA, transcription of arginine proceeds

High = arginine binds ArgR. so it binds the operator and prevents transcription

Question 19

What is the Lac operon?

Answer 19

Encodes machinery for breaking down lactose. Inducible system (catabolic)

Question 20

What is the LacI repressor protein?

Answer 20

Repressor of lac operon, binds the lac operator, prevents transcription

Question 21

What does LacI do when lactose is available vs absent

Answer 21

Available = lactose isomer (allolactase = inducer) binds LacI and inactivates it

Absent = LacI binds lac operator preventing transcription of lac operon (because it would make machinery for lactose breakdown; there is none present = wasted energy)

Question 22

What happens to the lac operon in the presence of glucose

Answer 22

cAMP production inhibited

Lac operon requires CRP (cAMP receptor protein) to bind cAMP. Together they would bind the promotor region & recruit RNAP

Question 23

What does the Lac operon require

Answer 23

Lactose and low glucose levels

Question 24

What is a direct inducer of lac operon? What is indirect?

Answer 24

Glucose - indirect
cAMP - direct

Question 25

What are some nucleotide based second messengers in bacteria?

Answer 25

cAMP, (p)ppGpp, cyclic-di-GMP

Question 26

What is ppGpp

Answer 26

Signaling molecule produced in response to aa starvation. Shuts down protein synthesis and induces aa biosynthesis in a process called stringent response

Question 27

What is quorum sensing

Answer 27

Chemical communication: sensing local density of cells through secretion/detection of specific molecules

Question 28

Why is quorum sensing important

Answer 28

Coordinate group behaviours like biolfilm formation, virulence

Question 29

What are autoinducers? How do they work in quorum sensing?

Answer 29

Produce small molecule (Autoinducers)
Only accumulate and detected at high density

Question 30

Name an autoinducer

Answer 30

Acyl homoserine lactones (AHL), common in gram -

Question 31

Name one example of an organism that uses quorum sensing

Answer 31

Vibrio fischeri (quid symbiont). Produces an enzyme that carries out bioluminescence, but one when present in high concentrations in the special light producing organ of the squid

Question 32

What are the proteins used in two-component regulatory system

Answer 32

Sensor kinase

Response regulator

Question 33

What is sensor kinase

Answer 33

Cytoplasmic membrane protein. Senses signals that activate kinase.

Question 34

What is the response regulator

Answer 34

Active once phosphorylated by sensor kinase. Binds DNA to regulate expression of genes (activate/repress)

Question 35

What is a local vs global regulator

Answer 35

Local regulator = control expression of limited number of genes

Global regulator = regulate large numbers of different genes in response to signal

Question 36

What is a Regulon?

Answer 36

Complete set of genes controlled by a given regulator

Question 37

What is an example of a two component system

Answer 37

PhoPQ two component system, that is a glocal regulator of virulence in Salmonella

Question 38

Is archaea transcription similar to euks or bacteria?

Answer 38

Similar to bacteria

Question 39

Give a brief description of transcription in eukaryotes

Answer 39

Activators/repressors bind DNA to affect recruitment of RNA pol

Question 40

Are two component systems found in archaea?

Answer 40

Yes, but not as common as bacteria