Copyright © 2013 Pearson Education, Inc.Lectures prepared by Christine L. Case

Chapter 5

Microbial Metabolism

© 2013 Pearson Education, Inc. Lectures prepared by Christine L. Case

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Catabolic and Anabolic Reactions

Metabolism: the sum of the chemical reactions in an organism

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Catabolic and Anabolic Reactions

Catabolism: provides energy and building blocks for anabolism

Anabolism: uses energy and building blocks to build large molecules

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Figure 5.1 The role of ATP in coupling anabolic and catabolic reactions.

Catabolism releases energyby oxidation of molecules

Energy isstored inmoleculesof ATP

Anabolism uses energy tosynthesize macromoleculesthat make up the cell

Energy isreleased byhydrolysisof ATP

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ANIMATION Metabolism: Overview

Catabolic and Anabolic Reactions

A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell

Metabolic pathways are determined by enzymes Enzymes are encoded by genes

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Collision Theory

The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide

Activation energy is needed to disrupt electronic configurations

Reaction rate is the frequency of collisions with enough energy to bring about a reaction

Reaction rate can be increased by enzymes or by increasing temperature or pressure

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Figure 5.2 Energy requirements of a chemical reaction.

Reactionwithout enzyme

Reactionwith enzyme

Reactant

Initial energy level

Final energy level

Products

Activationenergywithout enzyme

Activationenergywithenzyme

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Enzyme Components

Biological catalysts Specific for a chemical reaction; not used up in that

reaction

Apoenzyme: protein Cofactor: nonprotein component

Coenzyme: organic cofactor

Holoenzyme: apoenzyme plus cofactor

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Figure 5.3 Components of a holoenzyme.

Coenzyme Substrate

Apoenzyme (protein portion),

inactive

Cofactor(nonprotein portion),

activator

Holoenzyme(whole enzyme),

active

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Important Coenzymes

NAD+

NADP+

FAD Coenzyme A

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Figure 5.4a The mechanism of enzymatic action.

Substrate Active site

Enzyme–substrate

Products

Enzymecomplex

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Figure 5.4b The mechanism of enzymatic action.

Substrate

EnzymeSubstrate

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Factors Influencing Enzyme Activity

Temperature pH Substrate concentration Inhibitors

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Temperature and pH denature proteins

Factors Influencing Enzyme Activity

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Figure 5.6 Denaturation of a protein.

Active (functional) protein Denatured protein

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Figure 5.5a Factors that influence enzymatic activity, plotted for a hypothetical enzyme.

(a) Temperature. The enzymatic activity (rate of reaction catalyzed by the enzyme) increases with increasing temperature until the enzyme, a protein, is denatured by heat and inactivated. At this point, the reaction rate falls steeply.

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Figure 5.5b Factors that influence enzymatic activity, plotted for a hypothetical enzyme.

(b) pH. The enzyme illustrated is most active at about pH 5.0.

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Figure 5.5c Factors that influence enzymatic activity, plotted for a hypothetical enzyme.

(c) Substrate concentration. With increasing concentration of substrate molecules, the rate of reaction increases until the active sites on all the enzyme molecules are filled, at which point the maximum rate of reaction is reached.

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Enzyme Inhibitors: Competitive Inhibition

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Figure 5.7ab Enzyme inhibitors.

Normal Binding of Substrate Action of Enzyme Inhibitors

Substrate

Active site

Enzyme

Competitiveinhibitor

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Enzyme Inhibitors: Competitive Inhibition

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Enzyme Inhibitors: Noncompetitive Inhibition

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Figure 5.7ac Enzyme inhibitors.

Normal Binding of Substrate

Substrate

Active site

Enzyme

Action of Enzyme Inhibitors

Noncompetitiveinhibitor Allosteric

site

Alteredactive site

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Enzyme Inhibitors: Feedback Inhibition

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Figure 5.8 Feedback inhibition.

Substrate

PathwayOperates

Intermediate A

Intermediate B

End-product

Enzyme 1

Allosteric site

Enzyme 2

Bound end-product

Pathway Shuts Down

Fe

ed

ba

ck

In

hib

itio

n

Enzyme 3

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Oxidation-Reduction Reactions

Oxidation: removal of electrons Reduction: gain of electrons Redox reaction: an oxidation reaction paired with

a reduction reaction

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Figure 5.9 Oxidation-reduction.

Reduction

A oxidized B reduced

Oxidation

A B

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ANIMATION Oxidation-Reduction Reactions

Oxidation-Reduction Reactions

In biological systems, the electrons are often associated with hydrogen atoms

Biological oxidations are often dehydrogenations

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Figure 5.10 Representative biological oxidation.

Reduction

Oxidation

H+

(proton)

Organic moleculethat includes twohydrogen atoms

(H)

NAD+ coenzyme(electron carrier)

Oxidized organic

molecule

NADH + H+ (proton)(reduced electron

carrier)

H

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ATP is generated by the phosphorylation of ADP

The Generation of ATP

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The Generation of ATP

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Energy from the transfer of a high-energy PO4– to

ADP generates ATP

Substrate-Level Phosphorylation

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Substrate-Level Phosphorylation

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Oxidative Phosphorylation

Energy released from transfer of electrons (oxidation) of one compound to another (reduction) is used to generate ATP in the electron transport chain

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Photophosphorylation

Light causes chlorophyll to give up electrons Energy released from transfer of electrons

(oxidation) of chlorophyll through a system of carrier molecules is used to generate ATP

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Carbohydrate Catabolism

The breakdown of carbohydrates to release energy Glycolysis Krebs cycle Electron transport chain

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Glycolysis

The oxidation of glucose to pyruvic acid produces ATP and NADH

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Figure 5.11 An Overview of Respiration and Fermentation.

1

3

2

The Krebs cycle produces some ATP by substrate-level phosphorylation, reduces the electron carriers NAD+ and FAD, and gives off CO2. Carriers from both glycolysis and the Krebs cycle donate electrons to the electron transport chain.

In the electron transportchain, the energy of theelectrons is used toproduce a great deal ofATP by oxidativephosphorylation.

Glycolysis produces ATP and reduces NAD+ to NADH while oxidizing glucose to pyruvic acid. In respiration, the pyruvic acid is converted to the first reactant in the Krebs cycle, acetyl CoA.

In fermentation, the pyruvic acid and the electrons carried by NADH from glycolysis are incorporated into fermentation end-products.

brewer’s yeast

NADH

NADH

NADH

FADH2

NADH & FADH2

Glycolysis

Glucose

Pyruvic acid

Pyruvic acid(or derivative)

Formation offermentationend-products

ATP

ATP

ATPCO2

O2

Electrons

Acetyl CoA

Electrontransportchain andchemiosmosis

respiration fermentation

H2O

Kreb’scycle

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Preparatory Stage of Glycolysis

2 ATP are used Glucose is split to form 2 glucose-3-phosphate

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2 glucose-3-phosphate are oxidized to 2 pyruvic acid 4 ATP are produced 2 NADH are produced

Energy-Conserving Stage of Glycolysis

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Glycolysis

Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+ 2

pyruvic acid + 4 ATP + 2 NADH + 2H+

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Alternatives to Glycolysis

Pentose phosphate pathway Uses pentoses and NADPH Operates with glycolysis

Entner-Doudoroff pathway Produces NADPH and ATP Does not involve glycolysis Pseudomonas, Rhizobium, Agrobacterium

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Cellular Respiration

Oxidation of molecules liberates electrons for an electron transport chain

ATP is generated by oxidative phosphorylation

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Pyruvic acid (from glycolysis) is oxidized and decarboxylated

Intermediate Step

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The Krebs Cycle

Oxidation of acetyl CoA produces NADH and FADH2

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ANIMATION Electron Transport Chain: Overview

The Electron Transport Chain

A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain

Energy released can be used to produce ATP by chemiosmosis

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Figure 5.14 An electron transport chain (system).

Flow of electrons

Energy

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Figure 5.11 An Overview of Respiration and Fermentation.

1

3

2

The Krebs cycle produces some ATP by substrate-level phosphorylation, reduces the electron carriers NAD+ and FAD, and gives off CO2. Carriers from both glycolysis and the Krebs cycle donate electrons to the electron transport chain.

In the electron transportchain, the energy of theelectrons is used toproduce a great deal ofATP by oxidativephosphorylation.

Glycolysis produces ATP and reduces NAD+ to NADH while oxidizing glucose to pyruvic acid. In respiration, the pyruvic acid is converted to the first reactant in the Krebs cycle, acetyl CoA.

In fermentation, the pyruvic acid and the electrons carried by NADH from glycolysis are incorporated into fermentation end-products.

brewer’s yeast

NADH

NADH

NADH

FADH2

NADH & FADH2

Glycolysis

Glucose

Pyruvic acid

Pyruvic acid(or derivative)

Formation offermentationend-products

ATP

ATP

ATPCO2

O2

Electrons

Acetyl CoA

Electrontransportchain andchemiosmosis

respiration fermentation

H2O

Kreb’scycle

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Cytoplasm

Bacterium Mitochondrion

Intermembrane space

Mitochondrial matrix

Cellwall

Periplasmic space

Plasma membrane

Outer membrane

Inner membrane

Periplasmic space of prokaryote or intermembrane space of eukaryote

Prokaryoticplasmamembraneor eukaryoticinner mitochondrial membrane

Cytoplasm ofprokaryote ormitochondrialmatrix ofeukaryote

Figure 5.16 Electron transport and the chemiosmotic generation of ATP.

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Figure 5.15 Chemiosmosis.

High H+ concentration

Low H+ concentration

Membrane

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A Summary of Respiration

Aerobic respiration: the final electron acceptor in the electron transport chain is molecular oxygen (O2)

Anaerobic respiration: the final electron acceptor in the electron transport chain is NOT O2

Yields less energy than aerobic respiration because only part of the Krebs cycle operates under anaerobic conditions

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Respiration

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Pathway Eukaryote Prokaryote

Glycolysis Cytoplasm Cytoplasm

Intermediate step Cytoplasm Cytoplasm

Krebs cycle Mitochondrial matrix Cytoplasm

ETC Mitochondrial inner membrane Plasma membrane

Carbohydrate Catabolism

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Energy produced from complete oxidation of one glucose using aerobic respiration

Pathway ATP Produced NADH Produced

FADH2 Produced

Glycolysis 2 2 0

Intermediate step 0 2 0

Krebs cycle 2 6 2

Total 4 10 2

Carbohydrate Catabolism

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ATP produced from complete oxidation of one glucose using aerobic respiration

Pathway By Substrate-Level Phosphorylation

By Oxidative Phosphorylation

From NADH From FADH

Glycolysis 2 6 0

Intermediate step 0 6 0

Krebs cycle 2 18 4

Total 4 30 4

Carbohydrate Catabolism

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36 ATPs are produced in eukaryotes

Pathway By Substrate-Level Phosphorylation

By Oxidative Phosphorylation

From NADH From FADH

Glycolysis 2 6 0

Intermediate step 0 6 0

Krebs cycle 2 18 4

Total 4 30 4

Carbohydrate Catabolism

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Fermentation

Any spoilage of food by microorganisms (general use)

Any process that produces alcoholic beverages or acidic dairy products (general use)

Any large-scale microbial process occurring with or without air (common definition used in industry)

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Fermentation

Scientific definition: Releases energy from oxidation of organic molecules Does not require oxygen Does not use the Krebs cycle or ETC Uses an organic molecule as the final electron acceptor

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Figure 5.18a Fermentation.

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Figure 5.18b Fermentation.

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Fermentation

Alcohol fermentation: produces ethanol + CO2

Lactic acid fermentation: produces lactic acid Homolactic fermentation: produces lactic acid only Heterolactic fermentation: produces lactic acid and other

compounds

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Figure 5.19 Types of fermentation.

(a) Lactic acid fermentation

(b) Alcohol fermentation

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Figure 5.23 A fermentation test.

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Figure 5.21 Catabolism of various organic food molecules.

Electrontransportchain andchemiosmosis

Krebscycle

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Protein Amino acidsExtracellular proteases

Krebs cycle

Deamination, decarboxylation, dehydrogenation, desulfurization

Organic acid

Protein Catabolism

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Figure 5.22 Detecting amino acid catabolizing enzymes in the lab.

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Urease NH3 + CO2Urea

Protein Catabolism

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Clinical Focus: Human Tuberculosis – Dallas, Texas

Figure B The urease test.

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Used to identify bacteria

Biochemical Tests

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Clinical Focus: Human Tuberculosis – Dallas, Texas

Figure A An identification scheme for selected species of slow-growing mycobacteria.

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ANIMATION Photosynthesis: Overview

Photosynthesis

Photo: conversion of light energy into chemical energy (ATP) Light-dependent (light) reactions

Synthesis: Carbon fixation: fixing carbon into organic molecules Light-independent (dark) reaction: Calvin-Benson cycle

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Figure 4.15 Chromatophores.

Chromatophores

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Cyclic Photophosphorylation

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Figure 5.25a Photophosphorylation.

LightExcitedelectrons

Electrontransportchain

Electron carrier

In Photosystem I(a) Cyclic photophosphorylation

Energy forproductionof ATP

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Noncyclic Photophosphorylation

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Figure 5.25b Photophosphorylation.

Excitedelectrons

Excitedelectrons

(b) Noncyclic photophosphorylation

Electrontransportchain Energy for

productionof ATP

Light

Light

In Photosystem II

In Photosystem I

H+ + H+

12

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Calvin-Benson Cycle

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

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Use energy from chemicals Chemoheterotroph

Energy is used in anabolism

Glucose

Pyruvic acid

NAD+

NADH

ETC

ADP + P ATP

Chemotrophs

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Chlorophyll

Chlorophylloxidized

ETC

ADP + P ATP

Phototrophs

Use light energy

Photoautotrophs use energy in the Calvin-Benson cycle to fix CO2

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Figure 5.27 Requirements of ATP production.

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Figure 5.29 The biosynthesis of polysaccharides.

Glycogen(in bacteria)

Glycogen(in animals)

Peptidoglycan(in bacteria)

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Figure 5.30 The biosynthesis of simple lipids.

Krebscycle

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Figure 5.31a The biosynthesis of amino acids.

Krebscycle

Amination or transamination

Amino acid biosynthesis

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Figure 5.32 The biosynthesis of purine and pyrimidine nucleotides.

Krebscycle