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USMLE Step 1 > Molecular Biology > Flashcards

Molecular Biology Flashcards

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USMLE® Step 1 flashcards
1
Q

Describe the structure of chromatin.

A
  • Negatively charged DNA loops twice around a positively charged histone octamer, forming a nucleosome.
  • H1 (linker histone) binds to the nucleosome and to “linker DNA”, stabilizing the chromatin fiber.
  • Chromatin fibers condense to form supercoiled structure.
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2
Q

Histones are rich in which amino acids?

A

Lysine and Arginine (Note: positively charged)

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3
Q

What is heterochromatin?

A

Chromatin that is condensed, transcriptionally inactive, and sterically inaccessible.

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4
Q

What is euchromatin?

A

Chromatin that is less condensed, transcriptionally active, and sterically accessible.

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5
Q

What are the 2 forms of chromatin?

A

Heterochromatin

Euchromatin

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6
Q

What is the role of DNA methylation in prokaryotes?

A

Methylation of cytosine and adenine of the template strand during DNA replication allows mismatch repair enzymes to distinguish between old and new strands.

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7
Q

What is the role of DNA methylation in humans?

A

Methylation of CpG islands in DNA represses transcription.

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8
Q

What is the role of histone methylation?

A

Usually reversibly represses DNA transcription, BUT can activate it in some cases (depending on location).

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9
Q

What is the role of histone acetylation?

A

Relaxes DNA coiling (by neutralizing positive histone charge), allowing for transcription.

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10
Q

What is the most fundamental structural difference between purines and pyrimidines?

A

Purines have 2 rings and pyrimidines have 1.

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11
Q

What are the purines?

A

A, adenosine

G, guanine

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12
Q

What are the pyrimidines?

A

C, cytosine
T, thymine
U, uracil

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13
Q

Which nucleotide has a methyl group?

A

Thymine

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14
Q

How can uracil be produced from cytosine?

A

Deamination of cytosine.

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15
Q

What nucleotides are found in DNA? RNA?

A

DNA: A, G, C, T
RNA: A, G, C, U

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16
Q

What amino acid(s) are necessary for de novo purine synthesis?

A

Glycine
Aspartate
Glutamine
(and THF)

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17
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleotide is a nucleoside with a phosphate group linked to (deoxy)ribose by a 3’-5’ phosphodiester bond.

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18
Q

What DNA nucleotide bond is strongest? Why?

A

G-C is stronger than A-T given 3:2 hydrogen bonds.

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19
Q

What amino acid(s) are necessary for de novo pyrimidine synthesis?

A

Aspartate

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20
Q

Describe de novo purine synthesis in 2-3 steps.

A

1) Start with sugar + phosphate (PRPP).

2) Add base.

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21
Q

Describe de novo pyrimidine synthesis in 2-3 steps.

A

1) Make temporary base (orotic acid).
2) Add sugar + phosphate (PRPP).
3) Modify base.

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22
Q

Which metabolic pathway(s) involve carbamoyl phosphate?

A

De novo pyrimidine synthesis

Urea cycle

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23
Q

How does leflunomide affect nucleotide synthesis?

A

It inhibit synthesis of orotic acid during de novo pyrimidine synthesis.

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24
Q

How does mycophenolate affect nucleotide synthesis?

A

It inhibits IMP dehydrogenase during de novo purine synthesis.

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25
Q

How does ribavirin affect nucleotide synthesis?

A

It inhibits IMP dehydrogenase during de novo purine synthesis.

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26
Q

How does hydroxyurea affect nucleotide synthesis?

A

It inhibits ribonucleotide reductase (UDP -> dUDP) during de novo pyrimidine synthesis.

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27
Q

How does azathioprine (6-MP) affect nucleotide synthesis?

A

It inhibits de novo purine synthesis.

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28
Q

How does 5-FU affect nucleotide synthesis?

A

It inhibits thymidylate synthase (leading to decreased dTMP) during de novo purine synthesis.

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29
Q

How does methotrexate affect nucleotide synthesis?

A

It inhibits dihydrofolate reductase (leading to decreased dTMP) during de novo purine synthesis in HUMANS.

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30
Q

How does trimethoprim affect nucleotide synthesis?

A

It inhibits dihydrofolate reductase (leading to decreased dTMP) during de novo purine synthesis in BACTERIA.

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31
Q

How does pyrimethamine affect nucleotide synthesis?

A

It inhibits dihydrofolate reductase (leading to decreased dTMP) during de novo purine synthesis in PROTOZOA.

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32
Q

How does probenecid affect nucleotide metabolism?

A

It increases excretion of uric acid in urine.

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33
Q

How does allopurinol affect nucleotide metabolism?

A

It inhibits xanthine oxidase, thus inhibiting the degradation of purines to uric acid.

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34
Q

How does febuxostat affect nucleotide metabolism?

A

It inhibits xanthine oxidase, thus inhibiting the degradation of purines to uric acid.

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35
Q

What are the consequences of adenosine deaminase deficiency?

A
  • Excess ATP and dATP leads to feedback inhibition of ribonucleotide reductase, creating an imbalance in the nucleotide pool.
  • This prevents DNA synthesis and decreases lymphocyte count.
  • One of the major causes of AR SCID.
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36
Q

What is the pathophysiology of Lesch-Nyhan syndrome?

A
  • Defective purine salvage due to absence of HGPRT enzyme (which converts hypoxanthine -> IMP, and guanine -> GMP).
  • Results in excess uric acid and increased de novo purine synthesis.
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37
Q

What are the signs/symptoms of Lesch-Nyhan syndrome?

A 
HGPRT:
Hyperuricemia
Gout
Pissed off (aggression, self-mutilation)
Retardation
dysTonia
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38
Q

What is the treatment for Lesch-Nyhan syndrome?

A

Allopurinol (first line)

Febuxostat

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39
Q

What are key features of the genetic code?

A

Unambiguous (each codon specifies one amino acid).
Degenerate (most amino acids are coded by multiple codons).
Non-overlapping (read from fixed starting point).
Universal (conserved throughout evolution).

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40
Q

What is an origin of replication?

A

Particular consensus sequence of base pairs in genome where DNA replication begins.

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41
Q

What is a replication fork?

A

Y-shaped region along DNA template where leading and lagging strands are synthesized.

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42
Q

What is a helicase?

A

An enzyme that unwinds DNA templates at the replication fork.

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43
Q

What is the role of single-stranded binding proteins?

A

They prevent DNA strands from reannealing.

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44
Q

What is the role of a DNA topoisomerase?

A

It creates a single- or double-stranded break in the helix to add or remove supercoils.

45
Q

What is the mechanism of action of fluoroquinolones?

A

They inhibit prokaryotic topoisomerase II and IV.

46
Q

What is the role of a primase?

A

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

47
Q

What is the role of DNA polymerase III?

A

Only prokaryotes.

  • Elongates the leading strand by adding nucleotides 5’ -> 3’.
  • Elongates the lagging strand until it reaches primer of preceding fragment.
  • 3’ -> 5’ exonuclease activity proofreads each added nucleotide.
48
Q

What is the role of DNA polymerase I?

A

Only prokaryotes.

* Degrades RNA primer and replaces with DNA.

49
Q

What is the role of DNA ligase?

A

It catalyzes the formation of a phosphodiester bond (between Okazaki fragments) within a strand of double-stranded DNA

50
Q

What is the role of a telomerase?

A

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

51
Q

In terms of nucleotide changes, what are the types of DNA point mutations?

A

Transition: pur -> pur or pyr -> pyr.
Transversion: pur -> pyr or reverse.

52
Q

What are the 4 types of DNA mutations, in order of severity?

A

1) silent
2) missense
3) nonsense
4) frameshift

53
Q

What is a silent mutation?

A

Nucleotide substitution that encodes the same amino acid. (Often in the 3rd, “wobble”, position of codon.)

54
Q

What is a missense mutation?

A

Nucleotide substitution resulting in changed amino acid.

55
Q

What is a nonsense mutation?

A

Nucleotide substitution resulting in an early stop codon.

56
Q

What is a frameshift mutation?

A

Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream. (Often results in truncated, nonfunctional protein.)

57
Q

What is the lac operon?

A

A classic example of a genetic response to an environmental change.
Activation of the lac operon in E. coli leads to switch from glucose to lactose metabolism in glucose-poor environments.

58
Q

In a low-glucose environment, what mechanism leads to a change in the lac operon?

A

Low glucose results in the following sequence:

1) increased adenylyl cyclase activity.
2) increased generation of cAMP from ATP.
3) activation of CAP (transcription activator).
4) increased transcription along lac operon.

59
Q

In a high-lactose environment, what mechanism leads to a change in the lac operon?

A

High lactose results in the following sequence:

1) unbinding of repressor protein from repressor/operator site.
2) increased transcription along lac operon.

60
Q

Describe nucleotide excision repair.

A
  • Specific endonucleases release the oligonucleotides containing damaged bases.
  • DNA polymerase and ligase fill and reseal the gap, respectively.
61
Q

When does nucleotide excision repair occur?

A

G1 phase of cell cycle.

62
Q

What is the pathophysiology of xeroderma pigmentosa?

A

Defective nucleotide excision repair prevents repair of pyrimidine dimers caused by UV light exposure.

63
Q

Describe base excision repair.

A
  • Base-specific glycosylase removes altered base and creates AP site.
  • One or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end.
  • Lyase cleaves the 3’ end.
  • DNA polymerase-β fills the gap and DNA ligase seals it.
64
Q

When does base excision repair occur?

A

Throughout cell cycle.

65
Q

What defects are typically repaired through nucleotide excision?

A

Bulky helix-distorting lesions.

66
Q

What defects are typically repaired through base excision?

A

Spontaneous, toxic deamination.

67
Q

Describe DNA mismatch repair?

A
  • Newly synthesized stand is recognized and mismatched nucleotides are removed.
  • The gap is filled and resealed.
68
Q

When does mismatch DNA repair occur?

A

Predominantly in G2 phase of cell cycle.

69
Q

What defect underlies HNPCC (hereditary nonpolyposis colorectal cancer)?

A

Defective DNA mismatch repair.

70
Q

What is nonhomologous end joining?

A

Repair of double-stranded DNA breaks in which 2 ends of DNA fragments are brought together, without requirement for homology.

71
Q

What defect underlies ataxia telangiectasia?

A

Defective nonhomologous end joining (of double-stranded DNA breaks).

72
Q

What defect underlies Fanconi anemia?

A

Defective nonhomologous end joining (of double-stranded DNA breaks).

73
Q

In which direction is DNA synthesized?

A

5’ -> 3’

5’ end of nucleotide bears the triphosphate

74
Q

In which direction is RNA synthesized?

A

5’ -> 3’

5’ end of nucleotide bears the triphosphate

75
Q

In which direction is protein synthesized?

A

N-terminus to C-terminus

76
Q

In which direction is mRNA read?

A

5’ -> 3’

5’ end of nucleotide bears the triphosphate

77
Q

What are the start codon(s)?

A

AUG (rarely GUG)

78
Q

Which amino acid is encoded by the start codon?

A

Methionine (may be removed before completion of translation).

In prokaryotes, it’s N-formylmethionine.

79
Q

What role does N-formylmethionine play in the immune response?

A

N-formylmethionine is a prokaryotic amino acid which stimulates neutrophil chemotaxis.

80
Q

What are the stop codon(s)?

A

UGA, UAA, UAG

81
Q

What is a promotor (in gene expression)?

A

The DNA site where RNA polymerase II and multiple other transcription factors bind to DNA upstream from gene locus.

82
Q

What nucleotide sequences are common in promotor regions?

A

AT-rich, with TATA and CAAT boxes.

83
Q

What is an enhancer (in gene expression)?

A
  • A stretch of DNA that increases gene expression by binding transcription factors.
  • May be located close to, far from, or even within the gene whose expression it regulates.
84
Q

What is a silencer (in gene expression)?

A
  • A DNA site where negative regulators (repressors) bind.

* May be located close to, far from, or even within the gene whose expression it regulates.

85
Q

What are the RNA polymerase(s) in eukaryotes? What are their roles?

A

RNA polymerase I: makes rRNA
RNA polymerase II: makes mRNA
RNA polymerase III: makes tRNA

86
Q

What are the RNA polymerase(s) in prokaryotes? What are their roles?

A

Single RNA polymerase: makes rRNA, mRNA, tRNA

87
Q

What is the pathophysiology of death cap mushroom toxicity?

A

Contains α-amanitin which inhibits RNA polymerase II, causing severe hepatotoxicity.

88
Q

What is the mechanism of action of rifampin?

A

Inhibits the prokaryotic RNA polymerase.

89
Q

What is the mechanism of action of actinomycin D?

A

Inhibits RNA polymerases in both prokaryotes and eukaryotes.

90
Q

How is an RNA transcript initially altered within the nucleus?

A
  • Capping of 5’ end (with 7-methylguanosine).
  • Polyadenylation of 3’ end.
  • Splicing out of introns.
91
Q

What is the primary location for mRNA “quality control”?

A

Cytoplasmic P-bodies (contains exonucleases, decapping enzymes, microRNAs).

92
Q

What is the nucleotide signal for polyadenylation during RNA transcription?

A

AAUAAA

Note: poly-A polymerase does not require a template.

93
Q

Describe the process of pre-mRNA splicing.

A
  • Primary transcript combines with snRNPs and other proteins to form spliceosome.
  • Lariat-shaped intermediate is generated.
  • Lariat is released to precisely remove intron and join 2 exons.
94
Q

What is the target for anti-Smith antibodies?

A

Spliceosomal snRNPs.

95
Q

What are exons?

A

DNA segments that contain the actual genetic coding for a protein.

96
Q

What are introns?

A

Intervening noncoding segments of DNA.

97
Q

Describe alternative splicing.

A

Varied splicing of exons from a common DNA segment, allowing the productions of a large number of unique proteins.

98
Q

Describe the structure of tRNA.

A
  • 75-90 nucleotides long.
  • Has secondary structure, forming cloverleaf shape with 4 “arms/stems”:
    1) D-arm: recognition by correct aminoacyl-tRNA synthetase.
    2) Anticodon arm: Opposite 3’ aminoacyl end.
    3) T-arm: tRNA-ribosome binding.
    4) Acceptor stem: 5’-CCA-3’ at 3’ end accepts amino acid.
99
Q

Explain wobble.

A

Accurate base-pairing is usually required only in the first 2 nucleotide positions of an mRNA codon, so codons differing at the 3rd “wobble” position may code for the same tRNA/amino acid.

100
Q

What are the subunits of a eukaryotic ribosome?

A

40S and 60S

101
Q

What are the subunits of a prokaryotic ribosome?

A

30S and 50S

102
Q

Describe the initiation phase of protein synthesis.

A
  • Initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA.
  • mRNA and 60S ribosomal subunit assemble with complex and initiation factors are released.
103
Q

Describe the elongation phase of protein synthesis.

A
  • Aminoacyl-tRNA binds to the A site.
  • rRNA catalyzes peptide bond formation and transfers growing polypeptide to amino acid in A site.
  • Ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl-tRNA to P site.
104
Q

Describe the termination phase of protein synthesis.

A
  • Stop codon is recognized by release factor.

* Completed polypeptide is released from ribosome.

105
Q

What are the 3 ribosomal sites relevant for protein synthesis?

A

A site: accepts incoming aminoacyl-tRNA.
P site: holds growing peptidyl-tRNA.
E site: holds empty tRNA as it exits.

106
Q

What is post-translational trimming?

A

Removal of N- or C-terminal propeptides from zymogen to generate mature protein.

107
Q

List common post-translational covalent alterations.

A 
Phosphorylation
Glycosylation
Hydroxylation
Methylation
Acetylation
Ubiquitination
108
Q

What is a chaperone protein?

A

An intracellular protein involved in facilitating or maintaining protein folding.

USMLE Step 1 (4 decks)

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