Comp Exam-Ford

Question 1

replication:

template:

monomer:

enzymes:

polymer:

Answer 1

DNA

dNTPs

DNA Polymerase alpha, delta, epsilon

DNA

Question 2

transcription:

template:

monomer

enzymes:

polymer:

Answer 2

DNA

NTPs

DNA Polymerase I, II, III

RNA

Question 3

translation:

template:

monomer:

enzyme:

polymer:

Answer 3

RNA

amino acids

ribosome

protein

Question 4

replication:

• initiation
• elongation
• termination

Answer 4

• 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

Question 5

transcription:

• initiation
• elongation
• termination

Answer 5

• 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

Question 6

translation:

• initiation
• elongation
• termination

Answer 6

• eIF1/2/3/4F; ribosome; tRNA-met
• ribosome; eEF1A/1B/2; aminoacyl-tRNAs
• eRF1/3

Question 7

5 features of the genetic code:

1. ____ : no breaks within or between codons; colinear sequence from DNA → protein
2. ____ : 1 amino acid per codon
3. ____ : more than 1 codon per amino acid
4. ____ : codons do not share nucleotides
5. ____ : (almost) all life uses same code

Answer 7

1. continuous
2. unambiguous
3. degenerate
4. nonoverlapping
5. universal

Question 8

problems and solutions with eukaryotes:

1. size/complexity of genome →
2. linear genome →
3. compartmentalization →

Answer 8

1. histone; multiple origins of replication; introns; other RNA processing
2. telomeres
3. protein sorting

Question 9

4 features of genetic material and how DNA fits these features:

1. ____ of self :
2. ____ of information :
3. ____ of information :
4. variation through ____ :

Answer 9

1. replication: self-templating
2. storage : repair mechanisms available
3. expression : gene expression
4. mutation : gene duplication

Question 10

crossing over in meiosis, what DNA recombination mechanism is used

how does this process contribute to evolution

Answer 10

homologous recombination

gene duplication potential

Question 11

Base excision repair:

1. damage repaired:
2. DNA removed:
3. Polymerase used:
4. other enzymes:
5. accuracy:

Answer 11

1. modified bases
2. 1 nt
3. beta or lambda
4. glycosylase; AP endonuclease; DNA ligase
5. high

Question 12

nucleotide excision repair:

1. damage repaired:
2. DNA removed:
3. Polymerase used:
4. other enzymes:
5. accuracy:

Answer 12

• covalent adducts
• 10-30 nt
• epsilon or delta/kappa
• UVR enzymes; TFIIH; DNA ligase
• high

Question 13

translesion synthesis:

1. damage repaired:
2. DNA removed:
3. Polymerase used:
4. other enzymes:
5. accuracy:

Answer 13

1. covalent adducts
2. bypass
3. Rev 1; iota; eta; zeta
4. PCNA
5. low

Question 14

NHEJ:

1. damage repaired:
2. DNA removed:
3. Polymerase used:
4. other enzymes:
5. accuracy:

Answer 14

1. dsDNA breaks
2. at ssDNA site
3. TdT, mu or lambda
4. Ku; DNA Ligase IV
5. low

Question 15

homologous recombination:

1. damage repaired:
2. DNA removed:
3. Polymerase used:
4. other enzymes:
5. accuracy:

Answer 15

1. dsDNA breaks; stalled replication forks
2. exposed ends
3. delta; eta; zeta
4. RAD51; Spo11, MRN; RPA; BRCA2
5. high-ish

Question 16

RNA processing steps → description → function

1. 5’ cap →
2. 3’ PolyA tail
3. splicing

Answer 16

1. upside down G → resist degradation; initiate further processing; direct mRNA to cytosol; recruit eIFs
2. long string of A’s → define end of mRNA; resist degradation; circularize mRNA; bind eIFs
3. remove introns → retain exons; create diversity

Question 17

noncoding DNA: location → function:

1. noncoding RNA gene:
2. centromere
3. origin of replication
4. barrier/insulator
5. enhancer
6. promoter
7. telomere

Answer 17

1. euchromatin → transcribed
2. heterochromatin → attach sister chromatid
3. heterochromatin → replication start site
4. het/euchromatin junction → stops heterochromatin
5. upstream of promoter → transcription activator binding site
6. TATA box, INR, DPE, BRE → transcription start site
7. heterochromatin → ends of linear chromosomes (T loop)

Question 18

noncoding RNA: location → function:

1. rRNA
2. tRNA
3. snRNA
4. snoRNA
5. miRNA
6. siRNA
7. piRNA
8. lncRNA
9. TERC
10. introns
11. UTRs

Answer 18

1. nucleolus to cytosol → ribosome catalysis
2. cytosol → carry amino acids
3. nucleus, cajal bodies → part of spliceosome
4. nucleolus, cajal bodies→ RNA modification
5. cytosol → gene silencing
6. cytosol, nucleus → gene silencing
7. nucleus → silence transposons
8. nucleus, cytosol → signal, decoy, guide, scaffold
9. nucleus → telomerase template
10. remain in nucleus → removed from mRNA
11. part of mRNA → regulation of mRNA

Question 19

what are 2 signals that cue Nonsense Mediated Decay of mRNAs

Answer 19

retained intron

stop codon too far from 3’ UTR

Question 20

topological equivalencies:

1. nucleus = ____
2. secretory/endocytic pathway organelles = ____ , golgi, endosomes, lysosome

Answer 20

1. cytosol
2. ER