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114 Cards in this Set
- Front
- Back
The ____________ describes the relation between interatomic distances, electronic charge, solution dielectric, and free energies. |
van der Waals interaction |
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Protein ____________ defines the relation among subunits in a multisubunit lattice. |
quaternary structure |
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Protein _________ defines the amino acid sequence. |
primary structure |
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Protein ___________ defines the packing of helices, sheets, turns, etc. |
tertiary structure |
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Protein ___________ defines the motifs formed by short-range interactions between amino acids. |
secondary structure |
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A ___________ interaction involves polar O, N, or both with hydrogen and constitutes one of the important stabilization elements. |
hydrogen bond |
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__________ is used to determine the sequence of a protein based on sequential chemical reactivity. |
Edman degradation |
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A _____________ induces denaturation of proteins by disturbing the hydrophobic effect. |
chaotropic agent |
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Name the following protein structure: |
disulfide bond |
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A _____________ is a graph of the conformational torsion angles for the residues in a protein or peptide. A map of the structure of the polypeptide backbone (alpha helices and beta sheets etc.) |
Ramachandran plot |
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A _____________ has two charges which neutralize each other. |
zwitterion |
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The _____________ is the primary "force" of protein structural stabilization. |
hydrophobic effect |
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The _____________ is the characteristic speed of an enzyme's kinetics extrapolated to the time when a defined amount of substrate is added to the enzyme solution. |
initial rate |
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An act of _____________ does not change an enzyme and lowers the transition state free energy of the associated reaction. |
catalysis |
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The _____________ of an enzymatic catalysis reaction is the rate achieved when it is saturated with substrate. |
maximum velocity |
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The _____________ (or double reciprocal) equation defines parameters that are used to characterize the kinetics of an enzyme. |
Lineweaver-Burk |
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Km is the substrate concentration when Vo = Vmax / 2, or _____________. |
Michaelis-Menten constant |
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A _____________ is the enzyme-substrate combination formed during an enzyme catalysis event. |
Michaelis complex |
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The catalytic rate constant of an enzyme is abbreviated as: |
k_cat |
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_____________ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme. |
Competitive inhibition |
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_____________ of enzyme catalysis occurs when the inhibitor only binds to the enzyme-substrate complex. |
Uncompetitive inhibition |
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The _____________ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation. |
steady state approximation |
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Internal factors that limit the velocity of an enzymatic reaction: |
- hydrophobic effect - hydrogen bonding - disulfide bonds - van der Waals forces - ionic bonds (salt bridges) - dipole-dipole interactions |
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External factors that limit the velocity of an enzymatic reaction: |
- pH - solvent polarity - temperature - salt concentration(s) and types - presence of chaotropes - osmolytes |
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What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate? |
Amino acid : Serine Functional group : hydroxylate |
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Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a _____________. |
nerve gas antidote |
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What kind of reaction produces the reactivated enzyme? |
nucleophilic substitution |
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The bisubstrate-enzyme _____________ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively binding substrates. |
ping-pong |
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An _____________ works by amplifying an initial signal via several linked protease cleavage reaction stages. (e.g., blood clotting) |
enzyme cascade |
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A _____________ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage. |
zymogen |
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A decrease in the activity of an enzyme as a result of binding of a product from the reaction in question or subsequent reactions is referred to as _____________. |
feedback inhibition |
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_____________ involves binding of a regulatory molecule at a site other than the active site. |
Allosterism |
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_____________ and _____________ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and the Krebs cycle. |
Kinase ; phosphatase |
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_____________ regulates entry and exit from mitosis by catalyzing a covalent modification reaction. |
Cyclin kinase |
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Which two amino acids are phosphorylated in cyclin kinase? |
tyrosine and threonine |
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Examples of reversible factors that control the catalytic capability of an enzyme: |
- noncovalent modifications - pH and pKa changes - salt concentration changes |
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Examples of irreversible factors that control the catalytic capability of an enzyme: |
- covalent modification - proteolysis - irreversible inhibitors |
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The _____________ accounts for the temperature dependence of the rate of a reaction. |
Arrhenius equation |
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List the two "chemical modes of catalysis" |
- acid-base - covalent |
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List the two "binding modes of catalysis" |
- proximity effect - transition-state stabilization |
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A _____________ attacks an electropositive site in its role in a chemical (enzymatic) reaction. |
nucleophile |
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A common process used to produce a nucleophile is: |
acid-base catalysis |
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The most common amino acids used by enzymes to carry out acid-base catalysis is _____________. |
histidine |
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A catalytic triad of amino acids is typically present in (enzyme class name) |
serine proteases |
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The amino acids collaborate to accomplish _____________. |
acid-base catalysis |
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The most typically cited currency of energy in metabolism is: |
ATP |
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______ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions. |
Mg2+ |
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A coenzyme is either a loosely bound cosubstrate or a strongly bound _____________. |
prosthetic group |
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The heavy metal molybdenum is used to facilitate the biochemical reaction in _____________, a key enzyme in purine catabolism. |
xanthine oxidase |
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When ATP is used in some biochemical applications it yields AMP and _____________. |
pyrophosphate |
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The (vitamin) _____________ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions. |
nicotinamide |
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The other key redox coenzyme is abbreviated _____. |
FAD |
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The coenzyme _____________ often forms Schiff base with the E-amino group of a lysine residue in the enzyme. |
pyridoxal phosphate |
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What chemical group does coenzyme A typically carry in the course of its biochemical function? |
acetate |
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The _______-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique. |
biotin |
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The coenzyme _____________ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA. |
N5, N10 methylenetetrahydrofolate |
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Our understanding of this function can be used in a strategy for _____________ (treatment technique). |
anticancer chemotherapy |
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The coenzyme bound carbohydrates _____________ and glucose are required to synthesize lactose. |
UDP-galactose |
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Cis-retinal functions in _____________ the signal of a photon of light into a chemically recognizable form. |
transducing |
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The two important straight-chain forms of carbohydrate structure are the _________ and ________. |
ketose ; aldose |
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The two important ring forms of carbohydates are the ________ and _________. |
pyranose and furanose |
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The two important ring conformation of beta-D-glucopyranose are the _______ and _________. |
chair and boat |
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The cyclohexane ring containing the compound _____________ is released by phospholipase C in the phospholipid signal transduction mechanism. |
inositol triphosphate |
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The acronym NAG is used to abbreviate the name of the compound: |
N-acetyl-glucosamine |
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The key polysaccharide in starch is: |
amylopectin |
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The key polysaccharide in the liver is: |
glycogen |
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The antibiotic _____________ selectively inhibits cell wall peptidylglycan synthesis in bacteria. |
penicillin |
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Extra-cellular surface _____________ regulate the osmotic pressure around cells. |
carbohydrates |
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Phospholipase C produces two different second messengers in the phospholipid signal transduction pathway. The lipid-containing second messenger is _____________. |
diacylglycerol |
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The compound chondroitin sulfate _____________ cartilage and skeletal joints. |
lubricates |
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_____________ fatty acids of the same length have a lower melting temperature (Tm). |
Unsaturated |
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Lipid Tm values monitor the transformation form _____________ to dispersed forms. |
liquid crystal |
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Lipid _____________ are composed of two face-to-face monolayers while lipid _____________ form a biphasic sphere. |
bilayers ; micelles |
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The most popular model for a biological membrane is called the _____________ model. |
fluid mosaic |
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The four nucleic acid bases in RNA: |
adenosine, uracil, guanine, cytosine |
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The two normal base pairs in DNA and RNA are called _____________ base pairs. |
Watson-Crick |
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The _____________ bond in a nucleoside connects the base to the sugar. |
glycosidic |
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The _____________ can be used to determine if 2 single strands of DNA or RNA form a double helix. |
absorbance at 260nm |
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The face-to-face interaction between nucleic acid bases is called _____________. |
base stacking |
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Counterions bind all nucleic acids and are required to neutralize the ____________. |
phosphodiester phosphates |
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Protein complexes called _____________ serve this counterion function in the case of most chromosomal DNAs. |
histones |
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________ base pairs are less stable than _____ base pairs. |
A & T G & C |
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Differences between A and B forms of DNA: |
A form: 3' endo sugar conformation, base pairs tilted 20 degrees from helix axis, shorter central axial cavity, "fatter helices"
B form: 2' endo sugar conformation. Base pairs' perpendicular to helix axis, base pairs cross center of helix. |
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The 2' hydoxyl group catalyzes _____________ of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism. |
alkaline hydrolysis |
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An antisense oligonucleotide functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____________ binding. |
tRNA anticodon |
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Name the two most prevalent of the four classes of RNA. |
ribosomal RNA and transfer RNA |
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Some distinctive features of most eukaryotic mRNAs are: |
- m7G+ 5'-5' cap - monocistronic - contains introns and exons - poly(A) tail |
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A _____________ is used to detect the presence of a specific complementary nucleic acid sequence. |
DNA probe |
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_____________ are required to produce, manipulate and clone specific pieces of DNA. |
Restriction endonucleases |
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The two functional ends of transfer RNA are the anticodon and _____________. |
amino acid acceptor |
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The three most central catabolic pathways of intermediary metabolism are: |
- glycolysis |
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The four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are: |
- ATP - NADH - FADH2 - Coenzyme QH2 |
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The _____________ (Q) corrects or deviations from standard state concentrations (1M). |
mass action ratio |
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_____________ (#) steps in glycolysis control most of the flux through the pathway under actual cellular conditions. |
Three |
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What do those three reactions in glycolysis have in common? |
They are metabolically irreversible |
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Most of the reactions in glycolysis are: |
Near equilibrium |
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The kinetics of an enzyme reaction are most easily controlled when Km is approx. equal to ____________. |
the actual concentration of the reactant |
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The enzyme triose phosphate isomerase converts _____________ into glyceraldehyde-3-phosphate. |
dihydroxyacetone phosphate |
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When citrate negatively regulates the phosphofructokinase-1 reaction, the general name for this phenomenon is _____________. |
feedback inhibition |
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When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____________. |
feed-forward activation |
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The three possible catabolic fates of pyruvate: |
- acetyl CoA - ethanol - lactate |
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The enzyme alcohol dehydrogenase converts _____________ to ethanol |
acetaldehyde |
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_____________ uses the coenzyme lipoic acid in fueling the Krebs Cycle. |
Dihydrolipoamide acetyl transfease (DHP acetyl) |
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What symport reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction? |
pyruvate translocase |
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The two oxidative decarboxylation reactions of the Krebs Cycle are catalyzed by _____________ and _____________. |
isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase |
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The enzymes _____________ and malate dehydrogenase "fix" a carbonyl group on succinate in the production of oxaloacetate. |
fumarase |
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What crucial 2 carbon compounds is fixed to OAA? |
acetate |
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What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals? |
alanine and lactate |
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What energy sources are used to produce the protonmotive force? |
NADH, CoQH2, FADH2 |
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What enzyme complex uses the protonmotive force as the driving energy for ATP synthesis in oxidative phosphorylation? |
ATPase |
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How does electron transport drive production of the proton motive force? |
exports H+ from mitochondrion, creating a gradient |
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How many reactions does each round of beta oxidation of a fatty acid require? |
FOUR (oxidation, hydration, oxidation, thiolysis) |
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What are the products of one round of beta oxidation? |
- 1 CoQH2 |
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Which three steps of the Krebs Cycle do the first three steps of the fatty acid beta-oxidation cycle resemble? |
- succinate dehydrogenase - fumarase - malate dehydrogenase |