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EoM NBME > Molecular Biochemistry > Flashcards

Molecular Biochemistry Flashcards

1
Q

Components of a nucleoside

A

base and (deoxy)ribose

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2
Q

Components of a nucleotide

A

base, (deoxy)ribose, and phosphate

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3
Q

Side of a nucleotide chain which has the triphosphate

A

5’ end

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4
Q

Side of a nucleotide chain which has the hydroxyl

A

3’ end

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5
Q

Four important deamination reactions in nucleotides

A

1) cytosine -> uracil
2) adenine -> hypoxanthine
3) guanine -> xanthine
4) 5-methylcytosine -> thymine

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6
Q

Amino acids necessary for purine synthesis (3)

A

Glycine, aspartate, and glutamine

Mnemonic: “Cats PURr until they GAG”

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7
Q

Function of Leflunomide

A

Inhibits dihydroorotate

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8
Q

Function of Methotrexate (also trimethoprim and pyrimethamine)

A

Inhibit dihydrofolate reductase

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9
Q

Function of 5-fluorouracil (5-FU)

A

Form 5-F-dUMP, which inhibits thymidilate synthase (dec. in dTMP)

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10
Q

Function of 6-mercaptopurine

A

inhibit de novo purine synthesis

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11
Q

Function of hydroxyurea

A

Inhibits ribonucleotide reductase (purine and pyrimidine synthesis)

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12
Q

One of the major causes of autosomal recessive SCID (severe combined immunodeficiency). The deficient enzyme is required for degradation of adenosine and deoxyadenosine

A

Adenosine Deaminase Deficiency

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13
Q

Defective purine salvage due to absent HGPRT which converts hypoxanthine to IMP and guanine to GMP. Excess uric acid and de novo purine synthesis. X-linked recessive

A

Lesch-Nyhan syndrome

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14
Q

Lesch-Nyhan Syndrome symptoms and HGPRT mnemonic

A

Hyperurecimia, Gout, Pissed off (aggression, self-mutilation), Retardation, dysTonia

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15
Q

Genetic code feature: each codon specifies only 1 amino acid

A

Unamibigious

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16
Q

Genetic code feature: Most amino acids are coded by multiple codons

A

Degenerate / Redundant

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17
Q

Codons that differ in the 3rd base, may code for the same tRNA/amino acid.

A

Wobble

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18
Q

Genetic code feature: read from a fixed starting point as a continuous sequence of bases

A

Nonoverlapping

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19
Q

Genetic code feature: genetic code is conserved throughout evolution

A

Universal

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20
Q

What sort of nitrogenous bases would be heavily present in the origin of replication?

A

AT-rich sequences

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21
Q

Create a single or double stradned brea in the DNA helix to add or remove supercoils

A

DNA topoisomerases

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22
Q

Reverse transcriptase that adds DNA (TTAGGG) to 3’ ends of chromosomes to avoid loss of genetic material with every duplication

A

Telomerase

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23
Q

Subtype of point mutation: purine to purine or pyrimidine to pyrimidine

A

Transition

24
Q

Subtype of point mutation: purine to pyrimidine or vice versa

A

Transversion

25
Q

Nucleotide substitution but codes for the same amino acid; often base change in 3rd position of the codon

A

Silent mutation

26
Q

Nucleotide substitution resulting in changed amnio acid

A

Missense mutation

27
Q

Nucleotide substitution resulting in premature stop codon. Usually results in a nonfunctional protein

A

Nonsense mutation

28
Q

Deletion or insertion of a number of nucleotides not divisible by 3, resulting in a misreading of all nucleotides downstream.

A

Framshift mutation

29
Q

Mutation at a splice site, retained intron in the mRNA, protein with impaired or altered function.

A

Splice site mutation

30
Q

Specific endonucleases release the oligonucleotides containing damaged bases; DNA polymerase and ligase fill and reseal the gap, respectively. Repairs bulky helix-distorting lesions. Occurs in G1 phase of cell cycle

A

Nucleotide excision repair

31
Q

Inability to repair DNA pyrimidine dimers caused by UV exposure. Dry skin, extreme light sensitivity, skin cancer. Defect of exinucleases in nucleotide excision repairs

A

Xeroderma pigmentosum

32
Q

Base-specific glycosylase removes altered base and creates AP site (apurinic/apyrimidinic). One or more nucleotides are removed by AP-Endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA polymerase-beta fills the gap and DNA ligase seals it. Occurs throughout the cell cycle.

A

Base excision repair

33
Q

Which type of DNA repair is critical in repair of spontaneous/toxic deamination?

A

Base excision repair

34
Q

Newly synthesized strand is recognized, mismatched, nucleotides are removed, and the gap is filled and resealed. Occurs predominantly in S phase of cell cycle

A

Mismatch repair

35
Q

What process is defective in Lynch syndrome, also known as hereditary nonpolyposis colorectal cancer (HNPCC)

A

DNA mismatch repair

36
Q

Brings together 2 ends of DNA fragment to repair double-stranded breaks. No requirement for homology. Some DNA might be lost.

A

Nonhomologous end joining

37
Q

Requires two homologous DNA duplexes. A strand from the damaged dsDNA is repaired using a complementary strand from the intact homologous dsDNA template. Restores duplexes accurately without loss of nucleotides

A

Homologous recombination

38
Q

What process is defective in breast/ovarian cancers with BRCA1 mutation?

A

Homologous recombination

39
Q

Site where RNA polymerase II and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT box)

A

Promoter

40
Q

DNA locus where activator regulatory proteins bind, increase expression of a gene on the same chromosome

A

Enhancer

41
Q

DNA locus where repressor regulatory proteins bind, decreasing expression of a gene on the same chromosome

A

Silencer

42
Q

_____ and _____ may be located close to, far from, or even within the gene whose expression they regulate

A

Enhancers and silencers

43
Q

What is preprocessed mRNA called? (First aid uses a different term then we did)

A

heterogeneous nuclear RNA (hnRNA)

44
Q

What is the cap added in 5’ end mRNA processing?

A

7-methylguanosine

45
Q

What is added on the 3’ end of processed mRNA?

A

polyadenylation / poly A tail

46
Q

What is a good way to remember how RNA polymerases are numbered?

A

They’re numbered in the order they’re used. I - rRNA, II - mRNA, III - tRNA

47
Q

Product(s) of RNA Polymerase I

A

rRNA

48
Q

Product(s) of RNA Polymerase II

A

mRNA and snRNA

49
Q

Product(s) of RNA Polymerase III

A

5s rRNA, tRNA

50
Q

Small noncoding RNA molecules that posttranscriptionally regulate gene expression by targeting the 3’ untranslated region of specific mRNAs for degradation or translational repression.

A

microRNAs (miRNAs)

51
Q

What’s on the 3’ end of a tRNA

A

CCA acceptor stem for covalent binding to amino acids

52
Q

Function of the T arm on tRNA, which features a TΨC sequence

A

Tethers the tRNA molecule to the ribosome

53
Q

Arm of tRNA which is used in recognizion by the correct aminoacyl-tRNA synthetase

A

D-arm

54
Q

What charges tRNA with the correct amino acid

A

Aminoacyl-tRNA synthetase

55
Q

What are the triphosphate nucleotides used for charging tRNA and then translocation, respectively?

A

ATP and GTP

56
Q

Sites of a ribosome

A

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

EoM NBME (6 decks)

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