2. Metabolism A cell is a miniature factory A large number of Chemical reactions are occurring A (reactants) + B (reactants) ----> C (products) Chemical reactions are either endogonic (req. energy) or exogonic (release energy)

3. Enzyme Reduce Activation energy Contain specific active sites Substrates bind to active sites, forming the enzyme-substrate complex. Enzyme-substrate interaction results in product formation For ex. A + B ---> C

4. Enzymes Two types of enzyme-substrate inhibition 1.) Competitive – different substrates bind to the same active site. 2.) Allosteric – substrates cause the protein to change 3-D shape. Thus, the function changes.

5. Electron transfer Oxidation – when electrons are given up (donation) Reduction – when electrons are taken in (accepting)

7. Metabolism Catabolism - produce energy (ATP) - breakdown molecules (ex. glycolysis) Anabolism - use energy (ATP) - synthesize macromolecules (ex. DNA, lipids, etc.)

8. Metabolic Strategies All are based on energy, electron and carbon source: 1.) Chemoorganotrophic (chemoheterotroph) 2.) Chemolithotrophic (chemoautotroph) 3.) Photolithotrophic (photoautotroph) 4.) Photoorganotrophic (photoheterotroph)

9. Metabolism Catabolism Energy (ATP) Small molecules (precursors) Anabolism Large molecules

10. Catabolism - ex. Glycolytic pathway (glycolysis) - Two types of catabolism: 1.) respiration-aerobic( w/ oxygen) - anaerobic respiration (w/o oxygen) 2.) fermentation (does not use oxygen) - Glucose is taken in and broken down in order to generate energy and to use the glucose carbons as a source of carbon.

12. Glycolysis TCA Cycle GlycolysisRespiration Fermentation Oxidative phosphorylation Organic products

13. Respiration - Three phases - 1.) Glycolysis - 2.) TCA cycle - 3.) oxidative phosphorylation

14. Fermentation - Two phases - 1.) Glycolysis - 2.) Fermentation -high yield of product, ex. ethanol

15. Chemical reaction Metabolism involves chemical reactions A+B-->C+D, ex. Glycolysis Three events –1.) electron flow –2.) carbon flow –3.) energy production

16. Metabolism energyelectronscarbon Binary fission Flow of

17. Electron flow TCA electrons e-e- Coenzyme - NAD -->NADH Oxidative phosphorylation (electron transport chain) Coenzymes - NAD-->NADH NADH O2O2 Fermentation H2OH2O NAD NADH NADH->NAD e-e- NADH NAD

21. Reduction/oxidation (redox) - Electron flow involves redox reactions. - Reduction - a molecule accepts an electron. Reduced. Ex. NADH - Oxidation - a molecule donates an electron. Oxidized. Ex. NAD - H ion transfer is usually accompanied by electron transfer.

22. Reduction/Oxidation (Redox) Molecules involved in redox reactions Ex. Coenzymes: (oxidized)NAD + + H + + e - --> NADH (reduced) Occurs in glycolysis, TCA Ex. Electron transport chain (electron carriers accept electrons from NADH) Ex. 1/2O 2 + H 2 + e - ---> H 2 O Final electron acceptor can be oxygen, sulfate, nitrate, carbonate. (S,N, and C are anaerobic respiration)

23. Cycling : If both fermentation and respiration are possible, the reduced NADHs are used in the electron transport systems and fermentation. The oxidized NADs are used in respiration and/or fermention.

24. Glycolysis TCA Cycle NADH Electron transport chain (chemiosmosis ) H2OH2O Organic products RespirationFermentation NADH NAD NADH

25. Glucose (6 C molecule) Pyruvic acid (Two 3 C molecule) TCA Intermediates (3 or2 C) Carbon Flow CO 2 Biosynthesis (anabolism) Intermediates

26. Glycolysis (Breakdown of glucose) Glycolysis Pyruvic acid TCA Cycle NADH Electron transport chain (chemiosmosis ) H2OH2O Organic products RespirationFermentation NADH CO 2

27. Carbon flow Large molecules are broken into smaller molecules (catabolism) Critical intermediates are generated (ex. Pyruvic acid, etc.) They are used in the anabolism process as well as entry back into the catabolism process.

28. Energy Production 1.) Substrate-level phosphorylation- ADP + P ==> ATP (associated with glycolysis) 2.) Oxidative phosphorylation Ex. electron transport chain associated with the proton motive force. 3.) Photophosphorylation – converts light energy to chemical energy of ATP and NADPH. (Light +carbon dioxide+wate =>sugar=>glycolysis)

29. Substrate Level Phosphorylation - Occurs at certain steps in glycolysis - Fermentation generates most of its ATP using this process since no oxidative phosphorylation is present. - Level of ATP generation is less than oxidative phosphorylation. - Fermentation:Makes up difference by metabolizing large amounts of material, thus generating large amounts of product.

31. Oxidative Phosphorylation - Electron transport chain - Located in the cytoplasmic membrane - Transfer of electrons also exports H ions to one side of the membrane, creating a gradient (Proton motive force). -The H ions re-enter thru an ATPase, generating high levels of ATP. This process is call chemiosmosis

34. Photophosphorylation Light trapping pigments (chlorophylls) Sugars are synthesized with energy from light. The sugars are then metabolized (glycolysis).

35. Glycolysis Glucose Pyruvic acid TCA Cycle NADH Electron transport chain (chemiosmosis ) H2OH2O Organic products RespirationFermentation ATP CO 2 FADH 2

36. Respiratory Metabolism Conversion of carbohydrates to pyuvate – end of glycolysis (EM pathway) Oxygen is the final electron acceptor => water Includes the TCA cycle Includes Oxidative phosphorylation

37. Summary of Glycolysis (EM) Transfer electrons (oxidation-reduction) Generates NADH (oxidized) Generates small amounts of ATP (substrate level phosphosphorylation), compared to the oxidative phosphorylation. Generates critical intermediates

38. Summary of TCA Generates critical intermediates Generates oxidized coenzymes (NADH, FADH 2 ) Release carbon dioxide (reduces size of molecule)

39. Summary of ETS (oxidative phosphorylation) Accept electrons from oxidized coenzymes Electron carriers transfer electrons to other carriers. Transfer H ions to one side of cytoplasmic membrane (a gradient is formed) H ions move back into cytoplasm by way of the ATPase. Thus, ATP is generated in large amounts.

41. Alternate Glycolytic Pathway To supply coenzymes, critical intermediates, etc., during times of adaptation, absence of EM; other pathways are needed. Entner-Doudoroff pathway - aerobic bacteria (lack an EM enzyme), certain Archaea Less ATP generated Generates NADPH, rather than NADH

42. Alternate Glycolytic Pathway Modified ED pathway Partially nonphosphorylated Some Archaea (Halo, Thermo), Eubacteria Less to no net production of ATP, compared to EM.

43. Alternate to glycolysis Methylglyoxal pathway Eubacteria - during low phosphate concentrations. Less ATP generated, compared to EM.

44. Pentose Phosphate Pathway Directly linked to EM or glycolysis Major role is to generate ribose for the biosynthesis (anabolism) of DNA, RNA, ATP NAD, NADP. Normal process (operates in conjunction with EM)

46. Glycolysis supplies energy for anabolism Glucose Pyruvic acid TCA Cycle NADH Electron transport chain (chemiosmosis ) H2OH2O Organic products RespirationFermentation ATP CO 2

47. Metabolism Catabolism Energy (ATP) Small molecules (precursors) Anabolism Large molecules

48. Review Metabolism Shared with both respiration and fermentation Three phases of glycolytic pathway 1.) glycolysis 2.) TCA 3.) electron transport chain (oxidative phosphorylation) Three events during catabolism 1.)electron flow 2.)carbon flow 3.)energy production

49. Review continued 1.) Redox reactions Depends on reduction potential, positive value- more likely to accept electron. Participating molecules ex. NAD, NADH (electron donors or acceptors) 2.) 6C molecule to two 3C molecules C molecules (intermediates) enter biosynthesis or is released as CO 2

50. Review continued 3.) Three forms 1.) substrate level phosphorylation 2.) oxidative phosphorylation 3.) photophosphorylation Alternate forms of the glycolytic pathway exist in order to supply coenzymes, ATP, etc.

51. Fermentation Variety of products are synthsized. Use products to identify specific microoganim. Ex. Lactic acid, Ethanolic, Propionic Acid, Mixed Acid, Butanediol, Butyric acid, Amino acid, Acetic to methane Electron donor (substrate) and acceptor (product) are internal of the cell, thus less energy generated.

54. Mixed acid fermentation Methyl Red test - pH based test for acid production. Clinical labs use it to identify E. coli, urinary tract infections, etc. NADH is reoxidized to NAD

55. Butanediol fermentation Enterobacter, Serratia, Klebsiella- associated with opportunistic infections. Voges-Proskauer test - detects an intermediate metabolite. Used with MR test ex. VP-MR test Testing water supplies E.coli VP(-)MR(+), EnterbacterVP(+)MR(-)

56. Photoautotrophy Absorption of light energy Oxygenic photosynthesis- algae, cyanobacteria, release oxygen, two photosystems exist Anoxygenic photosynthesis-Green and purple bacteria, no O is released, one photosystem