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Biochemistry I - Enzymes

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    Study Guide Biochemistry I – Enzymes 1. Chemical Mechanisms of Enzyme Catalysis Enzymes can speed up chemical reactions by an extraordinary amount — sometimes by as much as a billion times . However, there is a physical limit to how fast an enzyme can work. An enzyme cannot catalyze reactions faster than it can encounter its substrate . In solution, enzymes collide with substrates at a rate of about 10⁸ – 10⁹ times per second . Inside cells, enzymes that act in the same metabolic pathway are often positioned close together. This arrangement reduces the need for substrates to diffuse long distances and makes reactions even more efficient. Even so, enzymes remain incredibly powerful catalysts because they use several clever chemical mechanisms to speed up reactions. 1.1 The Transition State For any chemical reaction to occur, reactant molecules must pass through a high - energy intermediate form called the transition state . • During a reaction, the energy of molecules temporarily increases • The transition state is unstable and short - lived • Once molecules pass this state, they can form products This explains why reactions usually happen faster at higher temperatures — more molecules can reach the transition state. On an energy diagram, the transition state appears as an energy barrier or hill . Catalysts, including enzymes, speed reactions by lowering this barrier , making it easier to reach the transition state.

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    Study Guide Figure 1 1.2 How Enzymes Stabilize the Transition State Enzymes use several mechanisms — often simultaneously — to make it easier for substrates to reach the transition state. 1. Proximity Effect Enzymes bring reacting molecules close together . In free solution, two specific molecules (such as ATP and glucose) rarely collide in the correct way because many other molecules are present. When both substrates bind to the enzyme’s active site , their effective concentration increases, and reaction becomes far more likely. 2. Orientation Effect Even if molecules collide with enough energy, a reaction will not occur unless they are properly oriented . Enzymes bind substrates in a precise orientation so that: • Energy from collisions is directed into the correct chemical bonds • The reaction proceeds efficiently

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    Study Guide 3. Induced Fit Enzymes are flexible , not rigid. When a substrate binds: • The enzyme changes shape • The substrate is forced into a strained or distorted form • This shape closely resembles the transition state Example: • The enzyme hexokinase closes around glucose like a clamshell • This movement pushes substrates into a reactive configuration This process is called induced fit . 4. Reactive Amino Acid Side Chains Some amino acid side chains are chemically active and can directly participate in catalysis. Examples: • Histidine can donate or accept protons • Serine can temporarily form covalent bonds with substrates during hydrolysis Placing these reactive groups close to the substrate greatly increases reaction speed. 5. Coenzymes and Metal Ions Enzymes sometimes need additional helpers to carry out reactions. Coenzymes • Small organic molecules • Not proteins • Assist catalysis but are not permanently changed • Provide chemical groups that amino acids lack Examples: • NAD ⁺ (nicotinamide adenine dinucleotide) – electron transfer

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    Study Guide • FAD (flavin adenine dinucleotide) – electron transfer • Pyridoxal phosphate (PLP) – amino group transfer

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    Study Guide

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    Study Guide Electron transfer reactions cannot be handled efficiently by amino acid side chains alone, so coenzymes are essential. Metal Ions • Found in the active sites of many enzymes • Can bind substrates, stabilize charges, or assist electron transfer 1.3 Coenzymes and Group Transfer Reactions Some reactions are especially difficult for amino acid side chains to perform. Example: • Amino group transfer • None of the 20 standard amino acids can easily accept an amino group The coenzyme pyridoxal phosphate (PLP) solves this problem because: • It contains a reactive carbonyl group • It can temporarily hold and transfer amino groups

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    Study Guide 1.4 Vitamins and Coenzyme Formation Vitamins are organic compounds required for growth and health. • Many microorganisms and plants can synthesize all needed organic molecules • Therefore, they do not require vitamins Humans, however, have lost this ability and must obtain vitamins from food. Many vitamins are precursors of coenzymes . Example: • Niacin (vitamin B ₃ ) is required to make NAD ⁺ • Deficiency of niacin leads to pellagra , which causes: o Skin problems o Digestive disorders o Neurological symptoms Niacin can be synthesized from the amino acid tryptophan , so pellagra usually results from deficiencies in both niacin and tryptophan . Key Takeaway • Enzymes speed reactions by stabilizing the transition state • They use proximity, orientation, induced fit, and reactive side chains • Coenzymes and metal ions expand catalytic possibilities • Many coenzymes are derived from vitamins • Vitamin deficiencies impair enzyme function 2. Chymotrypsin: An Enzyme at Work The general principles of enzyme catalysis can be clearly understood by studying the enzyme chymotrypsin . Chymotrypsin is a digestive enzyme found in the intestine, where it helps break down proteins into smaller peptides and amino acids.

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    Study Guide 2.1 What Does Chymotrypsin Do? Chymotrypsin hydrolyzes peptide bonds in proteins. Specifically, it cuts the peptide bond on the carboxyl side (the right side when written conventionally) of hydrophobic amino acids , such as phenylalanine, tyrosine, or tryptophan. Example: The small peptide glycyl - phenylalanyl - glycine (Gly - Phe - Gly) is cleaved into: • Gly - Phe • Gly This specificity is essential for efficient protein digestion. 2.2 The Active Site of Chymotrypsin The active site of chymotrypsin is specially designed to recognize and bind hydrophobic amino acid side chains. Hydrophobic Binding Pocket • The active site contains a deep pocket • This pocket is lined with hydrophobic amino acid side chains • Hydrophobic side chains (like phenylalanine) fit easily and favorably into this pocket • Charged or polar side chains do not bind well because they would lose favorable interactions with water Once the substrate is bound, the enzyme is positioned perfectly for catalysis.

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    Study Guide Figure 1: Step - by - step mechanism of chymotrypsin action in the hydrophobic pocket 2.3 The Catalytic Triad (Charge Relay System) Three specific amino acid side chains in the active site work together to catalyze the reaction. This group is called the catalytic triad : • Serine • Histidine • Aspartate How the Charge Relay System Works 1. Aspartate partially removes a proton from histidine 2. This makes histidine a stronger base 3. Histidine then removes a proton from serine 4. The deprotonated serine becomes highly reactive

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    Study Guide Normally, histidine alone would not be strong enough to remove a proton from serine. The presence of aspartate makes this possible. This cooperative interaction is called a charge relay system . 2.4 Formation of the Acyl - Enzyme Intermediate Once activated: • The oxygen atom of serine attacks the carbonyl carbon of the peptide bond • This breaks the peptide bond • An acyl - enzyme intermediate is formed, with the substrate temporarily covalently attached to the enzyme At the same time: • The proton originally on serine is transferred to the amino group of the peptide bond • One peptide fragment is released 2.5 Role of Water and Enzyme Regeneration Next: • Water enters the active site • Histidine accepts a proton from water • The hydroxyl group from water attacks the acyl - enzyme intermediate • This releases the second peptide fragment • The original enzyme structure is restored , ready for another catalytic cycle Thus, chymotrypsin is not consumed in the reaction. 2.6 Irreversible Enzyme Inhibitors The importance of the catalytic amino acids is demonstrated by irreversible inhibitors , which permanently inactivate the enzyme.

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