Biochemistry Exam #2 Study Guide

Biochemistry Exam #2 Study Guide - Biochemistry Exam#2...

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Biochemistry Exam #2 Study Guide Chapter 6: What is a catalyst? -A substance that increases the rate of a thermodynamically favored reaction without itself being changed or consumed in the overall process it may be reused in subsequent reactions -Living things use catalysts called Enzymes to increase the rates of chemical reactions What is an Enzyme? -Catalyst living systems use to increase the rates of chemical reactions -Most are proteins, but few are made of RNA -Chymotrypsin: Digestive protein that is synthesized in the pancreas and secreted into the small intestine, where it helps break down dietary proteins What is an active site? -Located in crevices on the enzyme surface -Where hydrolysis of polypeptide substrates take place (cleft between two domains) -Function groups inside active site are so carefully arranged that the enzyme can select its substrates from among many others that are similar in size and shape, and can then mediate a single chemical reaction involving those substrates Why do we need enzymes? How do they speed up reactions? -Chemical reactions require initial input of energy –usually in the form of increased heat Raising temp increases rate of vibration of molecules and the chance of collision Increase in concentration of reactants and heat can increase changes of chemical reaction occurring -Biological systems cannot raise heat or concentration at will enzymes act under mild conditions (do not need to raise the temp and therefore enhance rate of reaction) What is the difference between lock and key vs. induced fit models of substrate binding? -Lock and Key Model: emphasized the rigid 3D structure of the active site fitting closely with its substrate; tight binding -Induced Fit Model: views the active site as having a degree of flexibility Binding of substrate causes active site to undergo structural changes that will facilitate the enzyme-substrate reaction Strain and distortion by enzyme force substrate into the transition state (fits better than substrate) Solvent molecules (water) would hinder the reaction, active site excludes water by closing around substrates which lowers the energy barrier If water were present: increase in electrostatic interactions
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between substrate and enzyme; it could H bond and prevent low- barrier H bonds from forming (active site becomes non-aqueous when closed) What are the classes of enzymes and types of chemical reactions they catalyze? -Oxidoreductases Redox reactions, requires a cofactor such as NAD or FAD A- t B A t B- -Transferases Transfer of a functional group A-B + C A + B-C -Hydrolases Hydrolysis of functional group by water A-B +H2O A-H +B-OH -Lyases elimination to form double bond; or addition to a double bond X-A-B-Y A=B + X-Y -Isomerases isomerization reactions X-A-B-Y Y-A-B-X -Ligases ATP dependent joining to two molecules A + B +ATP A-B + ADP + Pi What is a transition state and how do enzymes affect it?
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