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Biological and Biochemical Foundations of Living Systems

Enzyme Structure and Function

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Function of enzymes in catalyzing biological reactions

An enzyme is a biological catalyst, in that it accelerates chemical reactions in a biological system. An enzyme accomplishes this acceleration by interacting with the reactants (the enzyme's substrates) in a manner which stabilizes their transition state (‡), which in turn lowers the activation energy (Ea) of the reaction, and a lower activation energy allows for the reaction to proceed faster.

Although an enzyme interacts with its substrates, it is not consumed in the reaction like a reactant. Once a reaction completes, the enzyme is again available to process new substrate. In a biological context, the reusable nature of enzymes to catalyze a particular reaction (the enzyme's specificity) offers a mechanism of controlling reactions by directing which enzymes are present and active, and in what quantities.

Enzyme classification by reaction type

Because of their specificity, a particular enzyme will only catalyze a singular or narrow set of similar reactions, allowing for classification by reaction type. Names for classes of enzymes are generally descriptive of the type of reaction they catalyze and usually end in the suffix -ase .

Major ClassDescription of reaction activity
Oxidoreductasesoxidation of a hydrogen (or electron) donor (loses) and reduction of the acceptor (gains)
Transferasesmove a functional group from a donor molecule to an acceptor molecule
Hydrolasescouple breaking a bond with hydrolytic cleavage (breaking water)
Lyasesbreaking a bond with elimination to form a double bond (or ring) or adding to a double bond
Isomerasesalter the geometry or structure of the reactant molecule (rearrangements)
Ligasescouple forming a bond (joining two molecules) with ATP hydrolysis

Reduction of activation energy

Over the duration of a reaction, the reactants must move through a high energy transition state before becoming products. The difference between the free energy of the reactant(s) and the free energy of the transition state is called activation energy. When the activation energy required to arrive at the transition state is lower, the reaction will proceed faster. Thus, in stabilizing the transition state, an enzyme reduces activation energy and increases reaction rate.

Substrates and enzyme specificity

Enzyme specificity describes the highly selective nature of an enzyme for a particular reaction or set of reactions. The reactants for a specific enzyme then are narrowly defined and called its substrates.

Active Site Model

The active site model describes the location on the enzyme where it interacts with its substrate. The shape and local chemical characteristics (functional groups) of an active site are responsible for the specificity of the enzyme. In their interactive state, the enzyme and its substrate, bound at the active site, are called the enzyme-substrate complex.

Induced-fit Model

The induced-fit model describes how the interaction of an enzyme and its substrate is often reliant on effects the substrate has on the enzyme as well as effects the enzyme has on the substrate. The binding of an enzyme to its substrate results in a release of free energy called binding energy, with which suitable substrate in close proximity to an enzyme may cause a small change in the shape of the enzyme that is enough to boost the enzyme's affinity for the substrate, a more complementary conformation, thus "inducing" a better fit for the enzyme and its substrate.

Mechanism of catalysis

A mechanism of catalysis is the way in which the chemical reaction is assisted in moving forward.

Approximationsimply brings reactants together in proximity and proper orientation
Covalent catalysisa reactive group on the enzyme is temporarily covalently bonded to the substrate
Acid-base catalysisa reactive group on the enzyme acts as a proton donor or acceptor
Metal ion catalysisassists in electrophilic or nucleophilic interactions or binds to substrate (increasing binding energy)


Cofactors are inorganic ions that assist an enzyme in its catalytic activity. Examples include Fe2+ and Mg2+. (The term cofactors is sometimes used to describe the superset of non-protein helper compounds with inorganic ions in one subset and organic molecules called coenzymes in another. In this usage, cofactors, inclusive of coenzymes, may be closely or covalently bound to the enzyme as a holoenzyme. Without the required cofactor, an enzyme is in an inactive state, or an apoenzyme.)


Coenzymes are small, organic molecules that assist an enzyme in its catalytic activity. Examples include heme, NAD+, and coenzyme A. Many coenzymes are derived from vitamins.

Water-soluble vitamins

Water-soluble vitamins include the series of B-vitamins and Vitamin C and are a dietary requirement as precursors to coenzymes (or as the coenzyme itself in the case of Vitamin C).

Effects of local conditions on enzyme activity

Enzyme activity can be dramatically affected by changes in temperature and pH. Low temperatures slow reaction rates, and high temperatures may increase reaction rates but also cause denaturing in protein enzymes. Fluctuations in pH can also denature a protein enzyme by disrupting the non-covalent interactions that stabilize its 2°, 3°, and 4° structures.

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