Lecture 2/26 Flashcards
what is the process called that makes DNA into messenger RNA (mRNA)?
transcription
what is a gene defined by?
its DNA region that is transcribed into RNA
does a gene need to be able to be made into a protein to be considered a gene?
no
why are genes a small fraction of the chromosome?
because much of the chromosome is non-coding
what is a promoter?
DNA sequence that provides a signal to RNA polymerase complex to start transcription in that region
what direction does RNA pol add nucleotides in?
5’ to 3’
what are the three main characteristics of RNA pol?
- it forms phosphodiester bonds using ribonucleotide triphosphates (ATP, CTP, etc. instead of DNTPs)
- hydrolysis of bonds in NTPs provides energy for transcription
- doesn’t need a primer for elongation to occur
what does a +1 and arrow indicate on DNA?
where transcription starts and the arrow is the direction that transcription will proceed in
what helps RNA pol complex bind to promoter at higher efficiency?
transcription factors
can an RNA pol complex bind to a promoter on its own? what happens to it?
not well, but basal transcription will occur
what do transcription factors/activators do?
bind to DNA and promote binding of RNA pol complex to a certain area
where is the promoter in relation to where transcription will start?
it is upstream, 5’ to the gene, in the minus region
do mammalian genes use one promoter per gene or multiple?
multiple
How much of a strand does a gene encompass?
a gene is on both strands of DNA, though only one strand is used as a template
what is the difference between a ‘transcription unit’ and a ‘coding region of a gene’
there is no difference, the phrasing is used interchangeably
what do transcriptional repressors do?
prevent binding of RNA polymerase complex
why aren’t the same proteins made in every cell if the genome is the same in every cell type?
TFs determine where and when a gene is expressed, and the different functions of different cells may require different proteins
what is a mutation?
an alteration in the DNA sequence
why do mutations occur?
mistakes in the cell cycle, environmental change
what is a LOF mutation
loss of function mutation, causes LOSS or NO protein function
what is it called when a mutation results in a complete loss of function?
null mutation
what is a GOF mutation?
gain of function mutations cause new or enhanced protein function
why is a GOF mutation bad?
you end up with a gene function different to what it’s supposed to do, or you get too much of the correct protein
what is a silent mutation?
it causes no change in protein function
what is a genotype?
genetic composition of an individual (what the DNA is as a whole or for a gene)
what is a phenotype?
observable characteristics of an individual (ie. hair color, eye color, height)
what is sigma factor and where is it found?
it is similar to a transcription factor, but in proks. it is needed for initiation of transcription
what does sigma factor do?
it recognizes core DNA sequences within a promoter and helps recruit the RNA pol complex
how many sigma factors are in proks?
many
what does sigma factor do with the RNA polymerase complex?
they physically interact to create a holoenzyme
can the core RNA pol complex elongate and terminate transcription without the sigma factor?
yes at a basal level, but it initiates poorly without the sigma factor
is helicase around during transcription?
no, RNA pol complex has helicase activity to melt H bonds and open the helix
what are three different functions of RNA polymerase?
- helicase
- polymerase (elongation and termination)
- proofreading
where is the proofreading cleavage site located in relation to the polymerization site in transcription?
it is the same site
how many nucleotides does the RNA pol complex cover?
30
at what point does the sigma factor leave?
it is displaced after 12-14 nucleotides are getting added
are both strands used as templates in transcription?
no, just one
what happens to the non-template strand during transcription?
it is moved out of the way (flipped out) so RNA can be made along the template strand
at what stage does sigma factor leave the RNA polymerase core complex?
during elongation
During transcription, how does the core RNA polymerase complex move?
it translocates along the DNA template strand in the 3’ to 5’ direction (which therefore causes nts to be added in the 5’ to 3’ direction on the mRNA)
what happens if there’s a mistake in transcription?
rna pol can remove 1-2 nts in proofreading
why is it more important to check for mistakes in DNA synthesis than for RNA
bc there is more than one transcript per gene bc you need lots of protein, so if one transcript has a mistake it will likely be fine. DNA is heritable
how many transcription bubbles are there in proks?
many
would the transcript be longer when closer to or further away from the promoter region?
further away from
what are the two ways to stop transcription in prokaryotes?
extrinsic signals (another protein comes in to block and dislodge the RNA pol complex) or intrinsic signals
what are the extrinsic signals to terminate transcription in proks?
rho factor, which is a hexamer (makes up ~20% of termination in bacteria)
how does rho-dependent termination work?
- the rho factor binds to a C rich region of the transcript (then it opens up and surrounds the region)
- hexamer core closes and Rho ATPase activity activates the helicase activity which causes complex translocation in the 5’ to 3’ direction
- Rho dislodges paused RNA pol complex from RNA
What do the intrinsic signals of termination for prok transcription need?
specific sequence type, doesn’t need additional factors
What sequences are instrinsic signals for termination of transcription?
RNA sequences ~40nt long of GC rich region 5’ to the polyU tract
what does the polyU tract in a transcript do?
it causes RNA pol to pause
How do the intrinsic signals of termination work?
GC rich region 5’ to polyU tract, the repeats in the polyU cause the RNA pol to pause, and the GC rich region forms hairpin loops and dislodges RNA from RNA pol complex, causing termination
Why can a hairpin be made for termination?
because the bottom part of the pin (not the loop) is complementary to each other – the GCs anneal to each other and it makes a hairpin
where does the hairpin form?
just before the 3’ end of the transcript (not at the end, 5’ to the end)
what is the more common form of termination for transcription in proks?
hairpin loops
does the hairpin get cleaved off?
no, it remains as part of the transcript
what is something in common between the extrinsic and intrinsic signals?
they are both based on the RNA transcript on the 3’ end
Which strand is the RNA-like strand?
the non-template strand
which template is the coding strand?
the non-template strand
Why is it called the RNA-like strand?
Because it is what the ensuing RNA will look like
What is the ensuing RNA strand called from transcription (in proks)?
the primary transcript
Why is there no splicing in proks?
bc there are no introns
do the numbers get bigger when going upstream or downstream?
downstream
What is conserved across promoters in proks?
the TATA box at -10 nts and TTGACA at -35nts upstream
in euks, how many genes to one promoter?
one
in proks, how many genes to one promoter?
one promoter can control multiple structural genes in proks
what is in the promoter region and where is it?
it is where the promoter is and where transcriptional factors bind, it is upstream to the start of transcription in proks
what is an operon?
a promoter with one transcript that has multiple coding regions but only one termination signal
are there operons in euks?
no
