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231 terms

Med Chem Exam 1

_______ is a recombinant enzyme (carboxypeptidase G2, CPDG2) which lowers bl levels of methotrexate, reducing its concentration to below the threshold for serious toxicity.
________ converts methotrexate to its inactive metabolites DAMPA and glutamate.
DAMPA and glutamate are metabolized by the _______, providing an alternative route of methotrexate eliminate to renal clearance during high-dose txm.`
________ is specifically indicated for the txm of toxic plasma methotrexate concentrations (>1 micromole/L) in pts w/ delayed methotrexate clearance due to impaired renal function.
What is the route of administration for Voraxaze (glucarpidase)? What is the recommended dose?
Single IV injection of 50 units/kg as bolus injection over 5 mins.
It takes _____ years on average for an experimental drug to travel from the lab to U.S. pts.
Only __ in 5,000 compounds that enter pre-clinical testing make it to human testing. __ of these is approved.
On average, it costs a company _________ to get one new med from the lab to U.S. patients.
$1.3 billion
Takes 6.5 years; lab and animal studies; assess safety, biological activity, and formulations, 5,000 compounds evaluated
Discovery/pre-clinical testing
Takes 1.5 years; 20-100 healthy volunteers; determine safety and dosage
Phase I
Takes 2 years; 100-500 patient volunteers; evaluate effectiveness, look for side effects
Phase II
Takes 3.5 years; 1,000-5,000 patient volunteers; confirm effectiveness, monitor adverse reactions from long-term use
Phase III
Additional post-marketing testing required by FDA
Phase IV
Proteins (catalysts) which speed up reactions utilized specific substrates (endogenous).
Recombinant tissue plasminogen activator; clot buster for acute MI (enzyme)
There are over __ mAbs approved for human use.
________ are produced from cell culture (biotech); exert effect on cell surface receptors or scavenge proteins in the ECM; rarely enter cells; very specific in action
Monoclonal Antibodies
Glycoprotieins that are soluble mediators in cell communication, represented by large groups (>100) of IL and IFNs; produced during effector phases of immune response or host defense
Cytokines exert their regulatory effects on specific organs/tissues _________ the site of excretion. aka ___________
nearby; paracrine
__________ is a recombinant granulocyte colony-stimulating factor
Neupogen (Filgrastim)
_______ is a GF used to enhance neutrophil proliferation and is indicated for CA patients receiving myelosuppressive chemo or BM transplant; pts w/ myeloid leukemia; pts w/ severe neutropenia
Neupogen (Filgrastim)
Most endogenous GFs are ________ that stimulate production of certain cell types.
A ________ is a substance produced by endocrine glands, released in very low concentrations into the bl stream.
A hormone exerts regulatory effects on specific organs/tissues _______ the site of site of secretion. aka ________
distant from; endocrine
Some hormones are not proteins, like ________.
__________ are synthetic molecules that bind to specific intracellular mRNA. They are made of about 13-25 nucleotides that are complementary to mRNA in a region of a coding sequence designed as a sense strand. By binding to mRNA, these stop translation.
Antisense oligonucleotides
__________ is used for the txm of CMV retinitis in persons w/ AIDS.
Vitravene (fomivirsen)
Vitravene is a(n) ______________.
antisense oligonucleotide (AS-ON)
__________ are RNA/DNA molecules that recognize specific proteins. They fold into a 3D structure and bind to proteins.
______ is an anti-VEGF inhibitor approved by the FDA for the txm of wet age-related macular degeneration (injected into eye)
Mucagen (pegaptanib Na injection)
pegaptanib sodium injection
Biologic drugs are homogeneous or heterogeneous mixtures?
Biologics have a logP of > or < 0.5?
logP < 0.5
LogP of > 0.5 means high or moderate-low solubility
Log P of < 0.5 means high or moderate-low solubility?
Biologics are distributed to any organ/tissue or are limited to plasma/extracellular fluid?
Limited to plasma/extracellular fluid
Are biologics routinely metabolized or catabolized to aa (peptides)?
catabolized to aa (peptides)
___________ is the movement of drug from the site of application into blood stream or target tissue.
___________ is the effect of drug on non-target tissues or cells.
___________ is the transformation, detoxification, conjugation, or bioactivation (prodrugs) of drugs
___________ is the movement of drug from blood to target site of action; greatly affected by plasma protein binding
Voraxaze converts methotrexate to its inactive metabolites ________ and ________.
DAMPA; glutamate
________ implies drug is administered by injection or infusion
For biologics, preferred routes of administration include _________ & ________.
parenteral; subcutaneous
What's a biologic (protein) that is administered by inhalation?
Exubera (inhaled insulin powder
_____ and _____ are examples of enzymes that don't end in '-ase' and catalyze the cleavage of peptides.
Trypsin; pepsin
The following are disadvantages of oral administration:
1) Drug-drug or drug-food interactions
2) First-pass effect (liver metab); can be advantageous for prodrugs
3) Liver enzyme induction
4) Digestive tract irritation
The following are disadvantages of parenteral administration:
1) High initial drug concentration
2) Invasive- risk of infection
3) Requires a certain skill level
The ratio of octanol solubility to water solubility is measured through LogP. A high log P is _______ and a low LogP is ________.
Lipid soluble; water soluble
H bond donors can occur between atoms of __, __, __, and a hydrogen.
N, O, F
Lapinski "Rule of Five (RO5)" must meet 3 out of 4 of the following criteria:
MW ______
# H bond acceptors ___
# H bond donors ___
___ < LogP < ___
< or equal to 500; < or equal to 10; < or equal to 5; -2 < LogP< 5
________ is a potent and selective leukotriene D4 receptor antagonist; indicated in adult and pediatric pts 2 y/o and older.
Singulair (montelukast Na)
_________ is used for the prophylaxis and chronic txm of asthma; the relief of daytime/nighttime s/s of seasonal/perennial allergic rhinits
Singulair (montelukast Na)
______ is a (IgG-1k) humanized mAb that blocks IgE-mediated mast cell degranulation
Xolair (omalizumab)
______ is indicated for adults and adolescents (12+) w/ moderate-severe persistent asthma who have a + skin test or in vitro reactivity to a perennial skin allergen and who s/s are inadequately controlled w/ inhaled corticosteroids.
Xolair (omalizumab)
Xolair (omalizumab) is administered ____________.
________ is an FDA-approved protein kinase inhibitor used in oncology.
_______ is another non '-ase' enzyme
Recently, patent expiration and loss of market exclusivity on several pharmaceuticals (biologics) stimulated a debate on the role of generic (____________) biologics.
Biosimilar; follow-on
___% of proteins are misfolded.
DNA = about ____ BP in humans and contains about _____ genes.
3 x 10^9; 25,000
Nuclear DNA contains about ___ Mb and ____ genes.
3,300; 25,000
Mitochondrial DNA contains about ___ kb and ___ genes.
16.6; 37
Out of nuclear DNA, __% is genes and __% is extragenic DNA.
25; 75
________ DNA are composed of repeats (tandem, clustered, or interspersed).
Out of nuclear genes, __% is coding DNA and __% is non-coding DNA (introns, UTR, fragments)
10; 90
In mitochondrial DNA, __ are rRNA genes, __ are tRNA genes, and __ are polypeptide encoding genes.
2; 22; 13
In the nuclear genome, replication utilizes strand-coupled mechanisms that use DNA pol ___ and ___.
Alpha; delta
In the mitochondrial genome, replication utilizes strand-coupled and strand-displacement models; only uses DNA pol ___.
Mitochondria can contain ___ 'plasmid-size' mitochondrial genomes.
A _________ is a very long, continuous piece of DNA, which contains genes, regulatory elements, and other intervening sequences; bundles w/ histones (major protein component of chromatin)
______ is a rare, progressive neurodegenerative disease caused by the decreased ability of cells to produce sufficient APT.
MELAS (mitochondrial encephalopathy lactic acidosis stroke-like episodes)
MELAS stands for....
Mitochondrial encephalopathy lactic acidsos stroke-like episodes
80% of those diagnosed w/ MELAS have a ________ mutation in dihydrouridine loop of tRNA.
3243 A --> G point
_________ explains the variation in severity of the disease among siblings.
_________ is the presence of a mix of more than one type of an organelle genome (mtDNA) w/in a cell. It is frequent for mutations to affect only some copies of mtDNA, while the remaining ones are undaffected.
Drugs most often used to treat MELAS include ________ and ________.
antioxidants and vitamins (like coenzyme Q10, L-arginine, B vitamins, Levocarnitine, etc.); no FDA-approved drugs yet.
The ribose has a -OH on the ___ C and deoxyribose does not.
The pyrimidines are __, __, and __; the purines are __ and __.
Uracil, cytosine, and thymine; adenine and guanine
A __________ has a nitrogen base linked by a glycosidic bond of C1' of a sugar (ribose/deoxyribose)
A nulceoside has a N base linked by a _________ to C1' of a sugar (deoxyribose/ribose)
glycosidic bond
Adenine and guanine become ________ and _______ when they are incorporated into nucleosides.
adenosine; guanosine
Cytosine and thymine become _______ and _______ when they are incorporated into nucleosides.
Cytidine; thymidine
Lamivudine, Brivudin, Valaciclovir, Valganciclovir, and Cidofovir are examples of ___________.
Nucleic acid analogs: antiviral drugs (shuts down replication)
Nucleotides are linked by ________ bonds.
Order of bases always read from _____.
5' --> 3'
C and Gs are linked by __ H bonds; A and Ts are linked by __ H bonds.
Physical properties of DNA:
__ nm in width
__ bases/turn
__ nm/turn
2.0; 10; 3.4
__________ compounds bind to DNA helices, forming intrastrand crosslinks b/t adjacent guanines in a similar way to cisplatin.
Dinuclear azole-bridged platinum
DNA is in a relaxed form, but ___________ can occur when ccDNA is subject to structural strain.
Strain is a result of __________ in ccDNA (DNA has fewer helical turns than would be expected for the B-form)
______ is a problem for both pro- and eukaryotic DNA
________ is an enzyme that helps to relieve torsional strain created by DNA replication.
______ catalyze addition of acetyl group to lysine side chain amino acid on proteins. (increase transcription)
HAT or histone acetyltransferase
______ catalyze the removal of acetyl groups (gene repression through chromatin condensation)
HDAC or histone deacetyltransferase
In human GI cancers, histone acetylation is globally reduced or increased?
________ cause the accumulation of acetylated histones and induces cell cycle arrest and/or apoptosis of some transformed cells (program cancers to self-destruct!)
HDAC inhibitors
________ have been shown to act selectively on gene expression, and are inducers of cell growth, arrest, differentiation, and death (in vitro and in vivo)
HDAC inhibitors
HDAC inhibitors have been shown to act selectively on _____________ and are inducers of cell growth, arrest, differentiation, and death (in vivo and in vitro)
gene expression
________ and ________ are examples of FDA-approved HDAC inhibitors used in cutaneous T-cell lymphoma (a type of non-hodgkin's lymphoma)
Vorinostat (Zolinza) [orally-active] and Romidepsin (Istodax) [IV infusion cyclic peptide
HDAC inhibitors (increase/decrease) acetylation of histones, thereby (increasing/decreasing) transcription of genes that have been silenced.
increase; increasing
HDAC inhibitors promote growth arrest by inducing the expression of __________ or _________ genes and are commonly used as anticancer drugs.
tumor-suppressor or pro-apoptotic
___ is the temperature it takes to unwind DNA.
90 C
_______ catalyzes dsDNA separation at origin.
_______ stabilize ssDNA that has been separated
DNA binding proteins
_______ catalyzes the addition of short RNA primers to template strand.
DNA primase
_______ catalyzes the addition of new nucleotides to form new strands.
DNA polymerase
_______ catalyzes removal of RNA primer and inserts the correct bases (DNA pol has this kind of activity)
_______ catalyzes the joining of Okazaki fragments and seals the sugar-phosphate backbone.
Initiation--the replication origin is at a consensus sequence of 245 bps in the genome that is rich in ___________.
GATC sequence repeats
___________ is the enzyme that stays in front of the replication fork; introduces a nick in the DNA backbone allowing the rotation of one strand around the other, relieving torsional strain which would otherwise accumulate in front of the advancing fork.
Topoisomerase I
Topoisomerase inhibitors can be anti-cancer agents (FDA-approved) and include ______ and _______.
topotecan; ironotecan
At the heart of the replicating machinery is _______, which catalyzes synthesis of new DNA using old DNA as a template.
DNA pol
In prokaryotes, there are 3 major DNA pol known, but DNA pol __ is the principal replication enzyme in bacteria.
DNA pol __ (eukaryotes) is responsible for the priming of replication of both strands.
DNA pol __ (euk) is responsible for the elongation of both strands.
_________ is a measure of the avg no. of nucleotides added by a DNA pol enzyme per association/disassociation w/ the template.
A ______ protein complex is required to keep DNA pol on the template and allow duplicaiton of long stretches of DNA
sliding clamp
In euk, the RNA primers are made at intervals of about ___ nucleotides on the lagging strand, and each primer is ___ nucleotides long.
200; 10
Primers are erased by _________ that recognized an RNA strand in an RNA/DNA helix and excise it; this leaves gaps that are filled by DNA pol III that can proofread.
DNA ligase catalyzes the formation of a _________ bond b/t the 3'-OH end of one fragment and the 5'-P end of the next, linking the sugar-phosphate backbones.
A thermostable _____ polymerase is used in PCR.
What are the 3 steps of PCR (in order)?
Denature, anneal, extend
In PCR, annealing is also called___________.
PCR primers are short, ssDNA mols that are about __ to __ bps long.
15-40 (primers are shorter in DNA replication)
______ quantifies PCR amplification as it occurs!
RT-qPCR (real time quantitative PCR)
After you amplify DNA, you can determine its sequence using the _______.
Sanger dideoxy chain termination reaction
_____________ automatically analyze DNA molecules label w/ any of 4 diff fluorescent dyes.
Fluorescence protocols
______ are regions of DNA containing tandem copies of di-, tri-, or tetranucleotide repeat units.
Short tandem repeats
STRs make up _____% of the mammalian genome.
STRs are also called _________.
You need topoisomerase in:
A) replication
B) transcription
C) both
The template strand is (sense/antisense), while the non-template strand is (sense/antisense).
anti-sense; sense
The following requires a primer:
a) DNA pol
b) RNA pol
c) both
For RNA synthesis to begin, RNA pol must first bind to the dsDNA at specific sequences called ____________.
promoters or promoter regions
In euk, promoters consist of a region -25 to -35 upstream from transcription start site, with a _____________.
TATA consensus sequence (TATA box)
Genes are in inactive states and require __________ to bind to the promoter -- help pol binding, transcription initiation, and expression of protein.
Transcription factors (activators)
In euk, RNA pol II binds a region of DNA (TATA box). _____ and _____ box are also important promoter regions.
CAAT (-80 to -110) and GC (-40 to -50)
In transcription, after about 20-30 nucleotides have been added to the growing RNA chain, a _____ is put on the 5' end.
G-cap (7-methylguanosine)
In transcription, the ___________ protects mRNA from degradation by endonucleases; also assists in binding to ribosome to initiate translation.
G cap
RNA that has just been synthesized is called the __________.
Primary transcript
2 important steps occur before the primary transcript becomes a mature transcript of mRNA that is ready for translation:
1) 3'-polyadenylation (poly-A tail addition) that protects is from exonuclease cleavage.
2) Splicing (removal of introns)
________ is the addition of 100-250 AAAAA to the 3'-end of a primary RNA transcript (coupled to termination)
Polymerization of aa is a(n) _______ reaction, which creates _______ bonds.
condensation (dehydration); amide (peptide)
What is the initiator codon?
AUG; Methionine (Met, M)
A string of mRNA codons represent a(n) ___________.
reading frame
Reading frame of mRNA of 50+ codons w/out a stop codon is called a(n) ___________.
open reading frame
What are the stop codons?
In translation, _________ catalyze the attachments of aa's to their appropriate tRNAs.
Enzyme aminoacyl tRNA synthetases
Eukaryotic ribosome is __S (__S and __S su); Prok is __S (__S and __S su)
80 (60S + 40S)
70 (50S + 30S)
_________ is an antimicrobial approved for the txm of infections caused by MRSA and vancomycin-resistant E. fecalis.
Linezolid (Zyvox)
________ is a drug that inhibits bacterial protein synthesis by directly binding to residues w/in the 23S ribosomal RNA of the 560S large su of bact ribosomes (prevents peptide bond formation)
Linezolid (Zyvox)
________ is a drug that inhibits translation initiation; it binds to the 16S rRNA of bact ribosome, which prevents the release of the growing protein (pp chain). Have 3 rings that are connected by ether bonds.
_______ is a drug that inhibits protein synthesis by blocking peptide transfer.
_______ are a class of drugs that block A site on bact ribosome, that prevents binding of aminoacyl-tRNA
_____ protein structure is the sequence of a chain of aa.
_____ protein structure occurs when the sequence of aa are linked by H bonds.
_____ protein structure occurs when certain attractions are present b/t alpha helices and pleated sheets (has domains)
_____ protein structure is a protein consisting of more than one aa chain (has subunits).
Although Met is the first aa of newly synthesized proteins, it's usually removed from mature proteins through a process called _________.
N-terminal excision (NME)
N-terminal excision is a (reversible/irreversible), (co-translational/post-translational) process.
irreversible; co-translational
NME is catalyzed by the enzyme ___________.
methionine aminopeptidase (MAP)
__________ are a large class of chaperones that that assist client proteins in folding (co-translational)
Heat shock proteins (HSP)
Post-translational modifications are examples of ________ changes, in addition to underlying genetics.
________ changes expand genes without altering the genome of the organism. (ex: chromatin remodeling)
Post-translational modifications (PTMs) alter the _________ of a protein (synthesis of membrane proteins)
PTMs alter energy metabolism, or ___________ in respiration.
Oxidative phosphorylation
Phosphorylation (pTyr, pSer, pThr) is involved in:
reversible, activation/inactivation of enzyme activity, modulation of molecular interactions, signaling
Acetylation is involved in:
protein stability, protection of N-terminus. Regulation of protein--DNA interactions (histones)
Methylation is involved in:
Regulation of gene expression
Glycosylation (N-linked, O-linked) is involved in:
excreted proteins, cell-cell recognition/signaling O-GlcNac, reversible, regulatory functions
Ubiquination is involved in:
destruction. After tryptic digestion, ubiquination site is modified w/ the Gly-Gly- dipeptide
Amino acid modifications are ________ modifications.
Physiologically, insulin is stored as a ___________ in the beta cells.
zinc-containing hexamer
___________ is a process/result of addition of saccharides (carbohydrates) to proteins; confers stability and helps w/ accurate folding
Nearly all proteins are glycosylated in the _______.
________ glycosylation involves the amide nitrogen of asparagine.
________ glycosylation involves the -OH oxygen of serine and threonine.
O-linked glycosylation
______, _______, and _______ are commonly phosphorylated by the action of protein kinases.
Serine, threonine, and tyrosine
> __% of all proteins are phosphorylated.
______ is the first-in-class drug first marketed in 2001; a kinase inhibitor for oncology
Gleevec (imatinib)
Most N-terminal groups of _____ are acetylated.
______, ______, ______, ______, and ______ are the most commonly N-methylated amino acids.
Lysine, arginine, histidine, glutamine, asparagine
Methylations are catalyzed by methyltransferases and cofactor _____.
Typically, three enzymes are involved in degrading misfolded proteins into innocuous small peptides:
ubiquitin-activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3)
The ______ is a professional protein-degrading organelle; abundant ATP-dependent protease; constitutes nearly 1% of all proteins; present in many copies throughout the cytosol and nucleus.
_______ is a proteosome inhibitor that is indicated for relapsing multiple myeloma and mantle cell lymphoma
Bertezomib (Velcade) --> IV infusion, new SC fomulation approved this yr
The boron atom in _______ binds to the catalytic site of the 26S proteasome w/ high affinity and specificty, preventing degradation of pro-apoptotic factors.
The following diseases are consequences of defects in the ubiquitin-proteasome pathway:
1) Alzheimer's
2) Parkinson's
3) Huntington's
4) Cancer
______ are substitutions of one base for another--altered RNA and perhaps protein--these don't alter transcription/translation mechanisms
Point mutations
_______ are the addition/removal of bases --- results in altered RNA and altered protein
_______ provide impediment to replication or transcription. Since replication is impaired, must be removed by another mechanism before replication
Structural distortions
_______ are changes in the genetic sequence that don't change the protein sequence. This occurs because of the redundancy of the genetic code. No obvious problems associated w/ disease.
Silent mutations
_______ are changes in DNA/RNA sequences that change the codon to a different aa. These lead to a mutated protein, experiencing misfolding; destabilizes it making it dys/non-functional. MOST COMMON
Missense mutations
PKU, a metabolic disease caused by mutations in phenylalanine hydroxylase is a ______ mutation.
_______ are changes in the genetic code that result in the coding for a stop codon rather than an aa; generally non-functional protein or impeded fxn; severe defects result
Nonsense mutations
Congenital primary aphakia (CPA) is a rare developmental disorder characterized by the absence of the lens is caused by a ______ mutation.
Nonsense mutation in the _____ gene results in defects in lens formation.
________ are the insertions/deletions of a number of bases; this alters the reading frame of the gene and results in premature stop codon or altered protein.
Frameshift mutations
Huntington's disease is an example of a _________ mutation.
________ are changes in the genetic sequence that occur at the boundary of exons and introns (e.g., keratoderma)
Splice or Splice-site mutations
Mismatch repair involves comparing parent dsDNA against daughter strands by __________.
Study of the organization and fxn of the complete genetic material of an organism
For a given trait, the genes associated w/ the trait is _________.
The genotype
The observable expression of the genotype as a clinical, biochemical, or molecular trait is a _________.
The tendency of certain disease phenotypes to appear at earlier ages and w/ increased severity in successive generations is ___________.
_________ is a term used if individuals are related by blood prior to marriage or mating (e.g., first cousins)
The proportion of people w/ a particular genetic change (a mutation in a specific gene) who exhibit s/s of a genetic disorder.
If people w/ a mutation don't develop features of the disorder, the condition is said to have ____________.
Reduced or incomplete penetrance
__________ is the extent to which a gene is expressed in one person. It can be graded as a %.
________ refers to whether the gene is expressed or not (how many people w/ the gen have the trait associated w/ the gene. ________ determines how much the trait affects/how many features of the trait appear in one person.
Penetrance; expressivity
The site on the chromosome at which a gene is located
Gene locus
Alternate forms of the same gene occupying the same locus on homologous chromosomes. These are called _________.
A chromosome that isn't a sex chromosome (humans 1-22)
(Dominant/Recessive) conditions usually involve structural proteins.
(Dominant/Recessive) conditions usually involve enzyme deficiencies.
_________ is a dominant disease in which the brain tissue gradually deteriorates in middle age. It is caused by the production of an inhibitor of brain cell metabolism.
huntington's disease
_________ is a dominant disease in which there is excessive CHO in the bl, leading to heart dz. It is caused by an abnormal form of CHO surface receptor.
______ is a recessive disease in which mucus clogs the lungs, liver, and pancreas. It is caused by the failure of Cl ion transport mechanisms. (affects 1/2,500 Caucasians)
_______ is a recessive disease caused by abnormal Hgb that results in poor blood circulation. (1/625 AA)
Sickle-cell anemia
_______ is a recessive disease caused by defective enzyme, hexosaminidase A. Results in the deterioration of CNS in infancy (1,3500 Jews)
_______ is a recessive dz caused by defective phenylalanine hydroxylase, where the brain fails to develop in infancy. (1/12,000)
_______ is a recessive dz caused by failure of proper thyroid development and results in increased birth wt, puffy face, constipation, and lethargy (1/1000 hispanics; 1/700 NA)
Congenital hyperthyroidism
______ is a sex-linked recessive disease caused by defective blood clotting factor VIII. (1/10,000 white males)
_______ is a dominant sex-linked disease caused by degradation of myelin coating of nerves stimulating msucles.
MD (Duchenne)
In this dz, the inherited mutation in this gene abnormally repeats the CAG segment from 36 to more than 50x (expanded trinucleotide repeat). Leads to long stretches of aa glutamine.
Huntington's (AD)