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Biochemestry > Molecular > Flashcards

Molecular Flashcards

1
Q

What are the stop codons

A

UAA
UGA
UAG

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2
Q

What happens when a ribosome encounters a stop codon

A

Releasing factor proteins bind to the ribosome and stimulate release of the formed polypeptide chain and dissolution of the ribosome-mRNA complex

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3
Q

What is the function of elongation factors

A

Facilitate tRNA binding and translocation steps of protein synthesis

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4
Q

Enzyme in charge of converting dUMP to dTMP

A

Thymidylate synthase

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5
Q

Cofactor needed by thymidylate synthase

A

5,10-methylene THF

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6
Q

Name the 2 types of silencing RNA

A
  1. micro RNA (miRNA)

2. small interfering RNA (siRNA)

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7
Q

Most important aminoacid in caspases and their function

A
  1. Cysteine

2. Cleavage of aspartic acid residues

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8
Q

Molecular charge of the histone octamer that allows it to attach to DNA

A

Positive (DNA has a negative charge)

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9
Q

Predominant aminoacids found in histones

A

Arginine and lysine

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10
Q

Histone in charge of stabilizing the chromatin fiber

A

H1

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11
Q

State of chromatin that appears darker on EM

A

Heterochromatin

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12
Q

State of chromatin that is highly methylated, and therefore, sterically inaccesible (transcriptionally inactive)

A

Heterochromatin

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13
Q

Barr bodies (inactive X chromosomes) exist in which state of chromatin

A

Heterochromatin

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14
Q

State of chromatin that is highly acetylated, and therefore, sterically accesible (transcriptionally active)

A

Euchromatin

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15
Q

Part of the DNA that, when methylated, represses transcription

A

CpG islands

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16
Q

Components of nucleosides

A

Base + (deoxy)ribose

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17
Q

Components of nucleotides

A

Base + (deoxy)ribose + phosphate

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18
Q

How many rings do purines and pyrimidines have

A

Purines have 2, while pyrimidines have 1

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19
Q

Deamination of cytosine makes…

A

Uracil

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20
Q

Deamination of adenine makes…

A

Guanine

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21
Q

Methylation of uracil makes…

A

Thymine

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22
Q

How many H bonds does the G-C bond have

A

3

*Therefore, if DNA is high in G-C bonds, melting temperatura will increase, making DNA more resistant

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23
Q

How many H bonds does the A-T bond have

A

2

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24
Q

Enzyme inhibited by leflunomide

A

Dihydroorotate dehydrogenase

*Part of the pyrimidine synthesis pathway

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25
Q

Enzyme deficient in a patient with orotic aciduria but without hyperammonemia

A

UMP synthase

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26
Q

Pyrimidine synthesis pathway enzyme that is inhibited by hydroxyurea

A

Ribonucleotide reductase

*Inhibited reaction: UDP to dUDP

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27
Q

Pyrimidine synthesis pathway enzyme that is inhibited by 5-FU

A

Thymidylate synthase

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28
Q

Pyrimidine synthesis pathway enzyme that is inhibited by methotrexate/trimethoprim/pyrimethamine

A

Dihydrofolate reductase (therefore, reducing deoxythymidine phosphate)

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29
Q

Purine synthesis pathway enzyme that is inhibited by 6-MP (and its prodrug, azathioprine)

A

PRPP amidotransferase

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30
Q

Purine synthesis pathway enzyme that is inhibited by mycophenolate and ribavirin

A

Inosine monophosphate dehydrogenase

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31
Q

Pathogenesis of adenosine deaminase deficiency

A

ADA is required for degradation of adenosine and deoxyadenosine, its deficiency causes an increase in dATP, which is toxic to lymphocytes

*One of the major causes of autosomal recessive SCID

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32
Q

Pathogenesis of Lesch-Nyhan syndrome

A

Defective purine salvage due to absent HGPRT, resulting in excessive uric acid and de novo purine synthesis

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33
Q

Signs and symptoms of Lesch-Nyhan syndrome

A
  • Hyperuricemia
  • Gout
  • Pissed off (aggression and self mutilation)
  • Retardation (intelectual disability)
  • dysTonia
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34
Q

Lesch-Nyhan syndrome treatment

A

Allopurinol or febuxostat

*They inhibit PRPP amidotransferase (as 6-MP), thereby reducing purine synthesis

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35
Q

Define the “wobble” feature of the genetic code

A

This refers to the fact that codons that differ in 3rd position may code for the same tRNA/aminoacid (base pairing is usually only required in the first 2 nucleotide positions of mRNA codon)

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36
Q

Organisms that can have multiple origins of replication

A

Eukaryotes

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37
Q

DNA replication direction

A

5’ to 3’ direction

38
Q

Enzyme that unwinds DNA template at replication fork

39
Q

Gene that codes for DNA helicase

A

BLM gene

*Deficiency leads to Bloom syndrome (growth retardation, facial abnormalities, photosensitive skin rash, and immunodeficiency)

40
Q

Molecule that prevents DNA strands from reannealing during DNA replication

A

Single-stranded binding proteins

41
Q

Molecules that create breaks in the DNA helix during DNA replication to add or remove supercoils

A

Topoisomerases

42
Q

Drugs that inhibit eukaryotic topoisomerase 1

A

Irinotecan/topotecan

43
Q

Drugs that inhibit eukaryotic topoisomerase 2

A

Etoposide/teniposide

44
Q

Antibiotics that inhibits prokaryotic topoisomerase 2 (DNA gyrase) and 4

A

Fluoroquinolones

45
Q

Molecule that adds an RNA primer on the template strands during DNA replication

46
Q

Molecule that during DNA replication, elongates leading strand by adding deoxynucleotides to the 3’ end

A

DNA polymerase 3 (only found in prokaryotes)

47
Q

Molecule active during DNA replication that has 5’ to 3’ synthesis and 3’ to 5’ exonuclease (proofreading) activities

A

DNA polymerases

48
Q

Molecule active during DNA replication (in prokaryotes only) that degrades the RNA primer and replaces it with DNA

A

DNA polymerase 1

*Excises primer with 5’ to 3’ exonuclease (only DNA polymerase with this activity)

49
Q

Molecule that catalyzes the formation of a phosphodiesther bond within a strand of double-stranded DNA during DNA replication (joins Okazaki fragments)

A

DNA ligase

50
Q

RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid los of genetic material

A

Telomerase

51
Q

Eukaryotic molecule that polymerizes the primer in eukaryotes

A

alpha DNA polymerase

52
Q

Most severe DNA mutation

A

Frameshift

53
Q

For point mutations, a change from purine to purine or pyrimidine to pyrimidine is called…

A

Transition

54
Q

For point mutations, a change from purine to pyrimidine (or viceversa) is called…

A

Tranversion

55
Q

What is a silent mutation

A

Nucleotide substitution that codes for the same aminoacid (often in 3rd position of codon)

56
Q

What is a missense mutation

A

Nucleotide substitution resulting in changed aminoacid (called conservative if new aminoacid is similar in chemical structure)

i.e. Sickle cell disease (substitution of glutamic acid with valine)

57
Q

What is a nonsense mutation

A

Nucleotide substitution resulting in early stop codon

  • Usually results in a nonfunctional protein
    i. e. beta talasemia major
58
Q

What is a frameshift mutation

A

Its a deletion or insertion of a number of nucleotides NOT DIVISIBLE BY 3, resulting in misreading of all nucleotides downstream

  • Protein may be shorter or longer, and its function may be disrupted or altered
    i. e. Duchenne muscular dystrophy, Tay-Sachs disease
59
Q

What is an in-frame mutation

A

Its a deletion or insertion of a number of nucleotides DIVISIBLE BY 3

i.e. Cystic fibrosis

60
Q

Type of mutation that results in a retained intron in the mRNA

A

Mutation at a splice site

61
Q

Región of the DNA recognized by RNA polymerase

A

Promoter region

62
Q

Mechanism of DNA repair in charge of repairing bulky helix-distorting lesions

A

Nucleotide excision repair

63
Q

Molecules used in nucleotide excision repair

A
  1. Specific endonucleases (reléase oligonucleotides containing damaged bases)
  2. DNA polymerase
  3. DNA ligase
64
Q

Nucleotide excision repair occurs during which phase of the cell cycle

65
Q

Defective nucleotide excision repair results in what patholgy

A

Xeroderma pigmentosum

66
Q

Mechanism of DNA repair in charge of repairing spontaneous/toxic deamination

A

Base excision repair

67
Q

Molecules used in base excision repair

A
  1. Glycolase (removes altered base and creates AP site)
  2. AP-Endonuclease (removes one or more nucleotides by cleaving the 5’ end)
  3. Lyase (cleaves de 3’ end)
  4. DNA Polymerase beta (fills the gap)
  5. Ligase (seals the thing)

“GEL PLease”

68
Q

DNA repair process deficient in Lynch syndrome

A

Mismatch repair

69
Q

DNA repair process that carries the risk of losing genetic material

A

Nonhomologous end joining

*Brings together 2 strands of DNA fragments to repair double-stranded breaks

70
Q

Prokaryotic aminoacid that is coded by the start codon and that, additionally, stimulates neutrophil chemotaxis

A

N-formylmethionine (fMet)

71
Q

Function of promoter regions in the regulation of gene expression

A

Sites where RNA polymerase 2 and other transcription factors bind to DNA upstream from gene locus

*AT-rich sequences (TATA and CAAT boxes)

72
Q

How many base pairs away are CAAT and TATA boxes from the site of transcription start

A
  • CAAT: 75 bp

* TATA: 25 bp

73
Q

Regions of DNA that alter gene expression by binding positive (transcription factors) or negative regulators

A

Enhancers and silencer

*May be located close to, far from, or within the gene

74
Q

Mechanism through which transcription factors alter gene expression

A

They facilitate bending of DNA

75
Q

Primary site of ribosomal RNA transcription

76
Q

State the types of RNA transcribed by each type of euokaryote RNA polymerase

A
  • RNA polymerase 1: rRNA
  • RNA polymerase 2: mRNA
  • RNA polymerase 3: tRNA

*1, 2, and 3 are numbered in the same order that their products are used in protein synthesis

77
Q

RNA polymerase inhibited by alpha-amanitin

A

RNA polymerase 2

78
Q

Modifications to hnRNA that take place in the nucleus before it can be considered mRNA

A
  1. Capping of the 5’ end (addition of 7-methylguanosine cap)
  2. Polyadenylation of 3’ end (~200 A’s)
  3. Splicing out of introns
79
Q

Cytosolic sites which contain exonucleases, decapping enzymes, and microRNAs; and where mRNAs can be stored for future translation

80
Q

Name the steps in pre-mRNA splicing

A
  1. Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form the spliceosome
  2. Lariat-shaped (looped) intermediate is generated
  3. Lariat is released to precisely remove intron and join 2 exons
81
Q

Antibodies to snRNPs (anti-Smith) are specific for what pathology

82
Q

What is the function of microRNAs

A

Regulate gene expression by targeting the 3’ untranslated region of specific mRNAs for degradation or translation repression

83
Q

Part of the tRNA that covalently binds aminoacids

A

The 3’ end is the acceptor stem, it is a CCA end

84
Q

tRNA arm in charge of binding to the ribosome

A

T-arm

*Contains ribothymidine, pseudouridine, cytidine / T-arm tethers tRNA molecule to ribosome

85
Q

tRNA arm necessary for tRNA recognition by the correct aminoacyl tRNA synthetase

A

D-arm

*Contains dihydrouridine residues

86
Q

Name the 2 groups of posttranslationsl modifications done to mRNA

A
  1. Trimming (removal of N- or C- terminal propeptides from zymogen to generate mature protein)
  2. Covalent alterations
87
Q

Function of chaperone proteins

A

Intracellulr proteins involved in facilitating and/or maintaining protein folding

88
Q

Enzyme required for the degradation of adenosine and deoxyadenosine into inosine

A

Adenosine deaminase (ADA)

89
Q

One of the enzymatic deficiencies that can lead to severe combined immunodeficiency (SCID) that can be found in the purine salvage pathwat

A

Adenosine deaminase (ADA)

90
Q

Substrate that is accumulated in adenosine deaminase (ADA) deficiency that inhibits ribonucleotide reductase

A

dATP

*This leads to inhibition of both nucleotide synthesis pathways

91
Q

Cell types that are most affected by adenosine deaminase (ADA) deficiency

A

T- and B-cells

Biochemestry (7 decks)

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