1.3: Prokaryotic Transcriptional Regulation Continued

Question 1

what is the difference between negative and positive regulation

Answer 1

for negative: when bound to dna, repressor protein prevents transcription
positive: when bound to dna, activator protein promotes transcription

Question 2

determine whether the following description matches the lac repressor or trp repressor: ligand binds to remove regulatory protein from dna. such that during negative regulation the addition of ligand switches gene on by removing repressor, and in positive regulation, the addition of ligand switches gene off by removing activator protein

Answer 2

lac repressor

Question 3

determine whether the following description matches the lac repressor or trp repressor: the ligand binds to allow regulatory protein to bind to dna. the removal of ligand swithces gene on by removing repressor protein (now in its inactive state) for negative regulation. and for positive, removing the ligand switches gene off by removing activator protein

Answer 3

trp repressor

Question 4

which binding motif does the tryptophan repressor contain

Answer 4

helix turn helix

Question 5

describe negative regulation

Answer 5

competition between rnap and repressor protein for promoter binding

Question 6

describe positive regulation

Answer 6

activator protein recruits rnap to the promoter to activate transcription

Question 7

cis regulatory elements/gene regulatory elements are typically close to which site of prokaryotic genes

Answer 7

the transcriptional start site

Question 8

other than the transcriptional start site, where can regulatory elements also be found in prokaryotes and eukaryotes?

Answer 8

• far upstream of the gene
• downstream of gene (eukaryotes)
• within gene (introns; eukaryotes)

Question 9

what is the NtrC protein

Answer 9

a transcriptional activator

Question 10

describe the type of mechanism allows the interaction of NtrC to interact w rnap; even if it is a distance away

Answer 10

dna looping allows NtrC to directly interact w rnap to activate transcription from a distance. the process involves the dna to conduct a looped activation intermediate to allow the temporary interaction between rnap and NtrC (called kissing) which turns it on

Question 11

what is a bacteriophage

Answer 11

virus that effects bacterial cell

Question 12

is the lifestyle of bacteriophage lambda regulated by positive or negative regulatory mechanisms

Answer 12

trick question, its both

Question 13

under what conditions are the prophage and lytic pathway favored

Answer 13

prophage: under favorable bacterial growth conditions
lytic: when the host cell is damaged

Question 14

the two gene regulatory proteins, ______ (cI) and ________ are responsible for initiating the switch between prophage and lytic pathways actually _______ each other’s synthesis

Answer 14

lambda repressor protein (cI), Cro protein, repress

Question 15

describe how the lambda repressor functions in the prophage state

Answer 15

the lambda repressor occupies the operator which blocks the synthesis of Cro, activates its down synthesis, most bacteriophage DNA is NOT transcribed

Question 16

describe how the cro protein function in the lytic state

Answer 16

Cro occupies the operator, blocks synthesis of cI/lambda repressor. allows its own synethesis. most bacteriophage DNA is extensively transcribed. dna is replicated, packaged, new bacteriophage released by host cell lysis

Question 17

t/f can the lambda repressor protein act as an activator

Answer 17

true

Question 18

t/f can the cro protein act as an activator

Answer 18

false

Question 19

describe what triggers the switch between prophage and lytic states

Answer 19

its host response to dna damage (induction event) which switches it to lytic state inactivates repressor.
under good growth conditions, lambda repressor protein turns off Cro and activates itself in a positive feedback loop to maintain the prophage state

Question 20

what type of feedback maintains the prophage state

Answer 20

positive feedback loop

Question 21

what type of feedback loop can be used to create cell memory

Answer 21

positive feedback loops - through the initial transient signal turning on expression of a gene and the cell will always remember it had that signal and the gene continues to be transcribed the the daughter cells regardless of signal

Question 22

what can feed forward loops measure and how

Answer 22

it can measure the duration of a signal.
as both a and b are required for the transcription of z. z is only transcribed given the input is accumulated sufficiently.

Question 23

describe how feed forward loops can decrease the sensitivity

Answer 23

crude example but just to help understand, if a or b is too sensitive to the signal - a splits in half (insufficient a to get both b and z going) so needs more signal to get enough such that z is transcribed

Question 24

what is synthetic biology

Answer 24

when scientists construct artificial circuits and examine their behaviour in cells

Question 25

describe the repressilator (tbh idk if we need to know this)

Answer 25

it’s an example of synthetic biology where scientists created a simple gene oscillator using a delayed(!!) negative feedback circuit. introduced the lac repressor, tet repressor (response to antibiotic), lambda repressor - tested out expressing and repressing diff genes. they observed increasing amplitude of fluorescence due to bacterial growth.

Question 26

define transcription attenuation

Answer 26

premature termination of transcription

Question 27

how is rna involved in transcription attentuation

Answer 27

rna adopts a structure that interferes with rnap, regulatory proteins can bind to rna and interfere with attenuation

Question 28

can prokaryotes, eukaryotes, or both be affected by transcription attenuation

Answer 28

both

Question 29

prokaryotes, plants, and some fungi can use _______ to regulate gene expression

Answer 29

riboswitches - NOT ALL RIBOSWITCHES DO TRANSCRIPTION ATTENUATION

Question 30

define riboswitches are

Answer 30

short rna seq that change conformation when bound by a small molecule

Question 31

provide an example of riboswitches and what is it regulated by

Answer 31

example: prokaryotic riboswitch that regulates purine (A,G) biosynthesis. regulated by low guanine levels

Question 32

describe how high and low guanine levels impact the riboswitch that regulates purine (A,G) biosynthesis

Answer 32

low guanine levels: transcription of purine biosynthetic gene is on.
high guanine levels: guanine binds to riboswitch and the riboswitch undergoes conformational change. causes rnap to terminate transcription by prying it off before it has the chance to get to the coding sequence - the transcription of purine biosynthetic genes is off

Question 33

t/f the flip flop device easy to draw

Answer 33

false