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Transcription I
Transcription II
Translation I
Translation II
Proteins
100
Purposes of 5' cap and poly-A tail?
In nucleus, escort/chaperone to cystoplasm (nuclear transport), cytoplasmic versions facilitate translation RNA stability
100
What is the strand of DNA that is NOT read during transcription?
Coding strand
100
Name the start & stop codons
Start: AUG Stop: TGA, TAA, TAG
100
Describe termination of translation
Stop codon makes up floor of A-site, no tRNA matches so releasing factor binds instead & breaks of ribosomal subunits
100
Difference between PK & EK proteins & why important?
Formyl group on initiation Met in PK EK cells use formyl group to recognize bacterial proteins
200
Which polymerase transcribes which types of RNA?
RNA polymerase II = microRNA RNA polymerase III = tRNA
200
How do sigma factor and TFIID differ? What do they have in common?
different=Protein vs. complex, other promoter regions; same=General, immediately upstream, do not remain associated to polymerase
200
Which direction do the ribosomes read the mRNA strand?
5' to 3' - start at the 5' methyl-G cap & scan until the first AUG!
200
How and why is the genetic code "redundant"?
multiple codons = same amino acid many more combinations than amino acids *wobble position (5' end of anticodon)
200
How/why do proteins fold?
hydrogen bonds, polarity/nonpolarity, covalent bonds (e.g. disulfide), chaperone proteins Shape = function!
300
Explain how transcription factors regulate transcription
Activators (bind enhancer elements) Repressors (bind repressor elements/operator elements)
300
Describe the fidelity of RNA polymerase and how this affects the end protein.
low-fidelity (fast and makes mistakes) 1/1000 nucleotides incorrect
300
What is gene silencing and how does it work?
Chemical modification of DNA (methylation), turns off promoter w/packaging Epigenetics
300
Describe initiation of translation in PK & EKs
PK: (IRES) 16S rRNA recognizes Shine-Delgarno AGGA, then lg subunit hops on EK: most 5' AUG = only start, sm rRNA subunit + tRNA carrying Met start at cap, find AUG, then stop & wait for lg subunit
300
What three amino acids have terminal OH groups and why is this chemical structure important?
Ser, Thr, Tyr Terminal OHs can participate in condensation rxns
400
Describe 3 modifications to EK pre-mRNA.
5' methyl-G cap: attached by pentose sugar 3' polyadenyl tail: after transcripiton, As polymerized w/out template RNA Splicing: 2' OH in intron grabs 5' end of intron (lariat), snRNAs bind to border sequences (AG|GU and AG|G) to create snRNPs, transesterification to link 3' of one exon to 5' to next exon
400
Describe 3 stages of EK transcription
Initiation: TATA box, general transcription factors (TFIID w/TBP first), then RNA polymerase, then TFIIH phosphorylates RNA polymerase to begin Elongation: 5' -> 3' Termination: after AAUAA, CstF & CSF snip and attract PAP for adding hundreds of As
400
Explain the three sites in the large subunit of rRNA and how they are involved in peptide bonding and elongation during transcription
from the 5' end of the mRNA, E - P - A; E site = exit, tRNA doesn't stay long; P site = peptidyl; A site = amino acyl; peptidyl transferase binds amino acids of tRNAs in A&P sites
400
What is an "operon"?
PK cell - promoters & all associated genes (polycistronic)
400
What is important about disulfide bonds and what forms them?
Covalent (rather than H) bond, can be inter- or intra-chain Do not form in cytoplasm, but found outside cell, lysosome, golgi, ER Cys - S group @ END of side chain
500
Describe 3 steps of PK transcription
Initiation: (-10 TATA box, -35), 2 alpha + 2 beta + 1 sigma (torque) Elongation: transcribe 5'->3' Termination: hairpin loop (torque)
500
What is RNA Splicing and how does it work?
Need sequences: (exon1)AG|GU(intron) A(branch point) (intron)AG|G(exon2); snRNAs + proteins = snRNPs & bind to border sequences; 2' OH on branch point A binds to 5' end of intron (makes lariat); then transesterification links 3' of exon1 to 5' of exon2
500
Explain how a EK gene can be "knocked down", and why
miRNA form hairpin in UTR dicer + RISC (RNase) Why: differentiation (esp. of stem cells)
500
What is the structure of tRNA, how does it function, and how is it different from other RNAs?
Structure: (*see slides), amino acid on 3' end, specific tRNAs with specific codons bind certain amino acids; Function: translation!, anticodon complementary to mRNA, with help of ribosome & enzymes, binding of amino acid to growing polypeptide chain Different: made from different RNA polymerase; contains psi (trident-shaped greek letter) - a modified U
500
What was unique about the structures Proline can form? How does it affect the polypeptide chain?
Pro's R-group loops around and binds to the amino acid's backbone (N); loop causes kink in chain