Biochemistry I - Enzymes - Quick Guides | Biochemistry

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Study GuideBiochemistry I–Enzymes1.Chemical Mechanisms of Enzyme CatalysisEnzymes can speed up chemical reactions by anextraordinary amount—sometimes by as much asa billion times. However, there is a physical limit to how fast an enzyme can work. An enzyme cannotcatalyze reactions faster than it canencounter its substrate.In solution, enzymes collide with substrates at a rate of about10⁸–10⁹ times per second. Inside cells,enzymes that act in the same metabolic pathway are often positioned close together. Thisarrangement reduces the need for substrates to diffuse long distances and makes reactions evenmore efficient.Even so, enzymes remain incredibly powerful catalysts because they use several cleverchemicalmechanismsto speed up reactions.1.1The Transition StateFor any chemical reaction to occur, reactant molecules must pass through ahigh-energyintermediate formcalled thetransition 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 productsThis explains why reactions usually happen faster at higher temperatures—more molecules can reachthe transition state.On an energy diagram, the transition state appears as anenergy barrier or hill.Catalysts, including enzymes, speed reactions by lowering this barrier, making it easier to reachthe transition state.

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Study GuideFigure 11.2How Enzymes Stabilize the Transition StateEnzymes use several mechanisms—often simultaneously—to make it easier for substrates to reachthe transition state.1. Proximity EffectEnzymes bring reacting moleculesclose together.In free solution, two specific molecules (such as ATP and glucose) rarely collide in the correct waybecause many other molecules are present. When both substrates bind to theenzyme’s active site,their effective concentration increases, and reaction becomes far more likely.2. Orientation EffectEven if molecules collide with enough energy, a reaction will not occur unless they areproperlyoriented.Enzymes bind substrates in a precise orientation so that:•Energy from collisions is directed into thecorrect chemical bonds•The reaction proceeds efficiently

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Study Guide3. Induced FitEnzymes areflexible, not rigid.When a substrate binds:•The enzyme changes shape•The substrate is forced into astrained or distorted form•This shape closely resembles thetransition stateExample:•The enzymehexokinasecloses around glucose like a clamshell•This movement pushes substrates into a reactive configurationThis process is calledinduced fit.4. Reactive Amino Acid Side ChainsSome amino acid side chains arechemically activeand can directly participate in catalysis.Examples:•Histidinecan donate or accept protons•Serinecan temporarily form covalent bonds with substrates during hydrolysisPlacing these reactive groups close to the substrate greatly increases reaction speed.5. Coenzymes and Metal IonsEnzymes sometimes needadditional helpersto carry out reactions.Coenzymes•Small organic molecules•Not proteins•Assist catalysis but arenot permanently changed•Provide chemical groups that amino acids lackExamples:•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 GuideElectron transfer reactions cannot be handled efficiently by amino acid side chains alone, socoenzymes are essential.Metal Ions•Found in the active sites of many enzymes•Can bind substrates, stabilize charges, or assist electron transfer1.3Coenzymes and Group Transfer ReactionsSome 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 groupThe coenzymepyridoxal 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 Guide1.4Vitamins and Coenzyme FormationVitaminsare organic compounds required for growth and health.•Many microorganisms and plants can synthesize all needed organic molecules•Therefore, theydo not require vitaminsHumans, however, have lost this ability and must obtain vitamins from food.Many vitamins areprecursors of coenzymes.Example:•Niacin (vitamin B₃)is required to makeNAD⁺•Deficiency of niacin leads topellagra, which causes:oSkin problemsoDigestive disordersoNeurological symptomsNiacin can be synthesized from the amino acidtryptophan, so pellagra usually results fromdeficiencies inboth 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 function2.Chymotrypsin: An Enzyme at WorkThe general principles of enzyme catalysis can be clearly understood by studying the enzymechymotrypsin. Chymotrypsin is adigestive enzymefound in the intestine, where it helps breakdown proteins into smaller peptides and amino acids.

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Study Guide2.1What Does Chymotrypsin Do?Chymotrypsinhydrolyzes peptide bondsin proteins. Specifically, it cuts the peptide bond on thecarboxyl side(the right side when written conventionally) ofhydrophobic amino acids, such asphenylalanine, tyrosine, or tryptophan.Example:The small peptideglycyl-phenylalanyl-glycine (Gly-Phe-Gly)is cleaved into:•Gly-Phe•GlyThis specificity is essential for efficient protein digestion.2.2The Active Site of ChymotrypsinTheactive siteof chymotrypsin is specially designed to recognize and bind hydrophobic amino acidside chains.Hydrophobic Binding Pocket•The active site contains adeep pocket•This pocket is lined withhydrophobic 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 interactionswith waterOnce the substrate is bound, the enzyme is positioned perfectly for catalysis.

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Study GuideFigure 1: Step-by-step mechanism of chymotrypsin action in the hydrophobic pocket2.3The Catalytic Triad (Charge Relay System)Three specific amino acid side chains in the active site work together to catalyze the reaction. Thisgroup is called thecatalytic triad:•Serine•Histidine•AspartateHow the Charge Relay System Works1.Aspartatepartially removes a proton fromhistidine2.This makes histidine astronger base3.Histidine then removes a proton fromserine4.The deprotonated serine becomes highly reactive

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Study GuideNormally, histidine alone would not be strong enough to remove a proton from serine. The presenceof aspartate makes this possible. This cooperative interaction is called acharge relay system.2.4Formation of the Acyl-Enzyme IntermediateOnce activated:•The oxygen atom ofserineattacks thecarbonyl carbonof the peptide bond•This breaks the peptide bond•Anacyl-enzyme intermediateis formed, with the substrate temporarily covalently attachedto the enzymeAt the same time:•The proton originally on serine is transferred to the amino group of the peptide bond•One peptide fragment is released2.5Role of Water and Enzyme RegenerationNext:•Waterenters 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•Theoriginal enzyme structure is restored, ready for another catalytic cycleThus, chymotrypsin isnot consumedin the reaction.2.6Irreversible Enzyme InhibitorsThe importance of the catalytic amino acids is demonstrated byirreversible inhibitors, whichpermanently inactivate the enzyme.

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