Metabolism Notes

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Learning Objectives	Check Your Understanding
5-1    Define metabolism , and describe the fundamental differences between anabolism and catabolism.	Distinguish catabolism from anabolism.
5-2    Identify the role of ATP as an intermediate between catabolism and anabolism.	How is ATP an intermediate between catabolism and anabolism?
5-3    Identify the components of an enzyme.	What is a coenzyme?
5-4    Describe the mechanism of enzymatic action.	Why is enzyme specificity important?
5-5    List the factors that influence enzymatic activity.	What happens to an enzyme below its optimal temperature? Above its optimal temperature?
5-6    Distinguish competitive and noncompetitive inhibition.	Why is feedback inhibition noncompetitive inhibition?
5-7    Define ribozyme.	What is a ribozyme?
5-8    Explain the term oxidation-reduction.	Why is glucose such an important molecule for organisms?
5-9    List and provide examples of three types of phosphorylation reactions that generate ATP.	Outline the three ways that ATP is generated.
5-10  Explain the overall function of metabolic pathways.	What is the purpose of metabolic pathways?
5-11  Describe the chemical reactions of glycolysis.	What happens during the preparatory and energy-conserving stages of glycolysis?
5-12  Identify the functions of the pentose phosphate and Entner-Doudoroff pathways.	What is the value of the pentose phosphate and Entner-Doudoroff pathways if they produce only one ATP molecule?
5-13  Explain the products of the Krebs cycle.	What are the principal products of the Krebs cycle?
5-14  Describe the chemiosmotic model for ATP generation.	How do carrier molecules function in the electron transport chain?
5-15  Compare and contrast aerobic and anaerobic respiration.	Compare the energy yield (ATP) of aerobic and anaerobic respiration.
5-16  Describe the chemical reactions of, and list some products of, fermentation.	List four compounds that can be made from pyruvic acid by an organism that uses fermentation.
5-17  Describe how lipids and proteins undergo catabolism.	What are the end-products of lipid and protein catabolism?
5-18  Provide two examples of the use of biochemical tests to identify bacteria in the laboratory.	On what biochemical basis are Pseudomonas and Escherichia differentiated?
5-19  Compare and contrast cyclic and noncyclic photophosphorylation.	How is photosynthesis important to catabolism?
5-20  Compare and contrast the light-dependent and light-independent reactions of photosynthesis.	What is made during the light-dependent reactions?
5-21  Compare and contrast oxidative phosphorylation and photophosphorylation.	How are oxidative phosphorylation and photophosphorylation similar?
5-22  Write a sentence to summarize energy production in cells.	Summarize how oxidation enables organisms to get energy from glucose, sulfur, or sunlight.
5-23  Categorize the various nutritional patterns among organisms according to carbon source and mechanisms of carbohydrate catabolism and ATP generation.	Almost all medically important microbes belong to which of the four aforementioned groups?
5-24  Describe the major types of anabolism and their relationship to catabolism.	Where do amino acids required for protein synthesis come from?
5-25  Define amphibolic pathways.	Summarize the integration of metabolic pathways using peptidoglycan synthesis as an example.

Key concepts:
Enzymes facilitate metabolic reactions.
ATP is used by microbes and other cells to manage energy needs.
Catabolic reactions couple with ATP synthesis.
Anabolic reactions couple with ATP breakdown

Chapter Summary

Catabolic and Anabolic Reactions (pp. 110–111)

ASM 3.1: Bacteria and Archaea exhibit extensive, and often unique, metabolic diversity (e.g. nitrogen fixation, methane production, anoxygenic photosynthesis).

ASM 3.3: The survival and growth of any microorganism in a given environment depend on its metabolic characteristics.

1. The sum of all chemical reactions within a living organism is known as metabolism.
2. Catabolism refers to chemical reactions that result in the breakdown of more complex organic molecules into simpler substances. Catabolic reactions usually release energy.
3. Anabolism refers to chemical reactions in which simpler substances are combined to form more complex molecules. Anabolic reactions usually require energy.
4. The energy of catabolic reactions is used to drive anabolic reactions.
5. The energy for chemical reactions is stored in ATP.

Enzymes (pp. 111–117)

1. Enzymes are proteins, produced by living cells, that catalyze chemical reactions by lowering the activation energy.
2. Enzymes are generally globular proteins with characteristic three-dimensional shapes.
3. Enzymes are efficient, can operate at relatively low temperatures, and are subject to various cellular controls.
4. When an enzyme and substrate combine, the substrate is transformed, and the enzyme is recovered.
5. Enzymes are characterized by specificity, which is a function of their active sites.

  

Naming Enzymes (p. 113)

6. Enzyme names usually end in -ase.
7. The six classes of enzymes are defined on the basis of the types of reactions they catalyze.

Enzyme Components (pp. 113–114)

8. Most enzymes are holoenzymes, consisting of a protein portion (apoenzyme) and a nonprotein portion (cofactor).
9. The cofactor can be a metal ion (iron, copper, magnesium, manganese, zinc, calcium, or cobalt) or a complex organic molecule known as a coenzyme (NAD⁺, NADP⁺, FMN, FAD, or coenzyme A).

Factors Influencing Enzymatic Activity (pp. 114–116)

ASM 3.2: The interactions of microorganisms among themselves and with their environment are determined by their metabolic abilities (e.g., quorum sensing, oxygen consumption, nitrogen transformations).

10. At high temperatures, enzymes undergo denaturation and lose their catalytic properties; at low temperatures, the reaction rate decreases.
11. The pH at which enzymatic activity is maximal is known as the optimum pH.
12. Enzymatic activity increases as substrate concentration increases until the enzymes are saturated.
13. Competitive inhibitors compete with the normal substrate for the active site of the enzyme. Noncompetitive inhibitors act on other parts of the apoenzyme or on the cofactor and decrease the enzyme’s ability to combine with the normal substrate.

   

Feedback Inhibition (pp. 116–117)

14. Feedback inhibition occurs when the end-product of a metabolic pathway inhibits an enzyme’s activity near the start of the pathway.

Ribozymes (p. 117)

15. Ribozymes are enzymatic RNA molecules that cut and splice RNA in eukaryotic cells.

Energy Production (pp. 117–119)

Oxidation-Reduction Reactions (pp. 117–118)

1. Oxidation is the removal of one or more electrons from a substrate. Protons (H⁺) are often removed with the electrons.
2. Reduction of a substrate refers to its gain of one or more electrons.
3. Each time a substance is oxidized, another is simultaneously reduced.
4. NAD⁺ is the oxidized form; NADH is the reduced form.
5. Glucose is a reduced molecule; energy is released during a cell’s oxidation of glucose.

  

The Generation of ATP (pp. 118–119)

6. Energy released during certain metabolic reactions can be trapped to form ATP from ADP and  (phosphate). Addition of a  to a molecule is called phosphorylation.
7. During substrate-level phosphorylation, a high-energy  from an intermediate in catabolism is added to ADP.
8. During oxidative phosphorylation, energy is released as electrons are passed to a series of electron acceptors (an electron transport chain) and finally to O₂ or another inorganic compound.
9. During photophosphorylation, energy from light is trapped by chlorophyll, and electrons are passed through a series of electron acceptors. The electron transfer releases energy used for the synthesis of ATP.

Metabolic Pathways of Energy Production (p. 119)

ASM 3.2: The interactions of microorganisms among themselves and with their environment are determined by their metabolic abilities (e.g., quorum sensing, oxygen consumption, nitrogen transformations).

10. A series of enzymatically catalyzed chemical reactions called metabolic pathways store energy in and release energy from organic molecules.

Carbohydrate Catabolism (pp. 119–131)

1. Most of a cell’s energy is produced from the oxidation of carbohydrates.
2. The two major types of glucose catabolism are respiration, in which glucose is completely broken down, and fermentation, in which it is partially broken down.

Glycolysis (p. 121)

3. The most common pathway for the oxidation of glucose is glycolysis. Pyruvic acid is the end-product.
4. Two ATP and two NADH molecules are produced from one glucose molecule.

   

Alternatives to Glycolysis (p. 121)

ASM 3.1: Bacteria and Archaea exhibit extensive, and often unique, metabolic diversity (e.g., nitrogen fixation, methane production, anoxygenic photosynthesis).

5. The pentose phosphate pathway is used to metabolize five-carbon sugars; one ATP and 12 NADPH molecules are produced from one glucose molecule.
6. The Entner-Doudoroff pathway yields one ATP and two NADPH molecules from one glucose molecule.

Cellular Respiration (pp. 121–127)

7. During respiration, organic molecules are oxidized. Energy is generated from the electron transport chain.
8. In aerobic respiration, O₂ functions as the final electron acceptor.
9. In anaerobic respiration, the final electron acceptor is usually an inorganic molecule other than O₂.
10. Decarboxylation of pyruvic acid produces one CO₂ molecule and one acetyl group.
11. Two-carbon acetyl groups are oxidized in the Krebs cycle. Electrons are picked up by NAD⁺ and FAD for the electron transport chain.
12. From one molecule of glucose, oxidation produces six molecules of NADH, two molecules of FADH₂, and two molecules of ATP.
13. Decarboxylation produces six molecules of CO₂.
14. Electrons are brought to the electron transport chain by NADH.
15. The electron transport chain consists of carriers, including flavoproteins, cytochromes, and ubiquinones.
16. Protons being pumped across the membrane generate a proton motive force as electrons move through a series of acceptors or carriers.
17. Energy produced from movement of the protons back across the membrane is used by ATP synthase to make ATP from ADP and .
18. In eukaryotes, electron carriers are located in the inner mitochondrial membrane; in prokaryotes, electron carriers are in the plasma membrane.
19. In aerobic prokaryotes, 38 ATP molecules can be produced from complete oxidation of a glucose molecule in glycolysis, the Krebs cycle, and the electron transport chain.
20. In eukaryotes, 36 ATP molecules are produced from complete oxidation of a glucose molecule.
21. The total ATP yield is less than in aerobic respiration because only part of the Krebs cycle operates under anaerobic conditions.

  

   

 

     

  

Fermentation (pp. 127–131)

ASM 3.2: The interactions of microorganisms among themselves and with their environment are determined by their metabolic abilities (e.g., quorum sensing, oxygen consumption, nitrogen transformations).

22. Fermentation releases energy from sugars or other organic molecules by oxidation.
23. O₂ is not required in fermentation.
24. Two ATP molecules are produced by substrate-level phosphorylation.
25. Electrons removed from the substrate reduce NAD⁺.
26. The final electron acceptor is an organic molecule.
27. In lactic acid fermentation, pyruvic acid is reduced by NADH to lactic acid.
28. In alcohol fermentation, acetaldehyde is reduced by NADH to produce ethanol.
29. Heterolactic fermenters can use the pentose phosphate pathway to produce lactic acid and ethanol.

   

Lipid and Protein Catabolism (p. 131)

1. Lipases hydrolyze lipids into glycerol and fatty acids.
2. Fatty acids and other hydrocarbons are catabolized by beta-oxidation.
3. Catabolic products can be further broken down in glycolysis and the Krebs cycle.
4. Before amino acids can be catabolized, they must be converted to various substances that enter the Krebs cycle.
5. Transamination, decarboxylation, and dehydrogenation reactions convert the amino acids to be catabolized.

  

Biochemical Tests and Bacterial Identification (pp. 131–133)

1. Bacteria and yeast can be identified by detecting action of their enzymes.
2. Fermentation tests are used to determine whether an organism can ferment a carbohydrate to produce acid and gas.

         

  

Photosynthesis (pp. 133–135)

1. Photosynthesis is the conversion of light energy from the sun into chemical energy; the chemical energy is used for carbon fixation.

   

The Light-Dependent Reactions: Photophosphorylation (pp. 134–135)

2. Chlorophyll a is used by green plants, algae, and cyanobacteria; it is found in thylakoid membranes.
3. Electrons from chlorophyll pass through an electron transport chain, from which ATP is produced by chemiosmosis.
4. Photosystems are made up of chlorophyll and other pigments packed into thylakoid membranes.
5. In cyclic photophosphorylation, the electrons return to the chlorophyll.
6. In noncyclic photophosphorylation, the electrons are used to reduce NADP⁺. The electrons from H₂O or H₂S replace those lost from chlorophyll.
7. When H₂O is oxidized by green plants, algae, and cyanobacteria, O₂ is produced; when H₂S is oxidized by the sulfur bacteria, S⁰ granules are produced.

   

The Light-Independent Reactions: The Calvin-Benson Cycle (p. 135)

8. CO₂ is used to synthesize sugars in the Calvin-Benson cycle.

  

A Summary of Energy Production Mechanisms (pp. 135–136)

1. Sunlight is converted to chemical energy in oxidation-reduction reactions carried on by phototrophs. Chemotrophs can use this chemical energy.
2. In oxidation-reduction reactions, energy is derived from the transfer of electrons.
3. To produce energy, a cell needs an electron donor (organic or inorganic), a system of electron carriers, and a final electron acceptor (organic or inorganic).

 

Metabolic Diversity among Organisms (pp. 136–140)

ASM 3.1: Bacteria and Archaea exhibit extensive, and often unique, metabolic diversity (e.g., nitrogen fixation, methane production, anoxygenic photosynthesis).

1. Photoautotrophs obtain energy by photophosphorylation and fix carbon from CO₂ via the Calvin-Benson cycle to synthesize organic compounds.
2. Cyanobacteria are oxygenic phototrophs. Green bacteria and purple bacteria are anoxygenic phototrophs.
3. Photoheterotrophs use light as an energy source and an organic compound for their carbon source and electron donor.
4. Chemoautotrophs use inorganic compounds as their energy source and carbon dioxide as their carbon source.
5. Chemoheterotrophs use complex organic molecules as their carbon and energy sources.

 

Metabolic Pathways of Energy Use (pp. 140–142)

   

Polysaccharide Biosynthesis (pp. 140–141)

1. Glycogen is formed from ADPG.
2. UDPNAc is the starting material for the biosynthesis of peptidoglycan.

Lipid Biosynthesis (p. 141)

3. Lipids are synthesized from fatty acids and glycerol.
4. Glycerol is derived from dihydroxyacetone phosphate, and fatty acids are built from acetyl CoA.

Amino Acid and Protein Biosynthesis (pp. 141–142)

5. Amino acids are required for protein biosynthesis.
6. All amino acids can be synthesized either directly or indirectly from intermediates of carbohydrate metabolism, particularly from the Krebs cycle.

Purine and Pyrimidine Biosynthesis (p. 142)

7. The sugars composing nucleotides are derived from either the pentose phosphate pathway or the Entner-Doudoroff pathway.
8. Carbon and nitrogen atoms from certain amino acids form the backbones of the purines and pyrimidines.

The Integration of Metabolism (pp. 142–143)

1. Anabolic and catabolic reactions are integrated through a group of common intermediates.
2. Such integrated metabolic pathways are referred to as amphibolic pathways.