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Home , Addition reaction, Enzyme kinetics, Substrate (chemistry)

Kinetics… Virtually All Reactions in Cells Are Mediated by • Enzymes catalyze thermodynamically favorable reactions, causing them to proceed at extraordinarily rapid rates • Enzymes provide cells with the ability to exert kinetic control over thermodynamic potentiality • Living systems use enzymes to accelerate and control the rates of vitally important biochemical reactions • Enzymes are the agents of metabolic function Enzymatic Role of enzymes • serve the same role as any other catalyst in chemistry • act with a higher specificity • acid and base catalyst possible due to proximal locations of amino acids • alter the structure location of quantity of the enzyme and you have regulated the formation of - try that in !

• Don't lose sight of what enzymes do. catalyze reactions – nothing more reactants -> products.

What do Enzyme ACTUALLY do?

Naming Enzymes •Enzyme commission for each enzyme based on the type of reactions. Kind of like IUPAC •Yeah right - the mother of invention – he/she who finds/discovers/purifies/clones the enzyme, names if. Trivial names rule…

• First recognition of an enzyme and naming – 1833: precipitate of malt extract converted starch into sugar – called diatase (first use of suffix –ase) • traditionaly are the only enzymes which don’t end in ‘ase’ and use ‘-in’ • Enzyme is coined after the Greek for “in yeast” • 1050s started need to use a standardized naming: Otto Hofmann-Ostenhof and Dixon & Webb – common, non-systematic names still rule.

Enzyme Nomenclature Provides a Systematic Way of Naming Metabolic Reactions O T H L I L

Enzyme reaction types: Enzymes are classified into six major classes based on the reaction they catalyze. 1) catalyze oxidation-reduction reactions. Most of these enzymes are known as , but some are called , , or . 2) catalyze group-transfer reactions (functional groups). Many require the presence of coenzymes. A portion of the usually binds covalently to these enzymes or their coenzymes. This group includes the ! 3) catalyze hydrolysis. They are a special class of transferases, with water serving as the acceptor of the group transferred 4) catalyze nonhydrolytic and nonoxidative elimination reactions, or lysis, of a substrate, generating a double bond. In other words these reactions catalyze group elimination to form double bonds. A that catalyzes addition reaction in cells is often termed a . 5) catalyze the reactions. Because these reactions have only one substrate and one product, they are among the simplest enzymatic reactions. 6) catalyze ligation or joining, of two substrates. These reactions require the input of chemical potential energy of a nucleoside triphosphate such as ATP. i.e. bond formation coupled to ATP hydrolysis. Ligases are usually referred to as synthetases. Often involved in joining carbon to N, S or O atoms.

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Enzyme specificity - One of the most powerful actions of enzymes. – Group complementation - the ability to recognize specific regions of the substrate to align reactants with catalytic site. – Based on non-covalent molecular interactions. – Lock and key vs. induced fit - both occur. Induced fit takes place when binding of one part of the substrate to the enzyme alters the conformation of the enzyme to make a true "fit" – Binding does not mean activity

Enzyme specificity An enzyme can bind and react stereo-specifically with chiral compounds This can happen due to a three point attachment – Binding can then only occur in one way and therefore the products are not a mixture.

General Information on Enzymology Enzyme nomenclature • • Substrate vs. reactant • Prosthetic groups, coenzyme and cofactors • Activity vs. reaction • Suffix -ase

Another important reminder - not all activity is on or off. Many times the enzyme has a low or constitutive activity that can be increased many times. It is a common mistake to think of enzymes being on or off.

Job of Enzyme Catalysts • Specifically bind substrate(s) (reactants), decrease energy to increase the rate (NOT thermodynamics) of a favorable reaction: • High specificity • Low side reactions • Ability to be regulated: Active site – amino acids and cofactors binding and “doing” the reaction, are regulated by the rest of the

How do enzymes work? • By reducing the energy of • This happens because the transition state is stabilized by a number of mechanisms involving the enzyme/protein • Without enzymes reactions occur by collisions between reactants or addition of various organic catalysts • The energy barrier between the reactants and product, is the free energy of activation. • The free energy (DG) of the reaction is what determines if a reaction is spontaneous.

Reactions are often multistep Two intermediate transition states. • Two step reactions will have a slow and fast step – based on activation energy • The higher activation step is the rate-limiting step of the reaction

Enzyme Kinetics • Kinetics is the branch of science concerned with the rates of reactions • seeks to determine the maximum reaction velocity that enzymes can attain and the binding affinities for substrates and inhibitors • Analysis of enzyme rates yields insights into enzyme mechanisms and metabolic pathways • This information can be exploited to control and manipulate the course of metabolic events

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Rates of a reaction… – the number of that must collide/interact for a reaction to occur. • For enzymes, molecules that are involved at the active site for a step of the reaction. • Unlike non-enzyme catalyzed reactions, the rate is too complex but often initially described as unimolecular or bimolecular • Remember, order – refers to , while molecularity defines the mechanism

Gen Chem – Rates of Reaction… Quick Review – MOST enzymes catalyze reactions in a first or second order reaction. - Less about collisions of freely moving molecules than binding and reacting on a surface of a catalyst (enzyme active site):

For single/uni-molecularity reactions – 1st order A->P The rate is proportional to the concentration of substrate

Enzyme Kinetics Kinetic defn.: Of or relating to or produced by motion. Kinetics defn.: the branch of chemistry or concerned with measuring and studying the rates of reactions.

Enzyme kinetics are defined differently than basic chemistry kinetics because of the large catalyst…

Measuring Rates of Enzyme Catalyzed Reactions Louis Michaelis and 's theory • assumes the formation of an enzyme-substrate complex • assumes that the ES complex is in rapid equilibrium with free enzyme • assumes that the breakdown of ES to form products is slower than 1) formation of ES and 2) breakdown of ES to re-form E and S Enzyme Kinetics An enzyme-catalyzed reaction of substrate S to product P, can be written

Actually, the enzyme and substrate must combine and E recycled after the reaction is finished, just like any catalyst. Because the enzyme actually binds the substrate the reaction can be written as:

The simplest reaction is a single substrate going to a single product. Rate or velocity of the reaction depends on the formation of the ES •The P -> ES is ignored •The Keq is based on the idea that the reaction is limited to the formation of the ES complex and that only K1 and K-1 are involved because the thermodynamics of the reversal of K2 cause it to be minimal

How fast an enzyme catalyzes a reaction is it's rate. The rate of the reaction is in the number of moles of product produced per second

[ES] Remains Constant Through Much of the Enzyme Reaction Time Course in Michaelis-Menten Kinetics

3 Time course for a typical enzyme-catalyzed reaction obeying the Michaelis-Menten, Briggs-Haldane models for enzyme kinetics. • The early state of the time course is shown in greater magnification in the bottom graph. Enzyme-Catalyzed Reactions • The relationship between the concentration of a substrate and the rate of an enzymatic reaction is described by looking at the concentration of S and v • At low concentrations of the enzyme substrate, the rate is proportional to S, as in a first-order reaction • At higher concentrations of substrate, the enzyme reaction approaches zero-order kinetics • This behavior is a saturation effect Psuedo First Order Kinetics For the most part enzyme reactions are treated as if there is only one substrate and one product. If there are two substrates, one of them is held at a high concentration (0 order) and the other substrate is studied at a lower concentration • so that for that substrate, it is a first order reaction. This leads us to the M and M equation.

•Mathematical model of the representation of the M&M eq. - For the reaction:

1) The Michaelis constant Km is:

Think of what this means in terms of the equilibrium. Large vs. a small Km

2) When investigating the initial rate (Vo) the Michaelis-Menten equation is:

Graphical representation is a hyperbola. Think of the difference between O2 binding of myoglobin and . •When [S] << Km, the velocity is dependent on [S] •When [S] >> Km, the initial velocity is independent of [S] •When [S] = Km, then Vo = 1/2 V max

Understanding Vmax The theoretical maximal velocity Vmax is a constant Vmax is the theoretical maximal rate of the reaction - but it is NEVER achieved in reality To reach Vmax would require that ALL enzyme molecules are tightly bound with substrate Vmax is asymptotically approached as substrate is increased

Understanding KmThe "kinetic activator constant" Km is a constant Km is a constant derived from rate constants Km is, under true Michaelis-Menten conditions, an estimate of the of E from S Small Km means tight binding; high Km means weak binding

Conditions for Michaelis -Menten Two assumptions must be met for the Michaelis-Menten equation 1) Equilibrium -the association and dissociation of the substrate and enzyme

4 is assumed to be a rapid equilibrium and Ks is the enzyme:substrate dissociation constant.

Two Assumptions… 2) - the enzyme substrate complex ES is at a constant value. That is the ES is formed as fast as the enzyme releases the product. For this to happen the concentration of substrate has to be much higher than the enzyme concentration. That is why we only study the initial velocity. Later in the reaction the substrate concentration is relatively lower and the rate of product starts to be limited by diffusion and not the mechanism of the enzyme.

Don't for get the two assumptions - They both lead to the same equation, the michaelis-menten equation.

What is this awe inspiring equation? The Michaelis-Menten kinetic model explains several aspects of the behavior of many enzymes. Each enzyme has a Km value that is characteristic of that enzyme under certain conditions. Determining Km and Vmax • Must be done experimentally/emperically • Measure rate of enzyme vs different concentrations of substrate

BUT YOU CAN’T GET THERE FROM HERE

Create a secondary plot to determine kinetic constants Linear Plots Can Be Derived from the Michaelis-Menten EquationLineweaver-Burk:

Begin with v = Vmax[S]/(Km + [S]) and take the reciprocal of both sides

Rearrange to obtain the Lineweaver-Burk equation:

A plot of 1/v versus 1/[S] should yield a straight line

Linear Plots Can Be Derived from the Michaelis-Menten Equation

Hanes-Woolf: Begin with Lineweaver-Burk and multiply both sides by [S] to obtain:

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Hanes-Woolf is best - why? Because Hanes-Woolf has smaller and more consistent errors across the plot

Other uses of Km The Turnover Number Defines the Activity of One Enzyme Molecule A measure of catalytic activity • kcat, the turnover number, is the number of substrate molecules converted to product per enzyme molecule per unit of time, when E is saturated with substrate. • If the M-M model fits, k2 = kcat = Vmax/Et • Values of kcat range from less than 1/sec to many millions per sec

The Turnover Number Defines the Activity of One Enzyme Molecule

The Ratio kcat/Km Defines the Catalytic Efficiency of an Enzyme The catalytic efficiency: kcat/Km An estimate of "how perfect" the enzyme is • kcat/Km is an apparent second-order rate constant • It measures how well the enzyme performs when S is low

The upper limit for kcat/Km is the diffusion limit - the rate at which E and S diffuse together The Ratio kcat/Km Defines the Catalytic Efficiency of an Enzyme So What? Or WDIC? Km • Km - relates to affinity ; Vmax relates to efficiency • Km tell how much substrate to use in an assay • If more than one enzyme share the same substrate, KM also will determine how to decide which pathway the substrate will take Vmax tells about pathways • Rate limiting enzyme in pathway • Km and Vmax can be used to determine effectiveness of inhibitors and activators for enzyme studies and clinical applications Enzyme Inhibitors Molecules which bind and act to alter the reaction kinetics of an enzyme. By binding to enzyme reducing the affinity, velocity, catalytic turnover or all of the above. - examples include poisons and

• Some inhibitors reversibly bind directly to active site competing with normal substrate (competitive inhibitor) • Some inhibitors reversibly bind to the protein away from active site – altering structure of protein so the enzyme does not function (either won’t bind or won’t react substrate). Non and Un-competitive and allosteric… • Other inhibitors bind covalently (irreversibly) to the active site, leaving the enzyme “dead”. Suicide Inhibitor

Competitive Inhibitors Compete With Substrate for the Same Site on the Enzyme

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Lineweaver-Burk plot of , showing lines for no I, [I], and 2[I].

Km is reduced but Vmax is unchanged

Pure Noncompetitive Inhibition – where S and I bind to different sites on the enzyme

Lineweaver-Burk plot of pure noncompetitive inhibition.

Note that I does not alter K but that it decreases V . m max

7 Mixed Noncompetitive Inhibition: binding of I by E influences binding of S by E

Lineweaver-Burk plot of mixed noncompetitive inhibition.

Note that both intercepts and the slope change in the presence of I.

Uncompetitive Inhibition, where I combines only with E, but not with ES

Note that both intercepts change but the slope (K /V ) remains constant in m max

the presence of I.

8 Kinetic Behavior of Bimolecular Reactions? Enzymes often catalyze reactions involving two (or more) substrates

Bisubstrate reactions may be sequential or single-displacement reactions or double-displacement (ping-pong) reactions

Single-displacement reactions can be of two distinct classes: 1. Random, where either substrate may bind first, followed by the other substrate 2. Ordered, where a leading substrate binds first, followed by the other substrate

Conversion of AEB to PEQ is the Rate-Limiting Step in Random, Single-Displacement Reactions

• In this type of sequential reaction, all possible binary enzyme-substrate and enzyme-product complexes are formed rapidly and reversibly when enzyme is added to a reaction mixture containing A, B, P, and Q.

In an Ordered, Single-Displacement Reaction, the Leading Substrate Must Bind First

• The leading substrate (A) binds first, followed by B. Reaction between A and B occurs in the ternary complex and is usually followed by an ordered release of the products, P and Q.

The Double Displacement (Ping-Pong) Reaction

• Double-Displacement (Ping-Pong) reactions proceed via formation of a covalently modified enzyme intermediate. Reactions conforming to this kinetic pattern are characterized by the fact that the product of the enzyme’s reaction with A (called P in the above scheme) is released prior to reaction of the enzyme with the second substrate, B.

How Can Enzymes Be So Specific? The “Lock and key” hypothesis was the first explanation for specificity The “Induced fit” hypothesis provides a more accurate description of specificity Induced fit favors formation of the transition state Specificity and reactivity are often linked. In the reaction, binding of glucose in the active site induces a in the enzyme that causes the two domains of hexokinase to close around the substrate, creating the catalytic site

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