BSC 2010 - Exam I Lectures and Text Pages

1. BSC 2010 - Exam I Lectures and Text Pages • I. Intro to Biology (2-29) • II. Chemistry of Life • Chemistry review (30-46) • Water (47-57) • Carbon (58-67) • Macromolecules (68-91) • III. Cells and Membranes • Cell structure (92-123) • Membranes (124-140) • IV. Introductory Biochemistry • Energy and Metabolism (141-159) • Cellular Respiration (160-180) • Photosynthesis (181-200)

2. P P P Adenosine triphosphate (ATP) H2O Energy + P i P P Adenosine diphosphate (ADP) Inorganic phosphate Figure 8.9 ATP: powers cellular work by coupling exergonic to endergonic reactions. • a.Type of nucleotide with an adenine, a ribose, and 3 phosphate groups (fig 8.8) • b. Phosphate groups are pulled off (hydrolysis) to release energy • fig 8.9: ATP + H2O  ADP + Pi (∆G = -7.3 kcal/mol) ATP (adenosine triphosphate) = energy currency of the cell

3. How ATP Performs Work Key to coupling exergonic w/ endergonic rxns is making a phosphorylated intermediate • a. Phosphorylation = transfer of a phosphate group to another molecule • b. Powered by hydrolysis of ATP (fig 8.11)

4. ATP hydrolysis to ADP + P i yields energy ATP synthesis from ADP + P i requires energy ATP Energy from catabolism (exergonic, energy yielding processes) Energy for cellular work (endergonic, energy- consuming processes) ADP + P i Figure 8.12 ATP is Renewable • ATP is renewable shuttle Pi + energy (fig 8.12) • Respiration & photosynthesisprovide energy to drive the endergonic process of ATP formation(∆G = +7.3 kcal/mol)

5. ENZYMES: Speed up Metabolic Pathways by Lowering Energy Barriers 1. Enzymes = catalytic proteins that speed up chemical rxns (don’t make rxns happen that would not happen on their own) 2. Converting a molecule into another involves contorting the original molecule into an unstable state • a. This takes energy = activation energy. (EA) = amt of energy you put into a rxn to get it over the hill so the downhill part of the rxn can start • b. Ex (fig 8.14): AB + CD  AC + BD 3. EA often supplied by adding heat (absorbed by reactant molecules) - usually too high a heat for rxns to happen at room temperature Why is it inappropriate to add a lot of heat to biological systems?

6. Enzymes speed up metabolic reactions by lowering energy barriers • Enzymes are catalysts. • A catalyst • Is a chemical agent that speeds up a reaction without being consumed by the reaction

7. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H Sucrase H OH H HO OH H HO H2O O + H H OH O HO CH2OH CH2OH OH H H H OH H OH OH Fructose Glucose Sucrose Figure 8.13 C12H22O11 C6H12O6 C6H12O6 The Activation Barrier • Every chemical reaction between molecules involves both bond breaking and bond forming • Hydrolysis is an example of a chemical reaction

8. A B D C Transition state B A EA D C Free energy Reactants B A ∆G < O C D Products Progress of the reaction Figure 8.14 The activation energy, EA • The activation energy, EA • Is the initial amount of energy needed to start a chemical reaction • Is often supplied in the form of heat from the surroundings in a system

9. Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy ∆G is unaffected by enzyme Course of reaction with enzyme Products Progress of the reaction Figure 8.15 Effect of enzymes on reaction rate • An enzyme catalyzes (speeds up) reactions by lowering the EA barrier

10. How an enzyme works: • 1. Substrate = reactant that enzymes acts on  forms an enzyme-substrate complex • 2. The 3-D structure of an enzyme gives it specificity • 3. Active site = specific site where an enzyme and substrate bind (typically a groove/pocket on the protein’s surface) • 4. Changes shape as substrate binds to it, so that it fits even more snugly around reactant (= induced fit, fig 8.16) • 5. Brings chemical groups of active site into position to enhance catalyzing the rxn • 6. Enzymes return to their original conformation after releasing converted substrate  they can be re-used

11. Substrate Specificity of Enzymes • The substrate • Is the reactant an enzyme acts on • The enzyme • Binds to its substrate, forming an enzyme-substrate complex

12. Substate Active site Enzyme Figure 8.16 (a) The Active Site • Is the region on the enzyme where the substrate binds, and where catalysis occurs.

13. Enzyme- substrate complex (b) Figure 8.16 Induced fit of a substrate • Induced fit of a substrate • Brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction

14. 1 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). 2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 3 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 Enzyme-substrate complex 6 Active site Is available for two new substrate Mole. Enzyme 5 Products are Released. 4 Substrates are Converted into Products. Figure 8.17 Products The catalytic cycle of an enzyme

15. Ways the active site can lower an EA barrier • The active site can lower an EA barrier by • Orienting substrates correctly • Straining substrate bonds and forcing transition states • Providing a favorable microenvironment (such as specific pH) • Covalently bonding (temporarily) to the substrate (direct participation)

16. Enzyme activity is affected by the environment: • 1. Temperature and pH can increase enzyme activity, but can also denature enzymes (fig 8.18) • 2. Cofactors and coenzymes are small molecules that bind to enzymes and are necessary for catalytic function. • Cofactors = non-protein helpers • Coenzymes = organic cofactors • 3. Enzyme inhibitors bind to an enzyme to make it inactive (fig 8.19) • a. Noncompetitive inhibitors change the 3-D structure of active site by binding elsewhere on the enzyme • b. Competitive inhibitors directly block substrate from active site

17. Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria Rate of reaction 80 0 20 100 40 Temperature (Cº) (a) Optimal temperature for two enzymes Figure 8.18 Effects of Temperature • Each enzyme has an optimaltemperature at which it can function best

18. Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Rate of reaction 5 6 7 8 9 3 4 0 2 1 (b) Optimal pH for two enzymes Figure 8.18 Effects of pH • Each enzyme has an optimal pH at which it can function best

19. Cofactors small molecules that bind to enzymes and are necessary for catalytic function. • Cofactors • Are nonprotein enzyme helpers • Coenzymes • Are organic cofactors

20. A substrate can bind normally to the active site of an enzyme. Substrate Active site Enzyme (a) Normal binding A competitive inhibitor mimics the substrate, competing for the active site. Competitive inhibitor Figure 8.19 (b) Competitive inhibition Enzyme Inhibitors • Competitive inhibitors bind to the active site of an enzyme, competing with the substrate

21. A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions. Noncompetitive inhibitor (c) Noncompetitive inhibition Figure 8.19 Enzyme Inhibitors • Noncompetitive inhibitors bind to another part of an enzyme, changing the function

22. Cells have to regulate enzyme activity (control metabolism): • They can either switch genes on/off • Or they can regulate the proteins once they’re made Regulating Proteins --- • A. Allosteric regulation = affecting an enzyme’s activity by attaching a regulatory molecule that changes its 3-D structure • 1. Feedback inhibition = when a metabolic pathway is switched off by inhibitory binding of its end product to an enzyme that acts early in the pathway (fig 8.21) • 2. Cooperativity These enzymes are usually composed of more than one polypeptide chain (fig 8.20). Inhibition/activation at one site affects all other active sites on the same molecule • B. Where are enzymes in the cell? This facilitates metabolic order. • 1. Embedded in phospholipid bilayers (membranes) • 2. In solution within an organelle (lysosomes)

23. Allosteric Regulation of Enzymes • Allosteric regulation • Is the term used to describe any case in which a protein’s function at one site is affected by binding of a regulatory molecule at another site • Function may be activated or inhibited.

24. Allosteric activatorstabilizes active from Allosteric enyzmewith four subunits Active site(one of four) Regulatorysite (oneof four) Activator Active form Stabilized active form Allosteric inhibitorstabilizes inactive form Oscillation Non-functionalactivesite Inhibitor Stabilized inactiveform Inactive form (a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again. Figure 8.20 Many enzymes are allosterically regulated • They change shape when regulatory molecules bind to specific sites, affecting function

25. Binding of one substrate molecule toactive site of one subunit locks all subunits in active conformation. Substrate Inactive form Stabilized active form (b)Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate. Figure 8.20 Cooperativity • Is a form of allosteric regulation that can amplify enzyme activity

26. Initial substrate(threonine) Active siteavailable Threoninein active site Enzyme 1(threoninedeaminase) Isoleucineused up bycell Intermediate A Feedbackinhibition Active site of enzyme 1 no longer binds threonine;pathway is switched off Enzyme 2 Intermediate B Enzyme 3 Intermediate C Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 Figure 8.21 End product(isoleucine) Feedback inhibition • In feedback inhibition, the end product of a metabolic pathway shuts down the pathway

27. Mitochondria, sites of cellular respiration Figure 8.22 1 µm Enzyme Location in the Cell • 1. Grouped into complexes and embedded in phospholipid bilayers (membranes) • 2. In solution within an organelle (lysosomes) • This facilitates metabolic order.