Glossary of Biochemistry Practice Final Exam

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The _____ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies.
Van der Waals interaction
Protein _____ defines the relation among subunits in a multisubunit lattice.
Quaternary structure
Protein _____ defines the amino acid sequence.
Primary structure
Protein _____ defines the packing of helices, sheets, turns, etc.
Tertiary structure
Protein _____ defines the motifs formed by short-range interactions between amino acids.
Secondary structure
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.
Hydrogen bond.
_____ is used to determine the sequence of a protein based on sequential chemical reactivity.
Edman degradation
A _____ induces denatration of proteins by disturbing the hydrophobic effect.
Chaotrophic agent
A _____ is a graph of a conformational torsion angles phi psi for the residues in a protein or peptide, a map of the structure of the polypeptide backbone.
Rachamandran plot
A _____ had two charges which neutralize each other.
The _____ is the primary “force” of protein structural stabilization.
Hydrophobic effect
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
An act of _____ does not change the enzyme and lowers the transition state free energy of the associated reaction.
The _____ of an enzymatic reaction is the rate achieved when it is saturated with substrate.
Maximum velocity
The _____ (or double reciprocal) equation defines parameters that are used to characterize the kinetics of an enzyme.
Km is the substrate concentration when vo=vmax/2, or _____
Michaelis-Menten constant
A _____ is the enzyme-substrate combination formed during an enzyme catalysis event.
Michaelis complex
The catalytic rate constant of an enzyme is abbreviated as _____
_____ of enzyme catalysis occurs when an inhibitor binds to the active site of an enzyme.
Competitive inhibition
_____ of enzyme catalysis occurs when an inhibitor only binds to the enzyme-substrate complex.
Uncompetitive inhibition.
The _____ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation.
Steady state approximation
Two internal factors that limit the velocity of and enzymatic reaction are _____ and _____.
Hydrophobic effect and H-bonding
Two external factors that limit the velocity of an enzymatic reaction are _____ and _____.
pH and temperature
What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate”
Serine, hydroxylate
PAM reactivates acetylcholine esterase, functioning as a _____.
Nerve gas antidote
What kind of reaction produces the reactivated enzyme?
Nucleophilic substitution
The bisubstrate-enzyme _____ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively binding substrates.
An _____ works by amplifying the initial signal via several linked protease cleavage reaction stages.
Enzyme cascade
A _____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage.
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
_____ involves binding of a regulatory molecule at a site other than the active site.
_____ and _____ reactions, involving phosphate addition and removal respectively, regulate both qlycolysis and the Krebs cycle.
Kinase and phosphatase
_____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction.
Cyclin kinase
What two amino acids are modified in the reactions catalyzed by cyclin kinase?
Tyrosine and threonine
Two example of reversible factors that control the catalytic capability of an enzyme are:
Noncovalent modifications, and pH changes
Two examples of irreversible factors that control the catalytic capability of an enzyme are:
Covalent modification, and irreversible inhibitors
The _____ accounts for the temperature dependence of the rate of a reaction.
Arrhenius equation
List two “chemical modes of catalysis”
Acid-base, and covalent
List two “binding modes of catalysis”
Proximity effect, and transition-state stabilization
A _____ attacks an electropositive site in i’s role in a chemical (enzymatic) reaction.
A common process used to produce a nucleophile is _____.
Acid-base catalysis
Probably the most common amino acid used by enzymes to carry out acid-base catalysis is _____.
A “catalytic triad” of amino acids is typically present in (enzyme class name) _____
Serine proteases
The amino acids “collaborate” to accomplish _____.
Acid-base catalysis (or protein cleavage)
The most typically cited currency of energy in metabolism is
_____ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions.
A coenzyme is either a loosely bound cosubstrate of a tightly bound _____.
He heavy metal molybdenum is used to facilitate the biochemical reaction in _____, a key enzyme in purine catabolism.
Xanthine oxidase
When ATP is used I some biochemical applications it yields AMP and _____.
The (vitamin) _____ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions.
The other key redox coenzyme is abbreviated _____
The coenzyme _____ often forms a Schiff base with the ε-amino group of a lysine residue in the enzyme.
Pyroidoxal phosphate
What chemical group does CoA typically carry in the course of its biochemical function?
The _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the “affinity capture” technique.
The coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA.
N5, N10 tetrahydrofolate
Our understanding of this function can be used in a strategy for (treatment technique) _____.
Anti-cancer chemotherapy
The coenzyme-bound carbohydrate _____ and glucose are required to synthesize lactose.
Cis-retinal functions in _____ the signal of a photon of light into a chemically recognizable form.
The two important straight-chain forms of carbohydrate structure are the _____ and _____.
Ketose and aldose
The two important ring forms of carbohydrate are the _____ and _____.
Pyranose and furanose
The two important ring conformations of β-D-glucopyranose are the _____ and _____.
Chair and boat
The cyclohexane ring containing compound _____ is released by phospholipase C in the phospholipids signal transduction mechanism.
Inositol triphosphate
The acronym NAG is used to abbreviate the name of the compound _____.
N-acetyl galactosamine
The key polysaccharide in starch is _____.
The key polysaccharide in the liver is _____.
The antibiotic_____ selectively inhibits cell wall peptidylglycan synthesis in bacteria.
Extra-cellular surface _____ regulate the osmotic pressure around cells.
Phospholipase C produce two second messengers in the phospholipids signal transduction pathway. The lipid-containing second messenger is _____.
The compound chondroitin sulfate _____ cartilage and skeletal joints.
_____ fatty acids of the same length have a lower melting temperature (Tm).
Lipid Tm values monitor the transformation from _____ to dispersed forms.
Liquid crystal
The most popular model for a biological membrane is called the _____ model.
Fluid mosaic
Liquid _____ are composed of two face-to-face monolayers while lipid _____ form a biphasic sphere.
Bilayers, micelles
The four nucleic acid bases in RNA are _____, _____, _____, and _____.
Adenine, guanine, cytosine, and uracil
The normal base pairs in DNA and RNA are called _____ base pairs.
The _____ bond in a nucleoside connects the base to the sugar.
The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA.
Absorbance at 260nm
The face-to-face interaction between nucleic acid bases is called______.
Base stacking
Counterions bind all nucleic acids and are required to neutralize the _____.
Phosphodiester phosphates.
The proteins called _____ serve this function in the case of most chromosomal DNA’s.
_____ base pairs are less stable than _____ base pairs.
A-T (or A-U), G-C
Two differences between A and B forms of DNA are:
A= 3’endo sugar confirmation, shorter, fatter helix
The 2’-hydroxyl group catalyzes _____ of RNA, a good example of anchiomeric assistance in a non-protein bimolecular mechanism.
Alkaline hydrolysis
An antisence oligonucleotide functionally inactivates an mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____ binding.
tRNA anticodon
Name the two most prevalent of the 4 classes of RNA.
Ribosomal RNA and transfer RNA
Two distinctive features of most eukaryotic mRNAs are _____ and _____.
7-Methyl G cap, poly A tail
A _____ is used to detect the presence of a specific complementary nucleic acid sequence.
DNA probe
_____ are required to produce, manipulate, and clone specific pieces of DNA.
Restriction endonucleases
Two functional ends of transfer RNA are the anticodon and _____.
Amino acid acceptor
The three most central catabolic pathways of intermediary metabolism are _____, _____, and _____.
Glycolysis, Kreb’s cycle, and electron transport/oxidative phosphorylation
The four major compounds in which energy is captured in a chemically usable form by metallic reaction pathways are _____, _____, _____, and _____.
ATP, NADH, FADH2, and coenzyme Q
The _____ (Q) corrects for deviations from standard stat concentrations (1M)
Mass action ratio
_____ (number) steps in glycolysis control most of the flux through the pathway under actual cellular conditions.
What do the 3 reactions that control most of glycolysis have in common?
They are metabolically irreversible
What do the reactions other than the 3 controlling reactions in glycolysis have in common?
They are near equilibrium
The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to _____.
The actual concentration of the reactant
The enzyme Triose phosphate isomerase converts ______ into glyceraldehydes-3-phosphate.
Dihydroxyacetone phosphate
When citrate negatively regulates (discourages) the phosphofructosekinase-1 reaction, the general name for this phenomenon is _____
Feedback inhibition
When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____.
Feedforward activation
The three possible catabolic fates of pyruvate are _____, _____, and _____.
Acetyl CoA, lactate, and ethanol
The enzyme alcohol dehydrogenase converts _____ to ethanol.
_____ uses the coenzyme lipoic acid in “fueling” the Kreb’s Cycle.
Dihydrolipoamide acetyl transferase
What “synport” reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction? (enzyme name)
Pyruvate translocase
The two “oxidative decarboxylation” reaction of the Krebs Cycle are catalyzed by _____ and _____.
Isocitrate dehydrogenase and α-ketogluterate dehydrogenase
List the reactions, coenzymes, cofactors, and enzymes involved in the “substrate-level phosphorylation” reaction of the Krebs Cycle.
Succinyl CoA synthetase
The enzymes _____ and malate dehydrogenase “fix” a carbonyl group on succinate in the production of oxaloacetate.
What crucial 2 carbon compound is then “fixed” to OAA?
What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals?
Alanine and lactate
What energy sources are used to produce the “proton motive force”?
What enzyme complex uses proton motive force as the driving energy for ATP synthesis in oxidative phosphorylation?
How does electron transport drive production of the proton motive force?
Exports H+ from mitochondrion (which creates a gradient, making them predisposed to flowing back in)
How many reactions of each round of β-oxidation of a fatty acid require?
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 steps of fatty acid β-oxidation. Name the four cofactors involved in this “siphon.”
Which three steps of the Krebs Cycle do the first three steps of β-oxidation resemble?
Succinate dehydrogenase, fumarase, malate dehydrogenase
Which three steps of the Krebs Cycle do the first three steps of β-oxidation resemble?

Succinate dehydrogenase, fumarase, malate dehydrogenase

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