CBG Lecture 5: Regulation of transcription

Question 1

what is transcription mainly controlled by

Answer 1

cis-acting DNA elements

trans-acting DNA elements`

Question 2

how can gene expression in prokaryotes be modified

Answer 2

by an interplay between transcription and translation

Question 3

what is attenuation

Answer 3

an interplay between transcription and translation

Question 4

what are cis-acting DNA elements?

Answer 4

regulate the DNA close to them by binding gene regulatory proteins
eg. promoter/operator/enhancer
sequences that have to be physically next to eachother to work are cis

Question 5

give some examples of cis acting DNA elements

Answer 5

promoter
operators
enhancers

Question 6

what are trans-acting DNA elements?

Answer 6

must be expressed a gene-regulatory protein to act ad can be relatively far away, even on different chromosomes eg. regulator DNA sequence
examples of trans-acting DNA sequence: Transcription factors, repressors, inducers

Question 7

give some examples of trans-acting DNA elements?

Answer 7

transcription factors
repressors
inducers

Question 8

what are transcription factors

Answer 8

DNA binding roteins

Question 9

give some examples of the main types of transcription factors and their structures

Answer 9

TATA binding protein (TBP) - beta scaffold (unusual for TF)
activator protein 1 (AP1) leucine zipper - generally binds in the major groove
CAP -catabolite activator protein (helix-turn-helix)
Early growth response protein 1 (EGR-1) -> Zinc fingers

Question 10

what is a TBP -give main structure

Answer 10

TATA binding protein

beta scaffold

Question 11

what is an AP-1 -give main structure

Answer 11

activator protein transcription factor

leucine zipper-generally binds in the major groove and straddles the DNA

Question 12

what is CAP-give main strucutre

Answer 12

transcription factor: catabolite activator protein: helix-turn-helix

Question 13

what is EGR-1-give main strucutre

Answer 13

early growth response pritein 1 - zinc fingers - have histidine/cysteine residues. fingers poke into major groove

Question 14

why does there need to be transcriptional regulation

Answer 14

so only express the proteins that are needed, as all cells have the same genome, but different genes expressed in different cells
different condns of same cell = different proteins needed

Question 15

what names do DNA sequences bound by TFs go by

Answer 15

low level sequences
OR
high level assemblies

Question 16

what are low level sequences?

Answer 16

response element = DNA sequence recognised by protein

eg. in bac: Pribnow box (E.coli) in euk: TATA,CAAT,BRE box ->assembled with large units

Question 17

what are high level assemblies?

Answer 17

DNA sequences bound by promoter =RNAP binding
for bac: operator
euk: enhancer, silencer, insulator

Question 18

what 2 things do trans regulatory elements need, to work

Answer 18

through interaction between
1)a transcribed and translated TF derived from the trans-regulatory element AND a DNA regulatory element thats adjacent to the regulated gene

Question 19

what control is the trp operon under

Answer 19

negative repressible control

Question 20

what is the trp operon regulated by

Answer 20

repressor protein

attenuation

Question 21

what is the trp operon composed of

Answer 21

trpR gene which synthesizes repressor protein
P:Promoter region where RNAP binds
O-operato region where effector binds (either a repressor or inducer) then structural gene regions trpA to L)
the structural genes encode the enzymes for trp synthesis

Question 22

what does repressible control mean

Answer 22

transcription is ON unless an effector is added

Question 23

what does negative control (of an operon) mean

Answer 23

transcription is turned OFF by binding to regulatory protein

Question 24

what are operons

Answer 24

they are how orikaryotes regulate gene sequences

Question 25

what happens to a prokaryote when concentration of tryptophan is high

Answer 25

1. repressor binds to co-repressor (trp) and becomes able to bind DNA 2. repressor/corepressor complex blocks transcription by binding operator 3. no tryptophan structural genes transcribed

Question 26

what happens to a prokaryote when concentration of tryptophan is low

Answer 26

turns the trp operon ON not enough typ available for TrpR to be in DNA-binding form No TrpR/trp blocking the operator so RNAP can transcribe operon

Question 27

what is autologous repression | give an example of this

Answer 27

repression by an element transcribed within the regulated gene in the lac operon, lacI represses its own transcription

Question 28

besides repressors, how else is the trp operon controlled

Answer 28

by attenuation

Question 29

why does attenuation not happen in eukaryotes

Answer 29

because you need interplay between transcription and translation without compartmentalisation using membranes (membranes present in EUKS)

Question 30

overall, what does attenuation do to trp operon

Answer 30

can prevent expression of trp biosynthesis genes when trp levels in cell are high

Question 31

how does attenuation work at high tRNAtrp concentration

Answer 31

ribosome reads through 1 easily and shields 2, 3&4 form a transcription terminator hairpin

Question 32

how does attenuation work at low tRNAtrp concentration

Answer 32

ribosome stalls in 1 waiting for tRNAtrp; 2 binds 3 3&4 cant form transcription terminator hairpin

Question 33

what happens when a 3&4 stem loop is present in trpL mRNa when a 2&3?

Answer 33

it acts with the attenuator (uracil rich sequence) to form a terminator for transcription at end of trpL gene when a 2&3 stem loop forms, attenuator doesnt form and transcription proceeds to trpE

Question 34

what determines whether ribosomal stalling will happen in mRNA

Answer 34

two adjacent trp codons being present in ribosome

Question 35

what are eukaryotic genes controlled by? | give flow chart of control

Answer 35

numerous enhancers | enhancer -> mediator -> basal TFs + RNAP (from a long looped distance)

Question 36

what sequence does the lac operon work by

Answer 36

tran acting sequence

Question 37

what genes are involved in the lac operon

Answer 37

lacI - codes repressor protein CBS - CAP binding site (catabolite activator protein binding site) Promoter Operator structural genes: lacZ - beta galactosidase lac Y - lactose permease lac A - importer protein

Question 38

how does the lac operon work

Answer 38

under negative inducible control repressor is inactivated by binding inducer - lactose repressor blocks transcription by binding operator

Question 39

what happens when E.coli has high concentrations of glucose and low [lactose]

Answer 39

lacI transcribed and translated repressor blocks transcription by binding operator RNAP cant bind therefore no structural genes transcribed

Question 40

what happens when E.coli has low [glc] and high [lac]

Answer 40

lacI transcribed and translated repressor blocking transcription by binding operator is INACTIVATED by binding allolactose inducer no lacI blocking operator so RNAP can transcribe operon

Question 41

what two ways is lac operon controlledq

Answer 41

positive control by CAP | negative inducible

Question 42

how is lac operon under positive control

Answer 42

by CAP low [glc] -> high [cAMP] -> CAP/cAMP able to bind CBS(CAP binding site) transcription is turned ON when regulatory protein (activator is CAP) binds to DNA and actively recruits RNAP