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Enzymes

Enzymes. Bio 11, November 9, 2007 Next Tuesday- last day to withdraw. Which is the most oxidized?. Carbon dioxide. Formaldehyde. Methane. Methanol. Which is the most reduced? Which is highest in energy? Which is lowest in energy?. Glycolysis is actually 10 chemical reactions.

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Enzymes

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  1. Enzymes Bio 11, November 9, 2007 Next Tuesday- last day to withdraw

  2. Which is the most oxidized? Carbon dioxide Formaldehyde Methane Methanol Which is the most reduced? Which is highest in energy? Which is lowest in energy?

  3. Glycolysis is actually 10 chemical reactions Each step in the reaction is catalyzed by a different enzyme 1 Glucose molecule yields 2 ATP, 2 NADH, 2 Pyruvate

  4. MITOCHONDRION CYTOSOL Pyruvate enters the mitochondrion, loses a carbon, and binds to coenzyme A to enter Krebs cycle NAD+ NADH + H+ Acetyl Co A CO2 Coenzyme A Pyruvate Transport protein

  5. The Krebs cycle is a set of many reactions • Each reaction is catalyzed by an enzyme • Such systems are called a metabolic pathways • Net result: 2ATP, 3 NADH, 1 FADH2/Glucose

  6. Inner mitochondrial membrane Oxidative phosphorylation: electron transport and chemiosmosis Citric acid cycle Glycolysis ATP ATP ATP H+ The electron transport system Generates a proton gradient, which powers ATP synthase H+ H+ H+ Cyt c Protein complex of electron carriers Intermembrane space Q IV III I ATP synthase II Inner mitochondrial membrane H2O 2H+ + 1/2 O2 FADH2 FAD NAD+ NADH + H+ ATP ADP + P i (carrying electrons from food) H+ Mitochondrial matrix Electron transport chain Electron transport and pumping of protons (H+), Which create an H+ gradient across the membrane Chemiosmosis ATP synthesis powered by the flow of H+ back across the membrane Oxidative phosphorylation Net result: ~32-34 ATP/glucose molecule

  7. Complete the table

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  12. Enzymes are protein catalysts • Catalyst- something that speeds up the rate of a reaction without being consumed by the reaction • They are shape-dependent • They are specific to a substrate • Most enzyme names end with “–ase”

  13. Diagramming a chemical reaction • Y axis = energy in chemical bonds of products and reactants • X axis = Reaction progress ( ≈ time) • Diagram shows an exergonic reaction • Ea = activation energy

  14. Enzymes can dramatically lower the activation energy for a reaction no enzyme with enzyme E a E Energy a reactants products Reaction Course Note that the equilibrium of the reaction is unaffected 12

  15. Substrate Binding and Reaction

  16. Example: b - galactosidase H O 2 galactose lactose b - galactosidase glucose (aka lactase in humans) 11

  17. b - galactosidase 10

  18. How enzymes work • Structure aids function • An active site (aka “activation site”) naturally fits substrate • Enzymes stabilize transition state of substrates

  19. Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. • Active site (and R groups of • its amino acids) can lower EA • and speed up a reaction by • acting as a template for • substrate orientation, • stressing the substrates • and stabilizing the • transition state, • providing a favorable • microenvironment, • participating directly in the • catalytic reaction. Substrates LE 8-17 Enzyme-substrate complex Active site is available for two new substrate molecules. Enzyme Products are released. Substrates are converted into products. Products

  20. Ways in which Enzymes help • The active site can lower an EA barrier by • Orienting substrates correctly • Straining substrate bonds • Providing a favorable microenvironment • Covalently bonding to the substrate ENZYMES CANNOT: -Act as an energy source -Turn an unfavorable reaction into a favorable one

  21. Effects of Local Conditions on Enzyme Activity • An enzyme’s activity can be affected by: • General environmental factors, such as temperature and pH • Chemicals that specifically influence the enzyme

  22. Effects of Temperature and pH • Enzymes have an optimal temperature and pH • Tertiary structure can be radically altered by changes in pH or temp

  23. Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Rate of reaction LE 8-18 40 0 20 60 80 100 Temperature (°C) Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Rate of reaction 2 3 6 7 9 10 0 1 4 5 8 pH Optimal pH for two enzymes

  24. Cofactors • Cofactors are nonprotein enzyme helpers • Coenzymes are organic cofactors • Many vitamins are cofactors for enzymes • Metal ions also can be essential to enzyme function

  25. Enzyme Inhibition • Competitive inhibitors bind to the active site of an enzyme, blocking the substrate • Noncompetitive inhibitors (aka allosteric) away from active site, changing enzyme shape • Many drugs are enzyme inhibitors (COX2 inhibitors, etc.) • Some toxins bind enzymes permanently, destroying them

  26. Regulation of enzyme activity helps control metabolism • Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated • To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes

  27. Allosteric Regulation of Enzymes • Allosteric regulation is the term used to describe cases where a protein’s function at one site is affected by binding of a regulatory molecule at another site • Allosteric regulation may either inhibit or stimulate an enzyme’s activity

  28. Cooperativity is a form of allosteric regulation that can amplify enzyme activity • In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

  29. Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Substrate LE 8-20b Inactive form Stabilized active form Cooperativity another type of allosteric activation

  30. Feedback Inhibition • In feedback inhibition, the end product of a metabolic pathway shuts down the pathway • Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

  31. Initial substrate (threonine) Active site available Threonine in active site Enzyme 1 (threonine deaminase) Isoleucine used up by cell Intermediate A Feedback inhibition Enzyme 2 Active site of enzyme 1 can’t bind theonine pathway off Intermediate B Enzyme 3 Intermediate C Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine)

  32. Specific Localization of Enzymes Within the Cell • Structures within the cell help bring order to metabolic pathways • Some enzymes act as structural components of membranes • Some enzymes reside in specific organelles, such as enzymes for cellular respiration being located in mitochondria

  33. Mitochondria, sites of cellular respiration LE 8-22 1 µm

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