Prokaryotic Gene Structure 4

Question 1

what are the two levels of control of bacterial gene expression?

Answer 1

1. @ diff levels of info transfer
* replication
* initiation of transcription
* transcriptional elongation
* post-transcription
* translation
* post-translation
2. global regulatory systems
* affect many genes & pathways at the same time

Question 2

what are the 3 types of gene expression

and brief description

Answer 2

1. constitutive genes (expressed continuously) ON
2. inducible genes (specifically activated for expression) OFF
3. repressible genes (specifically repressed expression) ON

Question 3

what are inducible genes?

Answer 3

genes that are off unless an inducer is present to promote gene expression

Question 4

what are repressible genes?

Answer 4

genes that are on except when an inhibitor/corepressor is present that suppresses gene expression

Question 5

what are activators & repressors?

Answer 5

regulatory proteins that bind to DNA & whose activity may be modulated by binding of inducers or inhibitors

Question 6

what do activators do

Answer 6

promote/induce transcription = positive control

Question 7

what do repressors do

Answer 7

repress/inhibit transcription = negative control

Question 8

what are small effector proteins/metabolites (3)

+ function

Answer 8

• non-covalently bind regulatory proteins as activators or repressors
• change activity of regulatory proteins
• affect transcription by interacting w regulatory proteins

Question 9

Inducible genes can be positively controlled and repressible genes can be negatively controlled depending on what ? (4)

Answer 9

• presence of activator & operator sites (cis sites) on DNA associated with specific gene.
• binding of activator and repressor regulatory proteins (inducers and/or inhibitors) on cis sites.
• positive regulatory control mechanisms for inducible genes and repressible genes.
• negative regulatory control mechanisms for inducible genes and repressible genes

Question 10

what is a cis-regulatory element?

+ examples

Answer 10

region of DNA/RNA involved in regulating expression of genes located on the same molecule

examples for DNA: consensus sequence
RNA: shine dalgarno, rut site

Question 11

ito of inducible genes, what happens in the absence of an inducer? (positive control)

Answer 11

activator cant bind to activator site & no transcription by RNA polymerase

Question 12

what does it mean for an inducible gene when an inducer is present? (positive control)

Answer 12

changes conformation of activator protein and allows it to bind to its activator site, which allows RNA polymerase transcription

Question 13

in the absence of an inducer, what is the difference in what happens to the inducible gene in negative and positive control

Answer 13

positive control = activator can’t bind to activator site & no transcription by RNA pol
negative control = repressor blocks transcription by RNA pol by binding to operator site within promoter region

Question 14

in the presence of an inducer, what is the difference in what happens to the inducible gene in negative and positive control

Answer 14

positive control = changes conformation of activator protein and allows it to bind to its activator site, which allows RNA polymerase transcription
negative control = changes conformation of repressor protein upon binding to it & releases it from operator site

Question 15

in the absence of an inhibitor, what is the difference in what happens to the repressible gene in negative and positive control

Answer 15

positive control = activator can bind to activator site & facilitates transcription by RNA pol
negative control = repressor unable to bind to operator site & transcription occurs

Question 16

in the presence of an inhibitor, what is the difference in what happens to the repressible gene in negative and positive control?

Answer 16

positive control = changes conformation of activator protein so can no longer to its activator site - prevents transcription
negative control = changes conformation of repressor protein upon binding & allows repressor + inhibitor to bind to operator site & no transcription

Question 17

why is the nucleotide sequence of the promoter (a cis regulatory element) important?

Answer 17

• it determines strength & stability of binding by RNA pol to promoter region (influences efficiency initiation of transcription)
• weak binding by RNA pol due to deviations from consensus sequence = weak transcription

Question 18

what is an example of trans-regulatory elements?

Answer 18

repressor & activator proteins

Question 19

what is an example of post-transcriptional regulation and explain how it works?

Answer 19

mRNA stability
mRNA half-life results in short or long translation window for ribosomes (short half life = few proteins produced from mRNA molecules)

Question 20

what is mRNA half-life?

Answer 20

when mRNA exists for a few seconds to several hours as a result of 3D struc of mRNA

Question 21

what type of regulation is the shine dalgarno sequence and how does it regulate?

Answer 21

• translational regulation
  poor shine delgarno = weak binding of ribosome (little protein produced)

Question 22

how do sRNAs (non coding RNAs) act as a form of regulation?

Answer 22

• translational regulation
• some sRNAs base pair to leader region of target mRNAs to block ribosome binding (and translation)
• some sRNAs promote translation by binding to mRNA - change secondary structure

Question 23

what is the general concept of a riboswitch?

Answer 23

small-molecule ligand binds to mRNA molecule to regulate the expression of the mRNA molecule

Question 24

what is the riboswitch region?

Answer 24

upstream of shine dalgarno in form of a hairpin loop that has binding site for ligand

Question 25

which sugar is always the sugar of choice for E.coli?

Answer 25

glucose

Question 26

what is catabolite repression?

Answer 26

synthesis of enzymes involved in catabolism of less-favoured sugars is prevented by the presence of the preferred sugar (glucose)

Question 27

what do each of the lac genes code for? (3)

Answer 27

lac z = beta-galactosidase (hydrolyses lactose)
lac y = permease (transports lactose into cell)
lac a = transacetylase

Question 28

what is diauxic growth

Answer 28

biphasic growth pattern - preferential use of one carbon source over another when both available in environment
second lag phase after preferred substrate is exhausted

Question 29

what are the 2 transcriptional units that the lac operon consists of

Answer 29

• lacI + promoter (placI)
• 3 struc genes (LacZ, lacY, lacA) under plac + operator (O) + CAP sites

Question 30

explain negative control of lac operon

Answer 30

regulated by lac repressor which binds to operator O site in presence of glucose

glucose is like an inhibitor

Question 31

explain positive control in lac operon

Answer 31

regulated by catabolite activator protein (CAP) which binds to CAP site in absence of glucose

Question 32

Why do bacteria growing in a medium containing both glucose and lactose not produce high levels of lac-operon proteins?

Answer 32

Glucose indirectly blocks the function of a positive regulator of the lac operon.

Question 33

what are the 2 forms CAP exists in ?

Answer 33

• active form when 3’5’ cAMP is bound to CAP
  active form binds CAP site on lac operon
• inactive form when cAMP conc is low

Question 34

when is adenylate cyclase active?

Answer 34

when there is little or no glucose present, makes cAMP

Question 35

how does glucose control cAMP concentration?

Answer 35

high glucose → low adenylate cyclase activity →
** low cAMP** (activator inactive)
low glucose → high adenylate cyclase activity → high cAMP (activator active)