CBG05 Flashcards
What is transcription of a gene regulated by?
Trans acting and cis acting sequence
What are trans acting elements?
Where are they found?
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.
What are cis regulatory elements?
Where are they found?
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.
What are transcription factors?
DNA binding proteins.
promoting as activators
blocking as repressors.
What is a structural motif?
a super secondary structure.
Give four examples of transcription factors and their structural motifs
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.
What can dna sequences bound by transcription factors be?
low level sequences
high level assemblies
What are low level sequences and examples?
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
What are high level assemblies and examples?
Essential for all transcribed genes, eg. RNA binding.
eukaryotes - enhancer, silencer, insulator
bacteria - operator
What is the Trp Operon?
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.
What happens when tryptophan is in the growth medium of the bacteria?
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.
How is blocking gene expression of Trp Operon regulated?
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
What kind of control is the Trp operon said to be under?
negative repressible
because active dna binding form of proteins turns genes off
Other than trytophan repressor repression how else is the trp operon regulated? What is the difference between the 2 and overall repression?
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
Why is attenuation only possible in prokaryotes?
As prokaryote ribosomes begin translating mRNA while RNAP is still transcribing
allowing process of translation to affect transcription of operon directly.
How does attenuation of Trp Operon work?
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)
What kind of control is the Lac operon under?
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
what does the lac operon code for?
proteins required to transport lactose into the cell and break it down.
What does cap do?
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.
When is the lac operon expressed?
when lactose is present and glucose is absent.
What kind of proteins does the lac operon code for?
catabolic
break down of lactose by beta galactosidase to glucose and galactosidase
What does the lac operon look like?
Lac1 —- CBS— P–O -LacZ-LacY-LacA–
Lac1= codes for repressor
cbs - cap binding site
What happens when glucose and lactose are present?
cap does not bind to cbs
the operon is off
What happens when glucose but not lactose is present?
the repressor binds to operator
cap not bound
operon is off
