Biochem - molecular

Question 1

Charge of DNA and histones

Answer 1

negatively charged DNA (bases are negative)

positively charged histone (rich in lysine/arginine)

Question 2

darker DNA on electron microscopy

Answer 2

heterochromatin, sterically inaccessible

Question 3

Location of DNA methylation

Answer 3

Cytosine and adenine (to signal replicated strand)

CpG island (to repress transcription, methylation makes mute)

Question 4

Purines vs. pyrimidines

Answer 4

purines = 2 rings (A, G)

pyrimidines = 1 ring (C, T, U)
deamination of cytosine makes uracil (which replaces thymine)

Question 5

Increased melting temperature of DNA

Answer 5

incr. C-G content (3 H bonds!)

Question 6

De novo purine synthesis

Answer 6

Glycine, Aspartate, Glutamine

sugar plus phosphate

then add base

Question 7

Purine synthesis inhibitors

Answer 7

6-MP

Mycophenolate, ribavirin

Question 8

Pyrimidine synthesis inhibitors

Answer 8

Leflunomide

Hydroxyurea (anti polycythemia)

5-FU

Methotrexate, trimethoprim (DHF reductase)

Question 9

Purine salvage deficiencies

Answer 9

Adenosine deaminase def. - excess ATP/dATP, decr. DNA and decr. lymphos (cause of SCID!)

Lesch-Nyan = absent HGPRT (hyperuricemia, gout, pissed off, retardation, dystonia)

Question 10

Prevents strands from reannealing

Answer 10

Single Strand Binding Proteins

Question 11

Proofreads each added nucleotide

Elongates leading strand to the 3’ end

Answer 11

DNA polymerase III

5’ to 3’ synthesis
proofreads with 3’ to 5’ exonuclease

Question 12

Degrades RNA primer, replaces with DNA

Answer 12

DNA polymerase I

Question 13

Catalyzes the formation of a phosphodiester bond within a strand of double-stranded DNA
ie. Joins Okazaki fragments

Answer 13

DNA ligase

Seals the strand

Question 14

Specific endonucleases release the oligonucleotides containing damaged bases

Gap is filled by DNA pol, sealed by ligase

Answer 14

nucleotide excision repair, occurs in G1

defective in xeroderma pigmentosum

Question 15

Newly synthesized strand is recognized, mismatched nucleotides removed and gap is filled and resealed

Answer 15

DNA mismatch repair

defective in HNPCC

Question 16

2 DNA fragments are brought together to repair dsDNA breaks

Answer 16

nonhomologous end joining

mutated in ataxia-telengiectasia, Fanconi anemia

Question 17

Order of RNA polymerase

Answer 17

1: rRNA (rampant)
2: mRNA (massive) - inhibited by death cap mushrooms (hepatotoxicity)
3: tRNA (tiny)

Question 18

Location of mRNA quality control

Answer 18

cytoplasmic P bodies

contain exonucleases, decapping enzymes, microRNAs

also can store mRNA for future translation

Question 19

tRNA structure

Answer 19

amino acid is bound to 3’ end (CCA)

T-arm: binds to ribosome
D-arm: recognized by aminoacyl tRNA synthetase

anti-codon loop: binds codon of mRNA

Question 20

mischarged tRNA

Answer 20

reads the usual codon but inserts the wrong amino acid

represents a mistake by aminoacyl-tRNA synthetase proofreading function

Question 21

ATP vs. GTP in the protein synthesis process

Answer 21

ATP = tRNA activation
GTP = tRNA gripping (to 40S subunit) and going places (translocation)

Question 22

Sites for elongation on ribosome

Answer 22

A site: incoming aminoacyl-tRNA
P site: accomodates growing peptide
E site: holds empty tRNA as it exits