lecture 21, 22, 23

Question 1

what is the purpose of regulating gene expression?

Answer 1

create different proteins for different activities or to conserve energy

Question 2

what is needed to regulate gene expression?

Answer 2

recognize environmental conditions and respond to such by turning genes off/on

Question 3

what does RNA pol need to transcribe?

Answer 3

it needs to be able to bind to a promoter and move from the promoter downstream without dissociating from DNA

Question 4

what is the process of binding to a promoter called?

Answer 4

recruiting

Question 5

how do activators work?

Answer 5

they allow for transcription by binding to activator binding sites on the DNA

Question 6

how do repressors work?

Answer 6

they block transcription by binding to operators on the DNA

Question 7

what are activators?

Answer 7

proteins that promote transcription by recruiting RNA pol and keeping it on the promoter

Question 8

what are repressors?

Answer 8

proteins that block transcription by blocking RNA pol recruitment and movement

Question 9

allosteric effectors

Answer 9

small molecules that bind to a protein in a specific site and regulates activity

Question 10

what is an effector that regulates activity in a positive way called?

Answer 10

an inducer

Question 11

what happens to a protein when an effector binds to its allosteric site?

Answer 11

it causes a confirmation/structural change in the protein

Question 12

what does the result of an effector binding to a protein result in?

Answer 12

it can allow or prevent proteins from binding DNA

Question 13

what happens if an activator doesn’t bind with an effector?

Answer 13

the activator is unable to bind with the activator binding site and is unable to promote transcription

Question 14

what happens if a repressor does not bind with an effector?

Answer 14

the repressor stays bound to the operator and continues to block transcription

Question 15

operon

Answer 15

a group of genes that are regulated together from the same promoer and transcribed into a singular mRNA

Question 16

what does it mean when genes in an operon are coordinately controlled?

Answer 16

one mRNA can translate into more than one protein

Question 17

what is the difference between an operon vs a single gene?

Answer 17

only one gene can be formed by the ribosome in a single gene, whereas in an operon the ribosome can create multiple proteins

Question 18

what controls the lac operon?

Answer 18

the repressor protein

Question 19

what is beta-galactosidase?

Answer 19

a protein that breaks down lactose

Question 20

what is permease?

Answer 20

a protein that transports lactose into the cell

Question 21

what is transacetylase?

Answer 21

a protein that modifies galactosides and detoxifies byproducts of lactose metabolism

Question 22

what proteins are required for lactose metabolism?

Answer 22

beta-gal and permease

Question 23

why is the repressor typically active in the lac operon?

Answer 23

to save energy if there is no lactose to be metabolized

Question 24

what does lactose get broken down into?

Answer 24

galactose and glucose

Question 25

apart from galactose and glucose, what else can beta-gal break lactose into?

Answer 25

allolactose

Question 26

what is the inducer in the lac operon system?

Answer 26

allolactose

Question 27

what happens when allolactose present in the system?

Answer 27

it binds to the repressor and is released from the operator, allowing for transcription

Question 28

when trying to study the lac operon, what issues can arise from a standard system?

Answer 28

lactose is broken down by beta-gal which drops the concentration during an experiment

Question 29

what was the solution Jacob and Monod came up with to work around the lactose concentration drop?

Answer 29

utilize IPTG as the allosteric inducer

Question 30

why was IPTG effective as an alternative to lactose?

Answer 30

it had similar properties to lactose and was not broken down by beta-gal

Question 31

what did Jacob and Monod do to be able to create a partial diploid in a haploid system?

Answer 31

utilized F' factors to introduce an additional copy of the gene

Question 32

inducible promoter

Answer 32

operon is expressed only in the presence of an inducer

Question 33

constitutive mutant

Answer 33

operon is expressed in the absence of an inducer

Question 34

cis acting element

Answer 34

activity occurs on the same DNA molecule as the element

Question 35

trans acting element

Answer 35

activity occurs on other DNA molecules of the element

Question 36

are operators cis or trans acting?

Answer 36

cis-acting

Question 37

are repressors cis or trans acting?

Answer 37

trans acting

Question 38

what occurred to lac operons that had mutated operators?

Answer 38

the operon would always be active because the repressor couldn't bind to the altered site

Question 39

what occurred to lac operons that had mutated lacl?

Answer 39

it would create super repressors that could not bind to the inducers or not create a repressor at all

Question 40

what is the preferred energy source for our cells?

Answer 40

glucose

Question 41

why is it better to have glucose over lactose?

Answer 41

it saves energy because its one less step in metabolism

Question 42

when glucose levels are high, what is the result?

Answer 42

ATP is high which reduces cAMP production

Question 43

when glucose is low, what is the result?

Answer 43

ATP is low which kickstarts cAMP production

Question 44

when there is less cAMP in the system, what effect does that have on the lac operon?

Answer 44

it is not able to be activated because the cAMP-cap complex is not formed

Question 45

when there is a lot of cAMP in the system, what effect does that have on the lac operon?

Answer 45

it causes the cAMP-cap complex to form which activates the lac operon

Question 46

describe the cAMP-cap complex

Answer 46

cAMP acts as an allosteric inducer to cap, whose binding site sits next to the promoter and activates the lac operon

Question 47

what happens to DNA when CAP binds to it?

Answer 47

DNA bends to enhance the interaction between RNA pol and the promoter

Question 48

what regulates the lac operon?

Answer 48

CAP

Question 49

what variables result in no lac mRNA being produced?

Answer 49

high amounts of glucose, no cAMP, and no lactose

Question 50

what variables result in a lot of lac mRNA being produced?

Answer 50

low amounts of glucose, high cAMP, and lactose

Question 51

in what case would lac mRNA be produced when theres glucose present?

Answer 51

lactose being present

Question 52

What function does AraC serve in the ara operon?

Answer 52

It can be an activator and a repressor

Question 53

what is the allosteric inducer of AraC?

Answer 53

Arabinose

Question 54

what happens when arabinose is not present in the ara operon?

Answer 54

AraC represses the operon by bending it

Question 55

what happens when arabinose is present in the ara operon?

Answer 55

transcription can occur

Question 56

in the trp operon, what represses it?

Answer 56

tryptophan

Question 57

what does it mean for mRNA production to attenuate?

Answer 57

to decrease production

Question 58

what happens when there's a high level of Trp?

Answer 58

the ribosome completely translates the leader region, region 3 pairs with 4 and terminates transcription

Question 59

what happens when there's a low level of Trp?

Answer 59

ribosome stays at leader region to encode for more Trp, region 2 pairs with 3 and transcription occurs

Question 60

lytic cycle

Answer 60

when a phage multiplies in a host cell and kills it

Question 61

lysogenic cycle

Answer 61

When a phage's DNA integrates with a host's chromosome

Question 62

what cycle will a phage go into if resources are abundant?

Answer 62

lytic cycle

Question 63

what cycle will a phage go into if resources are not available?

Answer 63

lysogenic cycle

Question 64

does a phage that undergoes lysogenic cycle stay like that forever?

Answer 64

no, it will eventually transition to the lytic cycle when resources become plentiful

Question 65

How is plaque created?

Answer 65

when phages kill their bacterial host

Question 66

cloudy plaque

Answer 66

some bacteria is alive and are of a wild-type temperate phage

Question 67

clear plaque

Answer 67

all bacteria has been lysed and is of a mutant phage that is lytic

Question 68

what promoters control what cycle a phage goes into?

Answer 68

Pr and Prm

Question 69

which gene will encode the lytic cycle?

Answer 69

cro

Question 70

which gene will encode the lysogenic cycle?

Answer 70

cl

Question 71

which promoters does the Cl repressor bind to from strongest to weakest affinity?

Answer 71

O1 > O2 > O3

Question 72

which promoters does the Cro repressor bind to from strongest to weakest affinity?

Answer 72

O3 > O2 > O1

Question 73

which gene encodes for virulence?

Answer 73

cro