Microbiology: A Systems Approach PowerPoint to accompany Microbiology: A Systems Approach Cowan/Talaro Chapter 8 Microbial Metabolism Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Chapter 8 Topics Metabolism Energy Pathways Biosynthesis

Metabolism Catabolism Anabolism Enzymes

Catabolism Enzymes are involved in the breakdown of complex organic molecules in order to extract energy and form simpler end products

Anabolism Enzymes are involved in the use of energy from catabolism in order to synthesize macromolecules and cell structures from precursors (simpler products)

The relationship between catabolism and anabolism. Fig. 8.1 Simplified model of metabolism

Enzymes Function Structure Enzyme-substrate interaction Cofactors Regulation

Function Catalysts for chemical reactions Lower the energy of activation

Structure Simple enzyme Conjugated enzyme Three-dimensional features protein alone Conjugated enzyme protein and nonprotein Three-dimensional features Enable specificity Active site or catalytic site

Conjugated enzymes contain a metallic cofactor, coenzyme, or both in order for it to function as a catalyst. Fig. 8.2 Conjugated enzyme structure

Specific active sites (amino acids) arise due to the folding of the protein (enzyme). Fig. 8.3 How the active site and specificity of the apoenzyme arise.

Enzyme-substrate interactions Substrates specifically bind to the active sites on the enzyme “lock-and-key” Induced fit Once the reaction is complete, the product is released and the enzyme reused

An example of the “lock-and-key” model, and the induced fit model. Fig. 8.4 Enzyme-substrate reactions

Cofactors Bind to and activate the enzyme Ex. Metallic cofactors Iron, copper, magnesium Coenzymes

Coenzyme Transient carrier - alter a substrate by removing a chemical group from one substrate and adding it to another substrate Ex. vitamins

An example of how a coenzyme transfers chemical groups from one substrate to another. Fig. 8.5 The carrier functions of coenzymes

Action Exoenzymes Endoenzymes Constitutive Induction or repression Types of reactions

Exoenzymes are inactive while inside the cell, but upon release from the cell they become active. In contrast, endoenzymes remain in the cell and are active. Fig. 8.6 Types of enzymes, as described by their location of action.

Constitutive enzymes are present in constant amounts, while regulated enzymes are either induced or repressed. Fig. 8.7 Constitutive and regulated enzymes

Types of Reaction Condensation Hydrolysis Transfer reactions

Condensation reactions are associated with anabolic reactions, and hydrolysis reactions are associated with catabolic reactions. Fig. 8.8 Examples of enzyme-catalyzed synthesis and hydrolysis reactions

Transfer reactions Transfer of electrons from one substrate to another Oxidation and reduction Oxidoreductase Transfer of functional groups from one molecule to another Transferases Aminotransferases

Examples of oxidoreductase, transferase, and hydrolytic enzymes. Table 8.A A sampling of enzymes, their substrates, and their reactions

Regulation Metabolic pathways Direct control Genetic control

The different metabolic pathways are regulated by the enzymes that catalyze the reactions. Fig.8.9 Patterns of metabolism

Competitive inhibition and noncompetitive inhibition are examples of direct control (regulation) of the action of the enzymes. Fig. 8.10 Examples of two common control mechanisms for enzymes.

Genetic control Repression Induction

Repression is when end products can stop the expression of genes that encode for proteins (enzymes) which are responsible for metabolic reactions. Fig. 8.11 One type of genetic control of enzyme synthesis

Summary of major enzyme characteristics. Table 8.1 Checklist of enzyme characteristics

Energy Cell energetics Redox reaction Electron carrier Exergonic Endergonic Redox reaction Electron carrier Adenosine Triphosphate (ATP)

The general scheme associated with metabolism of organic molecules, the redox reaction, and the capture of energy in the form of ATP. Fig. 8.12 A simplified model that summarizes the cell’s energy machine.

Redox reaction Reduction and oxidation reaction Electron carriers transfer electrons and hydrogens Electron donor Electron acceptor Energy is also transferred and captured by the phosphate in form of ATP

Electron carriers Coenzymes Respiratory chain carriers Nicotinamide adenine dinucleotide (NAD) Respiratory chain carriers Cytochromes (protein)

Electron carriers, such as NAD, accept electrons and hydrogens from the substrate (organic molecule). Fig. 8.13 Details of NAD reduction

Adenosine Triphosphate (ATP) Temporary energy repository Breaking of phosphates bonds will release free energy Three part molecule Nitrogen base 5-carbon sugar (ribose) Chain of phosphates

The phosphates capture the energy and becomes part of the ATP molecule. Fig. 8.14 The structure of adenosine triphosphate and its partner compounds, ADP and AMP.

ATP can be used to phosphorylate an organic molecule such as glucose during catabolism. Fig. 8.15 An example of phosphorylation of glucose by ATP

ATP can be synthesized by substrate-level phosphorylation. Fig. 8.16 ATP formation by substrate-level phosphorylation

Pathways Catabolism Embden-Meyerhof-Parnas (EMP) pathway or glycolysis Tricarboxylic acid cycle (TCA) Respiratory chain Aerobic Anaerobic Alternate pathways Fermentation

A summary of the metabolism of glucose and the synthesis of energy. Fig. 8.17 Overview of the flow, location, and products of Pathways in aerobic respiration.

Aerobic respiration Glycolysis Tricarboxylic acid (TCA) Electron transport

Glycolysis Oxidation of glucose Phosphorylation of some intermediates (Uses two ATPs) Splits a 6 carbon sugar into two 3 carbon molecules Coenzyme NAD is reduced to NADH Substrate-level-phosphorylation (Four ATPs are synthesized)

Glycolysis continued Water is generated Net yield of 2 ATPs Final intermediates are two Pyruvic acid molecules

The glycolytic steps associated with the metabolism of glucose to pyruvic acid (pyruvate). Fig. 8.18 Summary of glycolysis

TCA cycle Each pyruvic acid is processed to enter the TCA cycle (two complete cycles) CO2 is generated Coenzymes NAD and FAD are reduced to NADH and FADH2 Net yield of two ATPs Critical intermediates are synthesized

The steps associated with TCA cycle. Fig. 8.20 The reaction of a single turn of the TCA cycle

Electron transport NADH and FADH2 donate electrons to the electron carriers Membrane bound carriers transfer electrons (redox reactions) The final electron acceptor completes the terminal step (ex. Oxygen)

Electron transport continued Chemiosmosis Proton motive force (PMF)

Chemiosmosis entails the electron transport and formation of a proton gradient (proton motive force). Fig. 8.22 The electron transport system and oxidative phosphorylation

Electron transport chain Mitochondria eucaryotes Cytoplasmic membrane procaryotes

Total yield of ATP for one glucose molecule from aerobic respiration. Table 8.4 Summary of aerobic respiration for one glucose molecule

Anaerobic respiration Similar to aerobic respiration, except nitrate or nitrite is the final electron acceptor

Fermentation Glycolysis only NADH from glycolysis is used to reduce the organic products Organic compounds as the final electron acceptors ATP yields are small (per glucose molecule), compared to respiration Must metabolize large amounts of glucose to produce equivalent respiratory ATPs

The fermentation of ethyl alcohol and lactic acid. Fig. 8.24 The chemistry of fermentation systems

Types of fermenters Facultative anaerobes Strict fermenters Fermentation in the absence of oxygen Respiration in the presence of oxygen Ex. Escherichia coli Strict fermenters No respiration Ex. yeast

Products of fermentation Alcoholic fermentation Acidic fermentation Mixed acid fermentation

An example of mixed acid fermentation and the diverse products synthesized. Fig. 8.25 Miscellaneous products of pyruvate

Biosynthesis Anabolism Amphibolic Gluconeogenesis Beta oxidation Amination Transamination Deamination Macromolecules

Amphibolic Integration of the catabolic and anabolic pathways Intermediates serve multiple purposes

Intermediates can serve to synthesize amino acids, carbohydrates and lipids. Fig. 8.26 An amphibolic view of metabolism

Gluconeogenesis Pyruvate (intermediate) is converted to glucose Occurs when the glucose supply is low

Beta oxidation Metabolism of fats into acetyl, which can then enter the TCA cycle as acetyl CoA.

Examples of amination, transamination, and deamination. Fig. 8.27 Reactions that produce and convert amino acids

Macromolecules Cellular building blocks Monosaccharides Amino acids Fatty acids Nitrogen bases Vitamins