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ZBiochem > Molecular EC > Flashcards

Molecular EC Flashcards

1
Q

Which is transcriptionally active: heterochromatin or euchromatin?

A

Euchromatin is active

HeteroChromatin is Highly Condenced

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2
Q

What do DNA methylation and acetylation do?

A

Methylation makes DNA Mute (inactive)

Acetylation makes DNA Active

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3
Q

What amino acids are required for purine synthesis?

A

GAG

Glycine, Aspartate, Glutamine

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4
Q

What does ribonucleotide reductase do?

A

reduces nucleotides to deoxy forms

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5
Q

What cofactors are required for ribonucleotide reductase action?

A

thioredoxin and NADPH

*oxidized thioredoxin reduced/recycled by tioredoxin reductase

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6
Q

What is the rate limiting step of purine synthesis?

A

PRPP synthetase

*converts Ribose-5-P to PRPP

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7
Q

What ensures balance is maintained in purine synthesis? (2 things)

A

Cross regulation (GMP requires ATP and vice versa)

Each pathway has end-product inhibition

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8
Q

What is the rate-limiting step of pyrimidine synthesis?

A

CPS-II (formation of carbamoyl phosphate from CO2, glutamine and ATP)

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9
Q

What nucleotides is IMP a precursor to?

A

AMP and GMP

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10
Q

What nucleotides are UMP a precursor to?

A

CTP and TMP

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11
Q

What converts dUMP to dTMP?

A

Thymidylate synthase

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12
Q

What causes Orotic aciduria?

How does it present?

What is the treatment?

A

Defect in UMP synthase (converts orotic acid to UMP)

Presents as megaloblastic anemia UNRESPONSIVE to B12 or folate

Treat with lifetime uridine supplementation

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13
Q

What is the sequence from AMP to Uric acid?

A

AMP–>Adenosine–>Inosine–>Hypoxanthine–>Xanthine–> Uric acid

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14
Q

What is the sequence from GMP to Uric acid?

A

GMP–>Guanine–>Xanthine–>Uric acid

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15
Q

What is SCID?

What is its mechanism?

A

Severe Combined Immunodeficiency Disease

Adenosine deaminase deficiency (inability to convert adenosine to inosine)

  • ATP/GTP imbalance inhibits ribonucleotide reductase
  • prevents DNA synthesis
  • decreased lymphocytes count
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16
Q

What is Lesch-Nyhan syndrome?

What is its mechanism?

What are the findings?

A

Absence of HGPRT (& thus purine salvage)
“He’s Got Purine Recovery Troubles”

Results in excess uric acid production

Retardation
Self-mutilation
Aggression
Hyperurecemia/gout
Choreoathetosis
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17
Q

What is a silent point DNA mutation?

A

a mutation that codes for the same amino acid

often a change in the 3rd a.a. (tRNA wobble)

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18
Q

What is a missense mutation?

A

Wrong amino acid but similar chemical structure

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19
Q

What is a Nonsense mutation?

A

Change resulting in easly STOP codon

“STOP the NONSENSE”

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20
Q

What is a frameshift mutation?

A

Misreading all nucleotides downstream

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21
Q

Where are the p53 and RB genes located?

A

p53 is on chromosome 17

RB is on chromosome 13

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22
Q

Describe Mismatch Repair

A

Mismatch repair enzymes recognize mismatched nucleotides

GATC endonuclease makes incision in daughter strand
Removed and gap filled

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23
Q

Mutations in mismatch repair enzymes gives rise to what disease?

A

HNPCC (hereditary nonpolyposal colorectal cancer)

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24
Q

Describe base excision repair

A

Cytosine is spontaneously deaminated to uracil

Uracil DNA glycosylase removes Uracil

AP endonucleases cut DNA and nucleotide is replaced

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25
Q

Describe nucleotide excision repair

A

thymidine dimmers caused by UV light are removed by excision endonucleases

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26
Q

What is Xeroderma pigmentosum

A

Caused by a mutation in excision endonucleases responsible for repairing thymidine dimers

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27
Q

Describe direct DNA repair

A

Alkylation agents (temozolide) cause methylation of Guanine.

MGMT repairs (permanently inactivated and can be depleted)

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28
Q

What is nonhomologous end joining?

A

Repair of double stranded DNA breaks

Caused by iodinizing radiation or free radical oxidation

Mutated in ataxia telangiectasia

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29
Q

What phase of the cell cycle to 5-FU and Methotrexate act?

What is the mechanism?

A

S-phase specific

Inhibit dTMP synthesis to block DNA replication
(5-FU inhibits thymidylate synthase)
(Methotrexate inhibits DHF reductase)

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30
Q

In what part of the cell cycle do Bleomycin and Etoposide act?

By what mechanism?

A

S and G2 phases

Inhibit topoisomerase II (preventing strand sepparation)

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31
Q

What is the mechanism of Cyclophosphamide and Nitosoureas?

A

Alkylating agents that lead to copying errors and expression of abnormal proteins

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32
Q

What is the mechanism of Doxorubicin and Actinomycin D?

A

Intercalated into DNA rand block DNA/RNA polymerases

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33
Q

What phase of the cell cycle do vinca alkaloids (vincristine and paclitaxel) work?

What are their mechanisms?

A

M-phase specific

Vincristine inhibits mitotic spindle formation

Paclitaxel inhibits mitotic spindle breakdown

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34
Q

BCL2 proto oncogene function and associated tumors

A

Inhibits apoptosis

Mutated in follicular B cell lymphoma

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35
Q

ERBB2 proto oncogene function and associated tumors

A

Binds epidermal growth factor

Breast
Ovarian
Stomach

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36
Q

MYC proto oncogene function and associated tumors

A

Activates transcription

Burkitt’s Lymphoma
Neuroblastoma

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37
Q

RAS proto oncogene function and associated tumors

A

G protein that transducers growth factor signals

Bladder
Lung
Colon
Pancreas

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38
Q

APC tumor suppressor gene function and associated tumors

A

Inhibits MYC expression

FAP (familial Adenomatous Polyposis)
Colorectal cancer

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39
Q

BRCA1 and BRCA2 tumor suppressor gene function and associated tumors

A

DNA repair

BRCA1 
Breast 
Ovary
Colon
Prostate

BRCA2
Male and female breast

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40
Q

NF1 and NF2 tumor suppressor gene function and associated tumors

A

Control intra cellular signaling

Neurofibromatosis: optic nerve gliomas, meningioma, acoustic neuroma, pheochromocytoma

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41
Q

TP53 tumor suppressor gene function and associated tumors

A

Mediates G1 arrest and apoptosis

Li-Fraumeni
Breast
Brain
Leukemia
Sarcoma
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42
Q

RB1 tumor suppressor gene function and associated tumors

A

Mediates G1 arrest

Retinoblastoma
Osteosarcoma
Breast cancer

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43
Q

WT1 tumor suppressor gene function and associated tumors

A

Represses transcription in developing kidney

Wilm’s tumor

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44
Q

Ataxia telangiectasia

A

Defective DNA repair (double stranded breaks)

Lymphoma

Cerebellar ataxia; dilation of blood vessels in skin and eyes
Immunodeficiency (B and T cells)

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45
Q

Bloom’s syndrome

A

Defective DNA repair

Carcinomas, Leukemias, Lymphoma

Facial telangiectasia
Growth retardation
Immunodeficiency

46
Q

Fanconi’s anemia

A

DNA repair defect

Leukemia

Aplastic anemia
Pancytopenia
Congenital abnormalities

47
Q

HNPCC (hereditary nonpolyposis colorectal cancer)

A

Defective DNA repair (mismatch repair)

Colon, ovary

Tumors before 40

48
Q

Xeroderma pigmentosum

A

Defective DNA repair (nucleotide excision repair of thymidine dimers)

BCC, SCC, malignant melanoma

Severe skin lesions

49
Q

What is a pseudogene?

A

Produced by a retrovirus DNA from mRNA

Cannot be expressed (lack promoter and introns)

50
Q

What is a Transposon (jumping gene)?

A

DNA sequences that insert themselves into different areas of the genome

51
Q

What is a Retrotransposon?

What are examples of genetic diseases caused by Retrotransposons?

A

Jumping genes that use reverse transcriptase

Can prevent the expression of normal proteins

ei. Hemophilia and Duchenne Muscular Dystrophy

52
Q

What are some drugs that inhibit the G2 phase of the cell cycle?

A

Etoposide and Bleomycin

inhibit the synthesis of tubulin

53
Q

What are some drugs that inhibit the S phase of the cell cycle?

A

5-FU and Methotrexate

Inhibit DNA synthesis

54
Q

What are some drugs that inhibit the M phase of the cell cycle?

A

Colchicine
Paclitaxel
Vinca alkaloids

55
Q

What are CDKs and Cyclins?

A

CDKs phosphorylate proteins and activate them to promote cell cycle progression

Cyclins bind CDKs and activate them

56
Q

What are p53 and RB?

A

p53 inhibits G1 to S progression

UN-phosphorylated RB also inhibits G1 to S progression

57
Q

What is DNA Gyrase (topoisomerase II)?

A

Relaxes NEGATIVE supercoils in DNA replication

58
Q

What is DNA Helicase?

A

Separates DNA strands

59
Q

What are Single Stranded Binding Proteins?

A

Prevent strand from re-annealing

60
Q

What is DNA primase?

A

Makes RNA primer

DNA polymerase III can initiate from

61
Q

What is DNA polymerase III?

A

Elongates leading strand

Exonuclease activity “proofreads”

62
Q

What is DNA ligase?

A

Seals Okazaki fragments

63
Q

What is telomerase?

A

Adds DNA to 3’ end to maintain chromosome length

somatic cells do not have telomerase-aging

64
Q

Types of RNA and polymerases used to synthesize

A

rRNA (rampant)&raquo_space; RNA polymerase I
mRNA (massive)&raquo_space; RNA polymerase II
*inhibited by alpha-amanitin
tRNA (tiny) &raquo_space; RNA polymerase III

65
Q

What antibiotic inhibits prokaryotic RNA polymerase?

A

Rifampin

66
Q

What are 3 common sequences in the eukaryotic promoter?

A

TATA (binds TBP)
CAAT (binds NF1)
CG (binds SP1)

67
Q

hnRNA

A

primary mRNA transcript containing coding and noncoding sequences
(before introns are removed via splicing)

68
Q

What is the purpose of the cap and tail of the mRNA?

A

7-methylguanosine CAP orients mRNA on the ribosome

Poly(A) tail increases the half life

69
Q

snRNPs

A

aggregate at introns forming spliceosomes

SLE - autoantibodies against snRNPs

70
Q

lac operon: Low lactose, low glucose

A

No transcription

Repressors inhibit expression

71
Q

lac operon: High lactose, low glucose

A

Transcription

Allolactose inducer
No glucose –> cAMP elevated –> CAP-cAMP complex stimulates transcription

72
Q

lac operon: High lactose, High glucose

A

No transcription

Allolactose inducer
Glucose–>cAMP low–> no transcription stimulation

allows glucose to be used up first

73
Q

Describe drugs resistance in cancer cells due to amplication

A

The gene for dihydro folate reductase can be increased to levels 3000 times the lethal dose of methotrexate in normal cells.

74
Q

Name two examples of alternative splicing

A

Fibronectin : extracellular matrix, cell surface, and soluble all from same mRNA
*Removal of carboxy-terminal converts from membrane to soluble protein

IgG heavy chain in B cells

75
Q

mRNA editing of apolipoprotein B

A

In the GUT: ApoB-48 do not bind LDLR, encoded not to include binding domain

In the LIVER: Apo-100 has LDLR binding domain

76
Q

What are some examples of autosomal dominant diseases?

A 
Familial hypercholesterolemia, 
Marfan's, 
Osteogenesis imperfecta, 
Huntington's
von Williebrand's
Hereditary spherocytosis
Adult poly cystic kidney disease
Neurofibromatosis
77
Q

What are some examples of autosomal recessive diseases?

A 
Inborn errors of metabolism
Sickle cell
Cystic fibrosis
Adrenogenital syndrome
Wilson's disease
78
Q

What are some examples of X lined diseases?

A 
Duchenne's muscular dystrophy
Fabry's disease
Hemophilia A and B
Hunter's syndrome
Lesch-Nyhan syndrome
G6PD deficiency
79
Q

What antibiotics work on the 30S subunit?

A

Tetracyclins: Bind 30S and block incoming aminoacyl tRNA

Aminoglycosides: Inhibit 30S subunit

Streptomycin: Inhibit 30S subunit

80
Q

What antibiotics work on the 50S subunit?

A

Chloramphenicol:Inhibits peptidyltransferase activity of 50S

Erythromycin: Inhibits 50S translocation along mRNA

Clindamycin: Inhibits 50S translocation along mRNA

81
Q

What are some antibiotics that work on eukaryotic 60S subunit?

A

Shiga toxin
Shiga-like toxin (EHEC)
Ricin

~All cleave 28S of 60S subunit which prevents binding of aminoacyl tRNA

82
Q

How does diptheria toxin inhibit protein synthesis?

A

Inhibits EF-2 (elongation factor 2), inhibiting ribosome translocation

83
Q

What antibiotic targets eukaryotic peptidyl transferase?

A

Cyclohexamide: fungicidal and rat repellant

84
Q

Describe polypeptide translocation to the RER

A

Ribosome attaches to ER membrane via SRP

Translocon: directs into ER lumen

Amino end enters first, signal sequence cleaved

Msy be glycosylated in lumen

85
Q

I-Cell disease

A

Cannot form mannose-6-phosphate on enzymes targeted for lysosomes
~deficient in phosphotransferase needed to add M6P

Enzymes produced normally, but secreted into blood instead of lysosome

*presents with coarse facial features, clouded corneas, restricted joint movement.

86
Q

Ubiquitin

A

Tags proteins to be degraded in proteosome

87
Q

Vesicular trafficking proteins

A 
COP1: golgi>golgi (retrograde)
          golgi>ER
COPII: golgi>golgi (anterograde)
          ER>golgi
Clathrin:transGolgi>lysosomes
            plasma membrane>endosomes
88
Q

Molecular motor proteins

A

Dyenein: Retrograde microtubule (+>-)

Kinesin: Anterograde microtubule (->+)

89
Q

Chediak-Higashi syndrome

A

Pyogenic infections
Partial albinism
Peripheral neuropathy

Mutation in lysosome trafficking regulatory gene (LYST)

90
Q

Drugs that act on microtubules

A 
Mebendazole/thiabendazole (antihelminthic)
Griseofulvin (antifungal)
Vincristine/vinblastine (anti-cancer)
Paclitaxel (anti breast cancer)
Colchicine (anti-gout)
91
Q

Kartagener’s syndrome

A

immotile cilia
Dyenein arm deficiency

Infertility
Bronchiectasis
Recurrent sinusitis
Associated with siatus inversus

92
Q

Drugs that inhibit Na/K pump

A

Ouabain: inhibits binding to K site

Cardiac glycosides (digoxin/digitoxin)
directly inhibit ATPase
Leads to decreased Na/Ca exchange
Increased intracellular Ca and contractility
93
Q

Collagen types

A

Type I: Bone, Skin, Tendon
Type II:Cartilage
Type III: Reticulin
Type IV: Basement membrane

“Be (So Totally) Cool, Read Books”

94
Q

Type I collagen

A 
Bone
Skin
Tendon
Dentin
Fascia
Cornea
Late wound repair

Defective in osteogenesis imperfecta

95
Q

Type II collagen

A

Cartilage
Vitreous body
Nucleus pulposus

96
Q

Type III collagen

A

Reticulin (skin, blood vessels, uterus, fetus, granulation tissue)

Defective in Ehlers-Danlos

97
Q

Type IV collagen

A

Basement membrane

Defective in Alport syndrome

98
Q

Collagen synthesis

A

1) Synthesis (RER): Gly-X-Y
2) Hydroxylation (ER): of proline and lysine (required vit. C)
3) Glocosylation (ER): of hydroxylysine, hydrogen and disulfide bond formation
4) Exocytosis into extracellular space
5) Cleavage: of terminal regions into insoluble tropocollagen
6) Cross-link: Forming fibrils

99
Q

Multiple fractures, blue sclerae, hearing loss, dental imperfections

A

Osteogenesis imperfecta

100
Q

Congenital nephritis, deafness, and ocular disturbances

A

Alport syndrome (type IV collagen)

101
Q

Prader-Willi syndrome

A

Paternal allele not expressed

Retardation
Hyperphagia/obesity
Hypogonadism
Hypotonia

102
Q

Angelman syndrome

A

Maternal allele not expressed

Retardation
Seizures
Ataxia
Inappropriate laughter

103
Q

Trinucleotide repeat expansion diseases

A

Fragile X: (CGG)
Friedreich’s ataxia: (GAA)
Huntington’s: (CAG)
Myotonic dystrophy: (CTG)

“X-Girlfriends First-Aid Helped-Ace My-Test”

104
Q

Autosomal trisomies

A

21-Downsyndrome
18-Edwards (rocker-bottom feet, small jaw)
13-Patau’s (rocket-bottom feet, cleft palate, microophthalmia/cephaly, polydactyly)

“Drink at 21, Election at 18, Puberty at 13”

105
Q

Robertsonian translocation

A

Nonreciprocal chromosomal translocations
13,14,15,21,22
Long arms fuse @ centromere and short arms are lost

106
Q

Cri-du-chat syndrome

A

Microdeletion of short arm of chr 5

microcephaly, retardation, high-pitched crying/mewing, epicanthal folds, cardiac VSD

107
Q

Williams syndrome

A

Microdeletion of long arm of chr. 7

Elfin facies
Intellectual disability
Hypercalcemia (increased vit. D def)
Well-developed verbal skills/extreme friendliness
Cardiovascular problems
108
Q

22q11 deletion syndromes

A

Aberrant devo of 3rd and 4th branchial pouches

Cleft palate
Abnormal facies
Thymic aplasia
Cardiac defects
Hypocalcemia

“CATCH-22”

109
Q

DiGeorge syndrome

A

22q11 deletion

Thymus
Parathyroid
Cardiac defects

110
Q

Velocardiofacial syndrome

A

22q11 deletion

Palate
Facial
Cardiac defects

ZBiochem (9 decks)

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