Solution Manual for Microbiology with Diseases by Taxonomy 5th Edition Bauman 0134019199
9780134019192
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Microbial Metabolism
Chapter Outline
Basic Chemical Reactions Underlying Metabolism (pp. 123–130)
Catabolism and Anabolism
Oxidation and Reduction Reactions
ATP Production and Energy Storage
The Roles of Enzymes in Metabolism
Carbohydrate Catabolism (pp. 131–141)
Glycolysis
Cellular Respiration
◆ Interactive Microbiology: Aerobic Respiration in Prokaryotes
Pentose Phosphate Pathway
Fermentation
Other Catabolic Pathways (pp. 141–143)
Lipid Catabolism
Protein Catabolism
Photosynthesis (pp. 143–148)
Chemicals and Structures
Light-Dependent Reactions
Light-Independent Reactions
Other Anabolic Pathways (pp. 148–151)
Carbohydrate Biosynthesis
Lipid Biosynthesis
Amino Acid Biosynthesis
Nucleotide Biosynthesis
Integration and Regulation of Metabolic Functions (pp. 151–153)
Chapter Summary
Basic Chemical Reactions Underlying Metabolism (pp. 123–130)
Catabolism and Anabolism
Metabolism is the sum of the controlled complex biochemical reactions within an organism. The processes can be summarized as:
• Acquiring nutrients, the building blocks for metabolism
• Catabolism, the breakdown of nutrients
• Energy storage in the bonds of adenosine triphosphate (ATP)
• Catalytic enzymes break down nutrients into precursor metabolites.
• Other enzymes catalyze anabolic reactions using precursor metabolites and energy to assemble larger molecules
• Macromolecules are formed by polymerization reactions.
• Assembly of macromolecules into cellular structures produces cell growth.
• Cells typically divide in two when they have doubled in size.
Catabolism is the break-down of nutrient molecules in a series of steps known as a catabolic pathway. These pathways are exergonic, releasing energy, which is then stored in ATP molecules The resulting molecules are often the precursor metabolites for anabolic pathways Anabolic reactions synthesize macromolecules and use ATP energy (are endergonic).
Oxidation and Reduction Reactions
Oxidation-reduction (redox) reactions involve the transfer of electrons. These reactions always occur simultaneously because an electron gained by one molecule is donated by another molecule. The electron acceptor is said to be reduced. The electron donor loses an electron and is oxidized. If the electron is part of a hydrogen atom, the reaction is called a dehydrogenation reaction.
Free electrons are rare, they are carried from one site to another by electron carriers often as hydrogen atoms. Three electron carrier molecules often required in metabolic pathways are nicotinamide adenine dinucleotide (NAD+), nicotinamide adenine dinucleotide phosphate (NADP+), and flavin adenine dinucleotide (FAD).
ATP Production and Energy Storage
Energy from the chemical bonds of nutrients is concentrated in the high-energy phosphate bonds of ATP in a process called phosphorylation when inorganic phosphate (PO4 -3) is added to a molecule Substrate-level phosphorylation describes the transfer of phosphate from a phosphorylated organic nutrient to ADP to form ATP. Oxidative phosphorylation phosphorylates ADP using inorganic phosphate and energy from respiration. Photophosphorylation is the phosphorylation of ADP with inorganic phosphate using energy from light. There is a cyclical conversion of ATP from ADP and back with the gain and loss of phosphate.
The Roles of Enzymes in Metabolism
Catalysts increase reaction rates of chemical reactions but are not permanently changed in the process. Enzymes are the organic catalysts of metabolism.
Naming and Classifying Enzymes
Enzymes are often named for their substrates, which are the chemicals they act on, and enzyme names often end with -ase. Enzymes are classified into six categories based on their mode of action: hydrolases add hydrogen and hydroxide from the hydrolysis of water to split larger molecules into smaller ones; isomerases rearrange atoms in a molecule; ligases or polymerases join molecules; lyases split molecules without using water; oxidoreductases oxidize or reduce; and transferases transfer functional groups.
The Makeup of Enzymes
Many protein enzymes are complete in themselves. Other enzymes are composed of apoenzymes a protein portion and one or more nonprotein cofactors. Inorganic cofactors include ions such as iron, magnesium, zinc, or copper. Organic cofactors are made from vitamins and include NAD+, NADP+, and FAD. Organic cofactors are also called coenzymes. The combination of both apoenzyme and its cofactors is a holoenzyme.
RNA molecules functioning as catalysts are called ribozymes. Ribozymes process RNA molecules in eukaryotes. Ribosomal ribozymes catalyze the actual protein synthesis reactions of ribosomes; thus, ribozymes make protein enzymes.
Enzyme Activity
Activation energy is the amount of energy required to initiate a chemical reaction. Activation energy may be supplied by heat, but high temperatures are not compatible with life; therefore, enzymes are required to lower the activation energy needed. Substrates fit onto the specifically shaped active sites of enzymes. The complementary shapes of active sites of enzymes and their substrates determine enzyme-substrate specificity. The active site may change shape after substrate binding, described by the induced-fit model. In catabolism, an enzyme binds to a substrate, forming an enzyme-substrate complex, the bonds within the substrate are broken, the enzyme separates from the two new products, and the enzyme is released to act again. Temperature and pH can influence the rate of reactions.
Enzymes may be denatured by physical and chemical factors such as temperature and pH, which change their shape and thus their ability to bond. The change may be reversible or permanent.
The rate of enzymatic activity is also affected by the concentrations of substrate and enzyme. Enzyme activity proceeds at a rate proportional to the concentration of substrate molecules until all the active sites on the enzymes are filled to saturation.
Enzyme activity can be influenced in multiple ways. In allosteric activation, the binding of a cofactor to an allosteric site can cause the enzyme to be activated. Enzyme activity may be blocked by competitive inhibitors, which bind to and block but do not denature active sites. Noncompetitive inhibitors attach to an allosteric site on an enzyme, distorting the active site and halting enzymatic activity.
Feedback inhibition (negative feedback or end-product inhibition) occurs when the final product of a series of reactions is an allosteric inhibitor of some previous step in the series. Thus, accumulation of the end-product “feeds back” a stop signal to the process.
Carbohydrate Catabolism (pp. 131–140)
Carbohydrates are a primary energy source for many organisms. The process of cellular respiration breaks down carbohydrates completely into carbon dioxide and water. Incomplete break down and the production of organic waste products is called fermentation. Glycolysis is the starting point for both processes.
Glycolysis
Glycolysis (the Embden-Meyerhof pathway) involves the splitting of a glucose molecule in a series of 10 steps that ultimately results in the splitting of glucose into two molecules of pyruvic acid, and a net gain of two ATP and two NADH molecules. The 10 steps of glycolysis can be divided into three stages: energy-investment (steps 1, 2, and 3), lysis (steps 4 and 5), and energy-conserving (steps 6–10) ATP is produced by substrate-level phosphorylation. (Some organisms use the alternative Entner-Doudoroff pathway.)
◆ Video Tutor: Glycolysis
Cellular Respiration
◆ Interactive Microbiology: Aerobic Respiration in Prokaryotes
Cellular respiration is a three-stage metabolic process that involves oxidation of substrate molecules and production of ATP. The stages of respiration are synthesis of acetyl-CoA, the Krebs cycle, and electron transport.
Synthesis of Acetyl-CoA
The production of acetyl-coenzyme A (acetyl-CoA) begins with decarboxylation (removal of carbon as CO2) of pyruvic acid. Acetyl-CoA is formed when the two remaining carbons from pyruvic acid join coenzyme A in a high energy bond. Two molecules of acetyl-CoA, two molecules of CO2, and two molecules of NADH are produced.
The Krebs Cycle
Acetyl-CoA enters the Krebs cycle, a series of eight enzymatic steps that transfers energy and electrons from acetyl-CoA to coenzymes NAD+ and FAD. For every two molecules of acetylCoA that enter the Krebs cycle, two molecules of ATP, six molecules of NADH, and two molecules of FADH2 are formed. The Krebs cycle is also known as the tricarboxylic acid (TCA) cycle and the citric acid cycle. Six types of enzyme reactions take place in the Krebs cycle: anabolic, isomerization, redox, decarboxylation, substrate-level phosphorylation, and hydration.
Electron Transport
The electron transport chain is the stage in which the most energy is produced. It is a series of redox reactions that passes electrons from one membrane-bound carrier to another and then to a final electron acceptor Most organisms get electrons from organic molecules but lithotrophs use inorganic electron donors. The energy from these electrons is used to pump protons (H+) across the membrane. The proton gradient produced results in the synthesis ATP by a process called chemiosmosis
Electron transport chains are in the cytoplasmic membrane of prokaryotes and the inner membrane of mitochondria in eukaryotes. The four categories of carrier molecules in the electron transport system are flavoproteins, ubiquinones, metal-containing proteins, and cytochromes.
Aerobes use oxygen atoms as final electron acceptors in the electron transport chain in a process known as aerobic respiration, whereas anaerobes use other inorganic molecules such as sulfate, nitrate, and carbonate as final electron acceptors in anaerobic respiration.
◆ Video Tutor: Electron Transport
Chemiosmosis
Chemiosmosis is a mechanism in which the flow of ions down an electrochemical gradient across a membrane is used to synthesize ATP. For example, energy released during the redox reactions of electron transport is used to pump protons across a membrane, creating a proton gradient.
A proton gradient is an electrochemical gradient of protons that has potential energy known as a proton motive force. When protons flow down their electrochemical gradient through protein channels called ATP synthases (ATPases), ATP is synthesized. ATPases synthesize ATP in both oxidative phosphorylation and photophosphorylation.
About 34 ATP molecules are synthesized per pair of electrons traveling down an electron transport chain. Thus, there is a theoretical net yield of 38 ATP molecules from the aerobic respiration of one molecule of glucose via glycolysis (4 molecules of ATP produced minus 2 molecules of ATP used), the Krebs cycle (2 molecules of ATP produced), and the electron transport chain (34 molecules of ATP produced).
Pentose Phosphate Pathway
The pentose phosphate pathway is an alternative pathway for the catabolism of glucose, but yields fewer ATP molecules than does the Embden-Meyerhof pathway. However, it produces precursor metabolites not produced in glycolysis. The pentose phosphate pathway produces metabolites used in synthesis of nucleotides, amino acids, and glucose by photosynthesis
Fermentation
Fermentation is the partial oxidation of sugar to release energy using an organic molecule within the cell as the final electron acceptor when final electron acceptors for complete cellular respiration are unavailable. The essential function of fermentation is the regeneration of NAD+ for use in glycolysis. Two common fermentation pathways reduce pyruvic acid to lactic acid and ethanol, oxidizing NADH in the process. Some fermentation products are useful to health and industry while some are harmful. Fermentation reactions can be used to identify microbes.
Other Catabolic Pathways (pp. 141–143)
Lipid Catabolism
Fats are catabolized by lipases that break the glycerol–fatty acid bonds via hydrolysis. Glycerol is converted to DHAP, which is oxidized to produce pyruvic acid. Fatty acids are catabolized by beta-oxidation reactions to form acetyl-CoA and generate NADH and FADH2
Protein Catabolism
Proteins can be catabolized to produce energy and metabolites. Protein catabolism by prokaryotes involves protease enzymes secreted to digest large proteins outside their cell walls. The resulting amino acids move into the cell and are used in anabolism or deaminated to produce substrates for the Krebs cycle.
Photosynthesis (pp. 143–148)
Chemicals and Structures
Photosynthesis is a process in which light energy is captured by pigment molecules (the most important of which are chlorophylls) and used to drive synthesis of carbohydrates from CO2 and H2O The light-absorbing active center of chlorophylls contain a magnesium ion (Mg+2). Chlorophyll molecules and other pigments are held within a protein matrix in networks called photosystems. The photosystems are embedded in cellular membranes called thylakoids.
Prokaryotic thylakoids are infoldings of the cytoplasmic membrane, whereas eukaryotic thylakoids appear to be infoldings of the inner membranes of chloroplasts. Stacks of thylakoids within chloroplasts are called grana. The space between the thylakoids and the outer chloroplast membrane is the stroma There are two photosystems, photosystem I (PS I) and photosystem II (PS II), in order of their discovery, both of which carry out light-dependent reactions. The light absorption and redox reactions of photosynthesis are classified as light-dependent reactions (light reactions) and light-independent reactions (dark reactions). The latter synthesize glucose from carbon dioxide and water regardless of light conditions
Light-Dependent Reactions
A reaction center chlorophyll is a special chlorophyll molecule of photosystem I, which is excited by transferred energy absorbed by pigment molecules elsewhere in the photosystem. Excited electrons from the reaction center are passed to an initial acceptor of an electron transport chain, protons are pumped across the membrane, a proton motive force is created, and ATP is generated in a process called photophosphorylation.
Cyclic Photophosphorylation
In cyclic photophosphorylation, electrons return to the original reaction center chlorophyll after passing down the electron transport chain. The resulting proton gradient produces ATP by chemiosmosis. Photosystem I provides the excited electrons for cyclic photophosphorylation.
Noncyclic Photophosphorylation
In noncyclic photophosphorylation, photosystem II donates electrons to photosystem I, and the electrons are used to reduce NADP+ to NADPH in addition to ATP. Therefore, in noncyclic photophosphorylation, a cell must constantly replenish electrons to PS II. In oxygenic organisms, the electrons come from H2O. In anoxygenic organisms, the electrons come from inorganic compounds such as H2S.
Light-Independent Reactions
ATP and NADPH from the light-dependent reactions drive the synthesis of glucose by carbon fixation in the light-independent pathway of photosynthesis. The Calvin-Benson cycle of the light-independent pathway occurs in three steps: fixation of CO2 in which CO2 is combined with ribulose 1,5-bisphosphate (RuBP) then split to produce 3-phosphoglyceric acid; reduction by NADPH to form molecules of glyceraldehyde 3-phosphate (G3P), some of which join to form glucose while others are used for regeneration of RuBP to continue the cycle.
Other Anabolic Pathways (pp. 148–151)
Because anabolic reactions are synthesis reactions, they require energy and metabolites, both of which are often the products of catabolic reactions. Amphibolic reactions are metabolic reactions that can proceed toward catabolism or toward anabolism depending on the needs of the cell. Examples are found in the biosynthesis of carbohydrates, lipids, amino acids, and nucleotides.
Carbohydrate Biosynthesis
Gluconeogenesis refers to metabolic pathways that produce sugars, starch, cellulose, glycogen, and peptidoglycan from noncarbohydrate precursors such as amino acids, glycerol, and fatty acids. Amphibolic reactions are involved in this highly endergonic process.
Lipid Biosynthesis
Lipids are synthesized by a variety of routes. Fat is synthesized from glycerol and three molecules of fatty acid a reverse of the catabolic reaction. Steroids result from complex pathways involving polymerizations and isomerizations of sugar and amino acid metabolites. Waxes like mycolic acid are produced by long synthesis pathways requiring lots of energy.
Amino Acid Biosynthesis
Some amino acids can be synthesized from other amino acids. Essential amino acids are those an organism cannot synthesize and must obtain in its diet. Amino acids are also synthesized by amination, a process in which the amine group from ammonia is added to a precursor metabolite, and by transamination, a reversible reaction in which an amine group is transferred from one amino acid to another by the action of enzymes using the coenzyme pyridoxal phosphate
Nucleotide Biosynthesis
Nucleotides are composed of a 5-carbon sugar, a phosphate group, and a pyrimidine or purine base. These components are produced from precursor metabolites derived from glycolysis and the Krebs cycle: ribose and deoxyribose from ribose 5-phosphate, phosphate from ATP, and purines and pyrimidines from the amino acids glutamine and aspartic acid, ribose 5-phosphate, and folic acid
Integration and Regulation of Metabolic Functions (pp. 151–153)
Catabolic and anabolic pathways interact with each other in several ways. Energy released in catabolic reactions is used to drive anabolic reactions. Catabolic pathways produce precursor metabolites for use as substrates for anabolic reactions. Amphibolic reactions are anabolic or catabolic as needed.
Cells use a variety of mechanisms to regulate metabolism:
• Synthesizing and degrading channel and transporter proteins to regulate chemical concentrations
• Producing enzymes only when their substrate is present
• Catabolizing metabolites to produce lots of energy instead of low-energy metabolites
• Synthesizing metabolites only when they are needed
• In eukaryotes, separating metabolic processes in membrane-bound organelles
• Allosteric regulation of enzyme function
• Feedback inhibition
• Regulation pathways by regulating availability of cofactors
These regulatory mechanism can be categorized as control of gene expression, which controls enzyme production needed for metabolic pathways, or control of metabolic expression, in which the cells control enzymes that have been produced.
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