regulation of gene expression

Question 1

microbe response

Answer 1

microbes respond immediately to enviro changes

• chemotaxis: movement towards fuel or light source
• facultative aerobe: switch from O2 to alternate e-acceptor
• temperature change - increase or decrease in unsaturated FA in membrane

Question 2

how pathogens signal pathogenesis

Answer 2

express virulence factors to establish infection

- express genes to establish symbiont-host relationship

Question 3

gene expression in prokaryotes

Answer 3

start @ promotor
stop @ terminator
RNA polymerase creates single mRNA transcript form stuff in the middle

Question 4

polycistronic mRNA

Answer 4

one transcript encodes multiple polypeptides; ORF separated by stop codons + intercistronic regions of varying length

Question 5

what are polycistronic genes

Answer 5

high gene density on DNA. some genes read forward, others in reverse. tighlty regulated

Question 6

RNa polymerase, promoter + sigma factor recognition sites

Answer 6

need RNA pol+ sigma factor together to read off rna.

diff sigma factors interact w rna pol to get diff sequence from same/similar mrna strand

Question 7

what is probnow box?

Answer 7

10 nucleotides form start. from -10 to -35 sigma + holoenzyme start trasncribing from

Question 8

process of transcription

Answer 8

RNA pol + sigma factor come together at promoter region.
- sigma recognizes promotoer + initiation site
- trxn starts, sigma released. RNA chain grows to termination
- chain stops
- release polymerase and RNA
= once RNApol moves down, another guy can hop on at same time

Question 9

transcription termination

Answer 9

DNA contains inverted repeats
- complementary base-pair stem-loop inhibits continuation of trxn.
physical interference with movement of RNA pol

Question 10

coupled trxn and translation

Answer 10

both in cytoplasm. as RNa strand formed, ribosomes hop on and synthesize protein.

Question 11

polysome:

Answer 11

translation of single mRNA by several ribosomes

= rapid turn on/off. exponential synthesis

Question 12

4 ways of regulating activtiy

Answer 12

1. constitutive expression - no control
2. metabolic or posttranslational control of enzyme activity
3. regulation of enzyme synthesis at translation
4. regulation of enzyme synthesis at transcription

Question 13

regulation of enzymes

Answer 13

posttranslational
- direct control of enzyme activtiy
- rapid
allosteric regulation

Question 14

regulation of transcription

• operon
• structural genes
• operator
• promoter
• regulator

Answer 14

operon: genetic element that controls synthesis of several proteins in prokaryotes

structural genes that encode polypeptides

operator: starts/halts txn by binding protien factors
p: bind RNapol for txn

R: encodes single protein (green circle) which binds to operator to control gene expression

Question 15

negative transcriptional regulation

Answer 15

block mRNA synthesis

• enzyme overly abundant
• activity no longer necessary or detrimental to cell
• involves “repressor protein” to bind DNA and block RNApol

Question 16

positive transcriptional regulation

Answer 16

stimulate mRNA synthesis

• more enzyme needed in cell
• activator protein bind to DNA and promote transcription

Question 17

what are constitutive genes?

Answer 17

housekeeping

- no regulation

Question 18

repressible genes

Answer 18

expression stopped when product not needed

- level of enzyme decreases in presence of repressor and co-repressor

Question 19

inducible genes

Answer 19

expressed only when need arises
b-galactosidase induced when glucose is gone, lactose is present
- catalyze lactose hydrolysis to galactose and glucose
- level of enzyme rises in presence of repressor and inducer

Question 20

negative control - enzyme reduction ex: arginine added to e.coli on media.

Answer 20

enzyme for argninine shut down to conserve energy. arginie corepressor to prevent own synthesis.

Question 21

what is corepressor

Answer 21

repressor cannot bind operator alone. corepressor needed to bind to repressor to bind to operator. once bound no more synthesis

Question 22

negaative control: enzyme induction

Answer 22

e.coli growing on substrate other than lactose.

lactose added = enzymes induced + transcribed.
- de novo enzyme synthesis

Question 23

how lactose presence = enzyme induction

Answer 23

repressor bound at operator of lac operon.

lactose = inducer: binds to repressor causing its removal, txn allowed

Question 24

positive control

Answer 24

• activator protein promotes binding of RNA polymerase promoter
• non-continuous operons involved
• inducer molecule required for activator to bind DNA
• maltose is inducer

Question 25

catabolite repression

Answer 25

expression of genes to metabolize non-preferred sugar are repressed due to lack of catabolite (cyclic AMP). want to use preferred substrate first. non-preferred second.

Question 26

what is diauxic growth?

Answer 26

glucose metabolized first - gene expression for lactose metabolism turns on B-galactosidase - lag during switch in gene expression and de novo enzyme synthesis. biphasic growth curve.

Question 27

transcription of lac operon onlly occurs when?

Answer 27

glucose levels are low AND lactose is present

Question 28

Catabolite activator protein + lac operon?

Answer 28

CAP - bind to site upstream ofpromoter in lac operon to stimulate transcription (+regulator) CAP bound to catabolite, cAMP, to be active. glucose transport inhibits cAMP synthesis and lactose transport catabolite repression lifted by adding caMP to media

Question 29

lac operon under both positive and negative control

Answer 29

CAP binds to cAMP = cap-cAMP dimer. bind to lac operon increases binding of RNA polymrase at promoter - txn of lac genes begins -lactose required as inducer to remove repressor protein bound at operator (negative control of lac operon)

Question 30

summary of lac operon regulation

Answer 30

1. Lactose, no glucose. repressor inactive, CAP--cAMP stimulates txn 2. galactose + glucose. allolactose take off repressor. cAMP levels too low to activate CAP no trxn 3. no lactose, no glucose. both activator and repressor are active. no trxn 4. glucose, no lactose. no caMP and repressor block txn

Question 31

CAP as global regulator

Answer 31

regulates several operons under control of different catabolites - arabinose, galactose, maltose, + other carbon sources. - each operon under control of negative regulators too. - some features differ for each operon, binding by CAP-cAMP is same

Question 32

what is regulon

Answer 32

multiple operons responding to common regulatory protein - CAP operon. all the stuff that CAP moderates

Question 33

good things about global regulation

Answer 33

multiple operons allow bacteria to quickly adjust to changing enviro

Question 34

what happens when alternate sigma factors are produced?

Answer 34

sigma factor = nutrient deprivation, creates spore. global effects = cell differentiation = tolerance to abrupt temp changes = increase in osmolarity

Question 35

e. coli regulons

Answer 35

O2 both +/-, [caMP], temp, -NH3 oxygen radical damaged DNA

Question 36

two-component regulatory systems and phosphorelay

Answer 36

two component signals link external events to regulation of gene expression - transfer of phosphoryl group from one protein to another

Question 37

signal transduction - sensory kinase - response regulator

Answer 37

sK: respond to enviro signal "effector molecules". become phosphorylated RR: phosphorylated by sensor kinase. becomes activator of gene expression. dephosphorylated by phosphatase enzyme

Question 38

OmpF/OmpC porin proteins

Answer 38

f - wider diameter than c= more nutrients through. C protects against bile salts f - used when osmotic pressure is low. c when osmotic pressure is high

Question 39

regulation by two component signal transduction, envZ for OmpF repression

Answer 39

EnvZ - sensor kinase - sense increase in osmolarity. autophosphorylates and passes phosphoryl group to OmpR, the response regulator - ompR-P can bind to DNA to repress ompF and activate ompC expression

Question 40

quorum sensing

Answer 40

regulation in response to cell density. regulated by autoinducer. -> diffusible signaling, molecule in membrane: acetyl homoserine lactone (AHL) found in g- bacteria, species specific, and synthesized in cell and diffused out. triggers cascade - binds to regulator (enhancer) quorum binds to operator to recruit polymerase. lux increases. shift from none to lots of transcription when there are a certain number of cells

Question 41

lux operon

Answer 41

cells glow due to luciferase enzyme. = bioluminescent bacteria. encodes AHL synthase. luxR(activator) binds AHL (inducer) and positively regulates expression of lux genes = bioluminescence

Question 42

best studied bacterium for bioluminescence

Answer 42

vibrio fischeri. luminescence takes place only at hgih cell density when quorum sensing genes are induced.

Question 43

bacterial communications

Answer 43

cross-talk, "eavesdrop", sensing, signaling molecules. = stop cross talk may be antimicrobial drug source? no signal that enough cells to trigger infection = no onset of infection

Question 44

antisense RNA

Answer 44

transcribed from opposite DNA strand of mRNA. - base pair with mRNA to prevent translation,(+) control or degrate RNA. regulate synthesis from synthesized RNA

Question 45

translational control: riboswitches

Answer 45

g(-) bacteria = regulate translation of mRNA - absence of ligand, mRNA forms stem-loop and access to binding sequences (shine-dalgarno). in presence of ligand, diff interaction = diff stem-loop no access to ORF (shine-dalgarno)