topic 5: regulation of gene expression

Question 1

when do prokaryotes and eukaryotes change their gene expression?

Answer 1

in response to environmental changes

Question 2

what roles does gene regulation play in multicellular eukaryotes?

Answer 2

• regulates development
• responsible for differences between different cells types (cell specialization)

Question 3

how do bacteria respond to environmental change?

Answer 3

by regulating transcription (produce only the products that they need)

Question 4

what are two ways bacteria regulate metabolic pathways?

Answer 4

1. regulation of enzyme activity by feedback inhibition: controlled by allosteric regulation
2. regulation of enzyme production by gene expression regulation: controlled by the operons

Question 5

in the example of regulation of amino acid tryptophan in E.coli, what are the different methods to regulate gene expression?

Answer 5

[in the presence of tryptophan in the environment, there is no need to produce it]
1. regulation of enzyme activity (rapid response): tryptophan binds to Enzyme 1 and inhibits its activity

2. regulation of enzyme production (long-term response: the production of enzymes is inhibited to prevent the production of genes and using unnecessary cell resources

Question 6

what is an operon? what does it consist of?

Answer 6

• a prokaryotic DNA segment that includes:
• the operator
• the promoter
• a group of functionally related genes

Question 7

what is the operator?

Answer 7

• a segment of DNA which works as a regulatory switch (on-off) that controls a cluster of functionally related genes
• controls if transcription will take place
• consists of a specific sequence within the promoter of these genes

Question 8

what is the promoter?

Answer 8

a sequence where the RNA polymerase binds (the enzyme involved in transcription)

Question 9

what is the use of the group of functionally related genes?

Answer 9

the genes will be transcribed into different polypeptides, which form the enzymes that, for example, produce tryptophan

Question 10

what are other molecules/proteins that bacteria have that are involved in blocking or activating the transcription process?

Answer 10

• repressors
• co-repressors

Question 11

what are repressors?

Answer 11

• a protein that switches off the operon
• produced by a separate regulatory gene
• prevents gene transcription by binding to the operator and blocking DNA polymerase binding
• can be in an active or inactive form, depending on the presence of other molecules (ex: tryptophan or lactose)

Question 12

what is a co-repressor?

Answer 12

• a molecule that cooperates with a repressor protein to switch an operon off (operon inactivation)
• ex: tryptophan

Question 13

what is negative gene regulation? what are the two examples of it?

Answer 13

• negative gene regulation: operons are switched off by the active form of the repressor
  two types of such operons:
• repressible operons
• inducible operons

Question 14

describe repressible operons

Answer 14

• usually active
• usually regulate gene expression of enzymes involved in anabolic pathways
• their synthesis is repressed by high levels of the end product (co-repressor) which activates the repressor
• example: trp operon

Question 15

describe inducible operons

Answer 15

• usually inactive (INducible = INactive)
• usually regulate gene expression of enzymes involved in catabolic pathways
• their synthesis is induced by a chemical signal (inducer) which inactivates the repressor
• example: lac operon

Question 16

what does the trp operon contain?

Answer 16

it contains genes of enzymes involved in tryptophan synthesis

Question 17

‘transcription is normally on but can be inhibited when a small molecule binds allosterically to a regulatory protein’ the following describes?

Answer 17

repressible operon

Question 18

describe the process when each occurs:
(1) tryptophan is absent
(2) tryptophan is present

Answer 18

• (1) the repressor is inactive –> cannot bind to operator –> operon is ON –> RNA polymerase transcribes genes –> production of enzymes involved in tryptophan production –> tryptophan is synthesized
• (2) trp (a co-repressor) is present –> binds to the trp repressor protein –> repressor is activated –> binds to operator –> operon is OFF –> no production of tryptophan

Question 19

what does the lac operon contain?

Answer 19

it contains genes of enzymes used in lactose metabolism (lactose hydrolysis)

Question 20

‘transcription is normally off but can be activated when a small molecule binds allosterically to a regulatory protein’ the following describes?

Answer 20

inducible operon

Question 21

describe the process when each occurs:
(1) lactose is absent
(2) lactose is present

Answer 21

• (1) lac repressor is active by itself –> binds to operon –> operon is OFF –> lactose hydrolysis stops
• (2) allolactose (an inducer) is present –> binds to repressor and inactivates it –> lac operon is ON –> lactose hydrolysis is activated

Question 22

what is allolactose?

Answer 22

• a disaccharide similar to lactose (isomer)
• consists of the monosaccharides D-galactose and D-glucose linked through a β1-6 glycosidic linkage instead of the β1-4 linkage of lactose

Question 23

if both glucose and lactose are present, what do cells prefer and why?

Answer 23

cells always prefer glucose as it is a better energy source

Question 24

what is positive gene regulation?

Answer 24

when operons are switched on by the active form of the activator

Question 25

what is an activator? what is an example?

Answer 25

• a stimulatory protein (that stimulates transcription)
• example: catabolite activator protein (CAP) in E.coli which enhances transcription of the lac operon

Question 26

explain positive gene regulation in E.coli

Answer 26

(1) when glucose and lactose are both present: E.coli will prefer to use glucose –> there will be low quantities of the enzymes which are needed for lactose break down (low transcription)

(2) when only lactose is present and glucose is short in supply: E.coli will use lactose as an energy source –> sufficient quantities of enzymes are synthesized for lactose breakdown (enhanced transcription)

Question 27

what is the effect of having glucose absence?

Answer 27

enhanced transcription of enzymes that breakdown lactose (stimulated lactose hydrolysis)

Question 28

in what operon does both positive and negative gene regulation take place?

Answer 28

lac operon

Question 29

describe the process when each occurs:
(1) low glucose levels
(2) high glucose levels

Answer 29

(1) low glucose levels:
- increase in levels of cAMP (cyclic AMP)
- CAP is activated by binding to cAMP
- activated CAP attaches to the promoter of the lac operon, increases affinity of RNA polymerase, accelerates transcription of the lac operon
- hydrolysis of lactose to glucose & galactose

(2) high glucose levels:
- decrease in levels of cAMP
- CAP detaches from the lac operon
- decreased affinity of RNA polymerase, decreased transcription of the lac operon

Question 30

explain how active CAP can increase RNA polymerase affinity

Answer 30

active CAP binds before RNA polymerase, helps it attach better (on the promoter), therefore increasing its affinity, and transcribing at a faster rate

Question 31

a typical human cell expresses how much of its genes at a given time?

Answer 31

20%

Question 32

only ___% of DNA codes for proteins, the rest codes for what?

Answer 32

• 1.5
• RNA products (rRNAs and tRNAs) or is not transcribed at all

Question 33

abnormalities in gene expression lead to?

Answer 33

cancer

Question 34

what are the stages eukaryotic gene expression can be regulated at?

Answer 34

• regulation of chromatin structure
• regulation of transcription initiation
• post-translational regulation