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PHAR 411

Molecular Biology, Nucleotide Metabolism, & Pharmacogenomics

True/False: Promoters have similar structure and resemble a consensus sequence at the 5' end. True
What happens to cyclic AMP levels when glucose levels are high? Decreases
What happens to cyclic AMP levels when glucose levels are low? Increases
Under low lactose conditions the operator in the lac operon is bound by: Repressor
Under high lactose conditions the operator in the lac operon is bound by: RNA Polymerase (CRP-cAMP activation)
Under high glucose conditions the operator in the lac operon is bound by: Nothing
True/False: The leader peptide plays an indirect role in causing RNA polymerase to attenuate with no involvement of the mRNA. True
True/False: Trp codons in the leader peptide mRNA allow the system to respond to tryptophan levels in the cell. True
True/False: When tryptophan levels are low, mRNA synthesis at the trp operon is attenuated. False
The 2-3 mRNA structure promotes: Transcription
The 3-4 mRNA structure promotes: Attenuation
What two components are involved in steroid hormone action? Hormone-receptor complexes & Receptor-DNA interactions
True/False: UMP is the precursor for the pyrmidines. True
True/False: Deoxynucleoside triphosphates are used for DNA replication during the S phase of the cell cycle. True
True/False: Bases are always synthesized while attached to ribose or deoxyribose. True
How is PRPP synthesized? ATP and ribose 5'-phosphate
True/False: PRPP is required for both purine and pyrimidine de novo synthesis. True
What molecule does PRPP combine with in the first step of purine synthesis? Glutamine
What is the immediate precursor to dTMP? dUMP
What enzyme does tetrahydrofolic acid supply? Thymidylate synthase
True/False: dNTPs are used only for DNA synthesis. True
What antifolate drugs target dihydrofolate reductase? Trimethoprim & Methotrexate
What prodrug directly inhibits thymidylate synthase and results in decreased levels of dTMP? 5-fluoro-dUMP
What enzyme is found in the degradation pathway of AMP, what is the end product of the pathway, and what drug inhibits the enzyme causing the end product? Xanthine oxidase; uric acid; Allopurinol
What three purines can be directly salvaged? Guanine, adenine, & hypoxanthine
What is hypoxanthine-guanine phosphoribosyltransferase responsible for? Salvaging hypoxanthine and guanine to IMP and GMP, respectively.
What enzyme is responsible for salvaging adenine to AMP? Adenine phosphoribosyl transferase
Describe recombinant erythropoietin (Epogen). Glycoprotein produced in kidney that binds EPO receptor and stimulates red blood cell production (erythropoiesis).
Describe Bevacizumab (Avastin). Inactivated VEGF and blocks blood vessel growth. Used for colorectal and breast cancer.
Describe Trastuzumab (Herceptin). Signals HER2 which induces intracellular signaling that controls growth.
What is the antibiotic selection in E. coli? Ampicillin
What is the antibiotic selection in mammalian cells? Hygromycin
What reaction requires dNTPs, template DNA, thermostable DNA polymerase (Taq), two primers, and a thermal cycling machine? Polymerase chain reaction (PCR)
Somatic mutation Not passed on to progeny; external environmental factors
Germ line mutation Passed on to progeny
Explain why allopurinol is sometimes used by patients who are taking a chemotherapeutic agent. Chemotherapy causes cell death, which increases the concentration of purines. The degradation of AMP by xanthine oxidase to uric acid is inhibited by allopurinol.
If there is a decrease in 6-thio-IMP then AMP and GMP: Increase
How does allopurinol affect the metabolism of 6-mercaptopurine? It inhibits hypoxanthine-guanine phosphoribosyl transferase, the enzyme needed to convert 6-mercaptopurine to 6-thio-IMP.
What is the role of hypoxanthine-guanine phosphoribosyl transferase (HGPRT) in the metabolism of 6-mercaptopurine and 6-thioguanine? 6-Mercaptopurine is converted to 6-thio-IMP by Hypoxanthine-guanine phosphoribosyl transferase, and 6-thio-IMP is converted to 6-thioguanine by the same enzyme (HGPRT).
What are vinca alkaloids? Mitotic inhibitors that stop microtubule polymerization
What are taxanes? Mitotic inhibitors that stop microtubule depolymerization
What are two topoisomerase inhibitors? Irinotecan & etoposide
What three features does a vector generally have? (1) No more than one recognition site for a specific restriction enzyme, (2) replication origin(s), and (3) antibiotic resistance gene(s)
What four features are required to make recombinant DNA? (1) Restriction endonuclease(s), (2) vector, (3) host cell, and (4) ligase.
True/False regarding PCR: The boundaries of the amplified DNA are determined by the synthetic oligonucleotides used as primers. True
Are the primers of a polymerase chain reaction incorporated into the final DNA product? Yes
True/False: During the S phase of the cell cycle there is a high rate of dNTP synthesis. True
What is the significance of 5-FU? 5-fluorouracil is converted to 5-dUMP which inhibits thymidylate synthase.
What is the relationship of 5-FdUMP to thymidylate synthase and methylene tetrahydrofolate (MTHF)? Folinic acid can increase MTHF and potentiate action of 5-dUMP.
Which part of the cell cycle involves antimetabolites (antipurines, antipyrimidines, and antifolates)? S phase
Define haplotype. Set of polymorphisms that are inherited together
Define polymorphism. Variation in DNA sequence
What are two broad categories of genes that have polymorphisms that can affect an individual's response to a drug? Pharmacokinetics & pharmacodynamics
Synonymous single nucleotide polymorphism: Nucleotide change without a change in amino acid (silent)
Nonsynonymous single nucleotide polymorphism: Nucleotide change with a change in amino acid (missense)
Describe the P450 nomenclature system. First letters/numbers identify gene; number-letter after gene indicates nucleotide location; first number-letter represents wild type; second number-letter represents polymorphism.
What does UGT1A1*28 specifically refer to and how is this related to the metabolism of SN-38? UGT1A1*28 has 7 TA repeats and reduces metabolism
What are examples of CYP alleles related to drug metabolism? CYP2C9*1 NL enzyme activity, CYP2C9*2 decreased enzyme activity, CYP2C9*3 decreased enzyme activity; CYP2C19*1 NL enzyme activity, CYP2C19*2 no enzyme activity, CYP2C19*3 no activity
How can a poor metabolizer be at risk for drug-induced side effects for one drug and have lack of a therapeutic effect for another drug? Diminished drug elimination or lack of therapeutic effect resulting from failure to generate the active form of the drug.
What is abacavir's indication and mechanism of action? Indication: HIV/AIDS; Mechanism of action: Nucleoside analog reverse transcriptase inhibitor
What is the relationship between the HLA-B*57001 allele and abacavir? HLA-B*5701 confers high risk of abacavir-induced hypersensitivity
How can HER2 be measured? Immunohistochemistry (IHC) & gene amplification by fluorescent in situ hybridization (FISH)
What is Azathioprine's mechanism of action? Perturbs de novo purine synthesis with TPMT by inactivating 6-mercaptopurine
Describe TPMT*3A allele and how it affects azathioprine dosing. Intermediate TPMT increases risk of myelotoxicity; low/absent TPMT increases risk of severe life-threatening myelotoxicity
What are the genetic variants to warfarin? Variants in CYP2C9 decrease warfarin metabolism; variants in VKORC1 decrease levels of warfarin target
What is the potential role of UGT1A1 alleles in irinotecan metabolism? High expression of UGT1A1 results in increased SN-38 glucuronide (inactive metabolite)
Describe the potential role of CYP2C19 alleles in Clopidogrel metabolism. CYP2C19 metabolizes drug to active form; CYP2C19*1 functional; CYP2C19*2 nonfunctional (splicing); CYP2C19*3 nonfunctional (premature stop codon)
The polymorphic gene VKORC1 belongs to what drug? Warfarin
The polymorphic gene CYP2C9 belongs to what drug? Warfarin
The polymorphic gene HLA-B belongs to what drug? Abacavir
The polymorphic gene CYP2C19 belongs to what drug? Clopidogrel
The polymorphic gene UGT1A1 belongs to what drug? Irinotecan
The polymorphic gene TPMT belongs to what drug? Azathioprine
The polymorphic gene HER2 belongs to what drug? Trastuzumab
What genes have a polymorphism in their promoter? VKORC1 (-1639G>A) & UGT1A1 (6 TA repeats)
True/False: Individuals with the TPMT*3A/*3A genotype are more likely to experience toxicity with a conventional dose of azathioprine as compared to individuals that are homozygous wild type for TPMT. True
True/False: CYP2C9 polymorphisms are the principle polymorphisms responsible for individual differences in response to azathioprine. False - TPMT polymorphisms are
Which polymorphisms result in changes in the amino acid sequence of the corresponding enzyme? CYP2C9*3, CYP2C19*2 (splicing), and CYP2C19*3 (stop codon)
What polymorphisms affect pharmacokinetics? CYP2C9, CYP2C19, UGT1A1, TPMT
What polymorphisms affect pharmacodynamics? VKORC1, HLA-B, HER2
True/False: Polymorphisms in pharmacokinetic and pharmacodynamics parameters can explain the variability in warfarin toxicity. True
What enzyme is defective in hereditary fructose intolerance? Aldolase B
What enzyme is deficient in essential fructosuria? Fructokinase
For what purpose is fructose made in humans? Fuel for spermatazoa
In which tissue is fructose made for spermatozoa fuel? Seminal vesicles
What does the lacY gene do? Promotes cellular uptake of lactose
What does the lacA gene do? Modifies toxic products for excretion from bacteria
What does the lacZ gene do?
Created by: sdeck86



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