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First Aid Biochemistry > Molecular > Flashcards

Molecular Flashcards

1
Q

“beads on a string” Condensed DNA

A

Chromatin, H1 is the only histone that is not in the nucleosome core

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2
Q

Condensed, transcriptionally inactive, sterically inaccessible

A

heterochromatin

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3
Q

Transcriptionally active chromatin

A

euchromatin

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4
Q

DNA methylation

A

at CpG islands will repress transcription

allows mismatch repair enzymes to distinguish between old and new

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5
Q

Histone methylation

A

reverisbly represses DNA transcription

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6
Q

Histone acetylation

A

relaxes DNA coiling, allows DNA transcription

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7
Q

Uracil

A

Deaminated cytosine, found in RNA

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8
Q

C-G bond

A

3 H bonds, increase in these will increase in melting temp

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9
Q

A-T bonds

A

2 H bonds

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10
Q

Amino acids necessary for purine synthesis

A

Glycine, Aspartate, Glutamine
remember purines are A and G
pyrimidines are C, T, U

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11
Q

De novo Pyrimidines

A

make temporary base (orotic acid)
add sugar + PRPP
modify base

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12
Q

Leflunomide

A

inhibits dihydroorotate dehydrogenase

interferes with nucleotidee synthesis

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13
Q

Mycophenolate & Ribavirin

A

inhibit IMP dehydrogenase

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14
Q

Hydroxyurea in ribonucleotide synthesis

A

inhibits ribonucleotide reductase

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15
Q

inhibits dihydrofolate reductase in humans

A

methotrexate

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16
Q

inhibits dihydrofolate reductase in bacteria

A

trimethoprim

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17
Q

inhibits dihydrofolate reductase in protozoa

A

pyrimethamine

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18
Q

Lesch-Nyhan Syndrome

A

absent HGPRT, X-linked
hyperuricemia, Gout, agression, self-mutilation, retarded, dystonia
excess uric acid production and de novo purine synthesis

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19
Q

HGPRT

A

necesary for purine salvage

converts hypoxanthine to IMP and guanine to GMP

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20
Q

Adenosine Deaminase Deficiency

A

excess ATP and dATP

prevents DNA synthesis and thus decrease lymphocyte count

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21
Q

Unambiguous

A

each codon specifies only 1 amino acid

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22
Q

Degenerate/Redundant

A

most amino acids are coded by multiple codons

exceptions: methionine(AUG) and tryptophan (UGG)

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23
Q

Commaless, nonoverlapping

A

read from fixed starting point as a continuous sequence of bases

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24
Q

Universal

A

genetic code is conserved throughout evolution except in humans (mitochondria)

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25
Q

Helicase

A

unwinds DNA template at replication fork

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26
Q

single-stranded binding proteins

A

prevent strands from annealing

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27
Q

DNA topoisomerases

A

create a single- or double-stranded break in the helix to add or remove supercoils

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28
Q

fluoroquinolones

A

inhibits DNA gyrase (prokaryoktic topoisomerase II)

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29
Q

Primase

A

makes an RNA primer on which DNA polymerase III can initiate replication

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30
Q

DNA polymerase III

A

5’ => 3’ synthesis and proofreads 3’ => 5’ exonuclease
prokaryotes ONLY
elongates both leading and lagging strands

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31
Q

DNA polymerase I

A

Prokaryotic ONLY

degrades RNA primer and replaces it with DNA

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32
Q

DNA ligase

A

joins Okazaki fragments

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33
Q

Telomerase

A

An RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication

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34
Q

Transition mutation in DNA

A

purine to purine or pyrimidine to pyrimidine

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35
Q

Transversion mutation in DNA

A

purine to pyrimidine or vice versa

36
Q

Silent Mutation

A

nucleotide substitution by codes for same amino acid

37
Q

Missense Mutation

A

nucleotide substitution resulting in a changed amino acid like sickle cell disease

38
Q

Conservative missense mutation

A

new amino acids is similar to the replaced one in chemical structure

39
Q

Nonsense mutation

A

nucleotide substitution resulting in an early stop codon

40
Q

Frameshift Mutation

A

deletion of insertion or # of nucleotides not divisible by 3, results in a truncated non-fx protein
Ex. Duchenne muscular dystrophy

41
Q

Defective in xeroderma pigmentosum

A

nucleotide excision repair

42
Q

nucleotide excision repair

A

endonucleases to remove damaged bases
DNA polymerase and ligase to fill and reseal gap
repairs pyrimidine dimers from UV light

43
Q

Base Excision Repair

A

base-specific glycosylase to recognize altered base
1+ nucleotides are moved with AP-endonuclease cleaving 5’ end
lyase cleaves 3’ end
DNA-polymerase-beta fills gap and DNA ligase seals it

44
Q

Repair of spontaneous/toxic deamination

A

base excision repair

45
Q

Defective in hereditary nonpolyposis colorectal cancer

A

mismatch repair

46
Q

Mismatch repair

A

newly syn strand is recognized, mismatched nucleotides are removed, gap is filled and resealed

47
Q

DNA repair that is mutated in ataxia telangiectasia

A

Nonhomologous end joining

48
Q

repairs double-stranded breaks in DNA

A

Nonhomologous end joining

49
Q

Direction that mRNA and DNA are syn in

A

5’ to 3’

50
Q

mRNA is read in what direction?

A

5’ to 3’

51
Q

Start codon for Prokaryote

A

AUG, formylmethionine (f-met)

52
Q

Start codon for Eukaryote

A

AUG, for methionine

may be removed before translation is complete

53
Q

Stop codons

A

UGA, UAA, UAG

54
Q

Promoter

A

RNA polymerase finds to DNA upstream from gene locus (TATA box)

55
Q

Enhancer

A

DNA that alters gene expression by binding transcription factors

56
Q

Silencer

A

site where repressors bind

57
Q

RNA Polymerase I

A

in eukaryotes, makes rRNA (most numerous)

58
Q

RNA Polyermase II

A

in eukaryotes, makes mRNA, largest RNA

opens DNA at promoter site

59
Q

RNA Polymerase III

A

in eukaryotes, makes tRNA, smallest RNA

60
Q

alpha-amanitin

A

in Amanita phalloides, inhibits RNA polymerase II

61
Q

Prokaryotic RNA Polymerase

A

multisubunit complex, makes all 3 kinds of RNA

62
Q

initial RNA transcript

A

heterogenous nuclear RNA, hnRNA

63
Q

Processes in nucleus following transcription

A

Capping of 5’ end
Polyadenylation of 3’ end
Splicing of introns
thusly makes mRNA

64
Q

where mRNA is translated

A

cytosol

65
Q

AAUAAA

A

polyadenylation signal

66
Q

snRNPs

A

bind pre-mRNA at intron to aid in splicing

67
Q

Lariat

A

looped intermediated for splicing out introns from mRNA

when released, the 2 exons are joined

68
Q

antibodies to spliceosomal snRNPs

A

anti-Smith antibodies, highly specific for SLE

69
Q

Anti-U1 RNP antibodies

A

highly associated with mixed CT disease

70
Q

coding segment for protein

A

exons

71
Q

non-coding segments of DNA

A

introns

72
Q

tRNA 3’ end

A

CCA - for can carry aminos

73
Q

T-arm of tRNA

A

contains thymine, pseudouridine, cytosine, necessary for tRNA-ribosome binding

74
Q

D-arm of tRNA

A

contains dihydrouracil necessary for tRNA recognition to correct aminoacyl-tRNA synthetase

75
Q

mischarged tRNA

A

reads usual codon but inserts wrong amino acid

76
Q

aminoacyl-tRNA synthetase

A

scrutinizes AA before and after it binds to tRNA, if incorrect the bond is hydrolyzed

77
Q

tRNA wobble

A

codons differing in the 3rd wobble position may code for the same tRNA/amino acid due to degeneracy genetic code

78
Q

Protein Synthesis - Initiation

A

GTP hydrolysis, eIF help assemble 40S with initiator tRNA and are released when mRNA and 60S assemble

79
Q

2nd step of protein synthesis

A

Elongation

80
Q

A site

A

for incoming aminoacyl-tRNA (except for methionine)

81
Q

P site

A

rRNA catalyzes peptide bond formation, transfers growing polypeptide to AA in A site
growing peptide

82
Q

E site

A

hold empty tRNA as it exits

83
Q

Trimming

A

Post translational modification

removal of N or c terminal propeptides from zymogen to make mature protein

84
Q

Covalent Alterations

A

Post translational modification

phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination

85
Q

Chaperone Protein

A

Intracellular protein involved in facilitating and/or maintaining protein folding

86
Q

Heat Shock Protein

A

Ex of Chaperone protein, in yeast

HSP60, expressed at high temperatures to prevent protein denaturing and misfolding

87
Q

World’s shortest Joke: 2 women were sitting quietly

A

False. Your Penis.

First Aid Biochemistry (5 decks)

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