CHEM 113: BIOCHEMISTRY

LECTURE 3: Enzymes
___________________________________________________________________________________________________________

SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY

1ST SEMESTER | A.Y 2022 - 2023
• Transaminases – Catalyzes the transfer of amino
LEARNING OBJECTIVES group from one molecule to another
1 Understand concisely the function of enzymes • Kinases - Catalyzes the transfer of phosphate group
2 Explain properly the models of enzymatic reactions from ATP to give ADP and a phosphorylated product.
3 Enumerate completely the different classification of 3. Hydrolase
enzymes • Catalyzes the hydrolysis reaction
4 Know correctly the different uses of enzymes • Central to the process of digestion
• Carbohydrases, Proteases, and Lipases
• It is a compound usually a protein, that acts as a 4. Lyase – Catalyzes the addition of a group to a double
catalyst for a biochemical reaction bond or the removal of a group to form a double bond
• Cause cellular reaction to occur millions of times in a
faster manner that does not involve hydrolysis or oxidation
• Not consumed during the reaction but merely help 5. Isomerase
• the reaction occur more rapidly • Catalyzes the isomerisation of a substrate in a
• Mostly, are globular proteins. reaction converting it to a molecule isomeric with
itself.
ENZYME STRUCTURE • One reactant and one product in reactions.
6. Ligase – Catalyzes the bonding together of two
• Simple Enzyme – Composed only of protein molecules into one with the participation of ATP.
• Conjugate Enzyme – Has a non-protein part in
addition to a protein part MODLES OF ENZYME ACTION
o Apoenzyme – Protein of the conjugated enzyme
o Cofactor - Non – protein part of the conjugated • Enzyme active site
enzyme Holoenzyme o Small part of an enzyme’s structure that is
o Holoenzyme actually involved in catalysis.
- Biochemically active conjugated enzyme o A three – dimensional entity formed by groups
produced from an apoenzyme and a cofactor that come from different parts of the protein
- Combined apoenzyme and cofactor entity chains
- Coenzyme – Serves as a cofactor in a • Enzyme – Substrate Complex
conjugated enzyme o The intermediate reaction species that is formed
when a substrate binds to the active site of an
NOMERACLATURE & CLASSIFICATION OF ENZMYES enzyme.

• Named about the function of the enzyme, type of LOCK AND KEY MODEL
reaction catalyzed and the substrate identity.
• Substrate • Active site in the enzyme has the fixed, rigid
o Reactant in an enzyme – catalyzed reaction. geometrical conformation.
• Substrate with a complementary geometry can be
ASPECTS IN THE NAMING PROCESS OF ENYZMES accommodated.

• Suffix – most enzymes end in the suffix “ase”

o Ex. Urease, Sucrase, Lipase
o Exception: Digestive Enzymes
o Ex. Trypsin, Chymotrypsin, Pepsin
• Type of reaction catalyzed by an enzyme is often
used as a prefix
o Ex. Oxidase – Oxidation reaction
- Hydrolase – Hydrolysis reaction
• Identity of substrate and type of reaction catalyzed
o Ex. Glucose oxidase, pyruvate carboxylase,
succinate dehydrogenase

CLASSIFICATION OF ENYZMES

1. Oxidoreductase
• Catalyzes an oxidation – reduction reaction.
• Requires a coenzyme that is oxidized or reduced as
the substrate is reduced or oxidized
2. Transferase
• Catalyzes the transfer of a functional group from one
molecule to another
 CHEM 113: BIOCHEMISTRY
LECTURE 3: Enzymes
___________________________________________________________________________________________________________

SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY

1ST SEMESTER | A.Y 2022 - 2023
• PH
INDUCED – FIT MODEL o The charge on acidic and basic amino acids
located at the active site depends on pH
• Enzyme’s active site is not rigid and static. o small pH changes can result in enzyme
• There’s a constant change in shape denaturation and subsequent loss of catalytic
• Allows for changes in the shape or geometry of the activity.
active site of an enzyme to accommodate a substrate. o Biochemical buffers help maintain the optimum
• Result of the enzyme’s flexibility; it adapts the pH for an enzyme.
• incoming substrate. o Can also affect substrate, causing either
protonation or deprotonation of groups on the
substrate.
o Optimum pH
- pH at which an enzyme exhibits maximum
activity
- physiological pH ranges from 7.0 – 7.5
- Pepsin - Active in the stomach, functions best at
pH 2.0
- Trypsin – Operates in the small intestines,
function best at pH 8.0
ENZYME SPECIFITY • Substrate Concentration
o Increased concentration of substrate will obtain
• Extent to which an enzyme’s activity is restricted to a the enzyme activity.
specific substrate, a specific group of substrate, a o Turnover number – Number of substrate
specific type of chemical bond, or a specific type of molecules transformed per minute by one
chemical reaction. molecule of enzyme under optimum conditions of
• Degree of specificity is determined by the active site. temperature, pH and saturation.
• Enzyme Concentration
TYPES OF ENZYME SPECIFITY o Kept in a low number because enzymes are not
consumed in the reaction.
• Absolute Specificity o The greater the enzyme concentration, the
o Catalyze only one reaction greater the reaction rate.
o Most restrictive of all specificities
o Catalase – enzyme with absolute specificity EXTREMOZYMES
• Group Specificity
o Act only on molecules that have a specific • A microbial enzyme active at a conditions that would
functional group, such a hydroxyl, amino or inactivate human enzymes as well as enzymes
phosphate groups. present in other types of higher organisms
o Carboxylpeptidase is group specific. • Extremophile
• Linkage Specificity o Microorganisms that thrives in extreme
o Act on the particular type of bond, irrespective to environments
the rest of the molecular structure. o Acidophiles – Optimal growth at pH levels of 3.0
o Phosphatases hydrolyze phosphate – ester or below
bonds in all types of phosphate esters o Alkaliphiles – Optimal growth at pH levels of 9.0
o Most general of the common species or above
• Stereochemical Specificity – Act on a particular o Hyperthermophile – Temperature between 80C
isomer and 122C needed to thrive
• Halophiles
FACTORS THAT AFFECT ENZYME ACTIVITY • Cryophiles
• Enzyme Activity – Measures the raste at which an ENZYME INHIBITION
enzyme converts substrate to products in a
biochemical reaction • Enzyme inhibitor – Substance that slows or stops
• Factors that affects enzyme activity the normal catalytic function of an enzyme by binding
o Temperature, pH, Substrate Concentration, to it.
Enzyme Concentration • Reversible competitive Inhibition
• Temperature • Reversible Non-competitive inhibition
o Measure of kinetic energy of molecules. • Irreversible inhibition
o Higher temperatures mean molecules are moving
faster and colliding more frequently
o Optimum temperature
- Temperature at which an enzyme exhibits
maximum activity
 CHEM 113: BIOCHEMISTRY
LECTURE 3: Enzymes
___________________________________________________________________________________________________________

SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY

1ST SEMESTER | A.Y 2022 - 2023

REVERSIBLE COMPETITIVE INHIBITION ENZYME WITH TWO OR MORE PORTEIN CHAIN AND 2
KINDS OF BINDING SITES
• Competitive enzyme inhibitor
o Molecule that sufficiently resembles an enzyme • Regulators
substrate in shape and charge distribution that it o Substance that bind at the regulatory sites of
can compete with the substrate for occupancy of allosteric enzymes.
the enzymes active site o Positive Regulator
o Remains inchanged as it binds to the enzymes’s - Increase enzyme activity
active site. - The shape of the active site is changed such that
• Reversible process because it is maintained but weak it can more readily accept substrate.
interactions
• Can be reduced but increasing the concentration of o Negative Regulator
the substrate. - Decrease enzyme activity
- Changes to the active site are such that substrate
ENZYME INHIBITION less readily accepted.

• Reversible Non-Competitive Inhibition FEEDBACK CONTROL

o Non-Competitive enzyme inhibition
- Molecule that decreases enzyme activity by • A process in which activation or inhibition of the first
binding to a site on an enzyme other than the reaction in a reaction sequence is controlled by a
active site. product of reaction sequence.
- Presence of this causes a change in the structure • Negative Feedback
of the enzyme sufficient to prevent the catalytic
groups at the active site from properly effecting PROTEOLYTIC ENZYMES & ZYMOGENS
their catalyzing action.
• Irreversible Inhibition • Proteolytic Enzymes
o Irreversible enzyme inhibitor - Catalyzes the breaking of peptide bonds that
- Molecule that inactivates enzyme by forming a maintain the primary structure of protein.
strong covalent bond to an amino acid side – - Generated in an inactive form and converted to
chain group at the enzymes active site. active form when they are needed.
- Do not have structures similar to that of the • Zymogen
enzyme’s normal substrate. - Inactive precursor of a proteolytic enzyme.
- Activation of a zymogen requires an enzyme –
REGULATIION OF ENZYME ACTIVITY controlled reaction that moves some part of the
A cell that continually produces large amount of enzyme zymogen structure which changes the 3 –
for which substrate concentration is always very low is dimensional structure of zymogen,
1 wasting energy. The production of the which affects active site conformation.
enzyme needs to be “turned off”.
A product of an enzyme – Catalyzed reaction that is COVALENT MODFICATION OF ENZYME
present in plentiful amounts in a cell is a waste of
2 energy if the enzyme continues to catalyze the reaction Process in which enzyme activity is altered by
that produces the product. The enzyme needs to be covalently modifying the structure of the enzyme
turned off. through attachment of a chemical group or removal of a
chemical group from a particular amino acid within the enzyme
ALLOSTERIC ENZYME structure.
1 Have Quaternary Structure; (2 or more protein chains) • Phosphorylation – Process of addition of the
2 Have 2 kinds of binding sites (for substrates and for phosphate group to the enzyme by protein kinases
regulators). • Dephosphorylation – Removal of the phosphate
Active and regulatory binding sites are distinct from group from the enzyme by
3 each other in both location and shape. phosphatases.
Binding of a molecule at the regulatory site causes
changes in the overall three – dimensional structure MEDICAL USES OF ENYZMES
4 of the enzyme, including structural changes at the
active site. • Used to diagnose certain diseases.
• Appearance of these enzymes in the blood often
indicates that there is tissue damage in an organ and
that cellular contents are spilling out into the
bloodstream.
• Used in the treatment of disease.
 CHEM 113: BIOCHEMISTRY
LECTURE 3: Enzymes
___________________________________________________________________________________________________________

SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY

1ST SEMESTER | A.Y 2022 - 2023