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USMLE1 - Biochemistry > 1. Molecular Biochemistry > Flashcards

1. Molecular Biochemistry Flashcards

1
Q

Which histone ties DNA-histone nucleosome beads into more condensed structures?

A

H1. The only histone that is not in the nucleosome core.

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2
Q

DNA loops twice around histone octamer to form nucleosome bead. Which histones are these?

A

Histones H2A, H2B, H3, H4

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3
Q

Is DNA acidic or basic?

A

acidic

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4
Q

What type of aa are histones made of? Are they acidic or basic?

A

lysine and arginine; basic

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5
Q

Which is more accessible to transcription factors: heterochromatin or euchromatin?

A

Euchromatin

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6
Q

If a cell has a hyperchromatic nucleus, will it undergo transcription?

A

No. Heterochromatin are condensed, transcriptionally inactive and sterically inaccessible.

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7
Q

What are chromosomes? During what part of the cell cycle are they found? In what pathologic state would you see a lot of chromosomes?

A

Highly condensed forms of DNA; mitosis;

Neoplasia- highly dividing and thus hyperchromatic

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8
Q

What experiments look at chromosomes?

A

karyotyping

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9
Q

Heterochromatin and euchromatin: which have more methylated and/or acetylated histones?

A

Hypermethylation inactivates transcription (heterochromatin). Histone acetylation relaxes DNA coiling, allowing for transciprtion (euchromatin)

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10
Q

What does guanine have on it?

A

a ketone

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11
Q

What does thymine have on it?

A

a methyl

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12
Q

Deamination of what pyrimidine makes what?

A

cytosine to uracil

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13
Q

In what genetic code is uracil found in?

A

RNA

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14
Q

How many hydrogen bonds does a G-C and A-T connection have? Which one has a higher melting temperature?

A

GC (3) and AT (2). GC has a higher melting temperature because of the additional hydrogen bond.

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15
Q

What amino acids are required in purine synthesis and/or pyrimidine synthesis?

A

G-A-G (glycine, aspartate, glutamine) and Formyl-tetrahydrofolate for purine synthesis. Aspartate for pyrimidine synthesis.

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16
Q

What is the difference between a nucleotide and a nucleoside?

A

NucleoSide=base+ribose (Sugar)
NucleoTide=base+ribose+phosphaTe

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17
Q

Is PRPP added later or first in pyrimidine synthesis?

A

Later. Make temporary (orotic acid) base first, then ad surgar+phosphate (PRPP) and modify base.

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18
Q

What is PRPP? How is it made?

A

It is the ribose+phosphate; its made from PRPP synthetase + ATP using Ribose 5-P from the HMP shunt

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19
Q

What is the precursor for both purines?

A

IMP

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20
Q

What is the precursor for pyrimidines?

A

Orotic acid (plus PRPP) to make UMP -> UDP

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21
Q

Which intermediate is involved in both pyrimidine synthesis and the urea cycle?

A

Carbamoyl phosphate (which becomes orotic acid)

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22
Q

Why does a deficiency in ornithine transcarbamoylase result in an increased production pyrimidine?

A

Ornithine transcarbomoylase deficiency leads to an accumulation of carbamoyl phosphate, converting to orotic acid, the precursor of pyrimidine.

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23
Q

Is Carbamoyl phosphate synthetase I or II involved in pyrimidine synthesis?

A 
CPS I (mitochondria, urea cycle)
 CPS II (cytosol, pyrimidine metabolism)
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24
Q

What three enzymes lead to orotic acid accumulation? what reactions are they involved in?

A 
Ornithine transcarbamoylase (urea cycle, accumulation of carbamoyl phosphate)
 Orotic acid phosphoribosyltransferase and Orotidine 5'-phosphate decarboxylase (conversion of orotic acid to UMP)
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25
Q

What step in pyrimidine synthesis requires aspartate?

A

Conversion of carbamoyl phosphate to orotic acid (orotic acid phosphoribosyltransferase, orotidine 5’-phosphate decarboxylase)

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26
Q

What are the clinical symptoms of orotic aciduria?

A

Increased orotic acid in urine, megaloblastic anemia (does not improve with admin of vit B12 or folic acid), failure to thrive. No hyperammonemia (vs. OTC deficiency - increase oritic acid with hyperammonemia)

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27
Q

How do you differentiate the causes of orotic aciduria?

A

No hyperammonemia=defect in orotic acid hosphoribosyltransferase or orotidine 5’-phosphate decarboxylase (autosomal recessive)
Hyperammonemia=ornithine transcarbamoylase deficiency

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28
Q

What is unique about megaloblastic anemia from increased orotic acid?

A

Orotic aciduria megaloblastic anemia can not be corrected with folic acid or vit B12

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29
Q

How do you treat orotic aciduria? What is the mechanism for treatment?

A

oral uridine administration; provides nucleosides and provides feedback inhibition

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30
Q

What converts dUMP to dTMP? What drug blocks this?

A

Thymidylate synthase; 5-Fluorouracil

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31
Q

What enzyme is involved in convert UDP to dUDP? What drug blocks this?

A

Ribonucleotide reductase; hydroxyurea

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32
Q

What does ornithine transcarbamyolase do to carbamoyl phosphate?

A

Converts carbamoyl phosphate to citrulline

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33
Q

What does 6 mercaptopurine do?

A

6MP blocks de novo purine synthesis

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34
Q

Other than thymidylate synthase, what else is required to convert dUMP to dTMP?

A

N5N10 methylene THF

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35
Q

After N5N10 methylene THF donates a methyl for conversion of dUMP to dTMP what is it converted to?

A

DHF

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36
Q

What enzyme converts DHF to THF? What vitamin cofactor is used to transfer a methyl from an amino acid to DHF? What amino acid is that?

A

Dihydrofolate reductase; vitamin B12; homocysteine

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37
Q

What happens to homocysteine after converting a methyl?

A

Homocysteine becomes methionine

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38
Q

how is THF converted to N5N10 Methylene?

A

Using serine (which turns into glycine after reaction)

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39
Q

what does methotrexate do? what step is this enzyme involved in?

A

it inhibits conversion of DHF to THF by blocking dihyrdofolate reductase

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40
Q

what is the difference between methotrexate and trimethroprim?

A

trimethroprim inhibits bacterial dihyrofolate reductase

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41
Q

what is adenosine/AMP converted to? through what enzyme?

A

inosine/IMP; adenosine deaminase

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42
Q

GMP is degraded to guanosine which is degraded to guanine. What two options are next? by what enzymes?

A

either salvage by HGPRT and PRPP or converstion to xanthine and then to uric acid by xanthine oxidase

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43
Q

IMP is degraded to inosine and then to hypoxanthine. what two options are next? by what enzymes?

A

either salvage by HGPRT and PRPP or conversion to xanthine and then uric acid by xanthine oxidase

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44
Q

in what syndrome is HGPRT deficient? what is the inheritance pattern?

A

Lesch Nyhan syndrome; X linked recessive

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45
Q

what is main lab finding in Lesch Nyhan syndrome? due to what enzyme deficiency? what reaction is deficient?

A

uric acidemia; HGPRT; purine salvage

46
Q

what are the main clinical symptoms of Lesch Nyhan syndrome?

A

self mutilation, aggression, mental retardation, gout, hyperuricemia, choreathetosis

47
Q

what is the major cause of SCID? what does SCID stand for?

A

adenosine deaminase deficiency; Severe combined immunodeficiency disease

48
Q

what is the link between adenosine deaminase deficiency and decreased lymphocyte count?

A

excess ATP and dATP has negative feedback inhibition on ribonucleotide reductase which results in decreased DNA synthesis and thus decreased lymphocyte count

49
Q

what has negative feedback inhibition on ribonucleoside reductase?

A

ATP and dATP

50
Q

what is methotrexate?

A

a folic acid analogue

51
Q

what is given to prevent side effects when methotrexate is given? why does this work?

A

folinic acid; does not require DHF

52
Q

in the genetic code, what does unambiguous mean?

A

each codon specifies only one amino acid

53
Q

what does degenerate/redundant mean in terms of the genetic code?

A

codons may encode same amino acid since there are only ~20 aa

54
Q

what structures allows for degeneracy?

A

tRNA wobble

55
Q

what is the exception to degeneracy in the genetic code?

A

methionine is only encoded by AUG

56
Q

what is the exception to the nonoverlapping/commaless aspect of the genetic code?

A

some viruses

57
Q

what is the exception to the universal aspect of the genetic code?

A

mitochondria, archaebacteria, mycoplasma, and some yeasts

58
Q

what are the three types of point mutations?

A

silent, misssense, nonsense

59
Q

what is a clinical example of a missense mutation?

A

sickle cell disease- conversion of hydroophillic glutamic acid to hyrdophobic valine

60
Q

what is an example of a nonsense mutation?

A

beta thalassemia

61
Q

what creates a frameshift mutation? what are some clinical examples?

A

insertion or deletion of a number of nucleotides indivisible by 3; tay sachs, duchennes MD

62
Q

what does topoisomerase do? I or II eukaryotic?

A

creates nicks in DNA to prevent supercoiling; both!

63
Q

what is DNA gyrase?

A

a topoisomerase II

64
Q

what Ab class blocks DNA gyrase?

A

Flouroquinolones

65
Q

what is bleomycin?

A

an anti cancer agent that is a topoisomerase II and creates nicks in DNA

66
Q

what is etoposide? why does this not affect normal healthy cells?

A

a topoisomerase II inhibitor; because cancer cells use II more so than healthy cells

67
Q

what type of polymerase is primase?

A

DNA dependent RNA polymerase

68
Q

what type exonuclease activity does DNA polymerase III have? in what organisms is it found?

A

3’–> 5’; prokaryote only

69
Q

what type of exonuclease activity does DNA polymerase I have? in what organisms is it found? what is it used for?

A

5’–> 3’; prokaryote only; for removing RNA primer and filling it with DNA

70
Q

what type of drug are alkylating agents? how do they work? give a couple examples

A

antineoplastic agents; alkylate DNA!; cyclophosphamide and nitrosurea (aka lomustrine- a nitrosource)

71
Q

what two anti-neoplastic drugs work by blocking DNA and RNA polymerase?

A

dactinomycin, doxorubicin

72
Q

name two antineoplastic drugs that work by inhibiting the mitotic spindle by MT blocking.

A

vincrstine (vinca alkaloids) and paclitaxel

73
Q

how are senescent cells different from some neoplastic and germ cells? what does this substance do?

A

telomerase; an RNA polymerase that uses a RNA template to add DNA to the end of shortening 3’ ends

74
Q

what four enzymes are required for nucleotide excision repair?

A

endonucleases, exonucleases, DNA polymerase, DNA ligase

75
Q

what is the difference between exonucleases and endonucleases?

A

endonucleases are specific and break specific linking phosphodiester bonds, exonucleases are not sequence specific and just remove the nucleoside

76
Q

what type of enyzmes are used in base excision repair?

A

glycosylases (only remove the base- cut the bond between ribose and base)

77
Q

what is needed after the glycosylase in base excision repair?

A

an AP (apyrimidinic) endonuclease to cut the DNA, exonuclease then removes and then filled and sealed by enzymes

78
Q

what is most often mutated in xeroderma pigmentosum? what is the inheritance pattern? what are the clinical symptoms?

A

UV specific endonucleases for excision repair; AR; dry skin, photosensitivity, poikiloderma, susceptibility to skin cancers

79
Q

to what type of DNA damage are xeroderma pigmentation susceptible to?

A

UV nonionizing radiation causing thymidine dimers

80
Q

how does mismatch repair work? in what cancer is it mutated? what type of DNA is methylated?

A

immediately after replication, DNA is unmethylated and so it is a signal to be double checked; HNPCC; heterochromatin

81
Q

what kind of DNA damage does ionizing radiation cause? what type of repair helps with this?

A

double strand breaks; nonhomologous end joining

82
Q

which end carries the triphosphate? which end of DNA makes the hydoxyl attack?

A

5’ end; 3’ end

83
Q

what aa does AUG mRNA code for in eukaryotes? prokaryotes?

A

methionine; f Met (formyl methyl methionine)

84
Q

what is the difference between the promoter and enhancer? in what process are they used for?

A

promoter binds RNA Pol II and is very close (25 bases) to initiation site and is AT rich; enhancer/silencers bind TFs only, can be located close or far and regulate gene expression but not specifically initiation; transcription

85
Q

what do enhancers/silencers bind?

A

TFs

86
Q

do RNA polymerases have proofreading function? what does this mean for HIV?

A

no; increased mutation rate!

87
Q

which RNA polymerase synthesizes tRNAs and snRPs?

A

III

88
Q

which RNA polymerase synthesizes rRNA? where?

A

I; nucleolus

89
Q

how many RNA polymerases do prokaryotes have? what drug blocks prokaryotic RNA polymerase only? what is it used for?

A

1 for all three classes of RNA; Rifampin; TB

90
Q

What toxin causes liver failure by inhibiting RNA polymerase II if ingested? where does it come from?

A

alpha amanitin; mushroom caps

91
Q

what three steps are included in RNA processing? where does it occur?

A

5’ capping (with 7 methylguanosine), 3’ adenylation, splicing of introns; nucleus

92
Q

what is the signal for adenylation? what enzyme does? does it require a template?

A

AAUAAA; Poly A polymerase; no

93
Q

what is the RNA called before processing? and after?

A

hnRNA; mRNA

94
Q

what are required for splicing? encoded by what polymerase?

A

snRNPs; RNA polymerase III

95
Q

in what disease are there antibodies to snRNPs?

A

Lupus

96
Q

do introns or exons contain the genetic information?

A

exons

97
Q

what is alternative splicing? in what disease state does alt splicing occur unintentionally d/t early stop codons?

A

when different combination of exons get combined together; in Beta thallasemia

98
Q

where does splicing occur?

A

nucleus

99
Q

what are heat shock proteins?

A

assist in spontaneous refolding of proteins

100
Q

like mRNA has a poly A tail on the 3’ end, what does tRNA have on its 3’ end? what happens here?

A

CCA and chemically modified bases where amino acid is covalently bonded

101
Q

what is “charging” of tRNA? what enzyme regulates this? what does this reaction require? in what process is this?

A

when the amino acid is covalently binded to its corresponding tRNA; Aminoacyl tRNA synthetase; ATP; translation

102
Q

at what point is the amino acid correspondence to the mRNA code finalized?

A

in the charging reaction! for this reason aminoacyl tRNA synthetase double checks

103
Q

after addition of an aa, where does the aminoacyl tRNA now bind to?

A

30S ribosomal RNA (small one)

104
Q

what Abs block the binding between aminoacyl tRNA and rRNA by binding the 30S ribosome?

A

aminoglycosides and tetracyclines

105
Q

what toxins prevent elongation in translation in humans (by binding 40s)?

A

shiga toxin and ricin (protein in castor beans)

106
Q

what is significant about 50S/60S ribosomal unit?

A

it contains the peptidyltransferase activity (for elongation of protein

107
Q

what antibiotic inhibits peptidyltransferase activity?

A

chloramphenicol

108
Q

what fungicide/rat repellent inhibits the peptidyltransferase activity in humans?

A

cycloheximide

109
Q

Initiation of protein tranlsation is activated by ATP hydrolysis. T/F?

A

False; GTP hydrolysis

110
Q

Prokaryotes have what ribosomal units?

A

30S + 50S= 70S

111
Q

In protein translation, what is the “A” site for? “P” site? “E” site? what is the exception to this?

A

Incoming Aminoacyl tRNA; site where peptidyltransferase bond is made between growing peptide aa’s; the holds the empty tRNA as it exits; the initiator mRNA (met or f-met) starts off in E site rather than A site

USMLE1 - Biochemistry (6 decks)

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