Lec 8. Protein synthesis 1. Transcription Flashcards
What are the three steps to transcription?
Initiation, elongation, termination
What are the 4 characteristics of a genetic material?
Replication of self, storage of info, expression of info, and variation through mutation
What is the central dogma?
DNA to RNA via transcription. RNA to Protein via translation.
What enzyme helps DNA go to RNA?
RNA polymerase
What enzyme helps RNA translate to Protein?
Ribosome
What enzyme helps DNA replicate?
DNA pol
What are three exceptions to the Central Dogma?
Reverse transcription (RNA to DNA). RNA virus replication (RNA to RNA) and RNA directed DNA repair (RNA to DNA)
Rad52-dependent HR pertains to what exception of the central dogma?
RNA directed DNA repair (RNA to DNA)
What are the 5 features of the genetic code?
Continuous, Unambiguous, Degenerate, nonoverlaping, and universal
What does it mean that the genetic code is continuous?
Triplet codons are uninterrupted, no breaks between codons, order is colinear (not scrambled)
What does it mean that the genetic code is unambiguous?
Each codon specifies a single amino acid
What does it mean that the genetic code is degenerate?
Amino acids can be associated with multiple codons
What does it mean that the genetic code is nonoverlapping?
in mRNA, each nucleotide is only part of one codon
What does it mean that the genetic code is Universal?
Almost all life on earth uses the same code
Pertaining to the genetic code being continuous what are two colinear exceptions?
RNA editiing can change the nature of a codon, some ciliates scramble their germline genomes (the chromosomes used to transcribe mRNAs are not scrambled though). Ex Micronucleus gene is scrambled compared to the MACronucleus gene.
True or False? Overlapping genes share DNA space and RNA space
False, Overlapping genes share DNA space and not RNA space
Transcription and Translation pertaining to Prokaryotes are
Simultaneous and in a single location
Transcription and Translation pertaining to Eukaryotes are
sequential and in separate locations
What are the 5 steps to transcription?
- Promoter binding:RNA pol, TF. 2. Transcirption bubble opens. 3. Elongation of RNA strand. 4. Release of RNA strand. 5. Eukaryote complications
What are the two sub categories to Eukaryote complications?
1) Post-transcriptional processing: 3’ polyadenylation, 5’ cap, splicing. 2) Compartmentalization: remain in nucleus vs. exit to cytoplasm.
What are the three steps to Transcription initiation?
Specific sequences in the DNA are recognized by Transcription Factors (TF). RNA pol II is recruited to the promoter. Phosphorylation of the C-terminal tail of RNA pol II results in transcription factor release.
What is the role of the promoter?
Where we start transcription. Start making RNA
What are the steps to promoter recognition?
TFIID is recruited first. TBP (TATA Binding Protein) recognized the TATA Box, distorting the DNA helix. TFIID also simultaneously binds the INR (initiator element) and the DPE (Downstream Promoter Element). TFIIB is recruited second. Binds to the BRE (B recognition Element)
What is TFIID role in transition initiation?
Predominately binds to DNA. Recognizes promoter.
What is TFIIB role in transition initiation?
Binds to BRE element
What is TFIIF role in transition initiation?
Stabalizes RNA pol interaction with TBP and TFIIB, helps attract TFIIE and TFIIH
What is TFIIE role in transition initiation?
Attracts and regulates TFIIH
What is TFIIH role in transition initiation?
Unwinds DNA at the transcription start point. HELICASE.
Is TFIID necessary or sufficient to transcription?
Sufficient
Is TATA and initiator element necessary or sufficient?
Necessary
What 6 things do we need to recruit the pol?
TF, RNA pol, mediator, chromatin remodeling complexes, histone modifing enzymes, and activator protein.
What does the mediator do?
hold things together
What does the chromatin remodeling complexes do?
Remove add histones
What do histone modifying enzymes do?
writers and erasers of histone codes.
What does the activator protein do?
Gives specificity and to go on or off.
What is fidelity?
How well it does it correctly.
Pertaining to elongation fidelity, RNA poymerases dont have what?
Exonuclease domains
Does elongation fidelity of transcription have higher or lower fidelity than DNA repair and RT?
Higher
Does elongation fidelity of transcription have higher or lower fidelity than DNA replication?
Lower
Pertaining to elongation, prokaryotes vs eukaryotes, what is used for helical stress resolution?
Pro: Gyrase. Euk: Topisomerases
Pertaining to elongation, prokaryotes vs eukaryotes, what is the gene content?
Pro: Operons: 1 transcript=many genes. Euk: 1 transcript = 1 gene
Pertaining to elongation, prokaryotes vs eukaryotes, what is the RNA processing?
Prok: N/A. Euk: Concurrent with transcription
What are the three events for termination in transcription?
RNA pol II falls off, RNA trimmed, RNA polyadenylation
What are the two models for termination?
Torpedo Model and allosteric model
What is the Torpedo model?
Exonuclease XRN2 chews back RNA and kicks off RNA poll II when the 2 proteins collide
What is the allosteric model?
PolyA tail on mRNA signals RNA pol II to change shape and fall off
What are the two prokaryotic options for termination of transcription?
Dependent on either Rho protein or secondary structure (hairpin).
