Term
| van der waals interaction |
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Definition
| The _____ describes the relation betwee ineratomic distances, electronic charge, solution dielectric and free energies |
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Term
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Definition
| Protein ____ defines the realtion among subunits in a multisubunit lattice |
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Term
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Definition
| Protein ____ defines the amino acid sequence |
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Term
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Definition
| Protein ____ defines the packing of helices, sheets, turns, etc. |
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Term
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Definition
| Protein ____ defines the motifs formed by short-range interactions between amino acids |
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Term
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Definition
| a ____ interaction involves polar O, n, or both and the atom for which it is named, and constitutes one of the important protein stabilization elements |
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Term
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Definition
| ___ is used to determine the sequence of a protein based on sequential chemical reactivity |
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Term
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Definition
| a _____ induces denaturation of proteins by disturbing the hydrophobic effect |
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Term
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Definition
| A _____ is a graph of the conformational torsion angles phi and psy for the residues in a protein or peptide, a map of the structure of the polypeptide backbone |
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Term
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Definition
| A _____ has two charges whch neutralize each other |
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Term
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Definition
| the _____ is the primary force of protein structural stabilization |
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Term
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Definition
| 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 |
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Term
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Definition
| an act of _____ does not change an enzyme and lowers the transition state free energy of the associated reaction |
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Term
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Definition
| the _____ of an enzymatic catalysis reeaction is the rate achieved when it is saturated with substrate |
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Term
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Definition
| the _____ (or double reciprocal) equation defines parameters that are used to characterize the kinetics of an enzyme |
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Term
| Michaelis-Menten constant |
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Definition
| Km is the substrate concentration when v0=vmax/2, or _____ |
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Term
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Definition
| the catalytic rate constant of an enzyme is abbreviated _____ |
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Term
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Definition
| _____ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme |
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Term
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Definition
| _____ of enzyme catalysis occurs when the inhibitor only binds to the enzyme-substrate complex |
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Term
| steady state approximation |
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Definition
| the _____ prostulates that a constant input feed of substrate is supplied whose rate equals that of product formation |
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Term
| hydrophobic effect, H-bonding, disulfide bonds, van der waals forces, ionic bonds (salt bridges) or dipole-dipole interactions |
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Definition
| two internal factors that limit the velocity of an enzymatic reaction are _____ and _____ |
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Term
| pH, solvent polarity, temperature, salt concentration, and presence of chaotropes, osmolytes |
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Definition
| two external factors that limit the velocity of an enzymatic reaction are _____ and _____ |
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Term
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Definition
| What amino acid and functional group in the esterase site of acetylcholin esterase reacts with the substrate? |
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Term
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Definition
| Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a _____ |
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Term
| nucleophilic substitution |
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Definition
| What kind of reaction produces the reactivated enzyme? (acetylcholine esterase) |
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Term
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Definition
| the bisubstrate-enzyme _____ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively vinding substrates |
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Term
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Definition
| an _____ works by amplifying an initial signal via several linked protease cleavage reaction stages. (eg, blood clotting) |
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Term
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Definition
| a _____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage |
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Term
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Definition
| a decrase 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 _____ |
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Term
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Definition
| _____ involves binding of a regulatory moleculte at a site other than the active site |
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Term
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Definition
| _____ and _____ ractions, involving phosphate addition and removal respectively, regulate both glycolysis and the kreb's cycle |
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Term
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Definition
| _____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction |
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Term
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Definition
| What two amino acids are modified in the reactions catalyzed by cyclin kinase? |
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Term
| noncovalent modifications, pH and pKa changes, salt changes |
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Definition
| Two examples of reversible factors that control the catalytic capability of an enzyme are _____ and _____ |
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Term
| covelent modifications, proteolysis, irreversible inhibitors |
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Definition
| Two examples of irreversible factors that control the catalytic capability of an enzyme are _____ and _____ |
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Term
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Definition
| the _____ accounts for the temperature dependence of the rate of a reaction |
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Term
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Definition
| List the two chemical modes of catalysis |
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Term
| proximity effect, transition-state stabilization |
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Definition
| List the two binding modes of catalysis |
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Term
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Definition
| a _____ attacks an electropositive site in it's role in a chemical (enzymatic) reaction |
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Term
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Definition
| a commmon process used to produce a nucleophile is _____ |
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Term
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Definition
| probably the most common amino acid used by enzymes to carry out acid/base catalysis is _____ |
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Term
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Definition
| a catalytic triad of amino acids is typically present in _____ |
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Term
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Definition
| the amino acids colloborate to accomplish _____ |
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Term
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Definition
| the most typically cited currency of energy in metabolism is _____ |
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Term
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Definition
| _____ is typically required to achieve optimal activity with ATP cosubstrate enzyme reactions |
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Term
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Definition
| a conenzyme is either loosely bound cosubstrate or tightly bound _____ |
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Term
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Definition
| the heavy metal molubdenum is used to fascilitate the biochemical reaction _____, a key enzyme in purine cataboism |
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Term
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Definition
| when ATP used in some biochemical applications it yields AMP and _____ |
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Term
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Definition
| the (vitamin) _____ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions |
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Term
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Definition
| the other key redox coenzyme is abbreviated _____ |
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Term
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Definition
| the enzyme _____ often forms a schiff base with the e-amino group of a lysine residue in the enzyme |
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Term
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Definition
| What chemical group does coenzyme A typically carry in the couse of its biochemical function? |
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Term
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Definition
| the _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the affinity capture technique |
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Term
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Definition
| the coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA |
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Term
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Definition
| our understanding of DNA production can be used in a strategy for _____ |
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Term
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Definition
| The coenzyme bound carbohydrate _____ and glucose are required to synthesize lactose |
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Term
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Definition
| Cis-retinal functions in _____ the signal of a photon of light into a chemically recognizable form |
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Term
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Definition
| the two important straight -chain forms of carbohydrate structures are the _____ and _____ |
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Term
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Definition
| the two important ring forms of carbohydrates are the _____ and _____ |
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Term
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Definition
| the two important ring coformations of B-D-glucopyranose are the _____ and _____ |
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Term
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Definition
| the cyclohexane ring containing compoind _____ is released by phospholipase C in the phospholipid signal transductoin mechanism |
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Term
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Definition
| the acronum NAG is used to abbreviate the name of the compound _____ |
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Term
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Definition
| the key polysaccharide in starch is _____ |
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Term
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Definition
| the key polysaccharide in the liver is _____ |
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Term
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Definition
| the antibiotic _____ selectively inhibits cell well peptidylglycan synthesis in bacteria |
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Term
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Definition
| extra-cellular surface _____ regulate the osmotic pressure around cells |
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Term
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Definition
| phospholipase C produces two differnt second messengers in the phospolipid signal transduction pathway. The lipi containing second messenger is _____ |
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Term
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Definition
| the compound chondroitin sulfate _____ cartilage and skeltal joints |
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Term
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Definition
| saturated/unsaturated fatty acids of the same length have a lower melting temp (Tm) |
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Term
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Definition
| Lipid Tm values moitor the transformation from _____ to dispersed forms |
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Term
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Definition
| lipid _____ are composed of two face-toface monolayers while lipid _____ form a biphasic sphere |
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Term
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Definition
| the most popular model for a biological membrane is called the_____ model |
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Term
| adenine, guanine, cytosine, and uracil |
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Definition
| the four nucleic acid bases in RNA are _____, _____, _____, and _____ |
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Term
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Definition
| The two normal base pairs in DNA and RNA are called _____ base pairs |
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Term
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Definition
| the _____ bond in a nucleoside connects the base to the sugar |
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Term
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Definition
| The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA |
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Term
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Definition
| the face-to-face interaction between nucleic acids is called _____ |
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Term
| phosphodiester phosphates |
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Definition
| counterions bind all nucleic acids and are required to neutralize the _____ |
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Term
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Definition
| the proteins called _____ are counterions that bind and neutralize nucleic acids in the case of the most chromosomal DNA's |
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Term
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Definition
| GC/AT (or AU) base pairs are less stable than GC/AT (or AU) base pairs |
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Term
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Definition
| the 2'-hydroxyl group catalyzes _____ of RNA, a good exmaple of anchiomeric assistance in a non-protein biomolecular mechanism |
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Term
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Definition
| an antisense oligonucleotide functionally inactivarte a mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____ binding |
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Term
| m7G+ (5'-5') cap, monocistronic, contains introns and exons, poly(A) tail |
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Definition
| two distinctive features of most eukaryotic mRNAs are _____ and _____ |
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Term
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Definition
| a _____ is used to detect the presence of a specific complementary nucleic acid sequence |
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Term
| restriction endonucleases |
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Definition
| _____ are required to produce, manipulate, and clone specific peices of DNA |
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Term
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Definition
| the two functional ends of transfer RNa are the anticodon and _____ |
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Term
| glycolysis, Krebs cycle, and electron transport/oxidative phosphorylation |
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Definition
| the three most central catabolic pathways of intermediary metabolism are _____, _____, and _____ |
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Term
| ATP, NADH, FADH2, and Coenzyme QH2 |
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Definition
| the four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are _____, _____, _____, and _____ |
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Term
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Definition
| the _____ (Q) corrects for deviations from standard state concentrations (1M) |
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Term
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Definition
| _____ (number) steps in glycolysis control most of the flux through the pathway under actual cellular conditions |
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Term
| metabollically irreversible |
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Definition
| What do the three steps in glycolysis have in common? They are all _____ |
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Term
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Definition
| Most of the reactions in glycolysis are _____ |
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Term
| the actual concentration of the reactant |
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Definition
| the kinetics of an enzyme reaction are most easily controlle when Km is approximately equal to _____ |
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Term
| dihydroxyacetone phosphate |
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Definition
| the enzyme triose phosphate isomerase converts _____ into glyceraldehyde-3-phosphate |
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Term
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Definition
| when citrate negatively regulates (discourages) the phosphofructokinase-1 reaction, the general name for this phenomenon is _____ |
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Term
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Definition
| when fructose-1,6-bisphospahte stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____ |
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Term
| acetyl CoA, ethanol, and lactate |
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Definition
| the three possible catabolic fates of pyruvate are _____, _____, and _____ |
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Term
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Definition
| the enzyme alcohol dehydrogenase converts _____ to ethanol |
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Term
| dihydrolipoamide acetyl transferase |
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Definition
| _____ uses the coenzyme lipoic acid in fueling the kreb's cycle |
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Term
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Definition
| What symport reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction? |
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Term
| isocitrate dehydrogenase and a-ketoglutarate dehydrogenase |
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Definition
| the two oxidative decarboxylation reactions of the kreb's cycle are catalyzed by _____ and _____ |
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Term
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Definition
| list the reaction, coenzymes, cofactors, and enzymes involved in the substrate level phosphorylation reaction of the kreb's cycle |
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Term
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Definition
| the enzymes _____ and malate dehydrogenase fix a carbonyl group on succinate in the production of oxaloacetate |
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Term
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Definition
| what crucial 2 carbon compound is fixed to oxaloacetate? |
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Term
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Definition
| what amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenisis in mammals? |
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Term
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Definition
| What energy sources are used to produce the protomotive force? |
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Term
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Definition
| what enzyme complex uses protonmotive force as the driving energy for ATP synthesis in oxidative phosphorylation? |
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Term
| four (oxidaiton 1, hydration, oxidation 2, and thiolysis) |
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Definition
| How many reactions does each round of b-oxidation of a fatty acid require? |
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Term
| 1 CoQH2, 1 NADH, 1 H+, 1 acetyl CoA, 1 fatty acid (minus 2 C's) |
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Definition
| What are the products of one round of b-oxidation and what's the tally in terms of ATP equivalents of energy conserving products? |
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Term
| CoA, FAD/FADH, FE-S2+/3+, CoQ/CoQH2 |
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Definition
| A set of coupled cofactor regeneration cycles siphon off reducing equivalents then fix them into coenzyme Q in reactions that are coupled to the first oxidative step of fatty acid B-oxidation. Write down the names of the four cofactors involved in this siphon |
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Term
| succinate dehydrogenase, fumarase, malate dehydrogenase |
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Definition
| Which three steps of the Kreb's cycle do the first three steps of the fatty acid b-oxidation cycle resemble? |
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