Gene Transcription & RNA modification part 3 Flashcards
What are the 3 types of proteins needed for basal transcription at the core promoter?
- RNA polymerase 2
- General transcription factors (5 GTF)
- Mediator
Basal transcription
Baseline expression which has many genes & doesn’t have regulatory proteins
_____ are always need for RNA polymerase 2 to initiate transcription of genes
5 GTF
Describe the first 3 steps to form a open complex & start transcription?
- TFIID binds to TATA box
- TFIIB binds to TFIID
- TFIIB binds TFIIF & RNA polymerase
What are the last 3 steps to form a open complex & start transcription?
- TFIIE & TFIIH bind to RNA polymerase 2 to form a preinitiation complex (closed complex)(PIC)
- TFIIH acts as a helicase to form an open complex by unwinding the DNA & it also acts as as kinase
- TFIIB, TFIIE, & TFIIH released to form an open complex
Kinase
Adds phosphate & it then phosphorylates the tail of RNA polymerase 2
TFIID
Is a complex of proteins that includes the TATA binding protein (TBP) & severally TBP associated factors (TAFs)
Mediator
Medicates interactions between RNA polymerase 2 & regulatory transcription factors that bind to enhancers or silencers
Transcriptional termination of __________ occurs after the 3’ end of the transcript is cleaved near the polyadenylation signal sequence
RNA polymerase
What are the 2 models in termination
- Allosteric Model
2. Torpedo Model
Allosteric Model
After transcribing the polyadenylation signal sequence, RNA polymerase 2 is destabilized & falls off from the DNA (cause a change in its shape)
Torpedo Model
An exonuclease binds to the 5’ end of the RNA that is still transcribed & degrades it in the 5’ to 3’ direction & polymerase falls off
Describe termination process
- RNA polymerase 2 transcribed a gene past the polyadenylation signal sequence
- The RNA is cleaved just past the polyadenylation signal sequence
- Either the allosteric model is occurs or the torpedo model occurs to end termination
___________ occurs after transcription where rRNA remove spacers, tRNA adds CCA & mRNA cap, spliced, & polyadenylated
RNA modifications
________ formed in the nucleolus & it is transcribed, processed & bound to ribosomes where its modification makes mRNA short
rRNA
Exon
Contain coding sequences that are translated into proteins & found in mature mRNA
Introns
Found between exons & contain coding sequences that aren’t translated into proteins
What happens with tRNA?
Makes mRNA go from long to short where both ends are digested, CCA to 3’ end & modifies nucleotides
The production of tRNA molecules require what two things?
- Exonuclease
2. Endonuclease
Exonuclease (RNaseD)
Cleaves a covalent bond between two nucleotides at one end of a strand & digest a strand
Endonuclease (RNaseP)
Cleaves the bond between two adjacent nucleotides within a strand
What are the modified bases in tRNA?
- mG=methylguanosine
- P=pseudourine
- T= 4 - throuridine
- IP= 2-Isopentenyladensosine
Ribozyme
An RNA with catalytic activity (ex. RNaseP)
_______ is modified in the nucleus, spliced, capped, at the 5’ end, & poly-A at the 3’ end
mRNA
Prokaryotes has a _________
Co-linear info - same info from gene to protein (Eukaryotes are not always co-linear)
During transcription _______ contains introns & exons where the introns are removed & exons are connected to make a mature mRNA
pre-mRNA
________ removes all introns & some exons & links exons by phosphodiester bonds)
Splicing
What are the 3 mechanisms of splicing ?
- Group 1
- Group 2
- Spliceosome
______ & ______ occur via self splicing where the splicing doesn’t need the addition of a catalyst instead the mRNA features as its own ribozyme (catalyst)
Group 1 & Group 2
Describe group 1 splicing
- The guanosine break the bond bewteen the 1st exon & the intron where it becomes attached to the 5’ end of the intron
- The 3’- OH group of exon 1 then breaks the bond next to a different nucleotide that lies at the boundary between the end of the intron & exon 1 forms a phosphodiester bond with the 5’ end of exon 2
- The intron RNA is degraded
Maturases
Proteins that enhance the rate of self-splicing
pre-mRNA splicing occurs by __________
Spliceosome
Spliceosome
A large complex that spliced pre-mRNA in eukaryotes & contain several subunits call small riboproteins (snRNPs)(“snurps”)(Contaisn RNA & proteins)
Describe the splicing process
- The snRNPs designated U1 binds to the 5’ splice site & U2 binds to the branch site
- U4/U6 & U5trimer binds. The intron loops out & exons are brought closer together
- 5’ splice site is cut (1st splice site) & the 5’ end of intron is connected to the branch site to form a lariat where U1 & U4 are released
- 3’ splice site is cut (2nd splice site). Exon 1 is connected to exon 2 & the intron is released along with U2, U5, & U6. The intron will be degraded
- End up having two connected exons
_________ binds intron-exon boundary & correct orientation by catalyze reaction
Spliceosome
__________ regulates which exons occur in an RNA transcript, allowing different polypeptides to be made from the same protein-encoding gene
Alternative Splicing
Alernative Splicing
Phenomenon that pre-mRNA can be spliced in more than one way
What is an advatange of alternative splicing?
Since it allows two or more different polypeptides sequences to be derived from a single gene it can allow organisms to carry fewer genes it its genome
The ends of eukaryotic pre-mRNA have a ________ & ________
5’ cap & 3’ polyA tail
At their 5’ end most mature mature mRNA have a __________ covalently attached through capping
7-methylguanosine
_________ adds methylguanosine
Capping
Describe the process of capping
- Nucleotide at the 5’ end of the transcript has phosphate groups
- Guanyltransferase uses guanosine triphosphate (GTP) to attach a guanosine monophosphate (GMP) to the 5’ end
- Finally a methyltransferase attached a methyl group to the base guanine
Describe the 5’ Cap function
- Cap-binding proteins are requires for the proper exist of most mRNA from the nucleous
- The cap structure is recognized by initation factors that are needed during the early stages of translation
- The cap structure is needed in efficient splicing of intron (closes to the 5’ end)
At the 3’ end most mature mRNA have a string of adenine nucleotides called ______ which is important for mRNA stability, the exit out of the nucleus, & in synthesis of polypeptides
Poly A tail
A poly A tail is added to mature mRNA through __________
Polyadenylation
Describe polyadenlylation process
- The pre-mRNA contains a polyadenylation signal sequence near its 3’ end (usually AAUAAA)
- Anednoclease recognize the signal sequence & cleaves the pre-mRNA at a location 20 nucleotides before the 3’ end
- Poly-A polymerase enzyme attaches many adenine containing nucleotides
The nucleotide sequence of RNA can be modified by _________
RNA editing
RNA editing
Process of making a change in the nucleotide sequence of an RNA molecule that involves addition or deletions of particular nucleotides or substitution
Describe RNA editing by deamination
- A cytidine deaminase can remove an amino group from cytosine thereby creating uracil
- An adenosine deaminase can remove an amino group from adenine to make hypoxanthine ( I = G in translation)
_______ is important because it changes mRNA sequence which changed protein sequence which changes the way protein functions
mRNA editing
