7. Regulation

Question 1

common regulatory mechanisms in bacteria

Answer 1

regulation of gene expression
-transcription initiation
-transcription elongation
-translation

alter activity of enzymes and proteins
-postrtranslational

three domains of life differ in genome structure and regulatory mechanisms used

Question 2

regulation of transcription initiation

Answer 2

constitutive genes
inducible genes
repressible gene

Question 3

constitutive genes

Answer 3

housekeeping genes that are expressed CONTINUOUSLY by the cell

Question 4

inducible genes

Answer 4

genes that code for inducible enzymes needed only in certain environments (such as beta galactosidase) –> lac operon

Question 5

repressible genes

Answer 5

enzymes that function in biosynthetic pathways
-generally these enzymes are always present (until turned off) unless the end product in the biosynthetic pathway is available

Question 6

positive control

Answer 6

regulator protein ACTIVATES the binding of RNA polymerase to DNA

Question 7

positive control activation

Answer 7

maltose catabolism in E.coli
-maltose activator protein cannot bind to DNA unless it first binds maltose (inducer)
-subsequent binding

ACTIVATOR PROTEINS bind specifically to ACTIVATOR-BINDING SITE (certain DNA sequence that is not called an operator)
*inducer binds to activator protein which binds to activator binding site
*sometimes the activator binding site does not need to be next to the promoter

Question 8

Positive Control Structure

Answer 8

need activator protein for polymerase to bind
activator binding site
inducer (maltose) binds to maltose activator protein which allows RNA polymerase to bind to the mal Promoter

Question 9

negative control: repression and induction
the operon

Answer 9

cluster of consecutive genes whose expression is under control of a single operator
-all genes transcribed as single mRNA
-transcription physically blocked when repressor binds to operator

Question 10

enzyme induction can also be controlled by a

Answer 10

repressor

Question 11

addition of inducer…

Answer 11

inactivates repressor and transcription can proceed

Question 12

the repressor’s role is

Answer 12

inhibitory (preventing mRNA synthesis), so it is called negative control

Question 13

negative control of lac operon

Answer 13

inducible genes
-three structural genes coding for lactose uptake and metabolism
-lac repressor (lacI) binds operator, inhibiting transcription

enzymes normally not produced unless lactose is present

Question 14

lac operon structure

Answer 14

CAP site is regulatory
lac promoter (RNA polymeraSe binds here)
lac operator
lacZ, lacY, lacA

when the inducer (allolactose) binds to the repressor, RNA polymerase can proceed transcription

Question 15

diauxic growth

Answer 15

two exponential growth phases if two energy sources available
-better energy source consumed first, growth stops
-after lag, growth resumes with second energy source

*glucose preferentially used , then lactose *

Question 16

glucose low and lactose present

Answer 16

1. polymerase needs to associate
2. need to pull off repressor

glucose is low, cAMP is present since the cell is in starvation mode and ATP modified to cAMP

cAMP binds to CAP polymerase and can easily bind
lactose converted to allolactose (binds to repressor) and leaves

Question 17

regulation of lac operon by lac repressor

Answer 17

regulated by catabolite activator protein CAP
-regulates in response to presence or absence of glucose
-allows for preferential use of glucose

Question 18

regulation of transcription elongation

Answer 18

-transcription can also be regulated by controlling transcription termination
-this type of regulation, called attenuation, was first demonstrated with trp operon
-more recently riboswitches have been demonstrated to also play a regulatory role

Question 19

trp Opeorn Attenuation

Answer 19

in addition to transcription initiation control, transcription continuation is also controlled in this operon

attenuation is termination of transcription within the leader region (leader peptide)

occurs through stem-loop structures in the mRNA depending on trp level

Question 20

low trp level=

Answer 20

transcription continues

Question 21

riboswitches (sensory RNAs)

Answer 21

specialized form of transcription attenuation

folding of mRNA leader sequences (the riboswitch) determines if transcription will continue/ terminate

folding pattern altered in response to mRNA binding of an effector molecule

riboswitches in gram-positive bacteria function in transcriptional termination

Question 22

regulation of translation

Answer 22

riboswitches in gram-negative bacteria regulate translation of mRNA
-effector binding elements at 5’ end alters mRNA leader folding pattern

translation initiation can also be controlled by some small RNA molecules

Question 23

quorum sensing

Answer 23

cell-to-cell communication mediated by small signaling molecules such as N-acyl-homoserine lactone (AHL)

couples cell density and intercellular communication to transcription regulation

plays an essential role in the regulation of genes whose products are needed for the establishment of virulence, symbiosis, biofilm production, and morphological differentiation in a wide range of bacteria

Question 24

quorum sensing in v. fischeri

Answer 24

high concentrations of AHL produced by increased density of cells diffuse back into the cell, bind to the transcriptional regulator LuxR and activate transcription

LuxR stimulates transcription of the genes for AHL synthase (luxl) and proteins needed for light production

Question 25

response to autoinducers by v. harveyi

Answer 25

responds to three autoinducers
-maximizes expression of bioluminescence

low cell density
-low autoinducers
-LuxR not made, no bioluminescence

high cell density
-any combination of inducers
-LuxR made, bioluminescence occurs

Question 26

CRISPR

Answer 26

clustered regulatory interspaced short palindromic repeats
a prokaryotic “immune system” that evades viral destruction and maintains genome stability