LECTURE 13 Flashcards
what are direct removal of lesions methods?
error free systems because there is no synthesis of new DNA, which leads to errors
- thymine dimers (photoreactivation, photolyase)
- methyls (methylguanine methyltransferase)
- alkyls (alkyltransferase)
what does recombination repair deal with?
recombination is the last resort: deals with big problems
complex mutations such as double strand breaks or multiple lesions in one area
recombination repair picture:
there is 2 issues here: there is a thymine gap but also a gap opposite of that, which means you cannot use the opposing strand to synthesize DNA
a piece from strand A needs to go onto strand C to fix this problem
what types of RNA does transcription generate?
mRNAs
tRNAs
rRNAs (16S, 23S, 5S)
in what direction does RNA synthesis go?
5’ to 3’
at what rate does RNA polymerase go?
highly processive
adds 40 nucleotides/second at 37°C
how does RNA polymerase move on the gene?
forms a transcription bubble of 12-20 base pairs
where does transcription start/stop?
start: promoter
stop: terminator
characteristics of RNA structure?
- mostly single single stranded
- coils back on itself to make complementary base pairing
- secondary structure stem loops which can fold again to make tertiary structures
- sugars are riboses, contain OH group at the 2’ position
- the bases are ACGU
how does mRNA come out of the transcription bubble?
comes out during transcription
the first base still has the triphosphate, since it is not linked to any other base
when the RNA polymerase reaches the end, the mRNA is detached
what is the structure of a bacterial promoter?
- at -35 there is the RNA polymerase recognition site
- the consensus sequence is TTGACA
- at -10 there is the RNA polymerase binding site
- the TATA box, and the consensus sequence is TATAAT (also pribnow box)
the RNA polymerase binds to the TATA box and begins transcription
what is Rho?
protein factor
helicase involved in transcriptional termination
what are the two types of terminators for transcription in bacteria?
Rho independent:
- hairpin in the RNA strand
- 6 uridines after the hairpin structure
- no need for Rho
Rho dependent:
-no poly U tract
- sometimes no hairpin
how do the rho dependent vs rho independent terminators work?
Rho independent:
- the RNA pol is stuck on the hairpin
- AU base pair is so weak that this releases the mRNA and the RNA polymerase
Rho dependent:
-the RNA pol is stuck on the hairpin
- Rho, which follows the RNA polymerase, catches up to it, and the helicase action releases the mRNA and the polymerase
why do pictures of transcription of rRNA genes look like christmas trees?
bacteria needs lots of ribosomes
therefore need lots of rRNA
each branch coming out of the gene is an rRNA that is being synthesized
=> there are lots of RNA polymerases on each gene
as the rRNAs come out they already start to coil on themselves, making those secondary structures
differences between eukaryotic and prokaryotic mRNA?
what are polycistronic genes useful to bacteria?
genes on the same mRNA are usually related
very useful to express them at the same time, since they are most likely needed all together for the pathway in question
what does the 5’ end of eukaryotic mRNA look like?
has a 7-methylguanosine cap added to the 5’ end
the first base has a methyl added to it
what does the 5’ end of prokaryotic mRNA look like?
no cap and no methyl on the first nucleotide
what is coupled transcription and translation in bacteria?
translation and transcription happen in the same place, therefore they can happen simultaneously
as the mRNA exits the transcription bubble, a ribosome can bind to it to begin translation
what is a polysome?
an mRNA with multiple ribosomes on it
