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Flashcards in Biochem - molecular Deck (22):
1

Charge of DNA and histones

negatively charged DNA (bases are negative)

positively charged histone (rich in lysine/arginine)

2

darker DNA on electron microscopy

heterochromatin, sterically inaccessible

3

Location of DNA methylation

Cytosine and adenine (to signal replicated strand)

CpG island (to repress transcription, methylation makes mute)

4

Purines vs. pyrimidines

purines = 2 rings (A, G)

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

5

Increased melting temperature of DNA

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

6

De novo purine synthesis

Glycine, Aspartate, Glutamine

sugar plus phosphate

then add base

7

Purine synthesis inhibitors

6-MP

Mycophenolate, ribavirin

8

Pyrimidine synthesis inhibitors

Leflunomide

Hydroxyurea (anti polycythemia)

5-FU

Methotrexate, trimethoprim (DHF reductase)

9

Purine salvage deficiencies

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

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

10

Prevents strands from reannealing

Single Strand Binding Proteins

11

Proofreads each added nucleotide

Elongates leading strand to the 3' end

DNA polymerase III

5' to 3' synthesis
proofreads with 3' to 5' exonuclease

12

Degrades RNA primer, replaces with DNA

DNA polymerase I

13

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

DNA ligase

Seals the strand

14

Specific endonucleases release the oligonucleotides containing damaged bases

Gap is filled by DNA pol, sealed by ligase

nucleotide excision repair, occurs in G1

defective in xeroderma pigmentosum

15

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

DNA mismatch repair

defective in HNPCC

16

2 DNA fragments are brought together to repair dsDNA breaks

nonhomologous end joining

mutated in ataxia-telengiectasia, Fanconi anemia

17

Order of RNA polymerase

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

18

Location of mRNA quality control

cytoplasmic P bodies

contain exonucleases, decapping enzymes, microRNAs

also can store mRNA for future translation

19

tRNA structure

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

20

mischarged tRNA

reads the usual codon but inserts the wrong amino acid

represents a mistake by aminoacyl-tRNA synthetase proofreading function

21

ATP vs. GTP in the protein synthesis process

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

22

Sites for elongation on ribosome

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