Biochemistry I - Enzymes Overview

Biochemistry I - CHM219

• This course covers Enzymes, Biological Catalysts

Enzymes I: The Biological Catalysts

• Catalysts increase chemical reaction rates without being consumed
• Enzymes are biological catalysts, accelerating biochemical reactions.
• Enzymes are proteins, their structure is crucial for their activity.
• Denaturing or disassociating an enzyme usually destroys its catalytic activity

Outline:

• The Role of Enzymes: Brief overview, explains the concept of chemical catalysts and how enzymes function.
• Chemical Reaction Rates and the Effects of Catalysts - A Review: Examines how reaction rates are affected, providing background on kinetics. Introduces first-order reactions.
• How Enzymes Act as Catalysts: Principles and Examples: Details how enzymes bind to substrates, promote reaction, and the factors affecting their activity.
• The Kinetics of Enzymatic Catalysis: Focuses on how the rates of enzymatic reactions are measured and modeled.
• Enzyme Inhibition: Explains different types of enzyme inhibition mechanisms.
• Cofactors, Vitamins, and Essential Metals: Discusses the role of cofactors, vitamins, and essential metals as enzyme components.
• The Diversity of Enzymatic Function: Exploring a wide range of enzyme functions.
• Nonprotein Biocatalysts: Catalytic Nucleic Acids: Investigating non-protein biocatalysts (RNA catalysts).
• The Regulation of Enzyme Activity: Allosteric Enzymes: Examining allosteric regulation of enzyme activity.
• Covalent Modifications Used to Regulate Enzyme Activity: Explains how covalent modifications control enzyme activity.

History of Enzymes

• Biological catalysis recognized in late 1700s, focused on digestive processes.
• Research into enzyme activity continued through the 1800s, including exploring the processes of starch conversion to sugar.
• Louis Pasteur connected microbial fermentation processes to enzymes.

Enzymes are proteins

• James Sumner isolated and crystallized urease, proving that enzymes are proteins (1926).
• Northrop and Kunitz's confirmation of Sumner's work consolidated the understanding.

The Role of Enzymes

• Catalysts speed up chemical reactions without being consumed in the process.
• Enzymes catalyze hydrolysis of peptide bonds in proteins/polypeptides.
• The substance acted on by an enzyme is called the substrate.

Two Facts Deserve Emphasis:

• Catalysts remain unchanged during the chemical process.
• Catalysts do not change the equilibrium position of a reaction.
• Enzymes, like hemoglobin, are not true catalysts in some chemical processes.

Chemical Reaction Rates and Effects of Catalysts

• A first-order reaction's rate is proportional to the concentration of the reactant.
• A first-order reaction demonstrates a single, exponential decay of the reactant.

Determining First-Order Reactions

• Graphs of reactant concentration vs. time for first-order reactions show exponential decay.
• Graphs of the natural logarithm of reactant concentration vs. time yield a straight line.
• The slope of this line corresponds with the first-order rate constant.

First-Order vs. Second-Order Reactions

• First-order rate constants have time units.
• Second-order rate constants have concentration-based time units.
• Analysis of multi-step reactions is sometimes simplified by identifying a step that limits the overall reaction speed (rate-limiting step).

Activation Energy and Catalysts

• Chemical reactions need activation energy, the energy barrier.
• Catalysts lower this energy barrier for reactions.

Free Energy Diagrams

• Free energy diagrams illustrate free energy changes during chemical reactions.
• Transition states are high-energy, unstable states during chemical transformation.
• Catalysts stabilize the transition state, lowering its energy

Effect of Temperature and ΔG°+

• Reaction rates are related to the number of molecules with enough energy to overcome the activation energy.
• Higher temperatures increase the reaction rate by providing more molecules with required energy.

Rate Enhancement

• Rate enhancement equals the ratio of catalyzed/uncatalyzed reaction constants.

Enzymatic Rate Enhancements

• Each vertical bar represents rate enhancement.

Influence of Catalysts on Reactions

• Catalysts increase both forward and reverse reaction rate but do not change the equilibrium composition.
• Catalysts speed up reactions through altering the reaction pathways.

Effect of a Catalyst on Activation Energy

• Catalysts reduce the activation energy required for the reaction to proceed.
• This causes an increase in the reaction rate.
• The equilibrium point is unchanged.

How Enzymes Act as Catalysts

• Enzyme active sites are complementary in shape, charge, and polarity to transition states of the catalyzed reaction.
• Complementarity between the enzyme and substrate is crucial for enzyme specificity.

Catalytic Activity

• Enzymes rely on the integrity of their native protein conformation for catalytic function.
• Protein structure (primary, secondary, tertiary, and quaternary) is essential for enzyme activity.

Entropic and Enthalpic Factors in Catalysis

• Enzymes concentrate reactants in close proximity, favoring high-energy transition state formation.

Importance of Intermediate States

• Enzymes can accelerate reactions by creating intermediate states with lower energy levels similar to the transition state
• This accelerates the intermediate-state formation and product formation.

The Active Site of Lysozyme

• The lysozyme active site is accessible.
• The substrate is a trisaccharide (NAM-NAG-NAM).
• This carbohydrate substrate binds to and is cleaved from the active site.

The Mechanism of Lysozyme Action

• Initially, E35 acts as an acid to initiate glycosidic bond cleavage.
• Subsequently, E35 acts as a base to initiate attack by water.

Effect of pH on Lysozyme Activity

• The ideal pH optimum for lysozyme activity occurs within a pH range where both E35 and D52 amino acids are poised to function appropriately.

Evidence of Covalent Intermediate in Lysozyme Mechanism

• Studies on synthetic substrates, including NAG-2FGIcF, provide evidence for a transient covalent intermediate in the lysozyme reaction pathway.

Catalysis of Peptide-Bond Hydrolysis by Chymotrypsin

• Chymotrypsin's mechanism involves three key catalytic components (catalytic triad)
• The mechanism demonstrates a two-step process, highlighting the use of a serine residue.
• Initially, the hydroxyl group of a serine residue initiates the peptide bond cleavage.

Chymotrypsin's Serine Protease Catalytic Triad

• X-ray crystallography studies revealed the catalytic triad: His57, Ser195, and Asp102, which have particular spatial orientations facilitating catalysis.

Strategies Used by Lysozyme and Serine Proteases for Lowering ΔG°+

• Tables outlining the strategies used by different enzymes for lowering activation energy
• Lysozyme, using different catalytic strategies from serine proteases.

Timescale of Protein Motions

• Table summarizing timescales for different protein motions involved in catalysis.

Dynamic Conformational Changes in Dihydrofolate Reductase

• Diagram illustrating multiple, dynamic changes in the enzyme's conformation during the catalysis cycle.

Additional Note:

• Figures & diagrams are vital to understanding these concepts. Visualizing the mechanisms and pathways is crucial. Always review the associated graphs and illustrations.

This quiz explores the role of enzymes as biological catalysts, detailing their structure, function, and the kinetics of enzymatic reactions. Understand the principles behind how enzymes accelerate biochemical processes and how factors impact their activity.