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Biochem review USMLE > molecular biology > Flashcards

molecular biology Flashcards

1
Q

describe formation of chromatin

A

negatively charged DNA loops twice around positively charged histone octamer to form a nucleosome bead

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2
Q

what gives the histone octamer it’s positive charge?

A

arginine and lysine

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3
Q

which histones are present in the histone octamer?

A

2 x each: H2A, H2B, H3, H4

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4
Q

what is H1?

A

H1 is the only histone not in the octamer, it is responsible for tying beads together in a string

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5
Q

describe heterochromatin; transcription?

A

highly condensed form

transcriptionally inactive due to steric hindrance

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6
Q

describe euchromatin; transcription?

A

less condensed form

transcriptionally active

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7
Q

what is the consequence of DNA methylation? which bases are methylated?

A

parent/template strand is methylated during DNA replication allowing for mismatch repair enzymes to distinguish between old and new strands; cytosine and adenine can be methylated

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8
Q

role of histone methylation

A

inactivates DNA transcription

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9
Q

role of histone acetylation

A

allows for DNA uncoiling/transcription

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10
Q 
Purines = 
# of rings
A

PUR Adenine and guanine

2 rings

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11
Q 
pyrimidines = 
# of rings
A

PY Cytosine, uracil, thymine

1 ring

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12
Q

how do complementary DNA strands base pair?

A

A-T (2 H bonds)

C-G (3 H bonds)

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13
Q

DNA with higher ___ content will have a higher melting point

A

C-G

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14
Q

Amino acids required for purine synthesis

A

Glycine
Aspartate
Glutamate

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15
Q

nucleoside =

A

base + ribose sugar

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16
Q

nucleotide =

A

base + ribose sugar + phosphate

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17
Q

what type of bond links phosphate to sugar?

A

3’-5’ phosphodiester bond

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18
Q

Helicase

A

unwinds DNA template at replication fork by breaking H bonds

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19
Q

Single-Stranded binding proteins

A

stabilize strands to prevent reannealing and protect from degradation

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20
Q

DNA topoisomerase

A

creates “nicks” in the helix to relieve supercoiling during replication

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21
Q

drugs that inhibits prokaryotic DNA topoisomerase II (DNA gyrase)?

A

floroquinolones

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22
Q

drug that inhibits eukaryotic topoisomerase?

A

etopiside (cancer drug)

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23
Q

why must an RNA primer be added first?

A

RNA primer is required because DNA polymerase cannot initiate a strand, it can only add on and lengthen a strand

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24
Q

enzyme that adds primer

A

primase

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25
Q

DNA polymerases in prokaryotes

A

III and I

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26
Q

DNA polymerases in eukaryotes

A

alpha, delta

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27
Q

2 roles of DNA polymerase III

A
  • synthesizes DNA 5’ - 3’

- exonuclease activity 3’-5’ allowing for proofreading

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28
Q

role of DNA polymerase I

A

same as pol III plus excises RNA primer with 5’ - 3’ exonuclease activity and fills in the gap

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29
Q

what removes primer in eukaryotes?

A

RNase H

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30
Q

what fills in the gap left by the primer in eukaryotes?

A

DNA pol

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31
Q

what enzyme is responsible for joining Okazaki fragments together?

A

DNA ligase

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32
Q

why do prokaryotes not require telomerase

A

circular DNA

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33
Q

why is proofreading important in DNA replication?

A

yields “high fidelity” DNA product

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34
Q

leading strand is synthesized ___, ___ the fork

A

continuously, toward

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35
Q

lagging strand is synthesized ___, ___ the fork

A

discontinuosuly, away from

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36
Q

nucleotide excision repair occurs during-

A

G1

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37
Q

steps in nucleotide excision repair (3)

A

1- endonucleases remove damaged bases
2- DNA polymerase fills in gap
3- ligase seals

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38
Q

common defect that uses nucleotide excision repair

A

thymine dimer formation secondary to UV light exposure

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39
Q

disease with defect in nucleotide excision repair

A

Xeroderma pigmentosa (AR)- mutation in NER leads to inability to repair thymine dimers = freckling, early skin CA

40
Q

how is xeroderma pigments diagnosed

A

measure excision endonuclease levels in WBCs

41
Q

base excision repair occurs during-

42
Q

steps in base excision repair

A

1- glycosylases recognize and remove damaged bases
2- AP endonuclease cuts DNA on each side of defect
3- polymerase
4- ligase

43
Q

base excision repair is commonly used to-

A

remove cytosine that was deaminated to uracil; commonly by nitrates

44
Q

mismatch repair occurs during-

45
Q

mistmatch repair is responsible for-

A

removing mismatched nucleotides not recognized by the 3’-5’ exonuclease activity of DNA polymerase

46
Q

2 main genes for mismatch repair

47
Q

mutations in the mismatch repair enzymes lead to-

A

microsatellite instability –> cancer

48
Q

HNPCC

A

AD mutations in mismatch repair enzymes, leads to increased incidence of ovarian, colon, endometrial and gastric cancers

49
Q

HNPCC exhibits ___ penetrance

A

incomplete

50
Q

what is nonhomologus end joining?

A

type of double stranded DNA repair, 2 free ends are connected, homology is not required

51
Q

mutations in NHEJ are implicated in-

A

ataxia telangectasia

52
Q

describe rRNA

A

most abundant, made in nucleolus

53
Q

describe mRNA

A

most massive

made in euchromatin region of nucleus

54
Q

describe tRNA

A

smallest type

made in euchromatin region of nucleus

55
Q

when is some of each type of RNA made outside of the nucleus?

A

in mitochondria

56
Q

start codon?

codes for?

A

AUG
methionine in eukaryotes
N-formylmethionin in prokaryotes

57
Q

stop codons

A

UGA, UAA, UAG

58
Q

Does RNA polymerase require a primer?

59
Q

RNA pol are more prone to errors because-

A

unlike DNA pol, they lack proofreading abilities

60
Q

Eukaryotic RNA polymerases (3)

A

RNA pol I- rRNA
RNA pol II- mRNA
RNA pol III- tRNA and snRNAs

61
Q

toxin that inhibits RNA pol II, clinical effect

A

a-amanitin; hepatoxicity

62
Q

prokaryotic RNA pol

initiation/termination factors

A

only 1 RNA pol
initiation- sigma
termination- rho

63
Q

MOA of rifampin

A

inhibits prokaryotic RNA pol

64
Q

MOA of actinomycin D

A

chemotherapy agents that inhibits transcription in prokaryotes and eukaryotes

65
Q

immature mRNA is called

66
Q

3 processing steps

A

1) 5’ (7-methylguanosine) cap- added during transcription
2) poly-A tail- added after transcription
3) splicing of introns

67
Q

what is responsible for splicing?

A

spliceosome (snRNPs)

68
Q

which type of mRNAs lack poly A tail?

A

histone mRNA

69
Q

Lupus and snRNPs

A

SLE- antibodies against snRNPs (anti-smith)

70
Q

mRNA processing occurs at what location

71
Q

destiny of introns following splicing

A

remain in the nucleus, where they are degraded

72
Q

alternative splicing

A

combinations of different exons to form different products

73
Q

amino acid is bound to what part of the tRNA

A

3’ end at CCA

74
Q

what adds amino acid to tRNA? energy source?

A

aminoacyl-tRNA synthetase using 2 peptide bonds from ATP

75
Q

what is “wobble?”

A

accuracy of base pairing for translation only requires first 2 nucleotides to be correct (3rd position is wobble)

76
Q

3 basic steps in translation

A

initiation
elongation
termination

77
Q

describe initiation

A

40s binds to 5’ mRNA and seeks AUG, once AUG is located, 60s associates

78
Q

how much energy is required during translation?

A

2 ATP- activation/charing

2 GTP- gripping/grabbing

79
Q

describe elongation

A

t-RNA binds to A site
rRNA catalyzes peptide bond formation and transfers poly-peptide chain to t-RNA in A site
ribosome advances 3 NTs

80
Q

3 ribosomal sites

A

A- aminoacyl-tRNA
P- peptide
E- Exit

81
Q

what are the antibiotics that affect the ribosome?

A 
AT 30 (aminoglycosides, tetracyclines)
CCEL 50 (clinda, chloramphenicol, emycin, linezolid)
82
Q

“polysomes”

A

when multiple ribosomes bind to a single mRNA

83
Q

effect of shiga-toxin

A

removes adenine from 28s (60s)= arrest of protein synthesis

84
Q

effect of diphtheria/pseudomonas toxin

A

ADP-ribosylation of ef2= inhibits elongation

85
Q

process of degrading defective proteins

A

ubiquitination

proteasomal degradation

86
Q

only amino acids with one codon (2)

A

methionine

tryptophan

87
Q

3 destinies of proteins synthesized on RER

A

secretion
membrane-bound
lysosomes

88
Q

what is the “signal” that a protein is destined for secretion?

A

N- linked oligosaccharide

89
Q

which types of proteins are synthesized on free ribosomes? (2)

A

those intended to remain in the cell- cytoplasmic, mitochondrial

90
Q

3 main actions of golgi

A

1- modify N-oligosaccharides on asparagine
2- add O-oligosaccharides to serine/threonine
3- add mannose-6-phophate to signal trafficking to lysosomes

91
Q

I cell disease is due to

A

lack of mannose-6-phosphorylation on lysosomal proteins, instead of going to lysosomes, lysosomal enzymes are secreted out of the cell

92
Q

Symptoms of I cell disease

A

coarse facies, clouded corneas, high plasma levels of lysosomal enzymes; fatal in childhood

93
Q

COP I

A

retrograde transport (golgi to ER)

94
Q

COP II

A

anterograde transport (ER to golgi)

95
Q

clarthin

A

bidirectional
golgi to membrane
membrane to intracellular (receptor-mediated endocytosis)

96
Q

peroxisome duties (3)

A

B-oxidation of VLCFA
synthesize/degrade H2O2
degrade amino acids

Biochem review USMLE (11 decks)

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