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Step One Prep > Biochemistry-Molecular > Flashcards

Biochemistry-Molecular Flashcards

1
Q

Chromatin Structure

A
  1. Negatively charged DNA wrapped around positively charged histones
  2. Histone octomer with DNA= nucleosome. Rich in lysine and arginine. H2A, H2B, H3, H4
    H1- linker
  3. DNA and histone synthesis in S Phase
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2
Q

Heterochromatin

A

Highly condensed and transcriptionally inactive

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3
Q

Euchromatin

A

Less condensed and DNA is accessible. Transcriptionally active

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4
Q

DNA methylation

A

Differentiates between new and old strand. Methylation at cytosines and adenine . Allows for mismatch repair.
CpG lslands repress transcription= muted.

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5
Q

Histone methylation

A

Most of the time makes DNA mute

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6
Q

Histone acetylation

A

Relaxes DNA coiling and makes DNA active

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7
Q

Nucleotides

A

PURines (AG)- Pur As Gold
PYrimidies (CUT)- CUT Py
Thymies are methylated

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8
Q

What does deamination of cytosine create?

A

Uracil

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9
Q

Which bond is stronger G-C or A-T?

A

G-C because it has three hydrogen bonds as opposed to only two in A-T. Increased G-C = increased melting temperature

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10
Q

What three amino acids are necessary for purine synthesis?

A

Glycine, Aspartate, and Glutamate

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11
Q

What is a nucleoside?

A

base+(deoxy)ribose Sugar

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12
Q

What is a nucleotide?

A

Base+ (deoxy)ribose sugar+ Phosphate

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13
Q

Describe purine synthesis.

A

Start with a sugar (ribose 5-phosphate) + Phophoribsoyl Pyrophosphate (PRPP) and then add base.

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14
Q

Describe pyrimidine synthesis.

A

Make a temporary base (orotic acid). Then add sugar + phosphate (PRPP). Then modify the base

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15
Q

What is the function of ribonucleotide reductase?

A

Converts ribonucleotides to deoxyribonucleotides

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16
Q

What is the role of Leflunomide?

A

Inhibits the dihydroorotate dehydrogenase (important in the orotic acid production in pyrimidine synthesis)

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17
Q

What is the role of mycophenolate and ribavirin?

A

They inhibit IMP dehydrogenase (important in purine synthesis pathway)

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18
Q

What is the function of hydroxyurea?

A

Inhibits ribonucleotide reductase(enzyme important in pyrimidine synthesis)

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19
Q

What is the function of 6-mercaptopurine and prodrug azathioprine?

A

Inhibition of de nove purine synthesis

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20
Q

What is the function of 5-fluorouracil (5-FU)?

A

Inhibits thymidylate synthase which decreases deoxythymidine momophosphate which results in a decrease in dTMP

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21
Q

What is the function of methotrexate, trimethoprim and pyrimethamine?

A

All inhibit the function of dihydrofolate reductase (decrease dTMP) in humans, bacteria, and protozoa, repectively.

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22
Q

Describe Adenosine deaminase deficiency.

A

Creates an excess of ATP and dAT imbalances nucleotide pool via feedback inhibition of ribonucleotide reducatase and prevents DNA synthesis and thus low lymphocyte count.

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23
Q

What is one major cause of autosomal recessive SCID?

A

Adenosine deaminase deficiency

24
Q

What is hypoxanthine-guanine phosphoribosyltransferase?

A

An enzyme that converts hypoxanthine to IMP and Guanine to GMP.

25
Q

What enzyme is absent in Lesch-Nyhan syndrome?

A

Hypoxanthine-guanine phosphoribosytransferse which results in an excess of uric acid production and de novo synthesis of purine production

26
Q

What is the inheritance pattern of Lesch-Nyhan syndrome?

A

X-linked recessive

27
Q

What are the symptoms of Lesch-Nyhan syndrome?

A 
Results from HGPRT deficiency:
H-Hyperuricemia
G- Gout
P-Pissed off (aggression and self-mutilation)
R- Retardation
T-dysTonia
28
Q

What enzyme does fluoroquinolones inhibit?

A

DNA gyrase or prokaryotic topoisomerase II

29
Q

Please define a transition mutation.

A

A transition mutation is a mutation that changes a purine to another purine (e.g. A to G) or pyrimidine to antoher pyrimidine (C to T)

30
Q

Please define a transversion mutation.

A

A mutation that results in a change of a purine to a pyrimidine or vica versa.

31
Q

Please give an example of a missense mutation

A

Sickle cell anemia

32
Q

Please give an example of a frameshift mutation

A

Duchenne muscular dystrophy

33
Q

Please describe nucleotide excision repair mechanism and what type of mutations they fix.

A

Specific endonucleases release the oligonucleotide-containing damage bases; DNA polymerase and ligase fil and reseal the gap respectively. Repairs bulky helix-distorting lesions

34
Q

Describe xeroderma pigmentosum and what mutation causes it.

A

Mutation: Nucleotide excision repair mechanism so cell cannot repair pyrimidine dimers. Cuases early melanoma, basal cell carcinoma, and squamous cell carcinoma

35
Q

Please describe base excision repair and what type of mutations they fix.

A

Base-specific glycosylase recognizes altered base and creates AP site. ONe or more nucleotides are removed by AP-endomucleases, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA polymerase-beta fills the gap and DNA ligase seals it. It fixes spontaneous deamination

36
Q

Please describe mismatch repair.

A

Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed.

37
Q

Please name a disorder caused by a defect in mismatch repair mechanism.

A

Hereditary nonpolyposis colorectal cancer (HNPCC)

38
Q

Please describe nonhomologous end joining

A

Brings together 2 ends of DNA fragments to repair double-stranded breaks. Require no homology

39
Q

What causes ataxia telangiectasia?

A

mutation in nonhomologous end joining

40
Q

What do the start codons code for in eukaryotes and prokaryotes?

A

Eukaryotes- mthionine

Prokaryotes- formylmethionine

41
Q

Name the three stop codons

A

UGA- U Go Away
UAA- U Are Away
UAG- U Are Gone

42
Q

Describe a promoter.

A

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

43
Q

Enhancers/ Silencer

A

Stretch of DNA that alter gene expression. Can be thousands of bp up or downstream or in introns.

44
Q

Name and describe the functions of eukaryotic RNA polymerases.

A

RNA Pol I- makes rRNA
RNA Pol II- makes mRNA
RNA Pol III- makes tRNA

45
Q

Name the compound found in the death cap mushroom that inhibits RNA polymerase II.

A

Alpha-amanitin. Causes severe hepatotoxicity. Symptoms appear between 1-2 weeks

46
Q

How many RNA polymerases do prokaryotes have?

A

One

47
Q

Name three modifications that occur in the maturation process of mRNA.

A

5’ methylguanosine cap
3’ poly A tail
Splicing of introns

48
Q

What makes up the sliceosome?

A

Primary transcript + small nuclear ribonucleoproteins(snRNP)

49
Q

What causes SLE?

A

Antibodies to spiceosomal snRNPs

50
Q

Anti-U1 RNP antibodies cause…

A

mixed connective tissue disease

51
Q

Name the parts their function in tRNA

A

T Loop- recognition of ribosome
D Loop- recognition of correct aminoacyl tRNA synthetase
Anti-Codon- recognizes mRNA codon
3’ CCA- binds amino acid

52
Q

Describes aminoacyl-tRNA synthetase

A

Enzyme that loads amino acid onto the 3’ end of tRNA. If it adds the wrong amino acid it will hydrolyze and take it off

53
Q

Translation-Initiation

A

Initiated by GTP hydrolysis; initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex

54
Q

Translation- Elongation

A
  1. Aminoacyl-tRNA binds to A site
  2. rRNA catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site
  3. Ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl tRNA to P site
55
Q

Translation- Termination

A

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

56
Q

Name three posttranslational modification

A
  1. Trimming
  2. Covalent alterations
  3. Chaperone protein
57
Q

Name 7 covalent alterations that can be made on a protein.

A
  1. Phosphorylation
  2. Dephosphorylation
  3. Carboxylation
  4. Hydroxylation
  5. Methylation
  6. Acetylation
  7. Ubiquitination

Step One Prep (11 decks)

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