Comp Exam-Ford Flashcards
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
