Cell & Energetics

1. Cell & Energetics

2. Metabolism • totality of an organism’s chemical reactions • arises from interactions between molecules within the cell

3. Catabolic pathways • release energy • break down complex molecules into simpler compounds • Anabolic pathways • consume energy • build complex molecules from simpler ones

4. Thermodynamics • the energy of the universe is constant • Energy can be transferred and transformed • Energy cannot be created or destroyed • principle of conservation of energy • During every energy transfer or transformation, some energy is unusable, often lost as heat First Law Second Law

5. LE 8-3 CO2 Heat Chemical energy H2O First law of thermodynamics Second law of thermodynamics

6. Types of Reactions • exergonic reaction • net release of free energy • is spontaneous • exothermic • endergonic reaction • absorbs free energy from its surroundings • is nonspontaneous • endothermic

7. A cell does three main kinds of work: • Mechanical • Transport • Chemical • Cell energy management • energy coupling • the use of an exergonic process to drive an endergonic one

8. LE 8-8 ATP (adenosine triphosphate) Adenine Phosphate groups Ribose

9. ATP P P P Adenosine triphosphate (ATP) H2O + P P P + Energy i Adenosine diphosphate (ADP) Inorganic phosphate

10. ATP hydrolysis • Exergonic • the energy can be used to drive an endergonic reaction

11. LE 8-11 P i P Protein moved Motor protein Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP ATP + P i P P i Solute transported Solute Transport work: ATP phosphorylates transport proteins P NH2 NH3 P + + Glu i Glu Reactants: Glutamic acid and ammonia Product (glutamine) made Chemical work: ATP phosphorylates key reactants

12. Regeneration of ATP ATP Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (energonic, energy- yielding processes) P ADP + i

13. Enzymes

14. Enzymes • Catalytic proteins • Usually end in –ase • Ex. Sucrase • Hydrolyzes sucrose Sucrose C12H22O11 Glucose C6H12O6 Fructose C6H12O6 How Enzymes Work

15. Substrate Specificity of Enzymes • Substrate • The reactant that an enzyme acts on • Enzyme binds to its substrate • enzyme-substrate complex • Active site • The region on the enzyme where the substrate binds

16. Substrate Active site Enzyme-substrate complex Enzyme

17. The active site can lower an EA barrier by: • Orienting substrates correctly • Straining substrate bonds • Providing a favorable microenvironment • Covalently bonding to the substrate

18. 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 Enzyme-substrate complex Active site is available for two new substrate molecules. Enzyme Products are released. Substrates are converted into products. Products

19. Factors Affecting Enzyme Function • An enzyme’s activity can be affected by: • Environmental factors • Temperature • pH • Chemicals • Rate of reaction can also be affected by: • Amount of enzymes present • Concentration of substrate • Presence of cofactors/coenzymes • Presence of enzyme inhibitors

20. LE 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Rate of reaction 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

21. LE 8-19 A substrate can bind normally to the active site of an enzyme. Substrate Active site Enzyme • Enzyme Inhibitors • Competitive inhibitors • bind to the active site of an enzyme • competing with the substrate • Noncompetitive inhibitors • bind to another part of an enzyme • Cause the enzyme to change shape • make the active site less effective Normal binding A competitive inhibitor mimics the substrate, competing for the active site. Competitive inhibitor Competitive inhibition 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 Noncompetitive inhibition

22. Enzyme Regulation • Genes • Specific genes coding for specific enzymes are “turned on” or “turned off” • Allosteric regulation • protein’s function at one site is affected by binding of a regulatory molecule at another site • may either inhibit or stimulate an enzyme’s activity

23. Allosteric activator stabilizes active form. Allosteric Activation and Inhibition Allosteric enzyme with four subunits Active site (one of four) • allosterically regulated enzymes • Usually polypeptide subunits • has active and inactive forms • binding of an activator stabilizes the active form of the enzyme • binding of an inhibitor stabilizes the inactive form of the enzyme Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Allosteric inhibitor stabilizes inactive form. Non- functional active site Inhibitor Stabilized inactive form Inactive form Allosteric activators and inhibitors

24. Cooperativity • form of allosteric regulation • can amplify enzyme activity • binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

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

26. FeedbackInhibition Initial substrate (threonine) Active site available Threonine in active site • the end product of a metabolic pathway shuts down the pathway • prevents a cell from wasting chemical resources by synthesizing more product than is needed 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)

27. Energy Release

28. LE 9-2 Light energy ECOSYSTEM Photosynthesis in chloroplasts Organic molecules CO2 + H2O + O2 Cellular respiration in mitochondria ATP powers most cellular work Heat energy

29. becomes oxidized(loses electron) Xe- + Y X + Ye- becomes reduced(gains electron) Oxidation and Reduction • oxidation-reduction reactions • Aka. redox reactions • Chemical reactions that transfer electrons between reactants • Oxidation • a substance loses electrons • is oxidized • Reduction • substance gains electrons • is reduced (the amount of positive charge is reduced)

30. becomes oxidized C6H12O6 + 6O2 6CO2 + 6H2O + Energy becomes reduced • Cellular respiration • fuel (such as glucose) is oxidized • oxygen is reduced

31. Cellular Respiration • 3 stages: • Glycolysis • breaks down glucose into two molecules of pyruvate • The citric acid cycle • completes the breakdown of glucose • Oxidative phosphorylation • accounts for most of the ATP synthesis • it is powered by redox reactions

32. LE 9-6_1 Glycolysis Pyruvate Glucose Cytosol Mitochondrion ATP Substrate-level phosphorylation

33. LE 9-6_2 Glycolysis Citric acid cycle Pyruvate Glucose Cytosol Mitochondrion ATP ATP Substrate-level phosphorylation Substrate-level phosphorylation

34. LE 9-6_3 Electrons carried via NADH and FADH2 Electrons carried via NADH Oxidative phosphorylation: electron transport and chemiosmosis Glycolysis Citric acid cycle Pyruvate Glucose Cytosol Mitochondrion ATP ATP ATP Substrate-level phosphorylation Oxidative phosphorylation Substrate-level phosphorylation

35. Glycolysis • “splitting of sugar” • breaks down glucose • Produces two molecules of pyruvate • occurs in the cytoplasm • 2 major phases: • Energy investment phase • Energy payoff phase • Glycolysis

36. LE 9-8 Energy investment phase Glucose 2 ATP 2 ADP + 2 P used Citric acid cycle Glycolysis Oxidative phosphorylation Energy payoff phase formed ATP ATP ATP 4 ADP + 4 P 4 ATP 2 NADH + 2 H+ 2 NAD+ + 4 e– + 4 H+ 2 Pyruvate + 2 H2O Net 2 Pyruvate + 2 H2O Glucose 4 ATP formed – 2 ATP used 2 ATP 2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+

37. citric acid cycle (Krebs Cycle) • 8 steps: • 1st step • The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate • next seven steps • decompose the citrate back to oxaloacetate • NADH and FADH2 produced by the cycle relay electrons extracted from food to the electron transport chain • which powers ATP synthesis via oxidative phosphorylation

38. Electron Transport Chain • Located in the cristae of the mitochondrion • Most of the chain’s components are proteins • exist in multiprotein complexes • Carriers alternate reduced and oxidized states • Electrons drop in free energy as they go down the chain • Are finally passed to O2, forming water • generates no ATP • Function: • to break the large free-energy drop from food to O2 into smaller steps that release energy in manageable amounts

39. Chemiosmosis • the use of energy in a H+ gradient to drive cellular work • Example: • Electron transfer in the electron transport chain causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space • H+ then moves back across the membrane, passing through channels in ATP synthase • ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP

40. During cellular respiration, most energy flows in this sequence: • glucose NADH electron transport chain proton-motive force ATP • About 40% of the energy in a glucose molecule is transferred to ATP during cellular respiration • making about 38 ATP

41. Fermentation • consists of glycolysis plus reactions that regenerate NAD+ • Two common types: • alcohol fermentation • lactic acid fermentation • Fermentation

42. alcohol fermentation • pyruvate is converted to ethanol in two steps • the first releasing CO2 • Ex. Yeast - brewing, winemaking, and baking • lactic acid fermentation • pyruvate is reduced to NADH • forming lactate as an end product • no release of CO2 • Ex. some fungi and bacteria is used to make cheese and yogurt • Ex. Human muscle cells - generate ATP when O2 is scarce

43. Photosynthesis

44. Photosynthesis • Converts solar energy into chemical energy • Occurs in plants, algae, and some prokaryotes • Autotrophs • Sustain self without eating things derived from other organisms • Photoautotrophs • Ex. Most plants • Use solar energy to make organic molecules from water and carbon dioxide (PHOTOSYNTHESIS)

45. LE 10-2 Plants Unicellular protist 10 µm Purple sulfur bacteria 1.5 µm Multicellular algae Cyanobacteria 40 µm

46. Photosynthesis in plants • Primarily in leaves • Chlorophyll • green pigment • in chloroplasts • Absorbs light energy • Stomata • microscopic pores on leaf surface • CO2 enters • O2 exits

47. Chloroplasts • found mainly in cells of the mesophyll • interior tissue of the leaf • typical mesophyll cell = 30-40 chloroplasts • Thylakoids • membranes containing chlorophyll • Grana = stacks of thylakoid membranes • Convert solar energy into ATP and NADPH (chemical energy) • Stroma • dense fluid • Surrounds thylakoid

48. LE 10-3 Leaf cross section Vein Mesophyll Stomata O2 CO2 Mesophyll cell Chloroplast 5 µm Outer membrane Thylakoid Intermembrane space Thylakoid space Stroma Granum Innermembrane 1 µm

49. Photosynthesis 6 CO2 + 12 H2O + Light energy  C6H12O6 + 6 O2 + 6 H2 O

50. LE 10-4 12 H2O 6 CO2 Reactants: 6 O2 6 H2O C6H12O6 Products: