Ch 14 Gene Regulation in Prokaryotes

Question 1

What are constitutive genes

Answer 1

Unregulated genes. Often encode proteins that are continuously needed for survival of the bacterium.

Question 2

Why are gene regulated?

Answer 2

efficiency

so the right proteins can be produced at the right times, in the right amounts

Question 3

Name 3 common processes that are regulated at the genetic level

Answer 3

1. Metabolism. Ex: certain enzymes are needed for bacterium to process sugar; those are only required when sugar is present in the environment.
2. Response to environmental stress. Ex: proteins that help survive environmental shock (osmotic or heat shock)
3. Cell division. only needed when bacteria cell is getting ready to divide.

Question 4

In _____, transcription terminates soon after it has begun due to the formation of a transcriptional terminator

Answer 4

attenuation

Question 5

3 ways that gene regulation can happen at the translation level

Answer 5

1. Translational repressor proteins can bind to the mRNA & prevent translation from starting.
2. Riboswitches can produce an mRNA conformation that prevents translation from starting.
3. Antisense mRNA can bind to the mRNA and prevent

Question 6

2 ways gene regulation can happen post-translation

Answer 6

1. feedback inhibition

2. covalent modifications to the structure of a protein can alter its function

Question 7

Most common way genes are regulated in bacteria:

how is this done?

Answer 7

influencing the rate at which transcription is initiated.

sometimes referred to as “on/off” but really more “inc/dec”

regulatory proteins bind to the DNA - affects transcription of nearby genes

Question 8

Def of repressor & activator

Answer 8

repressor: regulatory protein that binds to DNA & inhibits transcription
= negative control

activator: regulatory protein that binds to DNA & increased rate of transcription
= positive control

Question 9

In conjunction with reg proteins _______ play a critical role in transcriptional regulation

+ how do they work?

Answer 9

small effector molecules

don’t bind directly to the DNA, instead binds to the activator/repressor. this causes a conformational change in the reg protein that influences its ability to bind to DNA.

Question 10

Describe reg protein’s binding sites

Answer 10

1 for DNA binding; 1 for effector molecule binding

Question 11

Inducer def

Answer 11

Small effector molecule that causes transcription to increase. Does this by:

• binding to a repressor protein & preventing it from binding to DNA, or
• can to an activator & cause it to bind to DNA

Genes regulated by inducers = inducible genes

Question 12

Corepressor def

Answer 12

small effector molecule that binds to a repressor protein, causing it to bind to DNA

Genes regulated by inducers = repressible genes

Question 13

inhibitor def

Answer 13

binds to an activator protein & prevents it from binding to DNA

Genes regulated by inducers = repressible genes

Question 14

14.1 comprehension

A repressor is a ____ that ____ transcription

Answer 14

regulatory protein

inhibits

Question 15

14.1 comprehension
Which of the following combinations will cause transcription to be activated?
a. repressor plus inducer
b. repressor plus corepressor
c. activator plus inhibitor
d. none of the above

Answer 15

a. repressor plus inducer

Question 16

Hi level, what does lac operon involve?

not sure if i like this question, might remove

Answer 16

repressor (reg protein) + activator (reg protein)

Question 17

enzyme adaptation (def)

Answer 17

refers to observations that a particular enzyme appears only after the cell has been exposed to the substrate for that enzyme

Question 18

What are the 4 key experimental observations Jacob & Monod made?

Answer 18

1. exposure of bacterial cells to lactose increased level of lactose-utilizing enzymes 1k - 10k x
2. Antibody & labeling techniques revealed that the inc in activity of these enzymes due to inc synthesis of proteins that form the enzymes
3. removal of lactose from the environment caused abrupt termination of enzyme synth
4. analysis of mutations in the lac operon revealed each protein involved with lactose utilization is encoded by a separate gene

Question 19

The lac operon encodes _____________

Answer 19

proteins involved in lactose metabolism

Question 20

operon def

Answer 20

group of 2+ genes transcribed from a single promoter

Question 21

an operon is flanked by a ___ that signals the beginning of transcription & a ___ that specifies the end

Answer 21

promoter

terminator

Question 22

describe organization of the lac operon

Answer 22

1. DNA elements:
   - promoter: binds RNA polymerase
   - operator: binds the lac repressor protein
   - CAP site: binds Catabolite Activator Protein
2. structural genes (used to metabolize lactose):
   - lacZ: enzymatically cleaves lactose & analogues; converts lactose to allolactose (acts as a SEM for lac operon)
   - lacY: encodes lactose permease (membrane protein required for the active transport of lactose into the cytoplasm)
   - lacA: covalently modifies lactose & analogues

Question 23

operator site def

Answer 23

aka, operator; sequence of bases that provides a binding site for a repressor protein called lac repressor

Question 24

the lacI gene

Answer 24

separate from the lac operon

has its own promoter (i)
lacI gene encodes the lac repressor, a protein that regulates the lac operon by binding to the operator site & repressing transcription

Question 25

lac repressor is a homotetramer. what does that mean?

Answer 25

protein composed of 4 identical subunits

Question 26

What are the ways lac operon can be regulated?

Answer 26

1. inducible under negative control (repressor protein + inducer SEM) 2. repressible under positive control (activator protein + inducer SEM) (check that one...) - it's a little confusing that this is called catabolite repression, bc CAP is an activator & cAMP is an inducer; they named this as a repressor before they really understood what was happening and I guess they were too proud to admit their mistake and rename it. Idiots....see top of pg 347 fpr details

Question 27

what are the genes are actually used to metabolize lactose?

Answer 27

lacZ, lacY & lacA

Question 28

describe lac operon + inducible under negative control

Answer 28

lac repressor protein is bound to the operator when no lactose in the environment. this prevent RNA polymerase to transcribe lac Z, Y & A. When 4 allolactose molecules bind to the lac repressor protein, a conformational change occurs and prevents the lac repressor protein from maintaining its bounds to the operator (lacO). the operon has been induced; transcription commences.

Question 29

If the lac repressor represses transcription of key lactose related genes, and it can only be induced by allolactose, which is converted from lactose by beta-galactosidase, how is the lac repressor ever induced?

Answer 29

in reality the lac repressor doesn't stop all transcription; therefore, there is always some amounts of lactose enzymes in the cell. this is how allolactose can be present to induce the lac repressor when needed

Question 30

A strain of bacteria containing the F' factor is called a _____, or partial diploid

Answer 30

merozygote

Question 31

Review lacI experiment, pg 342

Answer 31

done?

Question 32

catabolite def

Answer 32

a substance that is broken down inside the cell

Question 33

2nd way lac operon is transcriptionally regulated is catabolite repression, which is influenced by _______

Answer 33

the presence of glucose.

Question 34

What is the SEM in catabolite repression of lac operon?

Answer 34

cAMP (cyclic AMP) - binds to the CAP

Question 35

How does the CAP affect the lac operon?

Answer 35

Whenever there is no glucose present, the intracellular conc of cAMP is high, allowing it to induce the CAP. The CAP binds to the CAP site, enhancing RNA polymerase's ability to bind to the promoter site

Question 36

How many lac operator site are there?

Answer 36

3 (o1, o2 & o3)

Question 37

Explain how maximal repression of lac operon is obtained

Answer 37

lac repressor must bind to either: - O1 & O2, - O1 & O3, - BUT NOT O2 & O3 (this results in incomplete repression) Bc the sites aren't that close, DNA must form a loop for these binding combos to happen

Question 38

14.2 Comp What is an operon?

Answer 38

B - a group of genes under the control of a single promoter

Question 39

14.2 Comp The binding of ____ to lac repressor causes lac repressor to ___ to the operator site, thereby ____ transcription.

Answer 39

D - allolactose, not bind, increasing

Question 40

14.2 Comp On its chromosome, E coli has genotype lacI- lacZ+ lacY+ lacA+. It has an F' factor with a genotype of lacI+ lacZ+ lacY+ lacA+. What is the expected level of expression of the lac operon (Z, Y A) in the absence of lactose?

Answer 40

B. Neither lac operon will be expressed

Question 41

14.2 Comp How does the exposing of E coli cell to glucose affect the regulation of the lac operon via CAP?

Answer 41

D. cAMP doesn't bind to CAP, transcription is decreased

Question 42

What are the ways trp operon is regulated?

Answer 42

1. repressor protein - when trp levels in the cell are very low, trp repressor can't bind to operator site - RNA pol then transcribes the trp operon, cell expressed the genes needed to syn trp - once trp is synth, they act as a SEM corepressor, bind to trp repressor causing conf change -> binds to DNA & down regulated transcription 2. attentuation (transcription begins, but is halted prematurely)

Question 43

describe structure of trp operon

Answer 43

5 genes: E, D, C, B, A each encodes an enzyme In addition, also R & L play a big role. - L is part of the trp operon - R has its own promoter & is not part of trip; encoded the trp repressor

Question 44

How was trp attentuation discovered?

Answer 44

70's, Yanofsky discovered that mutant strains lacking trp repressor could still inhibit trp operon - mediated by the region that includes the trp L gene

Question 45

What segment of DNA is important in facilitating termination?

Answer 45

attenuation sequence

Question 46

Explain trp attentuation

Answer 46

- mRNA made from trpL has codons for 14 amino acids that form the trp leader peptide - 2 trp codons provide a way for bacterium to sense amount of available trp - mRNA from trpL has 4 regions that complement each other, causing stem-loops

Question 47

Operons involved in ____ are typically inducible, while operons involved in ____ are typically repressible

Answer 47

catabolism (breakdown of substances) anabolism (biosynth of substances)

Question 48

riboswitch def

Answer 48

an RNA molecule can exist in 2 difference secondary conformations - conversion of 1 -> other is due to binding of a small molecule - widespread in bacteria - 3-5% of all bacterial genes are regulated this way

Question 49

trans-effect def & ex

Answer 49

form of gen regulation that can occur even though two DNA segs aren't physically adjacent. ex: action of lac repressor on the lac operon . A reg protein, such as lac repressor, is called trans-acting