Microbiology - Microbial Metabolism (Ch. 5)

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Microbiology - Microbial Metabolism (Ch. 5)
2013-04-04 22:44:27

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  1. How do aldehydes work in killing microbes?
    They cross-link amino, hydroxyl, sulfhydryl, and carboxyl organic functional groups, thereby denaturing proteins and inactivating nucleic acids.
  2. What are the two alternative pathways that catabolize glucose? (Other than glycolysis)
    What coenzyme do they produce that glycolysis can't? What does that coenzyme do?
    • 1) Pentose-Phosphate Pathway (phosphogluconate pathway)
    • 2) Doudoroff Pathway

    They produce NADPH, which is a necessary coenzyme for anabolic enzymes that synthesize DNA nucleotides, steroids, and fatty acids.
  3. What is beta-oxidation and how does it work?
    Beta-oxidation is a catabolic process that degrades fatty acids into molecules of Acetyl-CoA. Enzymes repeatedly split off pairs of hydrogenated carbon atoms and join each pair to coenzyme A, forming acetyl-CoA.

    (5, 148)
  4. What is cellular respiration?
    Cellular respiration is a metabolic process that involves the complete oxidation of substrate molecules and then the production of ATP via a series of redox reactions.

    (5, 137)
  5. What are the four factors that affect enzymatic activity?
    • 1) Temperature
    • 2) pH levels
    • 3) Inhibitors
    • 4) Enzyme and substrate concentration

    (5, 130-133)
  6. Anabolic and catabolic reactions depend on what type of reaction in order to occur?
    Redox reactions
  7. What type of reaction do ligases/polymerases catalyze?
    They join two or more chemicals together (anabolic)

    (5, 128)
  8. What type of reaction do oxidoreductases catalyze?
    They remove electrons from (oxidize) or add electrons to (reduce) various substrates. They are used in both catabolic and anabolic pathways. 

    (5, 128)
  9. What two enzymes are most important to respiration and why?
    • 1) NADH
    • 2) FADH2

    They carry a substantial amount of the energy that is subsequently used to phosphorylate ADP to ATP.

    (5, 139)
  10. What is a dehydrogenation reaction?
    A biological oxidation that involves the loss of a hydrogen atom.

    (5, 127)
  11. List the 6 basic categories of enzymes.
    • 1) Hydrolases
    • 2) Isomerases
    • 3) Ligases (Polymerases)
    • 4) Lyases
    • 5) Oxidoreductases
    • 6) Transferases

    (5, 128)
  12. What are the three parts that together make up a holoenzyme? Briefly describe each one.
    • 1) Apoenzymes
    • Inactive proteins by themselves.
    • 2) Cofactors
    • Nonprotein substances, can be organic or inorganic.
    • 3) Coenzymes
    • Organic molecules that are required for metabolism but cannot be synthesized by certain organisms. They are either vitamins or contain vitamins.

    (5, 128)
  13. What type of reactions to lyases catalyze?
    They split chemicals (large molecules) into smaller parts without using water. (Catabolic)

    (5, 128)
  14. What are the six elements that must be present in order for organisms to survive?
    • 1) Carbon
    • 2) Hydrogen
    • 3) Nitrogen
    • 4) Oxygen
    • 5) Phosphorus
    • 6) Sulfur

    (5, Lecture)
  15. What are precursor metabolites? Where do they come from?
    • They are smaller molecules that can be used in anabolic reactions.
    • They are the resulting products of catabolism, or they can also be directly transported into the cell.

    (5, Lecture)
  16. Explain the 3 different types of enzymatic inhibitors.
    • 1) Competitive inhibitors
    • Bind to an enzymes active site and thus prevent the substrate form binding.
    • 2) Non-competitve inhibitors
    • Bind to an allosteric site located elsewhere on the enzyme, which in turn changes the shape of the active site, inhibiting substrates to bind.
    • 3) Feedback inhibition/Negative feedback/End-product inhibition
    • The end product of a series of reactions becomes an allosteric inhibitor of an enzyme in an earlier part of the reaction pathway.

    (5, 132-133)
  17. Summarize what happens during respiration.
    In summary, a number of redox reactions in glycolysis or alternate pathways and in the Krebs cycle strip electrons (which carry energy) from glucose molecules and transfer them to molecules of NADH and FADH2. In turn, NADH and FADH2 pass electrons to an electron transport chain. As the electrons move down the electron transport chain, proton pumps use the electrons' energy to actively transport protons (H+) across the membrane, creating a proton concentration gradient. This gradient is then used to create ATP.

    (5, 142)
  18. What is fermentation?
    Fermentation is the partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as the final electron acceptor.

    (5, 146)
  19. Compare and contrast cellular respiration and fermentation.
    • Both are processes that catabolize glucose. However, in cellular respiration glucose is completely broke down into carbon dioxide and water. In fermentation, organic waste products are produced.
    • Respiration leads to the Kreb Cycle and Electron Transport Chain, fermentation does not. Thus, fermentation results in the production of much less ATP than does respiration.

    (5, 133)
  20. What does it mean when an enzyme denatures?
    Can this be reversed?
    When the temperature rises beyond a certain critical point, non-covalent bonds (i.e. hydrogen bonds) will break, and the enzyme will lose its three-dimensional structure. They are now no longer functional.

    • Permanent denaturation is irreversible.
    • Reversible denaturation is reversible and the enzyme's non-covalent bonds reform upon return to normal conditions.

    (5, 131)
  21. Why is temperature a critical factor that can affect whether or not an enzymatic reaction will occur?
    The active sites of enzymes change shape as temperature changes.

    (5, 130)
  22. Which pathways are endergonic and why?
    Anabolic pathways are endergonic because they build molecules and require energy to do so.

    (5, 125)
  23. In terms of metabolism, what is a pathway?
    A series of catabolic or anabolic reactions.

    (5, 125)
  24. What is the difference between catabolic and anabolic pathways?
    • Catabolic pathways break larger molecules into smaller products.
    • Anabolic pathways synthesize large molecules from the smaller products of catabolism.

    (5, 125)
  25. What are enzymes?
    Enzymes are organic catalysts.

    (5, 127)
  26. What is the difference in the creation and destruction of bonds in catabolic reactions compared to anabolic reactions?
    • In catabolic reactions, bonds must be destabilized before they will break.
    • In anabolic reactions the reactants must collide with sufficient energy for the bonds to form between them.

    (5, 127)
  27. What is the difference between an active site and an allosteric site?
    • The active site is the enzyme's functional site which binds with the substrate.
    • The allosteric site is not the substrate binding site, but when activated by an inhibitor it induces a conformational change in the enzyme, altering its catalytic properties.

    (5, 129-132)
  28. Which pathways are exergonic and why?
    Catabolic pathways are exergonic because they break down large molecules and release energy while doing so.

    (5, 125)
  29. Which pathways produce ATP and which pathways use ATP?
    • Catabolic pathways produce ATP.
    • Anabolic pathways use ATP.

    (5, 125)
  30. What is chemiosmosis?
    Chemiosmosis is a general term for the use of ion gradients to generate ATP. It uses the potential energy from an electrochemical gradient to phosphorylate ADP into ATP.

    (5, 142)
  31. List and explain the three different ways cells phosphorylate ADP to form ATP.
    • 1) Substrate-Level Phosphorylation
    • Phosphate is transferred to ADP from another phosphorylated organic compound.
    • 2) Oxidative Phosphorylation
    • Energy from redox reactions of respiration is used to attach an inorganic phosphate to ADP.
    • 3) Photophosphorylation
    • Light energy is used to phosphorylate ADP with inorganic phosphate.

    (5, 127)
  32. Although not as energetically efficient as respiration, what is the benefit of fermentation?
    Fermentation allows for ATP production to continue in the absence of cellular respiration.

    (5, 146)
  33. What type of reaction do hydrolases catalyze?
    Hydrolysis reactions. Which are reactions that involve the cleaving of chemical bonds by adding water. (catabolic)

    (5, 128)
  34. What are the three stages of cellular respiration?
    • 1) Glycolysis (synthesis of Acetyl-CoA)
    • 2) The Krebs Cycle
    • 3) Electron Transport Chain (ETC) (a final series of redox reactions that pass electrons to  a final electron acceptor nor derived from the cell's metabolism)

    (5, 137)
  35. What is phosphorylation?
    Give an example.
    • Phosphorylation is a process in which inorganic phosphate (PO43-) is added to a substrate.
    • An example is ADP --> ATP.

    (5, 127)
  36. What type of reaction do tranferases catalyze?
    Transferases move a functional group from one molecule to another.

    (5, 128)
  37. Why do chemical reactions of life depend on catalysts in order to take place?
    Neither reactant concentration nor temperature is typically high enough within living organisms to ensure that bonds will form via anabolic reactions.

    (5, 127)
  38. What type of reaction do isomerases catalyze?
    Isomerases rearrange the atoms within a molecule.

    (5, 128)
  39. What are the end products of glycolysis?
    Glycolysis breaks down glucose and results in a yield of 2 pyruvic acid molecules and a total of 4 ATP molecules. However, because 2 ATP molecules are needed to start glycolysis, the net yield is actually 2 pyruvic acid molecules and 2 molecules of ATP.

    (5, 134-137)
  40. How is Acetyl-CoA (acetyl-coenzymeA) produced?
    Enzymes remove one carbon from pyruvic acid as CO2 and join the remaining two-carbon acetate to coenzymeA with a high energy bond. It also reduces a molecule of NAD+ to NADH.

    (5, 137)
  41. What is the proton motive force?
    It is the potential energy created by a proton gradient.

    (5, 143)
  42. What is the theoretical net maximum yield of ATP molecules produced from one molecule of glucose within eukaryotes?

    (5, 143)
  43. What are catalysts?
    Catalysts are chemicals that increase the likelihood of a reaction to occur but are not permanently changed in the process.

    (5, 127)