6. Enzymes – Mode of Action, Kinetics & Regulation

43 vocabulary flashcards covering definitions and key kinetic, structural and regulatory terms related to enzymes, their action, and their control in cells.

Enzyme

A biological catalyst, usually a globular protein (or RNA), that increases reaction rate without being consumed.

The 6 properties of enzymes

1. Mostly globular proteins

2. Increases rate of reaction

3. Operate at milder reaction conditions (pressure, temperature,PH)

4. Exhibit substrate specificity

5. Enzymes Nonmenclature (catalyse specific chemical reaction)

Biological catalyst

A substance produced by living organisms that lowers activation energy to speed up chemical reactions.

Active site

The precise 3-D groove on an enzyme where the substrate binds and catalysis occurs, which gives it its specific 3D conformation

What are the 3 types on amino acids found in active site?

• non catalytic: 3-12 aa

• Contact aa residues (interact reversible with substrate via weak H bonds, I bonds and hydrophobic interactions to position it in correct orientation. )

• Catalytic aa residues (catalyse the conversion of substrate to its product)

• Remaining polypeptide: provides framework that maintains the conformation of the aa

Substrate specificity

The ability of an enzyme to catalyse only one (or a narrow group of) reaction(s) because its active-site shape and charge complement the substrate.

Enzyme–substrate complex (ES complex)

A temporary complex formed when an enzyme binds its substrate, leading to product formation.

4 types of amino acid residues in enzyme

• contact residues

• - catalytic residues

• Structural;

• Non essential

Lock-and-Key hypothesis

1. Lock is enzyme, key is substrate

2. Conformation and charge complementary to enzymes

3. Form ES complex

4. Catalysis occur and product forms, products no longer fit, active site free to receive further substrates

5. Both not altered

Induced-Fit hypothesis

substrate binding induces a conformational change in the active site for a more precise fit such that enzyme can perform its catalytic function more effectively. #D conformational reverts back to original

Activation energy (Ea)

The minimum energy required for reactants to reach the transition state (at moderate temperatures) ; lowered by enzymes.

The absorption of thermal energy leads to…

1. Increase in KE of reactant molecules for more forceful collisions

2. Increase in frequency of collision of reactions

3. Increase in intramolecular vibrations (bonds more likely to break)

Transition state

The unstable, high-energy intermediate between substrate and product in a reaction.

What are the 5 mechanisms of activation energy?

1. Proximity effect

2. Strain effect

3. Orientation effects

4. Micro environment effects

5. Acid base catalysis

What is proximity effect

Temporary binding of reactants next to each other in the active site for→ increase chance of reaction

What is strain effect

Slight distortion of reactants as they bind to enzyme. This strains the bonds which are to be broken and increases chance of breakage

What is orientation effects

Reactants held by enzyme in such a way bonds exposed to chemical reactions

Micro environment effects

Hydrophobic aa create a water free zone where non polar reactants react more easily.

What is acid base catalysis

Acidic and basic aa in enzyme facilitate catalysis

Effective collision

A collision between enzyme and substrate with correct orientation and sufficient energy to form product.

Temperature coefficient (Q10)

Factor by which the rate of an enzyme reaction increases for every 10 °C rise (≈2 below optimum).

Optimum temperature

The temperature at which an enzyme’s reaction rate is maximal.

Denaturation

Loss of an enzyme’s 3-D structure (and function) due to disruption of bonds, often by heat or pH extremes.

Optimum pH

The pH at which an enzyme’s activity is highest.

Contact residues

Active-site amino acids that bind the substrate via weak interactions and position it correctly.

Catalytic residues

Active-site amino acids whose R-groups directly participate in the chemical transformation of substrate.

Structural residues

Amino acids that maintain the overall 3-D conformation of the enzyme.

Non-essential residues

Surface amino acids with no direct catalytic or structural role.

Absolute specificity

When an enzyme catalyses only one specific reaction (e.g., maltase on maltose).

Group specificity

When an enzyme acts on a particular type of bond in many substrates (e.g., proteases on peptide bonds).

Substrate concentration ([S])

Amount of substrate present; increasing [S] raises rate until enzyme saturation (Vmax).

Enzyme concentration ([E])

Amount of enzyme present; increasing [E] raises rate while other factors are non-limiting.

Why is it as time progresses rate of reaction drop?

Substrate concentration decreases (ENZYME DOES NOT) As there are less substrate molecules to collide effectively with enzyme molecules to form ES complex

Maximum velocity (Vmax)

The reaction rate when the enzyme is saturated with substrate; adding more substrate cannot increase rate.

Why do some enzymes have higher optimum temperature?

Higher proportion of disulfide bonds (strong covalent bonds) or numerous intramolecular interactions that hold the tertiary structure of the enzymes

What is temperature coefficient

Factor by which rate increases with each 10 degree rise in temperature:

Q10= rate of reaction @ (X+10) / rate of reaction at X

deviation from optimum PH is

Excess H+ or OH- ions neutrliase negatively and positively charged R groups of amino acids in enzyme respectively. The R groups belong to Strutural, contact, catalytic amino acid.

Michaelis constant (Km)

Substrate concentration at which reaction rate is ½ Vmax; inversely related to enzyme-substrate affinity.

When is Michaelis constant the same

For a particular enzyme (differs with diff enzyme)

What does low and high Km imply

Low: low substrate on cent ratio needed, high affinity between substrate and enzyme

High: high substrate conc needed, low affinity between enzyme and substrate

Enzyme saturation

Condition where all active sites are occupied; further [S] increase does not raise velocity.

Competitive inhibitor

Molecule bearing similar conformation and charge to substrate that binds the active site and block substrate from binding, raising Km but leaving Vmax unchanged. BINDS REVERSIBLY DUE TO WEAAK NON COVALENTLY BONDS

Can competitive inhibition be overcome

Yes. Increase substrate conc, increases chances of substrate binding to active site, if high enough can reach same max

Non-competitive inhibitor

Molecule bear no structural similarity, binding outside the active site, altering conformation of active site, substrate binds less effectively and lowering Vmax without changing Km. Decreases availability of enzymes

Diff in effects of eomcptitive and non competitive inhibitor

Competitive: Vmax same, increase Km

Non competitive: Vmax decreases, Km same

Can non competitive inhibitor be overcomed?

No. Increasing conc does not help as rate of reaction will continue to decrease.

Allosteric enzyme

Multimeric (2 or more subunits each. With active site + allosteric site) enzyme whose activity is regulated by allosteric inhibitor and activator.

• 2 conformational states: active/inactive → inhibitor/activattor binds to it, one is enough to inhibit or activate the activity of enzyme

• Cooperative binding: binding of first subunit changes conformation of other subunit, easier to accept subsequent subunits

Allosteric site

Specific location on an allosteric enzyme where regulators (activators or inhibitors) bind.

Allosteric inhibitor

Effector that stabilises the inactive conformation of an allosteric enzyme, decreasing activity.

Allosteric activator

Effector that stabilises the active conformation of an allosteric enzyme, increasing activity.

Cooperativity

Phenomenon where binding of a substrate to one subunit of an allosteric enzyme enhances binding to others, producing a sigmoid rate curve.

Feedback (end-product) inhibition

Regulatory mechanism where the final product of a metabolic pathway inhibits an early enzyme in that pathway/ metabolic pathway is inhibited by binding of end product of biochemical pathway to an enzyme that acts early in pathway.

(E.g. allosteric inhibitor, binds and alters conformation, rate of reaction decreased.

Cofactor

Non-protein helper (inorganic ion or organic molecule) required for enzyme function.

What are the 2 types of enzyme co factors

Inorganic ions (attach to enzyme and change shape) and Organic co factors: Coenzymes (bind loosely and briefly to enzyme) and Prosthetic group (permanently bound by strong covalent bonds)

Coenzyme

Organic cofactor that binds loosely and brieftly to an enzyme (e.g., NAD⁺).

Prosthetic group

Organic cofactor covalently bound permanently to an enzyme (e.g., haem in cytochrome oxidase).