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CBG > CBG05 > Flashcards

CBG05 Flashcards

1
Q

What is transcription of a gene regulated by?

A

Trans acting and cis acting sequence

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2
Q

What are trans acting elements?

Where are they found?

A

A DNA sequence that contains a gene.
This gene codes for a protein that will be used in the regulation of another target gene.
eg. regulatory sequences.
Can be found on the same chromsome as gene to be regulated or different.

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3
Q

What are cis regulatory elements?

Where are they found?

A

regions of non coding DNA which regulate transcription of nearby genes.
latin transaltes cis = ‘on this side’
Typically reguate genes by functioning as binding site for transcription factors.
Found in the vicinity of the gene they regulate.
Promoter, operator, enhancer genes.

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4
Q

What are transcription factors?

A

DNA binding proteins.
promoting as activators
blocking as repressors.

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5
Q

What is a structural motif?

A

a super secondary structure.

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6
Q

Give four examples of transcription factors and their structural motifs

A

TATA binding protein
- has a Beta scafffold

Activator preotin cFOS and cJun
-has a leucine zipper, repetition of leucine residues at
every 7th position.

Catabolite activator protein CAP

  • helix turn helix
  • 2 alpha helices joined by a short strand of AA’s found in many proteins that regualte gene expression

Early growth protein 1. EGR-1

  • zinc fingers.
  • contain one or more zic ions to stabilise the fold.
  • coordinated by 2 histine and 2 cystiene residues.
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7
Q

What can dna sequences bound by transcription factors be?

A

low level sequences

high level assemblies

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8
Q

What are low level sequences and examples?

A

low level sequences are response elements, the dna sequence is recognised by a protein
eg. in bacteria the pribnow boc
in eukaryoes, tata box, caat, box and bre

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9
Q

What are high level assemblies and examples?

A

Essential for all transcribed genes, eg. RNA binding.
eukaryotes - enhancer, silencer, insulator
bacteria - operator

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10
Q

What is the Trp Operon?

A

found in e.coli
5 genes that code for enzymes tha manufacture the AA tryptophan are arranged in a single operon, adjacent to one another and transcribed as a single long mRNA.

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11
Q

What happens when tryptophan is in the growth medium of the bacteria?

A

the enzymes expressed by trp operon are no longer needed so the operon is switched off.
Tryptophan repressor protein then binds to operator region within promoter, which blocks access to promoter region by RNAP, prevening expression of tryptophan producing enzymes.

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12
Q

How is blocking gene expression of Trp Operon regulated?

A

Tryptophan repressor = member of helix turn helix family.
to bind to operator it needs two molecules of tryptophan bound to it (corepressors)
the binding of the 2 tryptophans tilts the motif of repressor so it is presented properly to DNA major groove.
Without tryptophan the motif swings inward and the protein is unable to bind to operator

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13
Q

What kind of control is the Trp operon said to be under?

A

negative repressible

because active dna binding form of proteins turns genes off

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14
Q

Other than trytophan repressor repression how else is the trp operon regulated? What is the difference between the 2 and overall repression?

A

attenuation
repression system targets intracellular trp conc
attenuation responds to concentration of charged tRNA^trp
TrpR represses by factor of 70
attenuation x10
overall accumulated repression is 700 fold

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15
Q

Why is attenuation only possible in prokaryotes?

A

As prokaryote ribosomes begin translating mRNA while RNAP is still transcribing
allowing process of translation to affect transcription of operon directly.

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16
Q

How does attenuation of Trp Operon work?

A

Either of two stem loops can be formed in the RNA by complimentary base pairing.
Either between sequences 3 and 4 - a terminating loop
or between sequences 2 and 3
if a loop forms between sequences 2 and 3 then 3 is not available to loop with 4 and create the terminating loop.
The stem loop that is formed is determined by the speed of the ribosome following the RNAP and translating the mRNA into AA’s.
If tryptophan is lacking the ribosome stalls when it encounters two trp codons in mrna as trna^trp are in short supply
stalled ribosome allows stem loop 2-3 o forma dn 3-4 will not stall so transcription continues
(sequence 1 is 2 trp codons which are rare in proteins)

17
Q

What kind of control is the Lac operon under?

A

positive and negative inducible control by lac repressor protein and cap
normally transcription is off so called inducible
positive regulation by cap as when it bind its recruits RNAP

18
Q

what does the lac operon code for?

A

proteins required to transport lactose into the cell and break it down.

19
Q

What does cap do?

A

allow bacteria to use an alternative c-source in the absence of glucose, eg. lactose.
(cAMP) produced during glucose starvation
this binds to CAP causing a conformational change that allows CAP to bind to the CBS
CAP then makes a direct protein-protein interaction with RNA polymerase that recruits RNA polymerase to the lac promoter.

20
Q

When is the lac operon expressed?

A

when lactose is present and glucose is absent.

21
Q

What kind of proteins does the lac operon code for?

A

catabolic

break down of lactose by beta galactosidase to glucose and galactosidase

22
Q

What does the lac operon look like?

A

Lac1 —- CBS— P–O -LacZ-LacY-LacA–
Lac1= codes for repressor
cbs - cap binding site

23
Q

What happens when glucose and lactose are present?

A

cap does not bind to cbs

the operon is off

24
Q

What happens when glucose but not lactose is present?

A

the repressor binds to operator
cap not bound
operon is off

25
Q

What happens when neither glucose or lactose is present?

A

cap bound to cap binding site
repressor bound to operator
operon is off

26
Q

What happens when glucose is not present, but lactose is?

A

cap binds to cap binding site
no repressor protein
rnap cant bind to promoter
operon is on.

27
Q

What does the lac operon repressor protein do?

A

coded by Lac1 region at beginning of gene
transcribed and translated it then binds to operator region of promoter inhibiting transcription
if lactose is present this inhibits the repressor protein so it cannot bind to the operon
RNAP is then able to transcribe genes

28
Q

How are eukaryotic genes controlled?

A

complex control by numerous enhancers (short region of DNA that can be bound with proteins (activators) to activate transcription of a gene) - cis activating.
- in comparison to prokaryotes involves more proteins, longer dna and very complex.

29
Q

What is a central component in eukaryotic control?

A

mediator, 24 subunit complex which is a transcriptional coactivator in all eukaryotes and acts as a bridge between rnap and tfs

30
Q

What is the role of activators in eukaryotes?

A

attract position and modify general transcription factos, meciator and rnap11 at the promoter to begin transcription. by acting directly on these components and indirectly by changing chromatin structure around promoter.

31
Q

What is transcriptional synergy?

A

can be How where activator proteins work together and produce a transcription rate much higher than could be achieved individually.

32
Q

How do gene repressor proteins in eukaryotes differ from prokaryotes?

A

they dont directly compete with rnap for dna and often act through more than one mechanism at a given target gene

  • may work by direct interaction with transcription factors- blocking assembly etc
  • recruitment of chromatin remodelling complex that returns nucleosomal state of promoter to pre transcriptional form.
33
Q

What is autogolous, give an example?

A

controls self

eg. lac operon

34
Q

Describe the Arabinose operon?

A

duel positive and negative control
single dna binding protein araC may act as either a repressor or activator
Arabinose present - binds to araC which binds to initaitor region within promoter, allowing rnap to bind and transcribe.
without arabinose arac binds to araI and araO and causes looping so sigma and rnap cant bind.

35
Q

What is the arabinose operon?

A

codes for catabolic genes to break down arabinose.
araB
araA
araD
it is polycistronic so encodes more than one protein.

36
Q

What is a riboswitch?

A

regulated segment of mRNA that binds a small ,molecule resulting in a change in production of proteins encoded by mRNA
mRNA with riboswitch is directly involved in regulating its own activity in response to the concentration of effector molecules
could be a target for novel antibiotics
artifact of rna world hypothesis?

37
Q

what are enhancers?

A

short region of cis coding dna that can be bound by proteins to activate a gene

CBG (19 decks)

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