Chapter 5 Learning Objectives 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. List four features that are unique to living cells, compared to inert chemicals. Explain how each of the overarching biochemical principles of life contributes to a cell’s ability to reproduce. Distinguish between growth metabolism and nongrowth metabolism. Explain the connection between the ability to reproduce and entropy. Speculate about a different life form (on an imagined planet) that might not satisfy one or more of the four principles of chemical processes known to all Earth life. List two reasons why E. coli is a model organism for growth metabolism. List the two most common elements in a typical bacterium. List the two most abundant macromolecules in a typical bacterium. Explain why all cells need each of the four basic building blocks, regardless of what that cell is using as an energy or carbon source. List four cell functions that require energy. Explain why obligate parasites often have relatively small genomes. Speculate why the vast majority of a cell’s reducing power is used for protein synthesis. The broad processes of metabolism (fueling, biosynthesis, polymerization, assembly, and cell division) are interrelated by the fact that each requires starting materials that are the products of the preceding step. Identify the starting materials for each phase of metabolism. Speculate which processes of metabolism (fueling, biosynthesis, polymerization, assembly, and cell division) could be dispensable under certain circumstances (Hint: consider the effect of nutrition). Use the flowchart in Fig. 5.1 to explain how the metabolism of a cell would change if it was growing on different media (for example, a medium of simple salts and glucose compared to a rich medium with a mixture of peptides called tryptone, and yeast extract). Compare and contrast each of the following, with respect to source of energy and carbon: chemoheterotroph, photoheterotroph, chemoautotroph, and photoautotroph. Identify an example species that is a (i) chemoheterotroph and (ii) photoautotroph. Describe how the habitats of chemoheterotrophs and photoautotrophs might differ. Describe three processes that reducing power fuels in all life, regardless of energy source. Exam Resources: Microbe’s Chapter 5, Class Notes. Chapter 6 Learning Objectives 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. Support this statement with evidence: “All major metabolic pathways were evolved by the early prokaryotic cells.” Identify a reason why reducing power is equivalent to energy. Compare and contrast energy harvesting during fueling reactions for heterotrophs and autotrophs. Compare and contrast ATP generation by transmembrane ion gradients and substrate-level phosphorylation with respect to the mechanism of ATP generation and number of ATPs generated. Speculate reason that life on Earth has sustained two distinct pathways to generate ATP instead of a single pathway. Compare and contrast the oxidation and dehydration pathways for fueling reactions. Decide whether you would use ΔG, ΔG°, ΔG°’, to estimate the change in Gibbs free energy of a reaction in vivo. Predict the mechanism by which pH can alter the Gibbs free energy change. Give examples of bioenergetics processes and structures that all living organisms share. Explain why it is incorrect to state that energy is “stored” in the cell as ATP and reducing power. Discuss the process of fermentation. Summarize the mechanism by which fermentation microbes make valuable chemicals and products for humans. Describe the process of ATP generation by F1F0 ATP synthase. List four ways to generate transmembrane ion gradients. Identify the main mode of energy conservation during fermentation. State why fermentative fueling needs auxiliary pathways to make fermentation end products to achieve redox balance. List five products of microbial fermentation that you have enjoyed. Describe the role of the electron transport chain in respiration. Identify the difference in location of respiration between prokaryotes and eukaryotes. Compare and contrast aerobic and anaerobic respiration with respect to electron acceptor diversity and energy yielded. Discuss how metabolic diversity has allowed microbes to colonize and harness energy from almost any resource on the planet. State the implications of hierarchic placing of electron acceptors along the redox tower and the amount of energy harnessed from their respiration. Distinguish fermentation from anaerobic respiration. Speculate a reason why a microbe would ferment using substrate-level phosphorylation, rather than respire glucose, when the energy yield for glucose respiration is so much higher. Review the major differences between chemoautotrophs and chemoheterotrophs during respiration. Compare and contrast respiration and photosynthesis with respect to energy generation and generation of transmembrane ion gradients. Compare and contrast cyclic and noncyclic photosynthesis. Identify the role of electron acceptors and electron donors in energy harvesting via photosynthesis. Discriminate between anoxygenic and oxygenic photosynthesis. Identify a reason why anoxygenic phototrophs are well adapted to environments that are frequently subjected to fluctuations in energy and carbon availability. Describe the impact of oxygenic photosynthesis upon the evolution of the planet and life on Earth (including impacts on ancestral microbes and extant microbes). Exam Resources: Microbe’s Chapter 6, Class Notes. 1. Revised Chapter 7 Learning Objectives Describe each precursor metabolite in Central Metabolic Pathways and what they synthesize including amino acids, nucleotides, vitamins, lipids, LPS, murein, coenzymes, polyamine units, and prosthetic groups. 2. Identify two strategies microbes use to obtain building blocks, such as essential amino acids from exogenous sources. 3. Describe three major requirements needed for de novo synthesis reactions and summarize the purpose of each of the three stages of fueling reactions. 4. Describe three methods of molecular transport across the outer membrane of Gram-negative bacteria. 5. Compare and contrast simple diffusion and facilitative diffusion & compare and contrast ion-coupled transport, ABC transport, and group translocation. 6. Identify the purpose of feeder pathways for heterotrophs and autotrophs plus the role of RuBisCO in the autotrophic feeder pathway 7. Describe how glycolysis, the pentose phosphate pathway (PPP), and the TCA cycle are interconnected in the metabolic pathways. 8. List three auxiliary fueling pathways in central metabolism. 9. Describe how adaptations in metabolic pathways allow some bacteria to grow and survive under varying environmental conditions. 10. Differentiate the role and fate of NADH and NADPH in metabolism. 11. Define allostery and explain how biosynthetic pathways are regulated. 12. Contrast the assimilation of nitrogen, phosphorous, and sulfur. 13. Identify a reason why assimilation of phosphorous occurs at the fueling stage. 14. Describe why ammonia is the preferred form of nitrogen in microbes and list ways in which microbes can obtain nitrogen from environmental sources. 15. Identify a reason why nitrogen fixation is to energetically expensive and describe how environmental conditions prescribe the pathway of nitrogen assimilation. 16. State how amino acids are grouped by families and which amino acids are derived from what precursor metabolite in which pathway. 17. Justify the following statement with biochemistry-related evidence: "Cells, organelles, & all major metabolic pathways evolved from early prokaryotic cells” 18. Compare & contrast the main features of these Central Metabolic Pathways (Glycolysis, Pentose Phosphate pathway, Entner-Doudoroff Pathway , TCA cycle, Glyoxylate Cycle) (for each pathway & synthesis, name the starting material, major intermediates, starting materials, regulatory enzymes, and key regulatory step) 19. Describe the overall purpose of glycolysis, the Pentose Phosphate Pathway, Entner-Doudoroff (ED) Pathway & their reactants (plus enzymes) and products 20. Describe the overall purpose of the TCA cycle & describe the reactants and products of the TCA cycle (including how they relate to the fates of the breakdown products of carbohydrates, fatty acids, and amino acids) 21. Summarize and describe the reductive TCA pathway and the Glyoxylate Cycle 22. Describe the importance of the reactions catalyzed by glutamate dehydrogenase and glutamine synthetase/Gln OxoGlutarate Amino Transferase 23. Describe the role of glutamate and glutamine as the two ‘universal’ nitrogen donors 24. Describe the role of amino acid transaminases, serine acetyltransferase, and O-acetylserine sulfhydrylase Exam Resources: Microbe’s Chapter 7, Class Notes.