Transcription and repair Flashcards
folds of domain
- zinc finger C4 -found innuclear receptors
bind as dimers
found in multiples in proteins
common - leucine zippers because every 7th amino acid is a leucine fold of
bind as dimers
protein protein interaction site
2 alpha helices coiled around each other = coiled coil and then slide into major groove
- basic helix loop helix
coiled coil
doesnt have a leucine every 7th amino
doesnt contain a loop
reading as direct read out
classes of proteins that can read DNA sequence and bind to specific sequences
i.e. bacterial promoters
how to control protein levels
transcription = most efficient control of protein levels
post transcriptional modification of mRNA
mRNa degradation rates
Translation
post translational modification of proteins
Protein targeting
Protein egradation
transcription vs repliaation
all polymerases move 5 prime to 3 prime because magnesium is cofactors to co-ordinate the incoming nucleotides and new strand is made 5 prime to 3 prime both require template initiation elongation termination
difference
transcription dows not require primers but replication foes i.e okazaki
generally only one strand is copied in transcription
only segments of the DNA are copied in transcription
cis elements = promoters and control sequences
things on dna
transcription doesn’t need primer
polymerase can bind directly on promoter and initiate
simpler in prokaryotes but otherwise similar but dont work in each other
contain consensus sequences = very strong promoter - the further u are from consensus seq the weaker the promoter you are
minus 1 = last base of promoter
and plus 1 is first base of the transcribed unit
minus 10 and 35 promoter regions
in the direction of transcription = downstream
against = upstream
house keeping gene
always need to be turned on = constitutive promoter
promoter than drives a the housekeeping gene to produce lots of protein will be near the consensus
a gene which only requires a low level of protein for its housekeeping function will have a promoter far form the consensus
controls how much is made not control over activity of a given gene
how to you control if a given gene is on or off or how much that gene makes
trans acting elements
proteins that bind to cis elements i.e. dna dependent
RNA pol = does transcription
complex of 5 subunits and 6th is called sigma bind to polymerase to regulate which genes are turned on or off
transcription
initiation
polymerase will bind to promoter will recognise minus 10 and minus 35 sequences in the promoter and will move from a close to an open complex
@ minus 10 region is being mounted
promoter is cleared by the RNA polymerase
elongation = RNa polymerase moves along the DNa mounting DNA as it goes and making RNa strand
mounted bubble is 17bp long
8 of which is where new RNA is hybridises = hybrid hetero duplex template strand
till hits terminator sequences
can be Ro dependent or Ro independent
when formed in RNA forms hairpin = dissociation terminating transcription
topoisomerase
separation of strands = movement of transcription bubble creates topological pressures on DNA
normally negatively supercoiled
in front of transcription bubble are waves of positive supercoiling are generated
behind the transcription bubble
waves of negative supercoiling form
independent - sequence causes dissociation
Torpedo model =
Ro protein combines to RNA + races along RNA till meets DNA RNA hybrid region in polymerase and separates them
how to induce or repress a gene
use of specificity factors - sigma factors in RNA polymerase combine and change which sequence promoters it recognise
repressors activators
mediate response of cell to the presence of small molecules
negative regulation = molecule present and activate repressor to block binding or when molecules absent
based around operators
the promoter when the repressive binds to the operator is directly blocked by the RNA polymerase form binding to the promoter
positive
bind to sequences adjacent to promoter
stabilise reactoion of RNA polymerase to promoter
i.e. LAC operon
transcribed as one made into different proteins
driven by single promoter and overlapping is the operator where the repressor binds
in the absence of lactose or a derivative or it allolactose lac repressor binds to operator region adjacent to lac promoter blocking RNA polymerase = no transcription
no lactose = no metabolism of lactose proteins needed
presence of lactose converted to allolactose and points to lac repressor that causes the lateral repressor to fall off the operator = RNA polymerase binds = transcription = metabolise lactose
control when we want an exogenous gene turn on or off
also exhibits positive regulation activator site when binds to that stabilises polymerase
encodes genes in metabolism of lactose
-10 and -35 regions form core of promoter
overlapping that isthe operator sequence depending on the presence of alolactose and adjacent to the promoter CRP site regulates how much transcription you get in response to glucose
CRP bond to Camp = indicator of levels of glucose
high glucose = inhibit cAMP production
inversely related to lvel of glucose
for lac operon to be on presence of lactosebut absence of glucose
direct read out by transcriptional regulation - proteins recognise a given sequence - extrinsic info held by DNA
indirect readout - recognises the structural shape could be as a consequence of the bases but not directly the thing the protein recognises
DNA repair
DNA damage leaves distortions
mismatch repair base excision repair nucelotide excision repair direct repair deamination of recombinational dna repair error prone translesion dna synthesis
mismatch repair
3 to 5 exonuclease activity - high fidelity
taq doesnt have this ability
which strand is correct and which is wrong?how does it recognised self defamation?
the parent strand is correct
know this by methylating
adenine gets methylated
if both of the adenines are methylated the whole sequence is old
if only strand is methylated it must have just been methylated = daughter strand that needs repair
translocates pulls the DNA from both sides in and up = loop out
looking for methyl group
solution
daughter strand cleaves and removed with exoneuclease
dna polymerase 3 makes new strand
base excision repair
sponaneous deamination
DNA glycosylases and AP endonucleases - cut in the middle
cytosine deaminate to uracil = pair with A instead of G
know which strand is wrong = strand w uracil because doesnt occur in DNA
cut glycosidic bond between sugar and backbone = gap apurinic site = endonuclease at that site dna polymerase 1 fills in that site
nucleotide excision repair
thymine dimers - 2T on top of each other
cross link due to UV light - stools to polymerases
kinks in the DNA recognised by UvrA UvrB complex
thymine dimers causes defamation away from the b form of DNA
A helicase cuts on either side of lesion endonuclease - 2 cuts = unwinds and removes fragment
backbone cleaved 5prime and 3prime of the lesion
and then DNA pol 1 fills in the gap
UvrA replace UvrC
direct repair
base problem is drectly fixed
methylation of guanine to form O6 methly guanine with thymine instead of cytosine
repair back to guanine
taking of methyl group
1 O6methylguanine DNA methyltransfertase doesn’t turn over canny b reused has to be degraded
SOS response
recognise there is damage
turning on genes that respond to DNA damage
activated u wouldn’t want in a healthy cell
- repair is error prone
