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.
- zwitterion
- 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.
- Catalysis
- 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.
- Lineweaver-Burk
- 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 _____
- Kcat
- _____ 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.
- Ping-pong
- 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.
- Zymogen
- 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.
- Allosterism
- _____ 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 catalysisâ€
- Acid-base, and covalent
- List two “binding modes of catalysisâ€
- Proximity effect, and transition-state stabilization
- A _____ attacks an electropositive site in i’s role in a chemical (enzymatic) reaction.
- Nucleophile
- 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 _____.
- Histidine
- 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
- ATP
- _____ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions.
- Mg2+
- A coenzyme is either a loosely bound cosubstrate of a tightly bound _____.
- Cofactor
- 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 _____.
- pyrophosphate
- The (vitamin) _____ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions.
- Nicotinamide
- The other key redox coenzyme is abbreviated _____
- FAD
- 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?
- Acetate
- The _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the “affinity capture†technique.
- Biotin
- 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.
- UDP-galactose
- Cis-retinal functions in _____ the signal of a photon of light into a chemically recognizable form.
- Transducing
- 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 _____.
- Amylopectin
- The key polysaccharide in the liver is _____.
- Glycogen
- The antibiotic_____ selectively inhibits cell wall peptidylglycan synthesis in bacteria.
- penicillin
- Extra-cellular surface _____ regulate the osmotic pressure around cells.
- Carbohydrates
- Phospholipase C produce two second messengers in the phospholipids signal transduction pathway. The lipid-containing second messenger is _____.
- Diacylglycerol
- The compound chondroitin sulfate _____ cartilage and skeletal joints.
- Lubricates
- _____ fatty acids of the same length have a lower melting temperature (Tm).
- Unsaturated
- 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.
- Watson-Crick
- The _____ bond in a nucleoside connects the base to the sugar.
- Glycosidic
- 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.
- Histones
- _____ 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.
- 3
- 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.
- acetaldehyde
- _____ 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.
- fumarase
- What crucial 2 carbon compound is then “fixed†to OAA?
- acetate
- 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�
- NADH, FADH2, CoQH2
- What enzyme complex uses proton motive force as the driving energy for ATP synthesis in oxidative phosphorylation?
- F0F1ATPase
- 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?
- 4
- 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.â€
- CoA, FAD/FADH2, Fe-S, CoQ/CoQH2
- 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