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Biochemistry > Molecular Biochemistry > Flashcards

Molecular Biochemistry Flashcards

1
Q

What is chromatin?

A

Condensed, tightly coiled DNA wrapped around histones to fit into the nucleus and protect from DNA damage

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2
Q

What are histones? What amino acids are they rich in?

A

Positively charged protein octamer that DNA (negative) wraps around twice. Histones are rich in lysine and arginine.

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3
Q

Which histone is the linker? Which compose the nucleosome bead?

A

H1 is linker, H2A, H2B, H3 and H4 (x2) = nucleosome.

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4
Q

When does DNA and histone synthesis occur?

A

S phase

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5
Q

When does DNA condense to form chromosomes?

A

mitosis

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6
Q

What is heterochromatin? Classic example?

A

Highly condensed, inactive DNA. Appears darker on EM. Ex: barr bodies (inactive X).

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7
Q

What is euchromatin?

A

Less condensed, transcribable DNA. Appears lighter on EM.

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8
Q

What is CpG DNA methylation?

A

Addition of methyl group at cytosine-phosphate-guanine site, represses transcription. Methyl makes Mute.

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9
Q

What is histone methylation?

A

Usually reversibly represses DNA tx, can activate in some cases. Histone Methylation Mostly Makes Mute.

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10
Q

What is histone acetylation?

A

Relaxes DNA coiling, allowing for transcription. Histone Acetylation makes Active.

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11
Q

Which nucleotides are purines?

A

A, G. PURe As Gold.

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12
Q

Which nucleotides are pyrimidines?

A

C, T, Y. CUT the PY (pie).

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13
Q

Which nucleotides have 1 ring vs. 2 rings?

A

1 ring - PYrimidines, like pie. 2 rings = purines.

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14
Q

What is Uracil?

A

RNA uses Uracil instead of Thymine. Deamination of cytosine makes uracil.

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15
Q

Does thymine have a methyl?

A

Yes

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16
Q

Why does higher G-C content vs. A-T content of DNA raise the melting temperature of DNA?

A

G-C bond is 3 H bonds, A-T is 2 H bonds.

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17
Q

Which amino acids are necessary for purine synthesis?

A

GAG. Glycine, Aspartate, Glutamine.

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18
Q

What is a nucleoSide made of?

A

base + (deoxy)ribose. (Sugar).

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19
Q

What is a nucleoTide made of?

A

base + (deoxy)ribose + phosphaTe.

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20
Q

How is DNA linked?

A

3’-5’ phosphodiester bond.

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21
Q

De novo pyrimidine synthesis requires what three main steps?

A
  1. Make temporary base (orotic acid)
  2. Attach to sugar+phosphate (PRPP)
  3. Modify base to get either U/T/C
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22
Q

First, regulated step of de novo pyrimidine synthesis? What enzyme?

A

Creation of a ring from glutamine and CO2, to form carbamoyl phosphate. Enz: Carbamoyl phosphate synthetase II

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23
Q

What is required to get from carbamoyl phosphate to orotic acid?

A

Aspartate

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24
Q

What is PRPP?

A

Sugar (ribose 5-P) + phosphate that is added to nitrogenous bases to form nucleotides.

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25
Q

What enzyme converts ribonucleotides to deoxyribonucleotides? What drug inhibits this step?

A

Ribonucleotide reductase. Hydroxyurea.

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26
Q

What two pathways is carbamoyl phosphate involved in?

A

De novo pyrimidine synthesis and urea cycle.

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27
Q

How does leflunomide inhibit nucleotide synthesis?

A

Inhibits dehydroorotate dehydrogenase, an enzyme required in conversion of carbamoyl phosphate to orotic acid.

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28
Q

How does 6-MP/azathioprine inhibit nucleotide synthesis?

A

Inhibit purine synthesis - adding of nitrogenous purine base to PRPP.

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29
Q

How do mycophenolate and ribavirin inhibit nucleotide synthesis?

A

Inhibit conversion of IMP (precursor) to GMP.

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30
Q

How does 5-FU inhibit nucleotide synthesis?

A

Inhibits thymidylate synthase (adds methyl to dUMP, forming dTMP)

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31
Q

How do MTX, TMP, and pyrimethamine inhibit nucleotide synthesis?

A

Inhibit dihydrofolate reductase, indirectly necessary for methylation of dUMP to dTMP.

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32
Q

What does adenosine deaminase deficiency cause? How?

A

SCID. Without ADA, buildup of ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase. Prevents DNA synthesis, and thus lymphocyte count is reduced.

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33
Q

What does HGPRT do?

A

Converts hypoxanthine to IMP and guanine to GMP. Purine salvage.

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34
Q

What does HGPRT deficiency cause? Inheritance pattern? Symptoms?

A

Lesch-Nyan, X-Linked recessive. Defective purine salvage. Results in excess uric acid production. Hyperuricemia, Gout, Pissed off (aggression, self-mutilation), Retardation, dysTonia.

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35
Q

What does allopurinol do?

A

Inhibits xanthine oxidase, which creates uric acid.

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36
Q

What does febuxostat do?

A

Inhibits xanthine oxidase, which creates uric acid.

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37
Q

What does probenicid do?

A

Increases excretion of uric acid in the urine.

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38
Q

What does it mean to say the genetic code is “unambiguous”?

A

Each codon (3 base pairs) specifies only 1 amino acid.

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39
Q

What does it mean to say the genetic code is “degenerate”?

A

Most amino acids are coded by multiple codons.

40
Q

Which amino acids are encoded by only 1 codon?

A

Methionine (AUG) and Tryptophan (UGG).

41
Q

What does it mean to say the genetic code is “commaless or nonoverlapping”? What’s the exception?

A

Read from a fixed starting point as a continuous sequence of bases. Exception: viruses.

42
Q

What does it mean to say the genetic code is “universal”? The exception in humans?

A

Genetic code is conserved throughout evolution - same codons correspond to amino acids in different organisms. Exception: mitochondria have some variants.

43
Q

DNA helicase

A

Unwinds DNA template at replication fork

44
Q

Single-stranded binding proteins

A

Prevents strands from reannealing

45
Q

DNA topoisomerases

A

Create single/double stranded break in helix

46
Q

How do fluoroquinolones disrupt DNA replication?

A

Inhibit prokaryotic topo II (DNA gyrase) and topo IV

47
Q

Primase

A

Makes RNA primer on which DNA pol initiates replication

48
Q

DNA polymerase III

A

(Prok). Elongates leading/lagging strands 5’-3’ direction. Exonuclease proofreading activity 3’-5’ direction.

49
Q

DNA polymerase I

A

(Prok). Degrades RNA primer 5’-3’ (exonuclease). Otherwise same functions as DNA pol III.

50
Q

DNA ligase

A

Joins Okazaki fragments by forming phosphdiester bonds within strand of dsDNA.

51
Q

Telomerase

A

Euks only. RNA dependent DNA polymerase that adds DNA to 3’ end of chromosomes to avoid loss of genetic material.

52
Q

What is a “transition” DNA mutation?

A

Purine to purine or pyrimidine to pyrimidine mutation.

53
Q

What is a “transversion” DNA mutation?

A

Purine to pyr or pyr to purine mutation.

54
Q

Silent mutation?

A

Nucleotide substitution but codes for same amino acid. Often base change in 3rd position of codon (wobble).

55
Q

Missense mutation? “Conservative” means what?

A

Nucleotide substitution resulting in changed amino acid (conservative if AA is similar in structure).

56
Q

Sickle disease is caused by what mutation?

A

Missense. Substition of glutamic acid (hydrophilic) with valine (hydrophobic).

57
Q

Nonsense mutation?

A

Nucleotide substitution resulting in early stop codon.

58
Q

Frameshift mutation?

A

Deletion or insertion of number of nucleotides not divisible by 3, resulting in misreading of all subsequent nucleotides. Results in nonfunctional protein usually.

59
Q

Duchenne Muscular dystrophy has what kind of mutation?

A

Frameshift/deletion of gene coding for dystrophin.

60
Q

Three single strand DNA repair mechanisms?

A

Nucleotide excision repair, base excision repair, mismatch repair.

61
Q

What is nucleotide excision repair? What phase of cell cycle does this occur in?

A

Specific endonucleases release oligonucleos containing damaged bases, DNA pol and ligase fill and reseal the gap. Repairs helix-distorting lesions. Occurs in G1 phase.

62
Q

What is the defect in xeroderma pigmentosum?

A

Nucleotide excision repair. Prevents repair of pyrimidine dimers caused by UV light exposure.

63
Q

What is base excision repair? What phase of cell cycle does this occur in?

A

Base specific glycosylase finds altered base and removes it - creating “AP” site (apurinic/apyr). AP-endonuclease removes nucleotides by cleaving 5’ end, lyase cleaves 3’ end. DNA pol and DNA ligase fill in and seal. Occurs throughout cell cycle.

64
Q

What is mismatch repair? What phase of cell cycle does this occur in?

A

Newly synthesized strand is recognized, mismatched nucleotides are removed, and gap is filled and resealed. Occurs mostly in G2 phase of cell cycle.

65
Q

What is the defect in HNPCC?

A

Mismatch repair mechanism.

66
Q

What is non-homologous end joining?

A

Double stranded DNA repair mechanism. Brings together 2 ends of DNA fragments to repair double-stranded breaks. No requirement for homology. Some DNA may be lost.

67
Q

In which diseases are non-homologous end joining repair mechanism mutated?

A

Ataxia telangiectasia, Fanconi anemia.

68
Q

In what direction is DNA/RNA synthesis? Where is the energy source for the bond coming from?

A

5’-3’ direction. Energy source comes from the triphosphate on the 5’ end of the incoming nucleotide. This attaches to the 3’ hydroxyl on previous strand.

69
Q

Why do some drugs blocking DNA replication have modified 3’-OH?

A

Prevents addition of the next nucleotide; terminates the chain.

70
Q

In what direction is mRNA read? In what direction

A

It is READ in 5’ to 3’. (Vs. DNA template strands, which are read 3’ to 5’ so new strand can be built 5’ to 3’).

71
Q

In what direction is protein synthesized?

A

N-terminus to C-terminus.

72
Q

What are mRNA start codons? What do they code for?

A

AUG (rarely GUG). AUG inAUGurates protein synthesis. Euks: methionine (can be removed). Prok: Codes for N-formylmethionine (fMet).

73
Q

Fun fact about fMet?

A

Product of prokaryotic start codon. Stimulates neutrophil chemotaxis.

74
Q

What are the mRNA stop codons?

A

UGA (U Go Away), UAA (U Are Away), UAG (U Are Gone)

75
Q

Promoter region

A

Site where RNA pol II and other tx factors bind to DNA upstream from the gene locus. AT-rich sequence, “TATA box”.

76
Q

Enhancer region

A

Stretch of DNA that alters gene expression by binding transcription factors - not necessarily close to gene whose expression it regulates.

77
Q

Silencer region.

A

Stretch of DNA where negative regulators, “repressors” bind. Not necessarily close.

78
Q

What does RNA polymerase I do?

A

Makes rRNA (ribozyme), most numerous RNA. r for Rampant.

79
Q

What does RNA polymerase II do?

A

Makes mRNA, largest RNA, m for Massive. Opens DNA at promoter site. Makes snRNA.

80
Q

Why are Amanita phalloides mushrooms poisonous?

A

Contain alpha-amantin, which inhibits RNA pol II. Severe hepatoxicity.

81
Q

What does RNA polymerase III do?

A

Makes tRNA, smallest RNA, t for Tiny.

82
Q

What’s different about prokaryotic RNA polymerase?

A

Just one kind, a mulitsubunit complex, makes all 3 kinds of RNA.

83
Q

How does rifampin work?

A

Inhibits prokaryotic RNA polymerase.

84
Q

What does actinomycin D inhibit?

A

RNA polymerase in both prokaryotes and eukaryotes.

85
Q

What are snRNPs?

A

Sm proteins + snRNA. Used in splicing.

86
Q

What is splicing? What are the steps?

A

Removal of introns from pre-MRNA. 1) snRNPs attach to introns, form “sliceosome”. 2) Lariat/loop intermediate is formed. 3) Loop is removed, exons are joined.

87
Q

What are the classic Abs in SLE to?

A

Anti-Smith, anti Sm proteins that are part of snRNPs.

88
Q

What are anti-U1 RNP antibodies?

A

Abs to snRNPs, found in mixed connective tissue disease.

89
Q

What are the four arms of tRNA, what do they attach to?

A
  1. Acceptor stem, 5’CCA-3’ is amino acid acceptor site.
  2. T arm contains thymine psuedouracil cytosine - binds ribosome.
  3. D arm contains dihydrouracil, binds aminoacyl-tRNA synthetase.
  4. Anti-codon end is opposite acceptor stem.
90
Q

What is the function of aminoacyl t-RNA synthetase?

A
  1. Specific to an amino acid, is the matchmaker molecule to scrutinize amino acid before and after tRNA binds.
  2. If wrong, breaks bond. If correct, uses ATP to charge amino acid - tRNA bond, has energy for formation of peptide bond.
91
Q

What is the “initiation” step of translation?

A

GTP hydrolysis, initiation factors help assemble 40S with initiator tRNA. IFs released when mRNA and 60S subunit assemble.

92
Q

What are the subunits for Eurkaryotes and Prokaryotes?

A

40S, 60S –> 80S (Even, Euks).

30S, 50S –> 70S (Odd, prOkaryotes)

93
Q

What are the three steps of elongation?

A
  1. aminoacyl-tRNA binds A site
  2. ribozyme catalyzes peptide bond at P site, transfers growing polypeptide to amino acid in A site.
  3. Ribosome advances towards 3’ end, shifting peptidyl tRNA to P site (translocation). New tRNA comes to A site.
  4. E site is where Empty tRNA is while it Exits.
94
Q

When does termination of protein synthesis occur?

A

Stop codon is recognized by release factor, and completed polypeptide is released.

95
Q

What is trimming?

A

Removal of N or C terminal propeptides from zymogen to generate mature protein, e.g, trypsinogen to trypsin.

96
Q

What are chaperone proteins?

A

Intracellular protein involved in facilitating/maintaining protein folding. Eg heat shock proteins.

Biochemistry (11 decks)

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