Week 5 Flashcards
Which instrument can you see transcription taking place?
Electron micrograph
What is the molecular definitation of gene?
The entire nucleic acid sequence, that is necessary for the synthesis of protein or RNA. Or
SEGEMENTS OF GENES THAT ARE TRANSCRIBED INTO RNA.
What are the two types of genes when transcribed?
- The resulting RNA gets translated into a protein (mRNA)
- The resulting RNA functions as RNA and may not be translated into proteins (tRNA) (rRNA) and RNA in telomerase
True/ Fasle: Some RNA stop from making proteins
True
What do rates of transcription depend upon?
Neighbouring sequences, sequences that are not transcribed etc.
Typically does more mRNA mean more protien?
YES, not always though
True/ Flase: Uracil is in DNA
True, during deamination or depurification the C gets turned into U and rotates 90 deg.
Which direction is RNA added?
1) 5’ to 3’ (adding onto the three prime end)
2) made anti parallel and complementary to DNA. (G-C, A-U)
How is the dna template when making RNA?
it is read 3’ to 5’, compared to dna polemerase it is very similar.
How are RNA nucleotides linked together?
Phosphodiester bonds
think is it double strand or single strand….
What is the template strand for RNA?
ssDNA (3’ to 5’)
it is single stranded DNA going from 3’ to 5’.
What is the DNA-Rna strand in RNA polymerase held togther by?
Base pairing
What is a bean shaped protein that binds to the RNAP to find the promoter region?
The sigma factor
What makes the RNAP hallow enzyme?
Sigma factor + RNAP
How does RNA transcription occur?
- Sigma factor binds to the promoter sequence plus hallowenzyme
- Localized unwinding of DNA occurs
- Abortive transcription occurs: RNA polymerase trascribes the first 10 then lets go, then 10 then lets go.
- Leaves abortive transcription and goes into processive transcription, leaves behind the sigma factor as well. It is no longer hallowenzyme.
True/ False: Rna polymerase does not need a primer
True only DNA polymerase needs a primer
What is a promoter sequence? why is is importnat ?
Sigma factor binds to the promoter factor
It is everyting the sigma factor binds to and the sequence in between.
Which nucleotides are named +1?
The nucleotide pair that was first to be transcribed. (start site 1)
True/ False: The number of the sequence right behind the starting point of RNA is called 0
FALSE, It is -1! there is no 0!!
What is upstram and downstream?
+ are downstream, - are down stream.
so plus 1 is upstream of +200
What are promoter consenses?
it is the region on which sigma factor is on. say first end is on ACTGHHTT then second is ACTGTGTATAT then label them -35 and -10, so the promoter consenses are -35, -10
TRUE/FALSE: Bacteria has one sigma factor that binds to the promoter region.
NO, there are different sigma factors that bind with RNAP to make the hallowenzyme. The sigma factor depends on which type of protein you want to make.
What happens to the RNA as it leaves RNAP?
It forms base pairs with itself and forms loops.
What are the common base pairs of termination sequences?
bunch of CGCGCGC, then again CCGGCGC and then bunch of A’s, they then form a hairpin when Gs and Cs base pair, since they are strong the weaker AU bonds get broken. (intrensic transcription)
TRUE/FALSE: The initial steps of RNA synthesis are very inefficient
TRUE
- elongation mode of RNA is very processive
What are some characteristics of RNA termination signals?
-Hairpin like structure formed as a result of GC rich sequences
- At rich DNA sequences follow the hairpin sequence (they fall right off)
How do termination sequences help dissociate the RNA transcript from the poymerase?
They disrupt H-bonding of new mRNA transcript with DNA template.
What processes are coupled in prokaryotes?
Transcription and Translation are coupled, you can begin translation before you complete transcription.
Where does transcription occur in eukaryotes?
In the nucleus, wheras translation happens in the cytosol.
True/False: Exons have both coding and non-coding sequences.
True
Tr
What are the steps that take place from pre-MRA to MRA?
Polyadenylation
RNA splicing
5’capping
Does mature MRA has both introns and extrons?
No, it has only extrons but they code for both coding and non-coding regions.
What are the parts of mature RNA in a eukaryotic cell?
So it has no introns
Has extrons
5’ end has G tail
3’ has polyadenation tail
It has untranslated regions which control how much RNA is being translated.
Who has more RNA eukaryotes or prokaryotes?
Eukaryotes
Is each RNAP a multi-sub protein?
Yes
What does RNA polymerase 1 do in eukaryotes?
It transecribes the gene rRNA
W
What does RNA polymerase 2 do in eukaryotes?
It transcribes mRNA gene
What does RNA polymerase 3 do in eukarotes?
IT transcribes tRNA genes.
Does bacteria have RNA pol 1,2,3 ?
No thats eukaryotes, they are complicated!
what is the difference between the RNA pol 2 of eukaryotes vs that of RNA pol of bacteria?
RNA pol 2 in eukaryotes has a very special carboxyl termical domain not found in other RNAs.
RNAP in bacteria has 5 subunits
RNAP in eukaryotes has 12 subunits
What is the name of the protein that helps to place eukaryotic RNA polymerase in place at the promoter?
Its called the TRANSCRIPTION FACTOR
which polymerase has to deal with chromosomal structures?
Eukaryotic RNA polymerases
What are some points on eukaryotic promoters?
- they are more variable than bacterial promoters
- They have one or more specific sequences called elements
- The elements are at specific postitions
- These elements are regognised by General transcription fators which inturn help position the RNA polymerase.
What is a TATA box?
it is TATA highly conserved, about 30 bp upstream where the transcription start site.
What is the role of a TATA box?
It helps position the RNAP2 and the general transcription factors.
What ar the steps to initiate transcription in Eukaryotes?
- Binding of TBP (transcription binding protein) to find the TATA box. TBP is a subunit of a transcripiton factor Transcription 2 polymerase. (the one that transcribes mrna. )
2.It binds to the minor groove and mobilizes the binding of TF2B.
3.Other transcription factors like RNA pol 2 will be able to bind in thr correct orientation at the transcription site.
4.Then TF2H performs the helicase activity, and phosphoralation of C-terminal and the jobs of RNAP.
What are the roles of TF2H in a eukaryotic cell?
- Helps with phosphoralation of the special C terminal, which helps to kick start the RNAP from the abortion transcription
- Performs the role of RNAP initially
- Acts as helicase to unzip the strands.
What do enchancer proteins do on the mra of eukaryotic cell?
They serve as a binding spot for activation proteins.
What do activation proteins do?
They activate transcription by looping over and activating the mediator.
Does RNA pol 2 also have a C-terminal?
Yes, and it also has tandem repeats of 7 amino acids
How many aa repeats is present in human and yeast RNA pol 2?
52 and yeast 26
Is the aa repeats in RNA pol 2 required?
Yes it is very viable, for activation of mRNA sites.
How is RNA pol 2 activated?
Via phosphorylation
What is phosphoralated in RNA pol2?
The ser on Cterminal kicks off the initiation.
What happens after TF2H phosphoralates the RNAP2?
Differnent enzymes bind and chage the phosphoralation pattern.
Why is capping importnat?
It helps protect RNA from exonucleases from degration.
When is 5’ exonucleases capping done? Before or after mRNA is fully teanscribed?
Before its done (it is the first process that occurs)
Compare the gene strcuture of Prokayotes vs eukaryotes.
Bscterial gene does not have introns
- both have non coding sequences
How are introns removed?
1) Splisosomes get to the intron region and make a Branch-point A attack. So they attack the 5’ end to make a bond with 2’ C
2) Next they make 3’ form a bond with 5’ of next exons which makes it to release the intorn so a larient is created which is destroyed later.
Why can RNA be spliced but not DNA?
The splisosomes only make 2’ to 5’ bond, but DNA does not have OH on the 2’ end.
Do exon juntion hold the two strands of MRNA together after the splicing occurs?
No, they are covalently bonded. They are just a marker to show that introns were removed from there.
Can pre-mra self-splice?
No, the snRPS proteins in Splisomoes and other associated proteins assemlble on mRNA to remove introns.
How do snRNAs find introns?
They look for specific sequences on the mRNA and then bind
Are the A -cap coded in the genome?
No, only mrns is transcribed from the gemone. Once the two strands are seperated 3’end processing proteins recognize and make the 3’ poly a tail. the poly a binding proteins bind to it so 3’ endonucleuses cant bite it.
it goes from CTD direction to mRNA
Do you always need EJC’s (exon junction)?
No not every mrna has introns. To go out into the cytosol all you need is the cap binding proteins, tail binding proteins for sure, the ejc not always if no introns are present.
