Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, definitions in middle, relevant figures from 2nd edition on right).

Terms | Descriptions | Figures | Activated State | With respect to a chemical reaction, a transient high energy state of a reactant molecule (such as an unfavorable electron configuration or strained conformation) that enables the molecule to undergo the reaction. |  | Active Site | The site on an enzyme molecule where the substrate binds and where the reaction is facilitated. It is often a cleft or pocket in the surface of the enzyme. |  | Acute Pancreatitis | An extremely painful condition brought about by activation of trypsin in the pancreas. |  | Acyl-enzyme Intermediate | An intermediate formed during cleavage of a peptide bond by a serine protease. The intermediate contains the N-terminal part of the polypeptide substrate covalently (and transiently) bound to the enzyme. |  | Affinity Labeling | A process whereby an irreversible competitive inhibitor is bound to an enzyme's active site in order to label it. |  | Alcohol Dehydrogenase | A liver enzyme which catalyzes the reaction, Ethanol + NAD+<=> Acetaldehyde + NADH |  | Allosteric Activator | A heteroallosteric effector which shifts the T R equilibrium toward the R state |  | Allosteric inhibitor | A heteroallosteric effector which shifts the T R equilibrium toward the T state | Figure 11.34 | Allosteric Regulation | A type of enzymatic regulation in which the activity of an enzyme is affected by binding of a molecule by the enzyme. |  | Aspartate Carbamoyltransferase (Aspartate Transcarbamoylase, ATCase) | An allosteric enzyme that catalyzes a committed step in bacterial pyrimidine biosynthesis, conversion of carbamoyl phosphate and aspartate to N-carbalmoyl-L-aspartate. | Figure 11.35, Figure 11.37 | Autocatalytic | A molecule which catalyzes a reaction upon itself. |  | Biotin | A coenzyme involved in carboxylation reactions. |  | Carbamoyl Phosphate Synthetase II | An allosteric enzyme that catalyzes a committed step in eukaryotic pyrimidine biosynthesis, synthesis of carbamoyl phosphate from glutamine. It is inhibited by UDP, UTP, CTP, dUDP, and DUP-glucose, all of which prevent binding of the ATP substrate required by the enzyme. | Figure 11.35 | Carboxypeptidase A | A zinc-containing enzyme that catalyzes cleavage of polypeptide chains. |  | Catalase | An enzyme catalyzing the reaction, 2H2O2 -> 2H2O + O2 |  | Catalyst | A substance that increases the rate, or velocity, of a chemical reaction without itself being changed in the overall process. |  | Catalytic Antibodies | Antibodies that recognize molecules structurally analogous to transition states of particular substrates. Such antibodies act like enzymes. |  | Chymotrypsin | A serine protease that cuts preferentially on the carboxylate side of hydrophobic amino acid residues (such as phenylalanine) of a polypeptide. | Figure 11.13 | Coenzyme A | A coenzyme involved in acyl transfer reactions. |  | Competitive Inhibition | A type of inhibition of enzymatic catalysis in which the inhibitor is a molecule that resembles the substrate of the reaction and is accepted by the enzyme at the active site, but cannot undergo the catalytic step. | Figure 11.19 | Diisopropyl fluorophosphate (DFP) | An irreversible competitive inhibitor of enzymes having a serine in the active site. Enzymes include acetylcholinesterase and serine proteases. | Figure 11.24 | Eadie-Hostee Plot | A graph of enzymatic activity obtained by plotting V/[S] versus V, where V is the reaction velocity. |  | Enediol | An intermediate in a chemical reaction in which both carbons in a double bond are linked to hydroxyl groups. Such an intermediate occurs in the reaction catalyzed by triose phosphate isomerase. | Figure 11.17 | Enteropeptidase | A protease involved in activation of trypsinogen. |  | Enzyme | A protein that catalyzes a reaction |  | Enzyme-Substrate Complex | An intermediate in enzymatic catalysis in which the substrate is bound in the enzyme's active site in or near the transition state. |  | Epinephrine | Hormone interacting with cell surface that initiates a regulatory cascade to activate glycogen phosphorylase (and other enzymes). |  | Factor IX | Blood protein (also called Christmas factor) that, when activated by Factor XI, acts with Factor VII, Factor VI, and Tissue factor to activate Factor X | Figure 11.42 | Factor V | Blood protein that acts together with Factor X to activate prothrombin to thrombin. | Figure 11.42 | Factor VIII | Blood protein missing in classic hemophilia. Acts together with Factor IX to help activate Factor X | Figure 11.42 | Factor X | Blood protein that, after activation by Factors IX, VIII, VII, and Tissue factor, acts with Factor V to convert the inactive prothrombin to thrombin. | Figure 11.42 | Factor XI | Blood protein that, when activated by Factor XII, catalzyes activation of Factor IX. | Figure 11.42 | Factor XII | Blood protein that, when activated by kininogen and kallikrein, catalzyes activation of Factor XI. Also called Hageman factor. | Figure 11.42 | Factor XIII | Blood protein that converts Fibrin II to Fibrin I. | Figure 11.42 | FAD | A coenzyme which accepts electrons released in biological oxidations, forming FADH2. |  | Feedback Control | An enzymatic regulatory mechanism in which an end product of a multi-step pathway affects the activity of an enzyme early in the pathway. |  | Fibrin | Protein fibers that form a blood clot. | Figure 11.42 | Fibrinogen | Precursor form of the blood clotting protein, fibrin. | Figure 11.42 | Fibrinopeptides | Small peptides released from fibrinogen by proteolytic cleavage during enzyme activation. |  | First-Order Reaction | A reaction whose rate depends on the first power of the concentration of the reactant. |  | Free Energy Barrier | The difference between the free energy of a molecule in its initial state and the free energy of the molecule in its activated state. | Figure 11.10 | Fusion Proteins | Proteins coded for by genes that have been spliced together in vitro from two or more sources, making it possible to combine binding sites and catalytic sites in novel ways. |  | Glycogen Phosphorylase | An enzyme of skeletal muscle that catalyzes cleavage of glucose residues from glycogen by cleaving and phosphorylating residues from the nonreducing ends during glycogenolysis. The enzyme is largely regulated by covalent modification - phosphorylation/dephosphorylation. |  | Half-Life | In a first order reaction, the amount of time required for half of a reactant to be converted to product. |  | Heteroallostery | A property of an allosteric enzyme in which its activity is regulated by other, effector molecules. |  | Hexokinase | An enzyme catalyzing the reaction Glucose + ATP <=> Glucose-6-phosphate + ADP | Figure 11.8 | Homoallostery | A property of an allosteric enzyme in which it exhibits cooperativity in substrate binding. |  | Hydrolases | One of six classes of enzymes recognized by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). This one catalyzes hydrolytic cleavage. | Table 11.7 | Induced Fit Hypothesis | A mechanism of enzyme action, originally proposed by Daniel Koshland in 1958. It states that the enzyme active site best fits a substrate molecule induced to take up a configuration approximating that of the transition state. | Figure 11.7 | Intermediate States | In a chemical reaction, a catalyst can lower the activation energy of a chemical reaction by permitting an alternate pathway through the transition state. This altered pathway will have a state, such as this, which is considerably lower than the activation state of the uncatalyzed reaction. | Figure 11.5 | Irreversible Enzyme Inhibition | A process in which enzymatic catalysis is blocked by an inhibitor that covalently binds to the enzyme. |  | Irreversible Reaction | A reaction, such as the decay of radioactivity, that only occurs in one direction and cannot be reversed. |  | Isomerases | One of six classes of enzymes recognized by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). This one catalyzes intramolecular rearrangement. | Table 11.7 | Kallikrein | Along with kininogen, activates blood protein Factor XII | Figure 11.42 | Kininogen | Along with kallikrein, activates blood protein Factor XII | Figure 11.42 | KM | Also known as the Michaelis constant. A ratio of the rate constants for a specific enzymatic reaction, this entity gives information very characteristic of the reaction |  | Ligases | One of six classes of enzymes recognized by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). This one catalyzes reactions in which two molecules are joined. | Table 11.7 | Lineweaver-Burk Plot | Also called a double-reciprocal plot, this graph is made by plotting 1/V (velocity) versus 1/[S] for an enzymatic reaction. |  | Lock and Key Hypothesis | A mechanism to explain enzyme action, originally proposed by Emil Fischer in 1894. It states that an enzyme accommodates a specific substrate as a lock fits its specific key. A modification of this idea, the Induced Fit Hypothesis, better explains how catalysis is explained. | Figure 11.7 | Lyases | One of six classes of enzymes recognized by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). This one catalyzes removal of a group from or addition of a group to a double bond, or other cleavages involving electron rearrangement. | Table 11.7 | Metalloenzymes | Name for enzymes containing metal ions. |  | Michaelis Constant (KM) | A ratio of the rate constants for a specific enzymatic reaction, this entity gives information very characteristic of the reaction | Table 11.1 | Michaelis-Menten Equation | An equation that gives the rate of an enzyme-catalyzed reaction in terms of the concentrations of substrate and enzyme as well as two constants that are specific for a particular combination of enzyme and substrate: a rate constant for the catalytic production of product when the enzyme is saturated, and the Michaelis constant, KM |  | Mixed Inhibition | A kind of noncompetitive inhibition in which the enzyme-substate-inhibitor complex (ESI) has reduced catalytic activity or if binding of the inhibitor modifies both kcat and KM. |  | Nicotinamide Adenine Dinucleotide (NAD+), oxidized | A coenzyme which accepts electrons released in biological oxidations, for example in the reaction catalyzed by alcohol dehydrogenase of liver. | Table 11.5 | Nicotinamide Adenine Dinucleotide (NADH), reduced | A coenzyme which serves as an electron carrier. It can either donate electrons to a biological compound, reducing it, or can donate electrons to the electron transport system for use in oxidative phosphorylation. |  | Noncompetitive Inhibition | A type of enzymatic inhibition that occurs when a molecule or an ion can bind to a second site on the enzyme surface apart from the active site in such a way that it modifies kcat. | Figure 11.22 | Nonproductive Binding | A variant of competitive inhibition caused by binding of a normal substrate molecule to the active site in an alternate way in which the normal catalytic event cannot occur. |  | Ordered Substrate Binding | An enzymatic reaction mechanism for multiple substrate-binding in which one substrate must bind before the other one can be bound significantly. |  | Oxidoreductases | One of six classes of enzymes recognized by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). This one catalyzes oxidation-reduction reactions. | Table 11.7 | Pepsin | A protease produced in the stomach. |  | Phosphatase | An enzyme that removes phosphates from other molecules. Such an enzyme can convert the active form of glycogen phosphoryase (a) to the inactive form (b). |  | Phosphorylase a | The active form of glycogen phosphorylase. It arises from phosphorylation of the inactive form of the enzyme by phosphorylase kinase. |  | Phosphorylase b | The relatively inactive, unphosphorylated form of glycogen phosphorylase. The enzyme can be activated allosterically by AMP and strongly inhibited by ATP and glucose. |  | Phosphorylase Kinase | An enzyme catalyzing phosphorylation of the inactive glycogen phosphorylase b to the active form, glycogen phosphorylase a. |  | Ping-Pong Mechanism | An enzymatic reaction mechanism for multiple substrate-reactions in which one substrate is bound to an enzyme, a product is released, and then a second substrate binds and a second product is released. |  | Pre-steady-state | The period of time early in an enzymatic reaction before steady-state conditions are established. During this time, a "burst" of product can be produced rapidly | Figure 11.18 | Proteolytic Cleavage Control Mechanism | A covalent enzyme modification employed by some proteases, such as pancreatic proteases, which are inactive until proteolytically cleaved to activate them. Enzymes include trypsin, chymotrypsin, elastase, and carboxypeptidase, which are synthesized as inactive molecules called trypsinogen, chymotrypsinogen, proelastase, and procarboxypeptidase, respectively. | Figure 11.39 | Prothrombin | Precursor form of thrombin. | Figure 11.42 | Pyridoxal Phosphate | A coenzyme involved in group transfer reactions, especially transaminations. |  | Random Substrate Binding | An enzymatic reaction mechanism for multiple substrate-binding in which either substrate can be bound first. |  | Rate Constant | With respect to chemical reactions, a constant that relates the reaction rate for a particular reaction to substrate concentrations. |  | Rate-Limiting Step | In a multistep process, the slowest step, that determines how long the entire process takes. |  | Reaction Coordinate | A generalized measure of the progress of a chemical reaction. | Figure 11.2 | Reaction Rate (Velocity, V) | The rate with which the product of a reaction is produced. |  | Regulatory Cascade | A regulatory system controlling covalent modification of glycogen phosphorylase (and other enzymes) in which a series of phosphorylations of a set of enzyme provides tremendous amplification of a signal arsing from binding of a single hormone molecule to a cell surface, resulting in rapid activation of many enzyme molecules. |  | Reversible Enzyme Inhibition | A process in which enzymatic catalysis is blocked by an inhibitor without covalent binding to the enzyme. |  | Reversible Reaction | A chemical reaction which can occur in both directions, such as A <=> B. |  | Ribonuclease P | An RNA containing enzyme that catalyzes cleavage of precursors of tRNAs. The RNA can, under certain conditions, catalyze the reaction independent of the protein. |  | Ribozymes | RNA molecules that catalyze chemical reactions | Figure 11.29. | Second-Order Reaction | A reaction in which two reactant molecules must come together for the reaction to occur. The reaction is called second-order because the reaction rate depends on the square of reactant concentration (for two molecules of the same reactant) or on the product of two reactant concentrations (for two different reactants). |  | Secretory Pancreatic Trypsin Inhibitor | A trypsin inhibitor synthesized in the pancreas to prevent autocatalytic activation of trypsin. |  | Serine Proteases | A class of enzymes, including trypsin and chymotrypsin, that employ a serine residue in the reactions they catalyze - hydrolysis of peptide bonds in polypeptides and proteins. |  | Site-Directed Mutagenesis | A laboratory technique for making mutation(s) at a specific point in a DNA sequence. |  | Standard Free Energy of Activation | Symbolized by , it represents the additional free energy (above the average free energy of reactant molecules) that molecules must have to attain the transition state. |  | Steady State | Refers to a condition in an enzymatic reaction after the concentration of the enzyme-substrate (ES) complex builds up and then reaches a level at which it remains almost constant. In this condition, the rates of formation and breakdown of the ES complex are equal. | Figure 11.14 | Substrate | A substance acted on by an enzyme |  | Substrate-Level Control | Enzymatic regulation occurring through direct interaction of the substrates and products of each enzyme-catalyzed reaction with enzyme itself. The reaction catalyzed by hexokinase is under such control. |  | Suicide Inhibitor | Competitive inhibition of an enzyme by an irreversible competitive inhibitor. |  | Thiamine Pyrophosphate | A coenzyme involved in group transfer reactions. |  | Thrombin | Serine protease that catalyzes the proteolysis of fibrinogen to fibrin. | Figure 11.42 | Transferases | One of six classes of enzymes recognized by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology (IUBMB). This one catalyzes transfer of functional groups from one molecule to another. | Table 11.7 | Transition Energy | The amount of energy that must be added to a molecule to elevate its free energy from that of the initial state to that of the transition state. | Figure 11.2 | Transition State | In any chemical reaction, the high-energy or unlikely state that must be achieved by the reacting molecule(s) for the reaction to occur. |  | Triose Phosphate Isomerase | An enzyme that catalyzes the reaction Glyceraldehyde-3-phosphate Dihydroxyacetone Phosphate. The reaction proceeds via an enediol intermediate. | Figure 11.9 | Trypsin | A serine protease that cuts preferentially on the carboxylate side of basic amino acid residues in a polypeptide. |  | Turnover Number | Symbolized by kcat, this quantity is a measure of the amount of time it takes for an enzyme molecule to complete a reaction with one substrate molecule. | Table 11.1 | UDP-Glucose Epimerase | An NAD+/NADH containing enzyme that catalyzes interconversion of UDP-glucose and UDP-galactose. |  | Vitamins | Organic molecules that are essential to the biological processes of higher organisms, but cannot be synthesized by them. |  | Vmax (Maxiumum Velocity) | In an enzymatic reaction, a rate of reaction approached when substrate concentrations are much greater than KM. Under this state, the enzyme molecules are saturated with substrate. |  | Zymogen | A catalytically inactive precursor synthesized by a cell that must be activated to function. Examples include the pancreatic proteases. | Figure 11.39

Category - General

Query - Is contained in the left column below, solution in middle, figure on right

Reversal - there is no reversal

What does a catalyst do? | A catalyst acts to lower the activation energy for a chemical reaction. |  | Which scientist postulated a lock and key hypothesis to explain enzyme action? | Emil Fischer |  | What fits best into an active site of an enzyme? | A substrate molecule induced to take up a configuration approximating the transition state. |  | Who proposed the Induced Fit Hypothesis for enzyme action? | Daniel Koshland, in 1958. |  | What suffix is used to designate that a molecule is an enzyme? | -ase', as in hexokinase, for example. |  | What are common factors in all serine proteases? | 1. At the active site depression, an aspartate, a histidine, and a serine are all clustered. 2. A 'pocket' located close to the active site serine. |  | For a reaction obeying Michaelis-Menten kinetics, when does a reaction reach Vmax/2? | When [S] = KM |  | For a reaction obeying Michaelis-Menten kinetics, when does [S] = KM? | At Vmax/2 |  | In a two-step reaction, what does a large KM mean? | Low affinity of enzyme for substrate. |  | Under what conditions does the ratio kcat/KM behave as a second order rate constant for the reaction between substrate and free enzyme? | When [S]<<KM |  | Under what conditions will the ratio kcat/KM reach a maximum value? | When an enzyme has evolved to the maximum possible efficiency. |  | Name one enzyme whose kcat/KM value is close to the maximum possible value. | Triose phosphate isomerase. |  | On a Lineweaver-Burk plot, how does one find KM? | The value of the X-intercept is equal to -1/KM |  | On a Lineweaver-Burk plot, how does one find Vmax? | The value of the Y-intercept is equal to 1/Vmax. |  | What is the slope of an Eadie-Hofstee plot equal to? | -1/KM |  | What is the value of the X intercept of an Eadie-Hofstee plot? | Vmax |  | What is the value of the Y-intercept of an Eadie-Hofstee plot? | Vmax/KM |  | Trypsin inhibitor binding to trypsin is classified as what type of inhibition? | Reversible inhibition |  | What is the overall apparent effect of competitive inhibition? | The system acts as if the enzyme cannot bind substrate as well when the inhibitor is present. |  | Under competitive inhibition, what happens to KM and Vmax compared to the uninhibited reaction? | Vmax is unchanged, but KM increases, consistent with a lowered apparent affinity of enzyme for substrate. |  | Under non-competitive inhibition, what is the effect on KM and Vmax, compared to the uninhibited reaction? | Vmax is reduced. KM is unchanged. |  | Name a system with an irreversible competitive inhibitor. | 1. Diisopropyl fluorophosphate (DFP), which binds with serine hydroxyl groups and inactivates enzymes with serines in their active site, such as serine proteases or acetylcholinesterase. 2. N-tosyl-L-phenylalaninechloromethyl ketone (TPCK), which inhibits chymotrypsin because the inhibitor binds into the active site pocket, positioning the chlorine to react with the imidazole ring of histidine #57.

3. Physostignine, which is an alkaloid in calabar beans that is a potent inhibitor of acetylcholinesterase.

4. Penicillin antibiotics, which act as irreversible inhibitors of serine-containing enzymes used in bacterial cell wall synthesis.

5. Sarin, which binds with serine hydroxyl groups and inactivates enzymes with serines in their active site, such as serine proteases or acetylcholinesterase.

6. Parathion, which is a potent inhibitor of acetylcholinesterase.

Name two ribozymes

1. The RNA component of ribonuclease P

2. The L-19 IVS from a Tetrahymena preribosomal RNA

Name one enzymatic reaction under substrate-level control | The reaction catalyzed by hexokinase. | What is the effect of ATP on the allosteric enzyme, ATCase? | Activates it. | What is the effect of CTP on the enzyme ATCase? | Inhibits it. | Name a zymogen | 1. Trypsinogen 2. Chymotrypsinogen 3. Proelastase 4. Procarboxypeptidase 5. Fibrinogen

Category - General

Query - What type(s) of reaction is the following coenzyme involved in?

Reversal - there is no reversal

(coenzyme on left, reaction in middle, figures on right)

Nicotinamide Adenine Dinucleotide (NAD+), oxidized | Accepts electrons released in biological oxidations. |  | FAD | Accepts electrons released in biological oxidations, forming FADH2. |  | Thiamine Pyrophosphate | Group transfer reactions. |  | Coenzyme A | Acyl transfer reactions. |  | Biotin | Carboxylation reactions. |  | Pyridoxal Phosphate | Group transfer reactions, especially transaminations. |

Category - Enzymes

Query - What enzyme from chapter 11 contains the following metal ion?

Reversal

Category - General

Query - What metal is bound by the following metalloenzyme?

(coenzyme on left, reaction in middle, figures on right)

Fe | Cytochrome Oxidase or Catalase |  | Cu | Ascorbic Acid Oxidase |  | Zn | Alcohol Dehydrogenase or Carboxypeptidase A |  | Mn | Histidine ammonia-lyase |  | Co | Glutamate mutase |  | Ni | Urease |  | Mo | Xanthine Oxidase |  | V | Nitrate Reductase |  | Se | Glutathione Peroxidase |

Category - Lists

Query - In the fibrin production cascade, which step precedes/follows the one below?

[[Program should pick a step and whether a student is to give the preceding or following step - note here that the second term (after query) is actually the step from below that the computer randomly picks]].

1. In damaged tissue, the proteins kininogen and kallikrein activate factor XII (part of intrinsic pathway). or 1. Damage to blood vessels leads to release of tissue factor and activation of factor VII (start of extrinsic pathway). | 2. Factor XII activates factor XI (part of intrinsic pathway). | 3. The extrinsic and intrinsic pathways merge with activation of factor X. Activation of factor X by factor IX of the intrinsic pathway requires factor VIII (antihemophilic factor). | 4. Factor X activates prothrombin to thrombin | 5. Thrombin removes small fibrinopeptides from fibrinogen to form fibrin.