GIGUERE - LECTURE 2

Question 1

how is transcription regulated in prokaryotes?

Answer 1

Question 2

what is the general organization of operons

Answer 2

Question 3

how is expression of the operon determined

Answer 3

Question 4

how were operator/promoter sequences experimentally identified?

Answer 4

DNA footprint experiments:
protein is incubated with labelled DNA fragment containing sequence where the protein is thought to bind
digestion with DNAse cleaves the DNA backbone in exposed regions, but not where the DNA binding protein is bound
analysis of the DNase digests reveals the location of the protein binding site on the DNA

Question 5

what does the sugar metabolism operator nagC do?

Answer 5

nacC operator negatively regulates nagE and nagB expression by NagC

Question 6

what is induction vs repression

Answer 6

induction: increased synthesis of enzymes in response to metabolite
repression: the opposite of induction

Question 7

what is the main advantage of organizing genes in operons

Answer 7

Question 8

lac operon function and regulation by lactose

Answer 8

Question 9

what is the lac repressor and what do its domains bind to

Answer 9

lac operon is controlled by negative regulation
lacI is the repressor
lac operon is palindromic
lac repressor has a DNA binding domain on N terminus
C terminus binds the inducer (lactose)
lac repressor is a tetrameric protein

Question 10

what does the lac operon look like

Answer 10

Question 11

what is the mode of action of the Lac repressor in the absence and presence of lactose

Answer 11

Question 12

what is CAP and what does it do

Answer 12

Question 13

what control on the lac operon does CAP give when there is low glucose

Answer 13

Question 14

mode of action of the CAP activator in low vs high glucose

Answer 14

Question 15

summary of the lac operon regulation

Answer 15

Question 16

trp (tryptophan) operon characteristics

Answer 16

Question 17

trp operon in the presence vs absence of tryptophan

Answer 17

Question 18

trp repressor characteristics

Answer 18

Question 19

comparison of the lac and the trp operon

Answer 19

Question 20

negative vs positive control of gene expression

Answer 20

negative control: transcribed unless turned off by repressor
activation is the release from the negative control (only RNA pol needed)
positive control: expressed only if active regulator is present (RNA pol + activator needed)

Question 21

araBAD operon characteristics

Answer 21

Question 22

regulation of the araBAD operon by the combined action of CAP and AraC proteins

Answer 22

Question 23

what is a bacteriophage

Answer 23

Question 24

what is the structure of a bacteriophage

Answer 24

Question 25

how do bacteriophages operate?

Answer 25

Question 26

what is the bacteriophage lytic cycle

Answer 26

Question 27

what is the bacteriophage lysogenic cycle

Answer 27

Question 28

lytic vs lysogenic cycle comparison

Answer 28

Question 29

what decides whether the virus will follow the lytic or lysogenic cycle?

Answer 29

decision to enter lytic or lysogenic cycle is based on the binding of the Ci repressor or Cro to 3 operator regions in the viral genome

Question 30

how does regulation of the phage lambda cycle happen with Ci and Cro

Answer 30

Question 31

structure of the Cro protein

Answer 31

Question 32

structure of the Ci repressor and functions of its termini

Answer 32

Question 33

new phage particle synthesis control region

Answer 33

Question 34

what are the relative strengths of the PR and PRM promoter

Answer 34

PR is stronger than PRM and does not need the help of activators to recruit RNA polymerase the PR promoter at -35 and -10 only has one base that is different from the consensus region

Question 35

what happens on the gene during the lysogenic stage

Answer 35

Question 36

what happens on the gene during the lytic stage

Answer 36

Question 37

how do cells go from the lysogenic to the lytic cycle

Answer 37

Question 38

what is the structure of the repressor protein of lambda (Ci)

Answer 38

Question 39

how does the RecA cleavage of the repressor happen

Answer 39