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Transcription
Transcription Regulation and Chromatin Remodeling
RNA Processing
RNA Decay
Protein Synthesis
100
Pol II relies on many transcription factors.
True.
100
What is euchromatin vs. heterochromatin?
Euchromatin: regions with high transcriptional activity/loosely packed. Heterochromatin: Regions with low/no transcriptional activity and densely packed.
100
What is the RNA degradosome composed of?
endoribonuclease (RNase E) a 3'-->5' exoribonuclease polynucleotide phosphorylase (PNPase) a dead-box RNA helicase (RhlB helicase) glycolytic enzyme enolase
100
Is HPV-16 a DNA or RNA virus? What are the main cells it infects initially?
DNA virus. Infects basal layer of mucosal epithelium.
100
What are the three RNAs involved in translation? What do each contain?
mRNA, tRNA, and rRNA. mRNA: nucleotide sequence tRNA: anticodons to bind to mRNA, attached to aa rRNA: RNA component of ribosome: huge proteins/RNAs complex. helps catalyze peptide bond formation.
200
Name the three eukaryotic RNA polymerases and what they synthesize.
RNA polymerase I: pre-ribosomal RNA RNA polymerase II: mRNA, very fast/complex/highly regulated RNA polymerase III: tRNA and 5S rRNA
200
Name 4 ways to remodel chromatin
1) Nucleosome sliding 2) Histone exchange 3) Nucleosome eviction 4) Altered nucleosome structure
200
What are the steps of mRNA processing in eukaryotes?
1) Adding 5' cap 2) splicing out introns and rejoining any exons for a continous sequence 3) adding a 3' poly A tail 4) degradation of extra RNA
200
Name the exonuclease that cleaves from 5'-->3'
Xrn1
200
What would an insertion/deletion or both lead to in your mRNA?
Frameshift--shift reading frame and potentially get different proteins!
300
What are the steps of initiation for eukaryotic pol II transcription?
1) Pol II is recruited to DNA by transcription factors. Assembly of TBP (TATA-binding protein) with the promoter. 2) Helicase activity of TFIIH unwinds DNA at promoter. 3) Kinase activity in TFIIH phosphorylates the polymerase at the CTD (carboxy-terminal domain) changing the conformation and enabling RNA Pol II to transcribe.
300
Name 3 histone modifications, which one increases chromatin packing (lower transcription levels)
1) methylation 2) acetylation 3) phosphorylation Methylation increases packing. Acetylation and phosphorylation give a negative charge to the histones thereby giving a more relaxed state with DNA.
300
Do Group I ad Group II introns require ATP for splicing? How do Group I and Group II introns differ?
No ATP, they are self-splicing. Differ in splicing mechanism. Group I: 3' OH of free guanosine attacks phosphodiester bond between U and A of 5' splice site. Then the 3'OH of the U ending exon (5' exon) attacks the 5' end of the other exon and they rejoin. Group II: 2' OH of an A residue within the intron attacks the 5' splice site to form lariat structure. The 3'OH of the 5' exon acts as a nucleophile, completing the reaction.
300
True or false: splicing of tRNA only happens in eukaryotes.
True. Intro are present rarely in tRNA transcripts in eukaryotes.
300
What is wobble pairing?
In the codon, the first 2 bases follow a Watson-Crick pairing. The third base and the first base of the anticodon are wobbly and don't follow the Watson-Crick pairing. For this reason, there are only 32 tRNAs because it allows the tRNA to pair with more than 1 codon!
400
What is the CTD and why is it important?
C-terminal domain of Pol II. It is phosphorylated by kinase domain in TFIIH where it acts as a binding scaffold for TFs and coordinates nuclear process for mRNA elongation.
400
Name 3 types of DNA binding domains.
Helix turn helix (20 aa, in a-helical segments) Zinc fingers (30 aa, form loop X-linked by Zn+2, coordinated by 4 Cys/2Cys and 2 His Leucine Zipper (dimer of 2 amiphipathic a-helices+DNA binding domain)
400
How are spliceosomal introns spliced? What does this complex consist of? How does this complex work?
Spliced by spliceosomes. They consist of snRNP ("snurps" = small nuclear ribonucleoproteins). In these spliceosomes, introns undergoe splicing by the same lariat forming mechanism as the group II introns. Each snRNP contains one of a class of snRNAs (U1,2,4,5,6). The U1 snRNA has a sequence near its 5' end that is complementary to the splice site at the 5' end of the intron. U2 snRNA will also bind near 3' end of intron and form a complex with the other U4-6 to form an inactive spliceosome. U1 and 4 are expelled and U6 and 2 pair and the exons are spliced together. ATP required for assembly, not cleavage.
400
List the two eukaryotic mRNA decay pathways.
1) exonuclease mediated decay (shorten poly A tail) and assembly of complex of decapping activators to remove 5' or 3' ends (via exosomes with opposite polarity) 2) No deadenylation, but instead a cleavage within the mRNA (via endonuclease) and the degradation of the resulting fragments via exonucleases 5'-->3' or 3'-->5'
400
What enzyme carries the high energy reaction of attaching amino acids to corresponding tRNA? What is the intermediate before the amino acid that is added to tRNA? How do the two classes of these enzymes differ?
Aminoacyl-tRNA synthetase. Aminoacyladenylate intermediate. Differ in where they form the phosphodiester bond between amino acid and tRNA (class I on 2' OH and class II on 3' OH
500
Name 4 main features that differentiate bacteria from eukaryotes.
1) chromatin structure control access to promoters 2) Positive regulatory system are predominant (activators < repressors) 3) More complex regulatory proteins 4) Transcription and translation are separated
500
What is an enhancer? What does binding of Pol II on its promoter require?
An enhancer is a distant binding site for activators to bind to. Pol II requires transcription activators, architectural regulators, chromatin modification and remodeling proteins, and general transcription factors.
500
How can a gene give rise to multiple products? Give 2 examples.
Via differential RNA processing, like alternative splicing! 1) alternative cleavage/polyadenylation patterns to yield different mature mRNA depending on where the polyA tail is formed. 2) alternative splicing patterns where two different 3' splice sites exist and two forms of mature mRNA form as a result of the combination of splicing out the 5'-->3' splice sites.
500
How does rRNA processing in eukaryotes differ from prokaryotes?
Prokaryotes: pre-rRNA (30S) is methylated at specific bases and some uridine residues are turned into pseudouridine. Cleavage liberates precursors for rRNA and tRNA and nucleases form final 16S, 23S, and 5S mature RNAs. In Eukaryotes: 45S pre rRNA is incorporated into a 90S preribosomal complex. the 45S is methylated and some uridines converted to pseudouridines via snoRNA. Cleavage of 45S into 40S and 60S pre rRNAs. These are further cleaved in 18S, 5S, 5.8S, and 25S.
500
Name some translation inhibitors.
Tetracyclines Chloramphenicol and cycloheximide streptomycin