prokaryotic gene regulation

Question 1

direction of transcription

Answer 1

from origin of replication, outside is transcribed clockwise and inside is transcribed anticlockwise

Question 2

DNA packing

Answer 2

DNA is organised into a nucleoid with associated proteins that condense and compact DNA to form looped regulatory regions

Question 3

transcription

Answer 3

sigma factor associates with RNA polymerase to form holoenzyme which locates the promoter. sigma factor released as RNA polymerase moves along promoter

Question 4

bacterial promoters

Answer 4

-35 consensus sequence: recognised by RNA polymerase
-10 consensus sequence (pribnow box): binding site of RNA polymerase
strong promoter=more frequent transcription=more protein

Question 5

regulator genes

Answer 5

encode either regulatory RNA or proteins
regulator proteins have helix-turn-helix binding motif

Question 6

operons

Answer 6

group of structural genes (related in function and expressed as single mRNA molecule) and the regulatory sequences (promoter, operator)
Allow multiple genes to be transcribed together under the control of a single promoter

Question 7

operator

Answer 7

regulatory sequences on or near promoter region. is a binding
site for regulatory proteins that control transcription

Question 8

how operons work

Answer 8

a regulator gene (not part of operon and has own promoter) encodes a regulator protein that binds to operator to regulate transcription

Question 9

regulator proteins

Answer 9

activators: positive control
repressors: negative control

Question 10

activators

Answer 10

binds to sequence upstream from promoter region
helps recruit RNA polymerase to promoter
(transcription will initiate without this, just not as efficiently)

Question 11

repressors

Answer 11

binds to operator
blocks RNA polymerase binding or prevents its movement along the mRNA

Question 12

negative control with repressor proteins

Answer 12

negative repressible operons (on until turned off)
negative inducible operons (off until turned on)

Question 13

negative repressible operons: transcription normally ON

Answer 13

no core repressor=repressor (produced by regulator gene) inactive = transcription occurs
when the end product of the biosynthetic pathway builds up in sufficient quantities, it then acts as a core repressor
core repressor present= repressor binds to core repressor forming an active complex that blocks transcription

Question 14

Trp operon
(negative repressible operon)

Answer 14

tryptophan synthesis, 5 structural genes
trpR gene encodes repressor
tryptophan is core repressor at high levels
active repressor-corepressor complex binds to operator and prevents tryptophan being made

Question 15

negative inducible operon
(transcription normally OFF)

Answer 15

no inducer=repressor active and binds to operator=transcription blocked
inducer present, binds to repressor preventing it from binding to operator.
inducer allosterically modulates the repressor that is normally bound to DNA, causing it to release from the operator

Question 16

lactose metabolism in e.coli

Answer 16

glucose absent, lactose metabolised to glucose by beta galactosidase
permease in cell membrane facilitates lactose entry into cell

Question 17

lac operon: absence of lactose
negative inducible operon

Answer 17

lac l (regulator) encodes active repressor
repressor binds to operator and inhibits transcription
genes that code for proteins that break down lactose are not transcribed

Question 18

lac operon: presence of lactose

Answer 18

some lactose converted to allolactose
allolactose acts as an inducer that binds to repressor, changing its shape and making it inactive. removed from operator and transcription occurs, enzymes produced

Question 19

positive control with activator proteins

Answer 19

activator binds to site upstream from promoter
recruits RNA polymerase

Question 20

catabolite activator protein (CAP)
(positive control)

Answer 20

conc of cAMP inversely proportional to conc glucose
when glucose low, all ATP used so cAMP increases
cAMP allosterically activates CAP by conformational change

Question 21

effect of cAMP-CAP binding

Answer 21

CAP binds upstream from promoter, causing helix-turn-helix motif to interact with the DNA, bending it
enhances recognition and binding of RNA polymerase

Question 22

lac operon and CAP

Answer 22

transcription of lac operon only occurs when lactose is present and glucose is absent
low glucose=high cAMP=CAP activates transcription
high glucose=CAP cant activate operon

Question 23

where does cAMP come from

Answer 23

high levels of cAMP are produced from breakdown of ATP

Question 24

antisense RNA

Answer 24

regulatory RNA
complementary to specific mRNA
reduces translation by blocking ribosome from binding

Question 25

OmpF, antisense RNA

Answer 25

low osmolarity=cell produces OmpF protein (forms channels in membrane)
osmolarity increases=micF gene activated=micF RNA produced
pairs with 5’ of OmpF mRNA to block ribosome binding site. fewer channels made

Question 26

riboswitches

Answer 26

RNA sequences in mRNA that affect gene expression
either block ribosome binding sites or create a structure later in the mRNA causing premature termination of translation

Question 27

riboswitches when regulatory protein present

Answer 27

regulatory protein binds to riboswitch and stabilises a secondary structure, masking ribosome binding site and inhibits translation

Question 28

riboswitches when regulatory protein absent

Answer 28

riboswitch assumes alternatively secondary structure that makes the ribosome binding site available and translation occurs