Transcriptional regulation

Question 1

How to regulate activity of genes

Answer 1

-control abundance and activity of genes is essential for every cell l, it’s how cells adapt to their environments

Question 2

Regulation of transcriptional initiation

Answer 2

All levels of regulation are used (regulation protein, translation, transcription, protein activity)
- basic idea is to control whether or not RNA polymerase binds to promoter and initiated transcription / more accurately the rate at which it occurs
-DNA binding regulatory proteins called transcription factors are important
- sensing is key, you need to know which genes to turn on and off and when therefore we need to detect environmental cues and cellular status

Question 3

DNA binding regulatory proteins

Answer 3

-many regulatory proteins are DNA binding proteins
-they have DNA binding domains that usually bind the major groove of DNA helix
-DNA binding proteins often recognize consensus sequence (flexible)
-often DNA sequences it difect or inverted repeated are bound by homodimers -one monomer binds each repeat

Question 4

Activators

Answer 4

-transcription factors that promote transcription
-work by binding DNA at promoter and recruiting RNA polymerase (sigma factor) to begin gene transcription
-gene under positive control

Question 5

Repressor

Answer 5

-transcription factors that inhibit transcription
-bind DNA and often prevent RNAP DNA binding or transcriptional initiation after it binds
-sequence bound by repose or often called operator
-gene under negative control

Question 6

operator

Answer 6

sequence bound by repressor

Question 7

allosteric regularoy proteins

Answer 7

-some TF are regulated allosterically binding of an effector (small molecule) that activates or inactivates the protein
=-often works by altering whether it binds DNA
-induceers, coreprossors

Question 8

inducers

Answer 8

-effectors that turn on activator proteins or inactivate repressors
-allosteric regulatory proteins

Question 9

corepressors

Answer 9

effectors that activate repressor proteins
-allosteric regulatory proteins

Question 10

inducible system

Answer 10

-system that is off by default but can be turned on

Question 11

repressible system

Answer 11

is a system that is on by default but can be turned off

Question 12

is a single gene controlled by inducible or repressible system

Answer 12

both

Question 13

allosteric photo

Answer 13

Question 14

ArgR

Answer 14

-repressor protein that controls the expression of an argenine biosyntheis operon

Question 15

argenine biosynthesis

Answer 15

ArgR regulated multiple co-transcribed genes that function to produce arginine from precursor molecules in the cell
-when argenine is present rgR acts as a co-repressor
-when argine levels are low, ArgR is not bound by argenine and does bind DNA, genes are expressed and argenine is synthesized bt the cell
-When arginine levels are high it binds ArgR enabling ArgR to bind the operator and prevent transcription of this operon

Question 16

lac operon

Answer 16

-lactose good energy for ecoli
-machinery for breaking down lactose is encoded by the lac operon
–expressing these genes in absence of lactose is not useful so LacI reprossor protein binds lac operator preventing transcription
-when lactose is avaliable a lactose isomer (allolactose) binds LacI and inactivated it (allolactose is an inducer)

Question 17

lac operon in the presence of glucose

Answer 17

-glucose is better energy source than laxtose - catabolite repression
-in the presence of glucose production of cAMP is inhibited. Low cAMP levels in the cell
-lac operon needs CRP to be expressed to bind to cAMP
-cAMP bound CRP binds promoter region and recruits RNa polymerase
-lac operon requires lactose and low glucose levels
-glucose regulation is indirect

Question 18

cAMP as a signalling molecule

Answer 18

-cAMP is a signalling moleculd or second messenger
-in bacteria, nucelotide based molecules are extensively used for this
-produced in response to some signals, then regulate mutltiple processes in the cell
-impact the activity of multiple regulatory or non regilatory proteins

Question 19

ppGpp

Answer 19

signalling molecule produced in response to AA starvation
-ppGpp shits down protein synthesis and induced AA biosynthesis in a process called stringent response

Question 20

quorum sensing

Answer 20

-involves signalling molecules called autoinducers
-form of chemical communcation used by all domains
-involved sensing the local density of cells through secreting detecting specific molecules and regulating based on that info
-used to coordinate group behvaiours like biolfilm formation - only carry these activities at high cell densities

Question 21

basic idea of quroum sensing

Answer 21

-produce autoinducer it diffuses away, doesnt accumulate except at high density
-detect high density- know your in a group - activate group behvaiours

Question 22

common autoinducer in gram neg

Answer 22

AHL

Question 23

vibrio discehri

Answer 23

-produces an enzyme that carries out luminescent reaction but only when present at high concentration in specialized light producing organ of squid

Question 24

two component regulatory system

Answer 24

form of signal transduction that uses sensor kinase and response regulatory
-largest gene families in bacter
signal sesned by sensor kinase is often difficult to discern
-tightly regulated

Question 25

sensor kinaset

Answer 25

usually in the cytoplasmic membrane
-senses signal which activates kinase activity
-adds phosphate to response regulator
-in absence of signal dephosphorylates response regulator

Question 26

response regulator

Answer 26

when phosphorylated becomes active
-binds DNA to regulate expression of target genes

Question 27

two component regulatory systems

Answer 27

Question 28

transcriptional regulation in archaea

Answer 28

-different transcription mechanisms (4-1)
-TRANSCRIPTIONAL REGULATORY STSEMS IN ARACHEA OFTEN ANALOGOUS WITH ABCTERIAL SYSTEMS
-activators and repressors bidn DNA to affect recruitment of RNA polymerase
-have two component regulatory systems but not as common
-more complex regulation in eukarya