Download Micro Chapter 5 ppt. 11th edition

Chapter 5
Microbial
Metabolism
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Copyright © 2013 Pearson Education, Inc.
Lectures prepared by Christine L. Case
Lectures prepared by Christine L. Case
© 2013 Pearson Education, Inc.
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.
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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
ANIMATION Metabolism: Overview
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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.
Reaction
without enzyme
Reaction
with enzyme
Reactant
Activation
energy
without
enzyme
Activation
energy
with
enzyme
Initial energy level
Final energy level
Products
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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
Apoenzyme
(protein portion),
inactive
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Cofactor
(nonprotein portion),
activator
Substrate
Holoenzyme
(whole enzyme),
active
Important Coenzymes




NAD+
NADP+
FAD
Coenzyme A
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Enzyme Specificity and Efficiency
 The turnover number is generally 1 to 10,000
molecules per second
ANIMATION Enzymes: Overview
ANIMATION Enzymes: Steps in a Reaction
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Figure 5.4a The mechanism of enzymatic action.
Active site
Substrate
Enzyme
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Enzyme–substrate
complex
Products
Figure 5.4b The mechanism of enzymatic action.
Substrate
Enzyme
Substrate
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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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Factors Influencing Enzyme Activity
 Temperature and pH denature proteins
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Figure 5.6 Denaturation of a protein.
Active (functional) protein
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Denatured protein
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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Figure 5.7ab Enzyme inhibitors.
Normal Binding of Substrate
Substrate
Active site
Enzyme
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Action of Enzyme Inhibitors
Competitive
inhibitor
Enzyme Inhibitors: Competitive Inhibition
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Figure 5.7ac Enzyme inhibitors.
Normal Binding of Substrate
Substrate
Action of Enzyme Inhibitors
Altered
active site
Active site
Enzyme
Noncompetitive
inhibitor
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Allosteric
site
Figure 5.8 Feedback inhibition.
Substrate
Pathway
Operates
Pathway
Shuts Down
Enzyme 1
Intermediate A
Enzyme 2
Intermediate B
Enzyme 3
End-product
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Bound
end-product
Feedback Inhibition
Allosteric site
Ribozymes
 RNA that cuts and splices RNA
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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
A oxidized
B
Oxidation
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B reduced
Oxidation-Reduction Reactions
 In biological systems, the electrons are often
associated with hydrogen atoms
 Biological oxidations are often dehydrogenations
ANIMATION Oxidation-Reduction Reactions
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Figure 5.10 Representative biological oxidation.
Reduction
H
H+
(proton)
Organic molecule NAD+ coenzyme
that includes two (electron carrier)
hydrogen atoms
(H)
Oxidation
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Oxidized
organic
molecule
NADH + H+ (proton)
(reduced electron
carrier)
The Generation of ATP
 ATP is generated by the phosphorylation of ADP
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The Generation of ATP
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Substrate-Level Phosphorylation
 Energy from the transfer of a high-energy PO4– to
ADP generates ATP
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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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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.
Electron
transport
chain
Light Excited
electrons
Energy for
production
of ATP
Electron
carrier
In Photosystem I
(a) Cyclic photophosphorylation
Light Excited
electrons
Electron
transport
chain
In Photosystem I
Light Excited
electrons
In Photosystem II
(b) Noncyclic photophosphorylation
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Energy for
production
of ATP
Metabolic Pathways of Energy Production
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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.
respiration fermentation
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.
The Krebs cycle produces
some ATP by substratelevel 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 transport
chain, the energy of the
electrons is used to
produce a great deal of
ATP by oxidative
phosphorylation.
1
Glycolysis
Glucose
NADH
ATP
Pyruvic
acid
2
Pyruvic acid
Acetyl CoA
(or derivative)
NADH
FADH2
Kreb’s
cycle
NADH &
FADH2
Formation of
fermentation
end-products
CO2
ATP
3
Electrons
ATP
Electron
transport
chain and
chemiosmosis
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NADH
In fermentation, the
pyruvic acid and the
electrons carried by
NADH from glycolysis
are incorporated into
fermentation endproducts.
O2
H2O
brewer’s yeast
Preparatory Stage of Glycolysis
 2 ATP are used
 Glucose is split to form 2 glycerol-3-phosphate
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Figure 5.12 An outline of the reactions of glycolysis (Embden-Meyerhof pathway).
1 Glucose enters the cell and is phosphorylated. A
molecule of ATP is invested. The product is glucose 6-phosphate.
Glucose 6-phosphate
2
2 Glucose 6-phosphate is rearranged to form fructose
6-phosphate.
Fructose 6-phosphate
3 The P from another ATP is used to produce fructose 1,6diphosphate, still a six-carbon compound. (Note the total
investment of two ATP molecules up to this point.)
Fructose 1,6-diphosphate
4 An enzyme cleaves (splits) the sugar into two three-carbon
molecules: dihydroxyacetone phosphate (DHAP) and
glyceraldehyde 3-phosphate (GP).
Glyceraldehyde 3-phosphate (GP)
2-phosphoglyceric acid
DHAP is readily converted to GP (the reverse action may also occur).
6 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 highenergy bond between the sugar and a P . The three-carbon sugar now has
two P groups.
1,3-diphosphoglyceric acid
3-phosphoglyceric acid
5
7
The high-energy P 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.)
8
An enzyme relocates the remaining P of 3-phosphoglyceric acid to
form 2-phosphoglyceric acid in preparation for the next step.
Phosphoenolpyruvic acid (PEP)
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9 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.
10 This high-energy P 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.
Energy-Conserving Stage of Glycolysis
 2 glycerol-3-phosphate are oxidized to 2 pyruvic acid
 4 ATP are produced
 2 NADH are produced
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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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Intermediate Step
 Pyruvic acid (from glycolysis) is oxidized and
decarboxylated
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Figure 5.13 The Krebs cycle.
1 A turn of the cycle begins
as enzymes strip off the CoA
portion from acetyl CoA and
combine the remaining twocarbon acetyl group with
oxaloacetic acid. Adding the
acetyl group produces the sixcarbon molecule citric acid.
– 8 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.
6
5 ATP is produced by substratelevel phosphorylation. CoA is
removed from succinyl CoA,
leaving succinic acid.
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2 – 4 Oxidations generate
NADH. 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.
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
ANIMATION Electron Transport Chain: Overview
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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.
respiration fermentation
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.
The Krebs cycle produces
some ATP by substratelevel 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 transport
chain, the energy of the
electrons is used to
produce a great deal of
ATP by oxidative
phosphorylation.
1
Glycolysis
Glucose
NADH
ATP
Pyruvic
acid
2
Pyruvic acid
Acetyl CoA
(or derivative)
NADH
FADH2
Kreb’s
cycle
NADH &
FADH2
Formation of
fermentation
end-products
CO2
ATP
3
Electrons
ATP
Electron
transport
chain and
chemiosmosis
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NADH
In fermentation, the
pyruvic acid and the
electrons carried by
NADH from glycolysis
are incorporated into
fermentation endproducts.
O2
H2O
brewer’s yeast
Figure 5.16 Electron transport and the chemiosmotic generation of ATP.
Cell Periplasmic Plasma
Outer
wall space
membrane membrane
Inner
membrane
Intermembrane space
Mitochondrial matrix
Cytoplasm
Bacterium
Mitochondrion
Periplasmic space of prokaryote
or intermembrane space of
eukaryote
Prokaryotic
plasma
membrane
or eukaryotic
inner
mitochondrial
membrane
Cytoplasm of
prokaryote or
mitochondrial
matrix of
eukaryote
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Figure 5.15 Chemiosmosis.
High H+ concentration
Membrane
Low H+ concentration
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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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Anaerobic Respiration
Electron Acceptor
Products
NO3–
NO2–, N2 + H2O
SO4–
H2S + H2O
CO32 –
CH4 + H2O
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Carbohydrate Catabolism
Pathway
Eukaryote
Prokaryote
Glycolysis
Cytoplasm
Cytoplasm
Intermediate step
Cytoplasm
Cytoplasm
Krebs cycle
Mitochondrial matrix
Cytoplasm
ETC
Mitochondrial inner
membrane
Plasma membrane
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Carbohydrate Catabolism
 Energy produced from complete oxidation of one
glucose using aerobic respiration
ATP Produced
NADH
Produced
FADH2
Produced
Glycolysis
2
2
0
Intermediate step
0
2
0
Krebs cycle
2
6
2
Total
4
10
2
Pathway
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Carbohydrate Catabolism
 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
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Carbohydrate Catabolism
 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
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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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Table 5.4 Some Industrial Uses for Different Types of Fermentations*
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Figure 5.20 Lipid catabolism.
Lipase
Beta-oxidation
Krebs
cycle
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Figure 5.21 Catabolism of various organic food molecules.
Krebs
cycle
Electron
transport
chain and
chemiosmosis
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Protein Catabolism
Protein
Extracellular proteases
Deamination, decarboxylation,
dehydrogenation, desulfurization
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Amino acids
Organic acid
Krebs cycle
Figure 5.22 Detecting amino acid catabolizing enzymes in the lab.
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Figure 5.24 Use of peptone iron agar to detect the production of H2S.
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Protein Catabolism
Urea
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Urease
NH3 + CO2
Clinical Focus: Human Tuberculosis – Dallas, Texas
Figure B The urease test.
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Biochemical Tests
 Used to identify bacteria
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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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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
ANIMATION Photosynthesis: Overview
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Figure 4.15 Chromatophores.
Chromatophores
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Photosynthesis
 Oxygenic:
 Anoxygenic:
ANIMATION: Photosynthesis: Comparing Prokaryotes and Eukaryotes
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Figure 5.25a Photophosphorylation.
Electron
transport
chain
Light
Excited
electrons
Energy for
production
of ATP
Electron carrier
In Photosystem I
(a) Cyclic photophosphorylation
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Figure 5.25b Photophosphorylation.
Electron
transport
chain
Energy for
Light
production
Excited
of ATP
electrons
In Photosystem I
Light Excited
electrons
In Photosystem II
H+ + H+
1
2
(b) Noncyclic photophosphorylation
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Figure 5.26 A simplified version of the Calvin-Benson cycle.
Input
Ribulose diphosphate
3-phosphoglyceric acid
1,3-diphosphoglyceric acid
Calvin-Benson cycle
Glyceraldehyde
3-phosphate
Glyceraldehyde
3-phosphate
Output
Glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate
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Table 5.6 Photosynthesis Compared in Selected Eukaryotes and Prokaryotes
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Chemotrophs
 Use energy from chemicals
 Chemoheterotroph
Glucose
NAD+
ETC
Pyruvic acid
NADH
 Energy is used in anabolism
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ADP + P
ATP
Chemotrophs
 Use energy from chemicals
 Chemoautotroph, Thiobacillus ferrooxidans
2Fe2+
NAD+
ETC
2Fe3+
NADH
ADP + P
ATP
2 H+
 Energy is used in the Calvin-Benson cycle to fix CO2
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Phototrophs
 Use light energy
Chlorophyll
ETC
Chlorophyll
oxidized
ADP + P
ATP
 Photoautotrophs use energy in the Calvin-Benson
cycle to fix CO2
 Photoheterotrophs use energy
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Figure 5.27 Requirements of ATP production.
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Figure 5.28 A nutritional classification of organisms.
Light
Chemical
Organic compounds
O2
Not O2
Organic
Inorganic
compound
compound
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CO2
CO2
Organic compounds
Yes
No
Metabolic Diversity among Organisms
Nutritional Type
Photoautotroph
Energy Source
Light
Carbon Source
CO2
Example
Oxygenic:
Cyanobacteria, plants
Anoxygenic: Green
bacteria, purple
bacteria
Photoheterotroph
Light
Organic
compounds
Green bacteria, purple
nonsulfur bacteria
Chemoautotroph
Chemical
CO2
Iron-oxidizing
bacteria
Chemoheterotroph
Chemical
Organic
compounds
Fermentative bacteria
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Animals, protozoa,
fungi, bacteria
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.
Krebs
cycle
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Figure 5.31a The biosynthesis of amino acids.
Krebs
cycle
Amination or transamination
Amino acid biosynthesis
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Figure 5.31b The biosynthesis of amino acids.
Transamination
Glutamic acid Oxaloacetic
acid
Process of transamination
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α-Ketoglutaric
acid
Aspartic
acid
Figure 5.32 The biosynthesis of purine and pyrimidine nucleotides.
Krebs
cycle
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The Integration of Metabolism
 Amphibolic pathways: metabolic pathways that
have both catabolic and anabolic functions
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Figure 5.33 The integration of metabolism.
Krebs
cycle
CO2
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