05 lecture presentation.ppt - Professor Welday's Weebly...

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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© 2013 Pearson Education, Inc.

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Catabolic and Anabolic Reactions

5-1 Define metabolism, and describe the fundamental differences between anabolism and catabolism.

5-2 Identify the role of ATP as an intermediate between catabolism and anabolism.

Learning Objectives

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Metabolism: the sum of the chemical reactions in an organism

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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


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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Check Your Understanding


Distinguish catabolism from anabolism. 5-1 How is ATP an intermediate between catabolism

and anabolism? 5-2

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Enzyme

5-3 Identify the components of an enzyme.5-4 Describe the mechanism of enzymatic action.5-5 List the factors that influence enzymatic activity.5-6 Distinguish competitive and noncompetitive

inhibition.5-7 Define ribozyme.

Learning Objectives

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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 levelProducts

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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ANIMATION Enzymes: Steps in a Reaction

ANIMATION Enzymes: Overview

Enzyme Specificity and Efficiency

The turnover number is generally 1 to 10,000 molecules per second

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Figure 5.4a The mechanism of enzymatic action.

Substrate Active site

Enzyme–substrate

Products

Enzyme complex

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Figure 5.4b The mechanism of enzymatic action.

SubstrateEnzymeSubstrate

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Enzyme Classification

Oxidoreductase: oxidation-reduction reactions Transferase: transfer functional groups Hydrolase: hydrolysis Lyase: removal of atoms without hydrolysis Isomerase: rearrangement of atoms Ligase: joining of molecules; uses ATP

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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 Activity20


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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ANIMATION Enzymes: Competitive Inhibition

Enzyme Inhibitors: Competitive Inhibition

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Figure 5.7ab Enzyme inhibitors.

Normal Binding of Substrate Action of Enzyme Inhibitors

SubstrateActive site

Enzyme

Competitiveinhibitor

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Enzyme Inhibitors: Competitive Inhibition 27


ANIMATION Enzymes: Non-competitive Inhibition

Enzyme Inhibitors: Noncompetitive Inhibition

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Figure 5.7ac Enzyme inhibitors.

Normal Binding of Substrate

SubstrateActive site

Enzyme

Action of Enzyme Inhibitors

Noncompetitiveinhibitor Allosteric

site

Alteredactive site

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Enzyme Inhibitors: Feedback Inhibition30


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

Feed

back

Inhi

bitio

n

Enzyme 3

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Ribozymes

RNA that cuts and splices RNA

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What is a coenzyme? 5-3 Why is enzyme specificity important? 5-4 What happens to an enzyme below its optimal

temperature? Above its optimal temperature? 5-5 Why is feedback inhibition noncompetitive

inhibition? 5-6 What is a ribozyme? 5-7

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5-8 Explain the term oxidation-reduction.5-9 List and provide examples of three types of

phosphorylation reactions that generate ATP.5-10 Explain the overall function of metabolic

pathways.

Energy Production

Learning Objectives

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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 ATP39


The Generation of ATP 40


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

ADP generates ATP

Substrate-Level Phosphorylation41


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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Figure 5.14 An electron transport chain (system).

Energy

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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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Figure 5.25 Photophosphorylation.

Light Excitedelectrons

Electrontransportchain

Electron carrier

Energy forproductionof ATP

Excitedelectrons

Excitedelectrons

(b) Noncyclic photophosphorylation

In Photosystem I(a) Cyclic photophosphorylation Electron

transportchain Energy for

productionof ATP

Light

Light

In Photosystem II

In Photosystem I

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Metabolic Pathways of Energy Production 46




Why is glucose such an important molecule for organisms? 5-8

Outline the three ways that ATP is generated. 5-9 What is the purpose of metabolic pathways? 5-10

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Carbohydrate Catabolism

5-11 Describe the chemical reactions of glycolysis.5-12 Identify the functions of the pentose phosphate

and Entner-Doudoroff pathways.5-13 Explain the products of the Krebs cycle.5-14 Describe the chemiosmotic model for ATP

generation.5-15 Compare and contrast aerobic and anaerobic

respiration.5-16 Describe the chemical reactions of, and list some

products of, fermentation.

Learning Objectives

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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

GlycolysisGlucose

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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Glucose enters the cell and is phosphorylated. Amolecule of ATP is invested. The product is glucose 6-phosphate.

2 Glucose 6-phosphate is rearranged to form fructose 6-phosphate.

The from another ATP is used to produce fructose 1,6-diphosphate, still a six-carbon compound. (Note the total investment of two ATP molecules up to this point.)

An enzyme cleaves (splits) the sugar into two three-carbon molecules: dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GP).

DHAP is readily converted to GP (the reverse action may also occur).

The next enzyme converts each GP to another three-carbon compound, 1,3-diphosphoglyceric acid. Because each DHAP molecule can be converted to GP and each GP to 1,3-diphosphoglyceric acid, the result is two molecules of 1,3-diphosphoglyceric acid for each initial molecule of glucose. GP is oxidized by the transfer of two hydrogen atoms to NAD+ to form NADH. The enzyme couples this reaction with the creation of a high-energy bond between the sugar and a . The three-carbon sugar now has two groups.

The high-energy is moved to ADP, forming ATP, the first ATP production of glycolysis. (Since the sugar splitting in step 4, all products are doubled. Therefore, this step actually repays the earlier investment of two ATP molecules.)

An enzyme relocates the remaining of 3-phosphoglyceric acid to form 2-phosphoglyceric acid in preparation for the next step.

By the loss of a water molecule, 2-phosphoglyceric acid is converted to phosphoenolpyruvic acid (PEP). In the process, the phosphate bond is upgraded to a high-energy bond.

This high-energy is transferred from PEP to ADP, forming ATP. For each initial glucose molecule, the result of this step is two molecules of ATP and two molecules of a three-carbon compound called pyruvic acid.

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3

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6

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9

10

4

Glucose 6-phosphate

Fructose 6-phosphate

Fructose 1,6-diphosphate

Glyceraldehyde 3-phosphate (GP)

1,3-diphosphoglyceric acid

3-phosphoglyceric acid

2-phosphoglyceric acid

Phosphoenolpyruvic acid (PEP)

P

P

P

P

P

P

1

Figure 5.12 An outline of the reactions of glycolysis (Embden-Meyerhof pathway). 53


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

Energy-Conserving Stage of Glycolysis54


ANIMATION Glycolysis: Steps

ANIMATION Glycolysis: Overview

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 Step58


ANIMATION Krebs Cycle: Steps

ANIMATION Krebs Cycle: Overview

The Krebs Cycle

Oxidation of acetyl CoA produces NADH and FADH2

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Figure 5.13 The Krebs cycle.

A turn of the cycle begins as enzymes strip off the CoA portion from acetyl CoA and combine the remaining two-carbon acetyl group with oxaloacetic acid. Adding the acetyl group produces the six-carbon molecule citric acid.

– Oxidations generateNADH. Step 2 is a rearrangement. Steps 3 and 4 combine oxidations and decarboxylations to dispose of two carbon atoms that came from oxaloacetic acid. The carbons are released as CO2, and the oxidations generate NADH from NAD+. During the second oxidation (step 4), CoA is added into the cycle, forming the compound succinyl CoA.

ATP is produced by substrate-level phosphorylation. CoA is removed from succinyl CoA, leaving succinic acid.

– Enzymes rearrange chemical bonds, producing three different molecules before regenerating oxaloacetic acid. In step 6, an oxidation produces FADH2. In step 8, a final oxidation generates NADH and converts malic acid to oxaloacetic acid, which is ready to enter another round of the Krebs cycle.

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2 46 8

5

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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).

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

GlycolysisGlucose

Pyruvic acid

Pyruvic acid(or derivative)

Formation offermentationend-products

ATP

ATP

ATPCO2

O2

Electrons

Acetyl CoA


respiration fermentation

H2O

Kreb’scycle

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CytoplasmBacterium Mitochondrion

Intermembrane spaceMitochondrial 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. 64


Figure 5.15 Chemiosmosis.

High H+ concentration

Low H+ concentration

Membrane

65


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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ANIMATION Electron Transport Chain: Factors Affecting ATP Yield

Respiration67


Electron Acceptor ProductsNO3

– NO2–, N2 + H2O

SO4– H2S + H2O

CO32 – CH4 + H2O

Anaerobic Respiration68


Pathway Eukaryote ProkaryoteGlycolysis Cytoplasm Cytoplasm

Intermediate step Cytoplasm Cytoplasm

Krebs cycle Mitochondrial matrix Cytoplasm

ETC Mitochondrial inner membrane Plasma membrane

Carbohydrate Catabolism69


Energy produced from complete oxidation of one glucose using aerobic respiration

Pathway ATP Produced NADH Produced

FADH2Produced

Glycolysis 2 2 0

Intermediate step 0 2 0

Krebs cycle 2 6 2

Total 4 10 2



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


Krebs cycle 2 18 4

Total 4 30 4



36 ATPs are produced in eukaryotes

Pathway By Substrate-Level Phosphorylation

By Oxidative Phosphorylation

From NADH From FADH

Glycolysis 2 6 0


Krebs cycle 2 18 4

Total 4 30 4



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. 75


Figure 5.18b Fermentation. 76


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. 79


Table 5.4 Some Industrial Uses for Different Types of Fermentations* 80




What happens during the preparatory and energy-conserving stages of glycolysis? 5-11

What is the value of the pentose phosphate and Entner-Doudoroff pathways if they produce only one ATP molecule? 5-12

What are the principal products of the Krebs cycle? 5-13 How do carrier molecules function in the electron transport

chain? 5-14 Compare the energy yield (ATP) of aerobic and anaerobic

respiration. 5-15 List four compounds that can be made from pyruvic acid by

an organism that uses fermentation. 5-16

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Lipid and Protein Catabolism

5-17 Describe how lipids and proteins undergo catabolism.

5-18 Provide two examples of the use of biochemical tests to identify bacteria in the laboratory.

Learning Objectives

82


Figure 5.20 Lipid catabolism.

Lipase

Beta-oxidation

Krebscycle

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Figure 5.21 Catabolism of various organic food molecules.


Krebscycle

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Protein Amino acidsExtracellular proteases

Krebs cycleDeamination, decarboxylation,

dehydrogenation, desulfurization Organic acid

Protein Catabolism85


Figure 5.22 Detecting amino acid catabolizing enzymes in the lab. 86


Figure 5.24 Use of peptone iron agar to detect the production of H2S. 87


Urease NH3 + CO2Urea

Protein Catabolism88


Clinical Focus: Human Tuberculosis – Dallas, Texas

Figure B The urease test.

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Used to identify bacteria

Biochemical Tests90


Clinical Focus: Human Tuberculosis – Dallas, Texas

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

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What are the end-products of lipid and protein catabolism? 5-17

On what biochemical basis are Pseudomonas and Escherichia differentiated? 5-18

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Photosynthesis

5-19 Compare and contrast cyclic and noncyclic photophosphorylation.

5-20 Compare and contrast the light-dependent and light-independent reactions of photosynthesis.

5-21 Compare and contrast oxidative phosphorylation and photophosphorylation.

Learning Objectives

93


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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ANIMATION: Photosynthesis: Comparing Prokaryotes and Eukaryotes

Photosynthesis

Oxygenic:

Anoxygenic:

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ANIMATION Photosynthesis: Light Reaction: Cyclic Photophosphorylation

Cyclic Photophosphorylation97


Figure 5.25a Photophosphorylation.

LightExcitedelectrons

Electrontransportchain

Electron carrier

In Photosystem I(a) Cyclic photophosphorylation

Energy forproductionof ATP

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ANIMATION Photosynthesis: Light Reaction: Noncyclic Photophosphorylation

Noncyclic Photophosphorylation99


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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ANIMATION Photosynthesis: Light Independent Reaction

Calvin-Benson Cycle101


Figure 5.26 A simplified version of the Calvin-Benson cycle.

Ribulose diphosphate 3-phosphoglyceric acid

Input

1,3-diphosphoglyceric acid

Calvin-Benson cycle

Glyceraldehyde3-phosphate

Glyceraldehyde3-phosphate

Output

Glyceraldehyde 3-phosphate

Glyceraldehyde 3-phosphate

102


Table 5.6 Photosynthesis Compared in Selected Eukaryotes and Prokaryotes 103




How is photosynthesis important to catabolism? 5-19

What is made during the light-dependent reactions? 5-20

How are oxidative phosphorylation and photophosphorylation similar? 5-21

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A Summary of Energy Production

5-22 Write a sentence to summarize energy production in cells.

Learning Objective

105




Summarize how oxidation enables organisms to get energy from glucose, sulfur, or sunlight. 5-22

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Metabolic Diversity among Organisms

5-23 Categorize the various nutritional patterns among organisms according to carbon source and mechanisms of carbohydrate catabolism and ATP generation.

Learning Objective

107


Use energy from chemicals Chemoheterotroph

Energy is used in anabolism

Glucose

Pyruvic acid

NAD+

NADH

ETC

ADP + P ATP

Chemotrophs108


Use energy from chemicals Chemoautotroph, Thiobacillus ferrooxidans

Energy is used in the Calvin-Benson cycle to fix CO2

2Fe2+

2Fe3+

NAD+

NADH

ETC

ADP + P ATP2 H+

Chemotrophs109


Chlorophyll

Chlorophylloxidized

ETC

ADP + P ATP

Phototrophs

Use light energy

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

Photoheterotrophs use energy

110


Figure 5.27 Requirements of ATP production. 111


Chemical Light

Organic compounds CO2 Organic compounds CO2

NoYesO2 Not O2Organic

compoundInorganic

compound

Figure 5.28 A nutritional classification of organisms. 112


Nutritional Type Energy Source Carbon Source Example

Photoautotroph Light CO2 Oxygenic: Cyanobacteria, plantsAnoxygenic: Green bacteria, purple bacteria

Photoheterotroph Light Organic compounds

Green bacteria, purple nonsulfur bacteria

Chemoautotroph Chemical CO2 Iron-oxidizing bacteria

Chemoheterotroph Chemical Organic compounds

Fermentative bacteriaAnimals, protozoa, fungi, bacteria

Metabolic Diversity among Organisms113




Almost all medically important microbes belong to which of the four aforementioned groups? 5-23

114


ANIMATION Metabolism: The Big Picture

Metabolic Pathways of Energy Use

5-24 Describe the major types of anabolism and their relationship to catabolism.

Learning Objective

115


Figure 5.29 The biosynthesis of polysaccharides.

Glycogen(in bacteria)

Glycogen(in animals)

Peptidoglycan(in bacteria)

116


Figure 5.30 The biosynthesis of simple lipids.

Krebscycle

117


Figure 5.31a The biosynthesis of amino acids.

Krebscycle

Amination or transamination

Amino acid biosynthesis

118


Figure 5.31b The biosynthesis of amino acids.

Transamination

Process of transamination

Glutamic acid Oxaloaceticacid

α-Ketoglutaricacid

Aspartic acid

119


Figure 5.32 The biosynthesis of purine and pyrimidine nucleotides.

Krebscycle

120




Where do amino acids required for protein synthesis come from? 5-24

121


The Integration of Metabolism

5-25 Define amphibolic pathways.Learning Objective

122


The Integration of Metabolism

Amphibolic pathways: metabolic pathways that have both catabolic and anabolic functions

123


Figure 5.33 The integration of metabolism.

Krebs cycle

CO2

124




Summarize the integration of metabolic pathways using peptidoglycan synthesis as an example. 5-25

125

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