03/13 prokaryotic regulation

Question 1

what does I^S mean

Answer 1

it is a super repressor where the repressor is always on even with an inducer present

allolactose cannot bind to the repressor and allow it to release

Question 2

what is diauxic growth?

Answer 2

it is the use of two sugars by a bacterium

in this case it is glucose and lactose

Question 3

What if both lactose and glucose are present? why can the lac operon not be turned on simulataneously?

Answer 3

it is a waste of energy to create the enzymes needed to digest lactose when glucose is present

Question 4

when is catabolic repression alleviated in the lac operon?

Answer 4

when there is no glucose present, the catabolic repression is alleviated and the lac operon is turned on to digest lactose

Question 4

what is catabolic repression in the lac operon

Answer 4

it prevents the breakdown of lactose in the presence of glucose

Question 5

what is the role of the catabolite activator protein?

Answer 5

it is the activator protein that will bind to the CAP site in the lac operon in the absence of glucose

Question 6

is the CAP protein always active?

Answer 6

no, it is usually inactive until the inducer, cyclic AMP is present and binds to it

Question 7

what is the role of cAMP?

Answer 7

it is the effector molecule that binds to the CAP protein and activates it

Question 8

how is cAMP made?

Answer 8

it is made from ATP via the enzyme adenylyl cyclase when there are low levels of glucose

Question 9

what is the general role of cAMP?

Answer 9

it is a signalling molecule

Question 10

what is the cAMP-CAP complex?

Answer 10

it is the complex that binds near the lac operon that induces transcription under positive control

Question 11

in the presence of high levels of glucose, what happens to the enzyme adenylyl cyclase?

Answer 11

it is inhibited and cannot make cAMP

Question 12

in the presence of high levels of glucose, how is the lac operon affected?

Answer 12

if there is an abundance of glucose, the enzyme required to make cAMP is inhibited and the CAP activator protein cannot bind to the lac operon, thus the rate of transcription decreases

Question 13

what is the common role of the repressor and activator protein?

Answer 13

they are both induced by effector molecules that increase the rate of transcription

Question 14

what are the conditions to take the brakes off of the lac operon?

Answer 14

lactose must be present to make allolactose, which will bind to the repressor and cause it to release

Question 15

what are the conditions to put the gas on in the lac operon

Answer 15

glucose must be absent so the enzyme can make cAMP and the CAP protein can bind to the lac operon to activate it

Question 16

if there are high levels of glucose, what are the relative amounts of ATP and cAMP?

Answer 16

there are high levels of ATP and low levels of cAMP

Question 17

if there are low levels of glucose, what are the relative amounts of ATP and cAMP

Answer 17

there are low levels of ATP and high levels of cAMP

Question 18

what is common of allolactose and cAMP?

Answer 18

they are both inducer effector molecules that increase the rate of transcription

Question 19

what is bound to the operon in the presence of lactose and absence of glucose

Answer 19

the repressor is off and the activator is on (high amounts of cAMP)

Question 20

in the presence of lactose and absence of glucose, what is the rate of transcription at the lac operon

Answer 20

the rate is high

Question 21

what is bound to the operon in the absence of lactose and glucose

Answer 21

the repressor is on (no allolactose) and the activator is on (high amounts of cAMP)

Question 22

in the absence of lactose and glucose, what is the rate of transcription at the lac operon

Answer 22

the rate is low

Question 23

in the presence of lactose and glucose, what is bound at the lac operon

Answer 23

the repressor is off and the activator is off (low amounts of cAMP)

Question 24

in the presence of lactose and glucose, what is the rate of transcription

Answer 24

the transcription is at a low basal rate

Question 25

in the presence of glucose and absence of lactose what is bound at the operon?

Answer 25

the repressor is on (no allolactose) and the activator is off (low levels of cAMP)

Question 26

in the presence of glucose and absence of lactose, what is the rate of transcription

Answer 26

very low

Question 27

what is the purpose of the trp operon

Answer 27

it is involved in the biosynthesis of tryptophan

Question 28

what is the role of the trpR gene in the trp operon

Answer 28

it codes for the repressor protein

Question 29

what is the trpL gene

Answer 29

it is involved in the synthesis od a short polypeptide called the leader peptide that is involved in attenuation

Question 30

what is a catabolic process

Answer 30

it is the breakdown of something, like lactose metabolism

Question 31

what is an anabolic process

Answer 31

it is a process involved in "building up" ex) tryptophan biosynthesis

Question 32

how is the repressor in the trp operon different from the repressor in the lac operon

Answer 32

the repressor is initially inactive and not bound to DNA

Question 33

when does the repressor bind in the trp operon

Answer 33

it binds when there are high amounts of tryptophan which act as corepressors

Question 34

what type of effector molecule does the repressor in the trp operon act with?

Answer 34

a corepressor

Question 35

when there are large amounts of trptohan, the repressor is

Answer 35

bound

Question 36

when there is a low amount of tryptophan, the repressor is

Answer 36

not bound

Question 37

what is the effector molecule for the repressor in the trp operon

Answer 37

it is tryptophan

Question 38

is there an accelerator equivalent in the trp operon?

Answer 38

no, the operon is always on until a threshold amount of tryptophan has been synthesized

Question 39

what does it mean to attenuate?

Answer 39

it means to cut a process short

Question 40

how does the word attentuation describe the tryptophan operon?

Answer 40

it describes how transcription begins but stops at the attenuator sequence

Question 41

why does attenuation occur

Answer 41

it occurs in bacteria due to the coupling of transcription and translation and it stops transcription midway

Question 42

in the trp-L sequence, what are the critical regions?

Answer 42

1,2,3,4, these regions are complementary and can form stem loops

Question 43

between what regions do the stem loops form and what is the third alternate loop that forms

Answer 43

regions 1-2 and 3-4 bind 2-3 is the alternate loop

Question 44

what is the role of the 3-4 stem loop?

Answer 44

it functions as a terminator before the RNA polymerase can reach the structural genes

Question 45

when a 3-4 stem loop forms, what happens to gene expression

Answer 45

the genes will not be expressed and the mRNA is attenuatd

Question 46

if the 2-3 alternate stem loop forms, what will happen to gene expression

Answer 46

the genes will be expressed and will not be attenuated

Question 47

what causes one stem-loop to form over another?

Answer 47

the level of tryptophan

Question 48

if you have low levels of tryptophan, which stem loop will form?

Answer 48

the alternate 2,3 stem loop, this will allow transcription to occur to make new tryptophan

Question 49

if you have high levels of tryptophan, which stem loop will form

Answer 49

the 3-4 snd 1-2 stem loop will form, this terminates transcription

Question 50

why does the amount of tryptophan matter

Answer 50

it matters for determining whether or not transcription should occur based on the amount of charged tRNAs that are presemt

Question 51

when transcription is not coupled with translation in the trp operon, what occurs?

Answer 51

two stem loops form, the 1-2 and 3-4, which will terminate the RNA polymerase

Question 52

what is the role of the 3-4 stem loop in the trp operon?

Answer 52

it forms a rho-independent terminator that kicks off RNA polymerase

Question 53

when there are low levels of trptophan, what loop forms?

Answer 53

an alternative 2-3 loop that allows transcription to occur

Question 54

why is it important that the co-transcript and translation occur?

Answer 54

without transcription, the system would terminate

Question 55

why is it important that there are two trp codons?

Answer 55

it regulates the speed at which the ribosome translates it

Question 56

if there are high levels of tryptophan, how many charged tRNAs are present? why is this important

Answer 56

there are large amounts of charged tRNAs, this allows the ribosome to quickly translate the transcript and the 3-4 loop will form and terminate the RNA polymerase

Question 57

if there are low levels of tryptophan, how many charged tRNAs are present? why is this important?

Answer 57

there are small amounts of charged tRNAs, this will stall the ribosome and allow the alternative loop to form which allows transcription to occur

Question 58

if we do not have tRNAs for trptopan translation, what will occur?

Answer 58

the ribosome will stall and lead to the formation of a 2-3 alternate loop

Question 59

what regions can region 2 hydrogen bond with>

Answer 59

1 and 3

Question 60

what regions can region 3 hydrogen bond with?

Answer 60

2 and 3

Question 61

what are the two conditions where attenuation occurs?

Answer 61

when transcription and translation are not coupled and when there are high levels of tryptophan

Question 62

what is the situation where attenuation does not occur

Answer 62

when there are low levels of tryptophan