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. 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) Figure 8.9 P Adenosine triphosphate (ATP) H2OH2O + Energy Inorganic phosphate Adenosine diphosphate (ADP) PP PPP i 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 is Renewable ATP is renewable  shuttle Pi + energy (fig 8.12) ATP synthesis from ADP + P i requires energy ATP ADP + P i Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (exergonic, energy yielding processes) ATP hydrolysis to ADP + P i yields energy Figure 8.12 Respiration & photosynthesis provide 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. (E A ) = 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. E A 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. The Activation Barrier Every chemical reaction between molecules involves both bond breaking and bond forming Hydrolysis is an example of a chemical reaction Figure 8.13 H2OH2O H H H H HO OH O O O O O H H H H H H H CH 2 OH OH CH 2 OH Sucrase HO OH CH 2 OH H H H O Sucrose Glucose Fructose C 12 H 22 O 11 C 6 H 12 O 6 + H OHH

8. The activation energy, E A Free energy Progress of the reaction ∆G < O EAEA Figure 8.14 A B C D Reactants A C D B Transition state A B CD Products The activation energy, E A – 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. Effect of enzymes on reaction rate Progress of the reaction Products Course of reaction without enzyme Reactants Course of reaction with enzyme EAEA without enzyme E A with enzyme is lower ∆G is unaffected by enzyme Free energy Figure 8.15 An enzyme catalyzes (speeds up) reactions by lowering the E A 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. The Active Site Is the region on the enzyme where the substrate binds, and where catalysis occurs. Figure 8.16 Substate Active site Enzyme (a)

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

14. The catalytic cycle of an enzyme Substrates Products Enzyme Enzyme-substrate complex 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 E A 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. 4 Substrates are Converted into Products. 5 Products are Released. 6 Active site Is available for two new substrate Mole. Figure 8.17

15. Ways the active site can lower an E A barrier The active site can lower an E A 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. Effects of Temperature Each enzyme has an optimal temperature at which it can function best Figure 8.18 Optimal temperature for enzyme of thermophilic Rate of reaction 0 20 40 80 100 Temperature (Cº) (a) Optimal temperature for two enzymes Optimal temperature for typical human enzyme (heat-tolerant) bacteria

18. Effects of pH Figure 8.18 Rate of reaction (b) Optimal pH for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) 1 02 34 5 6789 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. Enzyme Inhibitors Competitive inhibitors b ind to the active site of an enzyme, competing with the substrate Figure 8.19 (b) Competitive inhibition A competitive inhibitor mimics the substrate, competing for the active site. Competitive inhibitor A substrate can bind normally to the active site of an enzyme. Substrate Active site Enzyme (a) Normal binding

21. Noncompetitive inhibitors bind to another part of an enzyme, changing the function Figure 8.19 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 Enzyme Inhibitors

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. Many enzymes are allosterically regulated – They change shape when regulatory molecules bind to specific sites, affecting function Stabilized inactive form Allosteric activator stabilizes active from Allosteric enyzme with four subunits Active site (one of four) Regulatory site (one of four) Active form Activator Stabilized active form Allosteric inhibitor stabilizes inactive form Inhibitor Inactive form Non- functional active site (a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again. Oscillation Figure 8.20

25. Cooperativity – Is a form of allosteric regulation that can amplify enzyme activity Figure 8.20 Binding of one substrate molecule to active 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.

26. Feedback inhibition Active site available Isoleucine used up by cell Feedback inhibition Isoleucine binds to allosteric site Active site of enzyme 1 no longer binds threonine; pathway is switched off Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A Intermediate B Intermediate C Intermediate D Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 End product (isoleucine) Figure 8.21 In feedback inhibition, the end product of a metabolic pathway shuts down the pathway

27. 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. 1 µm Mitochondria, sites of cellular respiration Figure 8.22