Comp Exam-Ford
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replication: template: monomer: enzymes: polymer:
DNA dNTPs DNA Polymerase alpha, delta, epsilon DNA
transcription: template: monomer enzymes: polymer:
DNA NTPs DNA Polymerase I, II, III RNA
translation: template: monomer: enzyme: polymer:
RNA amino acids ribosome protein
replication: • initiation • elongation • termination
• origin licensing/firing; ORC, MCM complex → CMG helicase, DNA polymerase epsilon • primase, RPC, PCNA, RPA, DNA Pol a/d/e, FEN1, Topo I, FACT, ASF1/CAF1 • FEN1, Topo II, telomerase
transcription: • initiation • elongation • termination
• TFIID/B/F/E/H, FACT, mediator (scaffold), activator, RNA Pol I, II, III, promoter-proximal pause, NELF, DSIF, P-TEFb • RNA Pol I, II, III; tpopisomerase; processing: PARP, CBC; spliceosome, PABP • Torpedo vs allosteric model
translation: • initiation • elongation • termination
• eIF1/2/3/4F; ribosome; tRNA-met • ribosome; eEF1A/1B/2; aminoacyl-tRNAs • eRF1/3
5 features of the genetic code: • ____ : no breaks within or between codons; colinear sequence from DNA → protein • ____ : 1 amino acid per codon • ____ : more than 1 codon per amino acid • ____ : codons do not share nucleotides • ____ : (almost) all life uses same code
• continuous • unambiguous • degenerate • nonoverlapping • universal
problems and solutions with eukaryotes: • size/complexity of genome → • linear genome → • compartmentalization →
• histone; multiple origins of replication; introns; other RNA processing • telomeres • protein sorting
4 features of genetic material and how DNA fits these features: • ____ of self : • ____ of information : • ____ of information : • variation through ____ :
• replication: self-templating • storage : repair mechanisms available • expression : gene expression • mutation : gene duplication
crossing over in meiosis, what DNA recombination mechanism is used how does this process contribute to evolution
homologous recombination gene duplication potential
Base excision repair: • damage repaired: • DNA removed: • Polymerase used: • other enzymes: • accuracy:
• modified bases • 1 nt • beta or lambda • glycosylase; AP endonuclease; DNA ligase • high
nucleotide excision repair: • damage repaired: • DNA removed: • Polymerase used: • other enzymes: • accuracy:
• covalent adducts • 10-30 nt • epsilon or delta/kappa • UVR enzymes; TFIIH; DNA ligase • high
translesion synthesis: • damage repaired: • DNA removed: • Polymerase used: • other enzymes: • accuracy:
• covalent adducts • bypass • Rev 1; iota; eta; zeta • PCNA • low
NHEJ: • damage repaired: • DNA removed: • Polymerase used: • other enzymes: • accuracy:
• dsDNA breaks • at ssDNA site • TdT, mu or lambda • Ku; DNA Ligase IV • low
homologous recombination: • damage repaired: • DNA removed: • Polymerase used: • other enzymes: • accuracy:
• dsDNA breaks; stalled replication forks • exposed ends • delta; eta; zeta • RAD51; Spo11, MRN; RPA; BRCA2 • high-ish
RNA processing steps → description → function • 5’ cap → • 3’ PolyA tail • splicing
• upside down G → resist degradation; initiate further processing; direct mRNA to cytosol; recruit eIFs • long string of A’s → define end of mRNA; resist degradation; circularize mRNA; bind eIFs • remove introns → retain exons; create diversity
noncoding DNA: location → function: • noncoding RNA gene: • centromere • origin of replication • barrier/insulator • enhancer • promoter • telomere
• euchromatin → transcribed • heterochromatin → attach sister chromatid • heterochromatin → replication start site • het/euchromatin junction → stops heterochromatin • upstream of promoter → transcription activator binding site • TATA box, INR, DPE, BRE → transcription start site • heterochromatin → ends of linear chromosomes (T loop)
noncoding RNA: location → function: • rRNA • tRNA • snRNA • snoRNA • miRNA • siRNA • piRNA • lncRNA • TERC • introns • UTRs
• nucleolus to cytosol → ribosome catalysis • cytosol → carry amino acids • nucleus, cajal bodies → part of spliceosome • nucleolus, cajal bodies→ RNA modification • cytosol → gene silencing • cytosol, nucleus → gene silencing • nucleus → silence transposons • nucleus, cytosol → signal, decoy, guide, scaffold • nucleus → telomerase template • remain in nucleus → removed from mRNA • part of mRNA → regulation of mRNA
what are 2 signals that cue Nonsense Mediated Decay of mRNAs
retained intron stop codon too far from 3’ UTR
topological equivalencies: • nucleus = ____ • secretory/endocytic pathway organelles = ____ , golgi, endosomes, lysosome
• cytosol • ER