Topic 6-L3 - Transcriptional regulation

Question 1

How to cells adapt to their environment

Answer 1

Controlling the abundance/activity of gene products

Question 2

Regulating transcriptional initiation

• transcription factors

Answer 2

control whether or not RNA polymerase binds a promoter and initiates transcription (more accurately, the rate at which that occurs). Largely accomplished by DNA-binding
regulatory proteins called transcription factors

Question 3

Many regulatory proteins are

Answer 3

DNA-binding proteins

Question 4

DNA-binding proteins have

Answer 4

DNA-binding domains such as the HTH domain that bind to DNA helix

Question 5

DNA binding proteins often recognize a

Answer 5

consensus sequence

Question 6

Often DNA sequences with direct or

inverted repeats are bound by homodimers, which are

Answer 6

one monomer binds each repeat,

dimerization required. Ensures specificity

Question 7

Transcription factors that promote transcription are called

Answer 7

activators

Question 8

Transcription factors that inhibit transcription are called

Answer 8

Repressors

Question 9

Activators often work by binding

Answer 9

DNA at promoter & recruiting RNA polymerase (sigma factor) to begin transcription. Gene under “positive control”

Question 10

Repressors bind DNA & (often)

prevent

Answer 10

RNAP DNA binding or transcriptional initiation after it binds. Sequence bound by repressor often called operator.
Gene under “negative control”

Question 11

Some transcription factors are regulated allosterically –

Answer 11

binding of an effector (usually a small molecule such as a metabolite) activates or inactivates protein

Question 12

Inducers

Answer 12

“turn on” activator proteins (or inactivate repressors)

Question 13

Corepressors

Answer 13

activate repressor proteins

Question 14

An inducible system is one

that is

Answer 14

off by default, but can be turned on.

Question 15

repressible system is one

that is

Answer 15

on by default, but can be turned off (a gene can be controlled by both)

Question 16

Example of a repressible system:

Answer 16

Arginine biosynthesis

Question 17

Arginine biosynthesis

Answer 17

ArgR is a repressor protein that controls the expression of an arginine
biosynthesis operon

Question 18

When arginine is present, acts as a

Answer 18

co-repressor.

Question 19

When arginine levels are high, it

Answer 19

binds ArgR, enabling ArgR to bind

the Operator & prevent transcription of this operon

Question 20

When arginine levels are low,

Answer 20

ArgR isn’t bound by arginine, doesn’t

bind DNA – genes are expressed and arginine is synthesized by cell

Question 21

Lac operon

Answer 21

Code for the breakdown for lactose (E source)

Question 22

Expressing these genes for lac operon in absence of lactose not useful – to prevent this,

Answer 22

LacI repressor protein binds lac Operator, prevents transcription

Question 23

When lactose is available, a

lactose isomer called

Answer 23

allolactose binds LacI & inactivates it

allolactose = inducer

Question 24

E. coli doesn’t want to use lactose if a better energy source is available –

Answer 24

Catabolite repression

Question 25

Lac operon expression requires both:

Answer 25

lactose AND low glucose levels.

Question 26

In the presence of glucose, production of cAMP is _________. Low cAMP levels in cell For lac operon to be expressed, also requires _____________ to bind cAMP. cAMP- bound CRP binds promoter region & recruits RNA polymerase

Answer 26

inhibited. CRP (cAMP receptor protein)

Question 27

Glucose regulation is

Answer 27

indirect (cAMP is direct inducer)

Question 28

(cAMP) is an example of a

Answer 28

signaling molecule or second messenger

Question 29

ppGpp produced in response to

Answer 29

amino acid starvation.

Question 30

ppGpp shuts down protein synthesis & induces amino acid biosynthesis in a process that is called

Answer 30

stringent response

Question 31

Quorum sensing also involves signaling molecules called

Answer 31

autoinducers

Question 32

Quorum sensing involves sensing the

Answer 32

local density of cells through | secreting/detecting specific molecules – regulating based on that info.

Question 33

Quorum sensing is used to

Answer 33

coordinate group behaviours like biofilm formation, virulence, etc. Only want to carry out these activities make certain genes at high cell densities

Question 34

Produce autoinducer (small molecule) – secrete – it diffuses away. Doesn’t accumulate in cell except at high density. Detect high density –

Answer 34

know you’re in a group – activate group behaviours

Question 35

Example of autoinducer

Answer 35

AHL

Question 36

Quorum sensing is a form of

Answer 36

chemical communication. | used by All 3 domains

Question 37

Quorum sensing using AHLs involves regulating the expression of numerous

Answer 37

genes in response to the concentration of AHLs sensed by the cell

Question 38

Different species produce/detect their own specific versions of

Answer 38

AHL (different R groups)

Question 39

Quorum sensing first discovered in

Answer 39

Vibrio fischeri

Question 40

A very common form of gene regulation in bacteria is the two-component regulatory system – form of

Answer 40

signal transduction

Question 41

Two-component regulatory system uses two protiens:

Answer 41

Sensor kinase and response regulator

Question 42

Sensor kinase:

Answer 42

Usually resides in cytoplasmic membrane. Senses specific signal(s), which activates kinase activity - adds phosphate to response regulator. In absence of signal, will dephosphorylate response regulator.

Question 43

Response regulator:

Answer 43

When phosphorylated, becomes active. Binds DNA to regulate expression of target genes (activator and/or repressor)

Question 44

Transcriptional silencing:

Answer 44

very tightly shutting off expression of genes by altering the genome structure at promoter regions

Question 45

Best known silencer is for transcriptional silencing

Answer 45

H-NS

Question 46

H-NS prevents

Answer 46

binds & restructures DNA to a rigid structure to prevent RNA polymerase from binding the DNA and/or carrying out transcription process

Question 47

H-NS binds regions of the genome that have a

Answer 47

high % AT

Question 48

high % AT in H-NS represent

Answer 48

horizontally-acquired DNA (genomes have a characteristic % AT).

Question 49

Counter-silencing DNA-binding activators bind

Answer 49

specific silenced loci and reverse effects of H-NS (re-structure DNA and/or remove H-NS) allow specific genes to be expressed

Question 50

Global regulators regulate large numbers of different genes in response to a

Answer 50

given signal or environmental cue

Question 51

A regulon is the

Answer 51

complete set of genes controlled by a given regulator

Question 52

``` Sigma factors, allosteric regulatory proteins, two-component systems, transcriptional silencers, second messengers, quorum sensing – all can potentially exert ```

Answer 52

global control

Question 53

PhoPQ acts as a

Answer 53

global regulator of many virulence- related processes in Salmonella

Question 54

Despite differences in transcription | mechanisms, transcriptional regulatory systems in Archaea often synonymous with

Answer 54

bacterial systems

Question 55

Activators/repressors bind

Answer 55

DNA to affect recruitment of RNA | polymerase

Question 56

Two -component regulatory systems | also present in

Answer 56

Arachaea, less common then in bacteria tho