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From MyMCAT

Contents 1 Introduction 2 Structure 3 Function 4 Mechanisms of Enzyme Action 5 Reaction Rates 5.1 Basic Regulation 5.2 Substrate Availability 5.3 Allosteric Regulation and Inhibition

Introduction

Enzymes are proteins (and sometimes unique RNA molecules) that act to catalyze a chemical reactions. The functions of enzymes are limitless, catalyzing reactions used in normal development, maintenance of the cell, defense against disease and they can function intracellularly, extracellularly, or even on the surface of a cell membrane.

Structure

Enzymes, like other proteins, are polymerase of amino acids that can also secondarily modified by additional other classes of molecules like lipids and sugars. The sequence of this polymer governs how it will fold and therefore determines the three dimensional structure of the protein. Unlike other proteins however, the shape of an enzyme is designed to distinctly carry out a chemical reaction using unique organizations of amino acid residues to facilitate the reaction. This distinctive site of the surface of the protein is known as the active site and generally allows substrates to fit uniquely and specifically. Enzymes also often employ secondary sites to regulate their function, these sites known as regulatory sites, allow binding of other molecules which cause the enzyme to slightly change shape and thus alter its ability to function. Just as other proteins can exist as multi-subunit complexes (like hemoglobin) so too can enzymes.

Function

Enzymes are true catalysts in that they are unchanged at the end of a reaction cycle and do NOT change a reactions equilibrium constant. Like other catalysts, enzymes function by lowing the activation energy of a reaction, the energy barrier that much be overcome before substrates can be converted to products. While the energy difference between reactants and products is unchanged between a catalyzed and uncatalyzed reaction, the energy that must be put in to cause the reaction (E activation) is reduced permitting reactions to occur at a faster rate than the uncatalyzed equivalent.

Mechanisms of Enzyme Action

Enzymes can improve reaction rates due to many effects. Firstly, by binding substrates together, enzymes are capable of holding reactants together effectively increasing the local concentration of reactants providing more time for them to react before they separate (whereas in an uncatalyzed reaction, the likelihood of reactants coming together long enough and in the correct orientation for a reaction to occur is often much less). Secondly, the shape of the active site forces reactants to assume a restricted range of shapes. This allows the enzyme to align segments of reagents in ways that permit functional groups to come together facilitating reactions to occur. This forced conformation is often known as the entropy effect (since it increases order in the reactants). Thirdly, the shape of the reagents in a bound enzyme are usually strained. This process is commonly known as induced fit which is a modification of the previously thought lock and key theory.

In the lock and key theory of enzyme mechanics, it was thought that substrates fit perfectly into an enzymes active site. This however, leaves the question: If they fit perfectly, why would they want to react, and secondly, why would the dissociate away from the enzyme afterward since they fit so nicely into the enzyme? The modern theory of induced fit answers both of these questions. Firstly, by causing substrates to strain, they become more unstable permitting reactions to occur more readily (and reach a transition state more easily). And secondly, by making the fit strained, energy can be released when the substrates (or products) are released as they are then able to return to a more stable free state.

Enzymes typically employ covalent catalysis and acid-base catalysis to carry out reactions. In these processes, amino acid residues in the enzyme react with groups in the substrates (often producing covalently linked enzyme-substrate complexes) to perform reactions. These processes are then completed by breaking the newly formed bonds in either reverse reactions or hydrolysis reactions to return the enzyme back to its original state but leaving the substrates modified.

Reaction Rates

Basic Regulation

Without considering regulatory and allosteric sites on an enzyme that may alter activity, the two most common regulatory effects are due to concentration of enzyme and enzyme reaction conditions. Firstly, the higher the concentration of enzyme the more reactions that can occur. To achieve this, either enzyme synthesis (through transcription and translation) should be increased, or the level of enzyme degradation should be reduced. Secondly, the conditions under which an enzyme is efficient is dependent on how the protein exists under those conditions. Protein structure can change depending on temperature, pH, and ionic strength and as a consequence an enzymes activity will be maximal under only a specific set of conditions. Pepsin, for instance, in found in the acidic conditions of the stomach and works optimally under these conditions. Under more basic conditions however, residues become modified altering the enzymes shape and its ability to react with substrates and as a consequence the enzyme's acitivity is decreased.

Substrate Availability

The rate of a reaction is intrinsicaly dependent on the concentration of the substrates. In an uncatalyzed reaction, the rate of a reaction depends on the probability of reactants colliding into one another (ie their concentration) and similarly in a catalyzed reactions, the rate depends on the probability of substrates occupying the enzymes active site. However, the effect of increasing substrate concentration on increasing the rate of the reaction is limited by how many enzymes are available. If one increases the substrate concentration, there becomes a point at which all of the available enzymes are occuped and thus increasing the substrate concentration wont make a difference as the excess substrate has no where to go. At this point, the enzyme is said to be saturated.

This phenomena can easily be understood if one plots the initial rate of a reaction based on the concentration of the substrate (where the amount of enzyme is held fixed). In this type of graph, only the initial reaction rate is used as the substrate concentration will begin to reduce otherwise as time goes on. This type of graph is known as a Michaelis-Menten graph.

Allosteric Regulation and Inhibition

A final way in which enzymes can be regulated is through the binding of other molecules or metabolites. Often, it is possible for an alternative molecule to enter an enzymes active site, this this case, the desired substrate is in competition with the other molecule and a reduced enzyme activity is commonly observed. A second method of regulation is through binding of molecules other than the active site. These sites, known as allosteric sites, have the ability to cause a change in enzyme activity (either positively or negatively) through conformational changes which occur when the molecule binds to the enzyme, as a consequence these changes result in alternations to the active site and in turn to the reaction kinetics of the enzyme. Inhibition is discussed in the next section.