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Microbiology Ch 05 lecture_presentation
1.
© 2015 Pearson
Education, Inc. Chapter 5
2.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • Metabolism • Collection of controlled biochemical reactions that take place within a microbe • Ultimate function of metabolism is to reproduce the organism
3.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • Metabolic Processes Guided by Eight Statements • Every cell acquires nutrients • Metabolism requires energy from light or catabolism of nutrients • Energy is stored in adenosine triphosphate (ATP) • Cells catabolize nutrients to form precursor metabolites • Precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions • Enzymes plus ATP form macromolecules • Cells grow by assembling macromolecules • Cells reproduce once they have doubled in size
4.
© 2015 Pearson
Education, Inc. Metabolism: Overview
5.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • Catabolism and Anabolism • Two major classes of metabolic reactions • Catabolic pathways • Break larger molecules into smaller products • Exergonic (release energy) • Anabolic pathways • Synthesize large molecules from the smaller products of catabolism • Endergonic (require more energy than they release)
6.
© 2015 Pearson
Education, Inc. Figure 5.1 Metabolism is composed of catabolic and anabolic reactions.
7.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • Oxidation and Reduction Reactions • Transfer of electrons from an electron donor to an electron acceptor • Reactions always occur simultaneously • Cells use electron carriers to carry electrons (often in H atoms) • Three important electron carriers • Nicotinamide adenine dinucleotide (NAD+) • Nicotinamide adenine dinucleotide phosphate (NADP+) • Flavin adenine dinucleotide (FAD)
8.
© 2015 Pearson
Education, Inc. Figure 5.2 Oxidation-reduction, or redox, reactions.
9.
© 2015 Pearson
Education, Inc. Oxidation-Reduction Reactions
10.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • ATP Production and Energy Storage • Organisms release energy from nutrients • Can be concentrated and stored in high-energy phosphate bonds (ATP) • Phosphorylation – inorganic phosphate is added to substrate • Cells phosphorylate ADP to ATP in three ways • Substrate-level phosphorylation • Oxidative phosphorylation • Photophosphorylation • Anabolic pathways use some energy of ATP by breaking a phosphate bond
11.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • The Roles of Enzymes in Metabolism • Enzymes are organic catalysts • Increase likelihood of a reaction
12.
© 2015 Pearson
Education, Inc. Enzymes: Overview
13.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • The Roles of Enzymes in Metabolism • Naming and classifying enzymes • Six categories of enzymes based on mode of action • Hydrolases • Isomerases • Ligases or polymerases • Lyases • Oxidoreductases • Transferases
14.
© 2015 Pearson
Education, Inc.
15.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • The Roles of Enzymes in Metabolism • The makeup of enzymes • Many protein enzymes are complete in themselves • Apoenzymes are inactive if not bound to nonprotein cofactors (inorganic ions or coenzymes) • Binding of apoenzyme and its cofactor(s) yields holoenzyme • Some are RNA molecules called ribozymes
16.
© 2015 Pearson
Education, Inc. Figure 5.3 Makeup of a holoenzyme. Inorganic cofactor Active site Coenzyme (organic cofactor) Apoenzyme (protein) Holoenzyme
17.
© 2015 Pearson
Education, Inc.
18.
© 2015 Pearson
Education, Inc. Figure 5.4 The effect of enzymes on chemical reactions. Reactants Activation energy without enzyme Activation energy with enzyme Products
19.
© 2015 Pearson
Education, Inc. Figure 5.5 Enzymes fitted to substrates. Active sites similar to substrate's shape Substrate Enzyme Enzyme-substrate complex; active sites become exact shape of substrate
20.
© 2015 Pearson
Education, Inc. 1 Enzyme- substrate complex Enzyme (Fructose-1,6- bisphosphate aldolase) Substrate (Fructose 1,6-bisphosphate) Dihydroxyacetone-PGlyceraldehyde-3P Products 2 3 4 Figure 5.6 The process of enzymatic activity.
21.
© 2015 Pearson
Education, Inc. Enzymes: Steps in a Reaction
22.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • The Roles of Enzymes in Metabolism • Enzyme activity • Many factors influence the rate of enzymatic reactions • Temperature • pH • Enzyme and substrate concentrations • Presence of inhibitors • Inhibitors block an enzyme's active site • Do not denature enzymes • Three types
23.
© 2015 Pearson
Education, Inc. Figure 5.7 Representative effects of temperature, pH, and substrate concentration on enzyme activity.
24.
© 2015 Pearson
Education, Inc. Figure 5.8 Denaturation of protein enzymes.
25.
© 2015 Pearson
Education, Inc. Competitive inhibitor Substrate Enzyme Reversible competitive inhibitor Substrate Increase in substrate concentration Enzyme Figure 5.9 Competitive inhibition of enzyme activity.
26.
© 2015 Pearson
Education, Inc. Enzymes: Competitive Inhibition
27.
© 2015 Pearson
Education, Inc. Active site Enzyme Allosteric site Allosteric (noncompetitive) inhibition Distorted, nonfunctional active site Allosteric inhibitor Distorted active site Substrate Active site becomes functional Allosteric activatorAllosteric site Allosteric activation Substrate Figure 5.10 Allosteric control of enzyme activity.
28.
© 2015 Pearson
Education, Inc. Enzyme-Substrate Interaction: Noncompetitive Inhibition
29.
© 2015 Pearson
Education, Inc. Figure 5.11 Feedback inhibition. Substrate Pathway shuts down Bound end-product (allosteric inhibitor) Enzyme 1 Allosteric site Pathway operates Feedback inhibition Intermediate A Enzyme 2 Intermediate B End-product Enzyme 3
30.
© 2015 Pearson
Education, Inc. Basic Chemical Reactions Underlying Metabolism • Tell Me Why • How can oxidation take place in an anaerobic environment, that is, without oxygen?
31.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Many organisms oxidize carbohydrates as primary energy source for anabolic reactions • Glucose is most common carbohydrate used • Glucose is catabolized by two processes • Cellular respiration • Fermentation
32.
© 2015 Pearson
Education, Inc. Glucose 2 Pyruvic acid Electrons KREBS CYCLE Acetyl-CoA Final electron acceptor Formation of fermentation end-products Pyruvic acid (or derivative) G L Y C O L Y S I S FermentationRespiration Figure 5.12 Summary of glucose catabolism.
33.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Glycolysis • Occurs in cytoplasm of most cells • Involves splitting of a six-carbon glucose into two three- carbon sugar molecules • Substrate-level phosphorylation – direct transfer of phosphate between two substrates • Net gain of two ATP molecules, two molecules of NADH, and precursor metabolite pyruvic acid
34.
© 2015 Pearson
Education, Inc. Glycolysis: Overview
35.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Glycolysis • Divided into three stages involving 10 total steps • Energy-investment stage • Lysis stage • Energy-conserving stage
36.
© 2015 Pearson
Education, Inc. Figure 5.13 Glycolysis.
37.
© 2015 Pearson
Education, Inc. Glycolysis: Steps
38.
© 2015 Pearson
Education, Inc. Figure 5.14 Example of substrate-level phosphorylation. Phosphoenolpyruvate (PEP) Holoenzyme Pyruvic acid Phosphorylation
39.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Cellular Respiration • Resultant pyruvic acid is completely oxidized to produce ATP by series of redox reactions • Three stages of cellular respiration 1. Synthesis of acetyl-CoA 2. Krebs cycle 3. Final series of redox reaction (electron transport chain)
40.
© 2015 Pearson
Education, Inc. Figure 5.15 Formation of acetyl-CoA.
41.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Cellular Respiration • Synthesis of acetyl-CoA • Results in • Two molecules of acetyl-CoA • Two molecules of CO2 • Two molecules of NADH
42.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Cellular Respiration • The Krebs cycle • Great amount of energy remains in bonds of acetyl-CoA • Transfers much of this energy to coenzymes NAD+ and FAD • Occurs in cytosol of prokaryotes and in matrix of mitochondria in eukaryotes
43.
© 2015 Pearson
Education, Inc. Carbohydrate Catabolism • Cellular Respiration • The Krebs cycle • Six types of reactions in Krebs cycle • Anabolism of citric acid • Isomerization • Redox reactions • Decarboxylations • Substrate-level phosphorylation • Hydration reaction
44.
© 2015 Pearson
Education, Inc. Figure 5.16 The Krebs cycle.
45.
© 2015 Pearson
Education, Inc. Krebs Cycle: Overview
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Education, Inc. Krebs Cycle: Steps
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Education, Inc. Carbohydrate Catabolism • Cellular Respiration • The Krebs cycle • Results in • Two molecules of ATP • Two molecules of FADH2 • Six molecules of NADH • Four molecules of CO2
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Education, Inc. Carbohydrate Catabolism • Cellular Respiration • Electron transport • Most significant production of ATP occurs from series of redox reactions known as an electron transport chain (ETC) • Series of carrier molecules that pass electrons from one to another to final electron acceptor • Energy from electrons is used to pump protons (H+) across the membrane, establishing a proton gradient • Located in cristae of eukaryotes and in cytoplasmic membrane of prokaryotes
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Education, Inc. Respiration Fermentation Path of electrons Final electron acceptor Figure 5.17 An electron transport chain.
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Education, Inc. Electron Transport Chain: Overview
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Education, Inc. Carbohydrate Catabolism • Cellular Respiration • Electron transport • Four categories of carrier molecules • Flavoproteins • Ubiquinones • Metal-containing proteins • Cytochromes • Aerobic respiration: oxygen serves as final electron acceptor • Anaerobic respiration: molecule other than oxygen serves as final electron acceptor
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Education, Inc. Figure 5.18 One possible arrangement of an electron transport chain. Bacterium Exterior Cytoplasmic membrane Intermembrane space Matrix Mitochondrion Cytoplasm Phospholipid membrane NADH from glycolysis, Krebs cycle, pentose phosphate pathway, and Entner-Doudoroff pathway FADH2 from Krebs cycle Cytoplasm of prokaryote or matrix of mitochondrion Exterior of prokaryote or intermembrane space of mitochondrion Ubiquinone FMN NADH FADH2 NAD+ Cyt c1 ATP synthase Cyt b H+ H+ 2 1 e– e– e– e– H+ H+ e– e– e– e– e– e– Cyt c Cyt a Cyt a3 H+ H+ e– e– H+ H+ 4 H+ H+ H+ H+ ADP 3 H2O ATP P+1/2 O2 H+ H+FAD + + H+
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Education, Inc. Electron Transport Chain: The Process
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Education, Inc. Electron Transport Chain: Factors Affecting ATP Yield
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Education, Inc. Carbohydrate Catabolism • Cellular Respiration • Chemiosmosis • Use of ion gradients to generate ATP • Cells use energy released in redox reactions of ETC to create proton gradient • Protons flow down electrochemical gradient through ATP synthases that phosphorylate ADP to ATP • Called oxidative phosphorylation because proton gradient is created by oxidation of components of ETC • Total of ~34 ATP molecules formed from one molecule of glucose
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Education, Inc.
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Education, Inc. Carbohydrate Catabolism • Alternatives to Glycolysis • Yield fewer molecules of ATP than does glycolysis • Reduce coenzymes and yield different metabolites needed in anabolic pathways • Two pathways • Pentose phosphate pathway • Entner-Doudoroff pathway
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Education, Inc. Figure 5.19 The pentose phosphate pathway.
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Education, Inc. Figure 5.20 Entner-Doudoroff pathway. Glucose Glucose 6-phosphate 6-Phosphogluconic acid 2-Keto-3-deoxy- 6-phosphogluconic acid Glyceraldehyde 3-phosphate (G3P) Pyruvic acid Pyruvic acid To Krebs cycle or fermentation Steps 6–10 of glycolysis
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Education, Inc. Carbohydrate Catabolism • Fermentation • Sometimes cells cannot completely oxidize glucose by cellular respiration • Cells require constant source of NAD+ • Cannot be obtained simply by using glycolysis and Krebs cycle • Fermentation pathways provide cells with alternative source of NAD+ • Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as final electron acceptor
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Education, Inc. Figure 5.21 Fermentation.
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Education, Inc. Figure 5.22 Representative fermentation products and the organisms that produce them.
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Education, Inc. Fermentation
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Education, Inc.
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Education, Inc. Carbohydrate Catabolism • Tell Me Why • Why do electrons carried by NADH allow for production of 50% more ATP molecules than do electrons carried by FADH2?
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Education, Inc. Other Catabolic Pathways • Lipids and proteins contain energy in their chemical bonds • Can be converted into precursor metabolites • Serve as substrates in glycolysis and the Krebs cycle
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Education, Inc. Figure 5.23 Catabolism of a fat molecule. Fatty acid chainsGlycerol Lipase 3 Glycerol + Fatty acids Hydrolysis DHAP To step 5 glycolysis Fatty acid To electron transport chain Acetyl-CoA To Krebs cycle Shorter fatty acid Beta-oxidation
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Education, Inc. Extracellular fluid Protease s Polypeptide Amino acids Cytoplasmic membrane Cytoplasm Deamination To Krebs cycle Figure 5.24 Protein catabolism.
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Education, Inc. Other Catabolic Pathways • Tell Me Why • Why does catabolism of amino acids for energy result in ammonia and other nitrogenous wastes?
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Education, Inc. Photosynthesis • Many organisms synthesize their own organic molecules from inorganic carbon dioxide • Most of these organisms capture light energy and use it to synthesize carbohydrates from CO2 and H2O by a process called photosynthesis
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Education, Inc. Photosynthesis: Overview
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Education, Inc. Metabolism
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Education, Inc. Photosynthesis • Chemicals and Structures • Chlorophylls • Type of pigment molecule that photosynthetic organisms use to capture light energy • Composed of hydrocarbon tail attached to light-absorbing active site centered on magnesium ion • Active sites are structurally similar to cytochrome molecules in ETC • Structural differences cause absorption at different wavelengths
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Education, Inc. Photosynthesis • Chemicals and Structures • Photosystems • Arrangement of molecules of chlorophyll and other pigments to form light-harvesting matrices • Embedded in cellular membranes called thylakoids • In prokaryotes – invagination of cytoplasmic membrane • In eukaryotes – formed from inner membrane of chloroplasts • Arranged in stacks called grana • Stroma is space between outer membrane of granum and thylakoid membrane
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Education, Inc. Figure 5.25 Photosynthetic structures in a prokaryote. Photosystem embedded in membrane (sectioned) Chlorophyll Thylakoid membrane Active site Tail (carbon chain) Thylakoid
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Education, Inc. Photosynthesis • Chemicals and Structures • Two types of photosystems • Photosystem I (PS I) • Photosystem II (PS II) • Photosystems absorb light energy and use redox reactions to store energy in the form of ATP and NADPH • Light-dependent reactions depend on light energy • Light-independent reactions synthesize glucose from carbon dioxide and water
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Education, Inc. Photosynthesis • Light-Dependent Reactions • As electrons move down the chain, their energy is used to pump protons across the membrane • Photophosphorylation uses proton motive force to generate ATP • Photophosphorylation can be cyclic or noncyclic
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Education, Inc. Acceptor Light Reaction center chlorophyll Possible path of energy transfer Photosystem: reaction center Figure 5.26 Reaction center of a photosystem.
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Education, Inc. Exterior of prokaryote or thylakoid space of chloroplast Cyclic photophosphorylation Cytochromes Cu Photosystem I Fe Reaction center Light Cytoplasm of prokaryote or stroma of chloroplast ATP synthase Membrane of prokaryote or of thylakoid in chloroplast Membrane of prokaryote or of thylakoid in chloroplast ATP synthase Photosystem I Cytochromes Fe Light Cytoplasm of prokaryote or stroma of chloroplast Light Quinone Reaction center Reaction center Cu Noncyclic photophosphorylation Exterior of prokaryote or thylakoid space of chloroplast To Calvin-Benson cycle NADPase Photosystem II Figure 5.27 The light-dependent reactions of photosynthesis: Cyclic and noncyclic photophosphorylation.
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Education, Inc. Photosynthesis: Light Reaction: Cyclic Photophosphorylation
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Education, Inc. Photosynthesis: Light Reaction: Noncyclic Photophosphorylation
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Education, Inc.
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Education, Inc. Photosynthesis • Light-Independent Reactions • Do not require light directly • Use ATP and NADPH generated by light-dependent reactions • Key reaction is carbon fixation by Calvin-Benson cycle • Three steps • Fixation of CO2 • Reduction • Regeneration of RuBP
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Education, Inc. Figure 5.28 Simplified diagram of the Calvin-Benson cycle.
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Education, Inc. Photosynthesis: Light-Independent Reaction
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Education, Inc. Photosynthesis • Tell Me Why • An uninformed student describes the Calvin-Benson cycle as "cellular respiration in reverse." Why is this student incorrect?
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Education, Inc. Other Anabolic Pathways • Anabolic reactions are synthesis reactions requiring energy and a source of precursor metabolites • Energy derived from ATP from catabolic reactions • Many anabolic pathways are the reverse of catabolic pathways • Reactions that can proceed in either direction are amphibolic
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Education, Inc.
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Education, Inc. Figure 5.29 The role of gluconeogenesis in the biosynthesis of complex carbohydrates.
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Education, Inc. Figure 5.30 Biosynthesis of fat, a lipid.
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Education, Inc. Figure 5.31 Examples of the synthesis of amino acids via amination and transamination.
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Education, Inc. Figure 5.32 The biosynthesis of nucleotides.
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Education, Inc. Other Anabolic Pathways • Tell Me Why • Why is nitrogen required for the production of amino acids by amination?
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Education, Inc. Integration and Regulation of Metabolic Function • Cells synthesize or degrade channel and transport proteins • Cells often synthesize enzymes only when substrate is available • Cells catabolize the more energy-efficient choice if two energy sources are available • Cells synthesize metabolites they need, cease synthesis if metabolite is available
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Education, Inc. Integration and Regulation of Metabolic Function • Eukaryotic cells isolate enzymes of different metabolic pathways within membrane-bounded organelles • Cells use allosteric sites on enzymes to control activity of enzymes • Feedback inhibition slows/stops anabolic pathways when product is in abundance • Cells regulate amphibolic pathways by requiring different coenzymes for each pathway
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Education, Inc. Integration and Regulation of Metabolic Function • Two types of regulatory mechanisms • Control of gene expression • Cells control amount and timing of protein (enzyme) production • Control of metabolic expression • Cells control activity of proteins (enzymes) once produced
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Education, Inc. Integration and Regulation of Metabolic Function • Tell Me Why • Why is feedback inhibition necessary for controlling anabolic pathways?
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Education, Inc. Figure 5.33 Integration of cellular metabolism (shown in an aerobic organism).
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Education, Inc. Metabolism: The Big Picture
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Education, Inc. Important topics • Chloroplast – Structure – Function • Photosynthesis vs. Calvin-Benson cycle • Gluconeogenesis • ETC (Electron Transport Chain)
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