Metabolism, Photosynthesis, and Cellular Respiration

1. Chapters 8, 9, and 10 Metabolism, Photosynthesis, and Cellular Respiration

2. Chapter 8 • 8.1: An organism’s metabolism transforms the matter and energy, subject to the laws of thermodynamics • Metabolism – totality of an organism’s chemical reactions • Emergent property of life that comes from molecular interactions

3. Organization of the Chemistry of Life into Metabolic Pathways • Metabolic pathway – begins with a specific molecule, molecule is altered in a series of steps, results in a specific product • One enzyme per step A Starting molecule

4. Catabolic Pathways • Degradative processes • Release energy • Complex molecules into simpler molecules • Think: CATs (CATabolic pathways) tear things apart

5. Anabolic Pathways • Consume energy • Simpler molecules combined into a more complex one • Sometimes called biosynthetic pathways • Example: protein synthesis from amino acids • Bioenergetics: study of how energy flows through living organisms

6. Forms of Energy • Energy – the capacity to cause change • The ability to arrange a collection of matter • Can be used to do work • Kinetic energy – energy associated with the relative motion of objects • Heat (thermal energy) – kinetic energy associated with the random movement of atoms or molecules • Light is also energy

7. Forms of Energy • Potential energy – energy that is not kinetic; energy that matter possesses because of its location or structure • Chemical energy – term used by biologists to refer to the potential energy available for release in a chemical reaction • E.g. potential energy available through a catabolic reaction

8. Laws of Energy Transformation • Thermodynamics – the study of energy transformations that occur in a collection of matter • Systems – matter under study • Surroundings – everywhere outside of the system • Isolated system – unable to exchange energy or matter with surroundings • Open system – exchanges energy and matter with surroundings • organisms

9. First Law of Thermodynamics • The energy of the universe is constant • Energy can be transferred and transformed, but it cannot be created or destroyed • Also known as the principle of conservation of energy

10. Second Law of Thermodynamics • Every energy transfer or transformation increases the entropy of the universe • Entropy – measure of disorder or randomness • Spontaneous – process that can occur without input of energy • Must increase entropy of the universe • For a process to occur spontaneously, it must increase the entropy of the universe

11. Biological Order and Disorder • Living systems increase the entropy of their surroundings • Ordered structures created from less organized materials • Can go the other way as well • Entropy of a particular system can decrease, as long as the universe becomes more random at the same time

12. 8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously • Free-Energy Change, Delta G • Gibbs free energy, or free energy – portion of s system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell • Delta G = delta H – TdeltaS • DeltaH – change in the systems enthalpy (equivalent to total energy) • DeltaS - entropy

13. Free Energy, Stability, and Equilibrium • DeltaG = final G – initial G • Negative G is spontaneous • Tendency of a system to change to a more stable state • Equilibrium • Reversible • Does not mean that forward and backward reactions stop • Same rate or reaction, relative concentrations stay constant • Refer to Figure 8.5

14. Free Energy and Metabolism • Exergonic and Endergonic Reactions in Metabolism • Exergonic • “Energy outward” • Proceeds with a net release of free energy • DeltaG is negative • Endergonic • “energy inward” • Absorbs free energy from its surrounding • DeltaG is positive • Refer to Figure 8.6

15. Equilibrium and Metabolism • Reactions in an isolated system would reach equilibrium and not be able to do any work • A cell that has reached metabolic equilibrium is dead • Metabolism as a whole is never at equilibrium

16. 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions • Three main kinds of work • Chemical work – pushing of endergonic reactions • Transport work – pumping of substances across membranes against the direction of spontaneous movement • Mechanical work – actions such as beating of cilia, contracting of muscles, etc. • Energy coupling – the use of an exergonic reaction to power an endergonic one • ATP usually responsible

17. The Structure and Hydrolysis of ATP • ATP (adenosine triphosphate) • Contains ribose, adenine, and three phosphate groups • One of the nucleoside triphosphates used to make ATP • Bonds broken by hydrolysis • ATP + H2O  ADP + HOPO32- • High energy phosphate bonds

18. How ATP Performs Work • Hydrolysis of ATP releases heat • Shivering • Heat usually harnessed to perform cellular work • Phosphorylation – the transfer of a phosphate group from ATP to some other molecule; the other molecule is now phosphorylated • Transport and mechanical work are nearly always powered by ATP hydrolysis • Leads to a change in shape in the protein

19. The Regeneration of ATP + ATP H2O Energy from catabolism (exergonic, energy-releasing processes) Energy from catabolism (exergonic, energy-releasing processes) ADP + P

20. 8.4: Enzymes speed up metabolic reactions by lowering energy barriers • Figure 8.13 • Enzyme – macromolecule that acts as a catalyst • Catalyst – a chemical agent that speeds up a reaction without being consumed by the reaction

21. The Activation Barrier • Activation energy (free energy of activation) – The initial investment of energy for starting a reaction • energy required to contort reaction molecules so that they can break • Often supplied in the form of heat from surroundings • Refer to Figure 8.14

22. How Enzymes Lower the EA Barrier • Figure 8.15 • Heat can be used to speed up a reaction, but most organisms would die. • Lowering the EA barrier enables the reactants to absorb enough energy to reach the transition state without reaching high temperatures.

23. Substrate Specificity of Enzymes • Substrate – the reactant an enzyme acts on • Forms an enzyme-substrate complex when the enzyme and substrate have joined together • Enzyme + Substrate  Enzyme-substrate complex Enzyme+Products • Most enzyme names end in -ase

24. Substrate Specificity of Enzymes • Active site – region where the enzyme binds to the substrate; where catalysis occurs • Induced fit model

25. Catalysis in the Enzyme’s Active Site • Figure 8.17 • Occurs very quickly • Reusable

26. Catalysis in the Enzyme’s Active Site • Variety of mechanisms to lower EA • Provides template for substrates to come together • Enzyme can stretch substrates to transition-state form • Active site provides optimal microenvironment • Direct participation of active site in reaction • Rate related to initial substrate concentration

27. Effects of Local Conditions on Enzyme Activity • Temperature • pH • Chemicals

28. Effects of Temperature and pH • Up to a point, ROR increases with temperature • Optimal pH value usually between 6 and 8 • Figure 8.18

29. Cofactors • Cofactors– nonprotein helpers for catalytic activity • May be tightly bound to enzyme permanently, or loosely bound with substrate • Inorganic • Coenzyme – cofactor that is an organic molecule • vitamins

30. Enzyme Inhibitors • Certain chemicals inhibit the action of specific enzymes • Two kinds: • Competitive inhibition • Block substrates from entering active sites • Noncompetitive inhibition • Bind to another part of the enzyme so that it changes its shape, preventing the substrate from binding • Figure 8.19

31. 8.5: Regulation of enzyme activity helps control metabolism • REGULATION IS IMPORTANT

32. Allosteric Regulation of Enzymes • Allosteric regulation – term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to another site • Like reversible noncompetitive inhibition • Figure 8.20

33. Allosteric Activation and Inhibition • Enzymes made up of subunits • Subunits made up of polypeptide chains • The binding of an activator stabilizes the active form of the enzyme • The binding of an inhibitor stabilizes the inactive form of the enzyme

34. Identification of Allosteric Regulators • Not that many metabolic enzymes are allosterically regulated • Pharmaceutical companies interested in allosteric regulators • Exhibit higher specificity than do inhibitors binding to the active site • Figure 8.21

35. Feedback Inhibition • Feedback inhibition – in which a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme early in the pathway • Figure 8.22

36. Specific Localization of Enzymes Within a Cell • “The cell is not a bag of chemicals with thousands of different kinds of enzymes and substrates in a random mix.” • Compartmentalized

37. Cellular Respiration: Harvesting Chemical Energy Chapter 9

38. 9.1: Catabolic pathways yield energy by oxidizing organic fuels • The breakdown of organic molecules is exergonic • Fermentation – a partial degradation of sugars that occurs without O2 • Aerobic respiration – consumes organic molecules and O2 and yields ATP • Anaerobic respiration is similar to aerobic respiration but consumes compounds other than O2

39. Cellular Respiration • Contains both aerobic and anaerobic processes, but usually used to refer to aerobic respiration • C6H12O6 + 6 O2 6 CO2 + 6 H2O + Energy (ATP + heat) • The breakdown of glucose is exergonic

40. Redox Reactions • Oxidation and Reduction • Releases energy stored in organic molecules • LEO the lion says GER • Oxidizing agent gets reduced, and reducing agent gets oxidized • Changing of electron sharing as opposed to transferring

42. Stepwise Energy Harvest via NAD+ and the Electron Transport Chain • In cellular respiration, glucose and other organic molecules are broken down in a series of steps • Electrons from organic compounds are usually first transferred to NAD+, a coenzyme • As an electron acceptor, NAD+ functions as an oxidizing agent during cellular respiration • Each NADH (the reduced form of NAD+) represents stored energy that is tapped to synthesize ATP

43. Electrons passed to ETC by NADH • Series of steps instead of all at once

44. Stages of Cellular Respiration • Glycolysis – breaks down glucose into two molecules of pyruvate • The citric acid cycle – completes the breakdown of glucose • Oxidative phosphorylation -most of the ATP synthesis

45. 9.2: Glycolysis harvests chemical energy by oxidizing glucose to pyruvate • Glycolysis means “sugar splitting” • Glucose (six-carbon sugar) is split into two three-carbon sugars • Smaller sugars oxidized • Remaining molecules turned into pyruvate

46. Glycolysis • Occurs in the cytoplasm • Divided into: • Energy investment • Cell spends ATP • Energy payoff • ATP is produced with substrate-level phosphorylation and NAD+ is reduced to NADH • Figure 9.9

47. 9.3: The citric acid cycle completes the energy yielding oxidation of organic molecules • Pyruvate enters mitochondrion • Must be converted to acetyl coenzyme A (acetyl CoA) before the citric acid cycle can begin • Figure 9.10 • Citric acid cycle also called the Krebs cycle or the tricarboxylic acid cycle

48. The Citric Acid Cycle • Takes place within the mitochondrial matrix • Figure 9.11 • Figure 9.12