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Enzymes

BIOCHEMISTRY (Polytechnic University of the Philippines)

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ENZYMES

• Is a compound, usually a protein, that acts as a catalyst for a biochemical reaction.

• Each cell in the human body contains thousands of different enzymes because almost every
reaction in a cell requires its own specific enzyme.

• Enzymes are not consumed during the reaction but merely help the reaction occur more rapidly.

• Enzymes undergo all the reactions of proteins including denaturation.

Activation energy

Enzyme structure

• Simple enzymes: is an enzyme composed only of protein ( amino acid chains)

• Conjugated enzymes: is an enzyme that has a non-protein part in addition to a protein part.

• Apoenzyme:

• Cofactor: it provides additional chemically reactive functional groups beside those

present in the amino acid side chains of apoenzyme.

• Coenzyme: is a small organic molecule that serves as a cofactor in a conjugated

enzymes.

Nomenclature and classification of enzymes

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• Enzymes are commonly named by using a system that attempts to provide information about
the function (rather than the structure) of the enzyme.

• The typed of the reaction and the substrate identity are the focal points for the nomenclature of
an enzyme.

• Substrate: it is the reactant in an enzyme-catalyzed reaction. Substrate is a substance

upon which the enzymes ” acts ”.

Three important aspects of the enzyme-naming process are the following:

1. The suffix –ase identifies a substance as an enzyme.

2. The type of reaction catalyzed by an enzyme is often noted with a prefix. Oxidase, hydrolase.

3. The identity of the substrate is often noted in addition to the type of reaction. Infrequently, the
substrate but not the reaction type is given.( urease, lactase)

Classification of enzymes

• Oxidoreductase

• Transferase

• Hydrolase

• Lyase

• Isomerase

• Ligase

Oxidoreductase

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1. Label the reaction to indicate which compound is oxidized and which compound is reduced.

2. Lactate dehydrogenase is the enzyme. What is the name of the term given to NAD + in this
reaction?

Transferase

Ligase

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Hydrolase

Isomerase

Models of enzyme action

• Active site: is the relatively small part of an enzyme’s structure that is actually involved in the
catalysis.

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• Enzyme-substrate complex: catalyst offer an alternative pathway with lower activation energy
through which a reaction can occur. An enzyme-substrate complex is the intermediate reaction
species that is formed when a substrate binds to the active site of an enzyme.

Lock-and-key model

Induce-fit model

Enzyme specificity

1. Absolute specificity: the enzyme will catalyze only one reaction.

2. Group specificity: the enzyme will act only on molecules that have specific functional group,
such as hydroxyl, amino or phosphate groups.

3. Linkage specificity: the enzyme will act on a particular type of chemical bond. (phosphatases)

4. Stereochemical specificity: the enzyme will act on a particular stereoisomer.

Factors that affect enzyme activity

• Temperature

• pH

• Substrate concentration

• Enzyme concentration

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Temperature

• Higher temperatures means molecule are moving faster and colliding more frequently. This
concept applies to collision between substrate molecules and enzymes. As the temperature of
an enzymatically catalyzed reaction increases, so does the rate of the reaction.

• Optimum temperature:

Ph

• Most enzyme exhibit maximum activity over a very narrow pH range.

• Optimum pH:

• How does gastric ulcer occur? What is the causative agent for this condition?

Substrate concentration

• When the concentration of an enzyme is kept constant and the concentration of substrate is
increased, the enzyme activity pattern is obtained. This activity pattern is called .

Enzyme concentration

• The greater the enzyme concentration, the greater the reaction rate.

Enzyme inhibition

• The rates of enzyme-catalyzed reactions can be decreased by a group of substances called

inhibitors.

• Enzyme inhibitor: is a substance that slows or stops the normal catalytic function of an enzyme
by binding to it.

• Reversible competitive inhibition, reversible noncompetitive inhibition and irreversible

inhibition.

Reversible competitive inhibition

• Competitive enzyme inhibitor: is a molecule that sufficiently resembles an enzyme substrate in

shape and charge distribution that it can compete with the substrate for occupancy of the
enzyme’s active site.

example: of competitive inhibitor

• Anti-histamines are competitive inhibitors of histidine decarboxylation, the enzymatic reaction

that converts histidine to histamine.

Reversible noncompetitive inhibition

• Noncompetitive enzyme inhibitor: is a molecule that decreases enzyme activity by binding to a

site on an enzyme other than the active site.

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Example of noncompetitive inhibitor

• Metal ions (Pb2+, Ag2+ and Hg2+ )

• The binding sites for these ions are sulfhydryl (-SH) groups located away from the active site.

• Metal sulfide will affect the secondary and tertiary structure of the enzyme.

Irreversible inhibition

• Irreversible enzyme inhibitor: is a molecule that inactivates enzymes by forming a strong

covalent bond to an amino acid side-chain group at the enzyme’s active site.

Example of irreversible inhibitor

• Chemical warfare agents (nerve gases)

• Nerve agents (sarin, soman, cyclosarin, tabun)

• Vesicating or blistering agents (mustards, lewisite)

• Respratory agents (chlorine,phosgene, diphosgene)

• Cyanide

• Antimuscarinic agents (anticholinergic compounds)

• Opioid agents (opioid derivatives)

• Riot control agents ( pepper gas, cyanide)

• Vomiting agent (adamsite)

• Organophosphate insecticides

Regulation of enzyme activity

• A cell that continually produces large amounts of an enzyme for which substrate concentration
is always very low is wasting energy. The production of the enzyme needs to be “turned off”.

• A product of an enzyme-catalyzed reaction that is present in plentiful(more than needed)

amounts in a cell is a waste of energy if the enzyme continues to catalyze the reaction that
produces the product. The enzyme needs to be “turned off”.

“turned off” and “turned on” mechanism of enzymes

1. Feedback control associated with allosteric enzymes

2. Proteolytic enzymes and zymogens

3. Covalent modification

Feedback control associated with allosteric enzymes

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• Allosteric enzymes: is an enzyme with two or more protein chains and two kinds of binding sites
( substrate and regulator)

• Many, but not all, enzymes responsible for regulating cellular processes are allosteric enzymes.

-Characteristics of Allosteric Enzyme-

• All allosteric enzymes have quaternary structure.

• All allosteric enzymes have two kinds of binding sites.

• Active and regulatory binding sites are distinct from each other in both location and
shape.

• Binding of a molecule at the regulatory site causes changes in the overall three
dimensional structure of the enzyme, including changes at the active site.

• Feedback control: is a process in which activation or inhibition of the first reaction in a reaction
sequence is controlled by a product of the reaction sequence.

• The product of each step is the substrate for the next enzyme.

Proteolytic enzymes and zymogen

• Proteolytic enzymes: is an enzyme that catalyzes the breaking of peptide bonds that maintain
the primary structure of a protein.

• Zymogen: is the inactive precursor of a proteolytic enzyme.

Covalent modification of enzymes

• Covalent modification: is a process in which enzyme activity is altered by covalently modifying

the structure of the enzyme through attachment of a chemical group or removal of a chemical
group from a particular amino acid within the enzyme’s structure.

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