Metabolism. Topic 11&12 (ch8) Microbial Metabolism. Metabolic Balancing Act. Topics. Catabolism Anabolism Enzymes
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1 Topic 11&12 (ch8) Microbial Metabolism Topics Metabolism Energy Pathways Biosynthesis 1 Catabolism Anabolism Enzymes Metabolism 2 Metabolic Balancing Act Catabolism Enzymes involved in breakdown of complex organic molecules to extract energy and form simpler end products Anabolism Enzymes involved in the use of energy from catabolism to synthesize macromolecules and cell structures from precursors (simpler products) 3 1
2 Catabolism and Anabolism Simple Model 4 Energy to Drive Cellular Work Energy released from dephosphorylation of ATP drives cellular work, including anabolic pathways. ATP is regenerated through phosphorylation, harnessing the energy found in chemicals or from sunlight. (credit: modification of work by Robert Bear, David Rintoul) 5 Enzymes what are they? Function Structure Enzyme-substrate interaction Cofactors Action Regulation 6 2
3 Enzyme are Made of Many protein enzymes are complete without additions Apoenzymes are inactive if not bound to non-protein cofactors (inorganic ions or coenzymes) Binding of apoenzyme and its cofactor(s) yields holoenzyme Some are RNA molecules called ribozymes 7 Enzymes in 3D Essential to Function! 8 Cofactors Bind to and activate the enzyme Ex. Metallic cofactors Iron, copper, magnesium Coenzymes 9 3
4 Coenzyme Transient carrier - alter a substrate by removing a chemical group from one substrate and adding it to another substrate Ex. vitamins 10 Types of Enzyme (Based on Structure) Simple enzyme protein alone Conjugated enzyme protein and nonprotein Three-dimensional features Enable specificity Active site or catalytic site 11 A Conjugated Protein Enzyme 12 4
5 Another Example of Conjugated Enzymes 13 Enzyme Function What can they do? Catalysts for chemical reactions Lower the energy of activation 14 What Affects Enzymes? 15 5
6 Unfolding Kills Enzymes 16 Enzyme-substrate Interactions Substrates specifically bind to the active sites on the enzyme, possibilities: Induced fit lock-and-key (next slide) When the reaction is complete, product is released, enzyme reused 17 Lock-and-key Model, Cannot Induce Fit 18 6
7 Enzyme Activity Interfered ( or Controlled) Competitive = binds/blocks substrate site Noncompetitive = binds other place that distorts the regular binding site 19 Binding Can Control Enzyme Activity - Feedback Regulation Bind Allosteric Inhibitor = decrease enzyme activity Bind Allosteric Activator = increase enzyme activity What s going on? 20 Apoenzyme Becoming Holoenzyme Sperm zinc / motility example 21 7
8 Example: Coenzyme Transfers Chemical Groups Between Substrates 22 Enzyme Actions and Reactions Exoenzymes Endoenzymes Constitutive Induction or repression Types of reactions 23 Exoenzymes vs. Endoenzymes Exoenzymes - inactive inside the cell, active after release. Endoenzymes remain in the cell and are active 24 8
9 Constitiutive and Regulated Enzymes Constitutive enzymespresent in constant amounts Regulated enzymes are either induced or repressed. 25 So Many Reactions! Arghhh! 26 Saved! Only 3 Reaction Types! Condensation (associated with anabolic reactions) Hydrolysis (associated with catabolic reactions) Transfer reactions 27 9
10 Enzyme-catalyzed Synthesis And Hydrolysis Reactions 28 Transfer Reactions Transfer of electrons from one substrate to another Oxidation (add O 2 to a compound with a loss of electrons, increase charge) Reduction (add e - to a compound, decrease charge) Oxidoreductase Transfer of functional groups from one molecule to another Transferases Aminotransferases 29 How To Remember Re-Dox? LEO goes GER Losing Electrons is Oxidation Gaining Electrons is Reduction Image from
11 Example Oxidoreductase, Transferase, And Hydrolytic Enzymes 31 Enzyme Regulation Mess With The Substrate Binding Site! Bind Allosteric Inhibitor = decrease enzyme activity Bind Allosteric Activator = increase enzyme activity Feedback can be positive or negative! 32 Enzymes Can Also Be Regulated Via: Metabolic pathway manipulation Direct control Genetic control 33 11
12 Patterns Of Metabolism Different metabolic pathways are regulated by the enzymes that catalyze the reactions. 34 Two Common Direct Control Mechanisms- Competitive And Noncompetitive Inhibitions 35 Another Example of Feedback Inhibition Metabolic Diseases 36 12
13 Genetic Control Repression Induction 37 Energy Cell energetics Exergonic Endergonic Redox reaction (change in oxidation number) Electron carrier Adenosine Triphosphate (ATP) 38 Endergonic (in) vs Exergonic (out) 39 13
14 Cell Energy Model (Simplified) 40 Redox Reaction (again) Reduction and oxidation reaction (LEO goes GER): Oxidation: loss of electrons, or gain of oxygen, gives increase in oxidation number. Reduction: gain of electrons, or loss of oxygen, gives decrease in oxidation number. Electron carriers transfer electrons and hydrogens Electron donor Electron acceptor Energy is also transferred and captured by the phosphate in form of ATP 41 Electron Carriers Coenzymes Nicotinamide adenine dinucleotide (NAD) Respiratory chain carriers Cytochromes (protein) 42 14
15 NAD Reduction simple annotated 43 Adenosine Triphosphate (ATP - $$!) Temporary energy repository - energy storage! Break phosphates bonds to release free energy Three part molecule: Nitrogen base 5-carbon sugar (ribose) Chain of phosphates 44 AMP grows to ATP, each stage higher in energy 45 15
16 Carbohydrates Most Important Many organisms oxidize carbohydrates as primary energy source for anabolic reactions Glucose most common carbohydrate used Glucose catabolized by two processes: Cellular respiration Fermentation 46 Phosphorylation of Glucose by ATP Make Glucose 6P from ATP Make ATP from TCA Glycolysis (Glucose intermediate) ATP can phosphorylate an organic molecule like glucose during catabolism 47 ATP Can Be Synthesized By Substrate-level Phosphorylation 48 16
17 Various Pathways To Get Energy And Make Products Catabolism Embden-Meyerhof-Parnas (EMP) pathway or glycolysis Tricarboxylic acid cycle (TCA) Respiratory chain Aerobic Anaerobic Alternate pathways Fermentation 49 Metabolism Summary of Glucose and Energy 50 Aerobic Respiration (O 2 ) Three stages: Glycolysis Tricarboxylic acid (TCA) Electron transport 51 17
18 Basics of Glycolysis In cytoplasm for most cells Divided into three stages involving 10 total steps Energy-investment stage Lysis stage Energy-conserving stage (cont. next slide) 52 Basics of Glycolysis In cytoplasm for most cells Oxidation of glucose Phosphorylation of some intermediates (Uses two ATPs) Splits a 6 carbon sugar into two 3 carbon molecules Coenzyme NAD is reduced to NADH Substrate-level-phosphorylation (Four ATPs are synthesized) 53 (cont. next slide) Basic of Glycolysis (continued) Water is generated Net yield of 2 ATPs Final intermediates are two Pyruvic acid molecules (notice that it require 2 different, parallel pathways to finally generate both pyruvic acid molecules ) 54 18
19 Glycolysis Overview 55 Glycolytic Steps: Metabolism of Glucose to 2 Pyruvic Acid molecules (pyruvate) 56 TCA Cycle Each pyruvic acid is processed to enter the TCA cycle (two complete cycles) CO 2 is generated Coenzymes NAD and FAD are reduced to NADH and FADH 2 Net yield of two ATPs Critical intermediates are synthesized 57 19
20 Some Krebs Intermediates Make Other Molecules 58 TCA Cycle Steps Each cycle handles one 3 carbon molecule. This means it takes two cycles to burn up one 6 carbon glucose molecule. 59 Electron Transport NADH and FADH 2 donate electrons to the electron carriers Membrane bound carriers transfer electrons (redox reactions) The final electron acceptor completes the terminal step (ex. Oxygen) 60 20
21 Electron Transport (continued) Driven by: Chemiosmosis Proton motive force (PMF) 61 e - Transport 62 Chemiosmosis and the electron transport system, with oxidative phosphorylation e- transport and formation of a proton gradient 63 21
22 ATP Synthase Spans Membrane H + flows down electrochemical gradient, provides energy for ATP production by oxidative phosphorylation. (credit: modification of work by Klaus Hoffmeier) Which membrane? Same for Eukaryotes AND Prokaryotes? 64 Electron Transport Chain Locations Eukaryotes mitochondria Prokaryotes Cytoplasmic membrane 65 ATP Yield: One Glucose Molecule, Aerobic Respiration 66 22
23 Anaerobic respiration (No O 2 ) Similar to aerobic respiration, except nitrate or nitrite is the final electron acceptor 67 Fermentation Glycolysis only NADH from glycolysis is used to reduce the organic products Organic compounds as the final electron acceptors ATP yields are small (per glucose molecule), compared to respiration Must metabolize large amounts of glucose to produce equivalent respiratory ATPs 68 Types Of Fermenters Facultative anaerobes Fermentation in the absence of oxygen Respiration in the presence of oxygen Ex. Escherichia coli Strict fermenters No respiration Ex. yeast 69 23
24 Why Fermentation? Sometimes cells cannot completely oxidize glucose by cellular respiration Cells require constant source of NAD + Cannot be obtained simply using glycolysis and Krebs cycle Fermentation pathways provide cells with alternate 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 70 So Many Products Of Different Fermentations! Alcoholic fermentation Acidic fermentation Mixed acid fermentation 71 Fermentation Of Ethyl Alcohol And Lactic Acid 72 24
25 Pyruvate Mixed Acid Fermentation - Diverse Products! 73 Some Fermentation Products 74 Respiration Comparison 75 25
26 Biosynthesis Anabolism Amphibolic ( ) Gluconeogenesis Beta oxidation Amination Transamination Deamination Macromolecules 76 Amphibolic Integration of the catabolic and anabolic pathways Intermediates serve multiple purposes 77 Overview Of Anabolic And Catabolic Relationships 78 26
27 Gluconeogenesis Pyruvate (intermediate) converts to glucose Occurs when the glucose supply is low 79 Gluconeogenesis 80 Beta Oxidation Or How To Get That Energy Back Out Of Fat! Metabolism of fatty acids into acetyl- CoA Krebs (TCA cycle) 4 steps: Oxidation by FAD Hydation of C2=C3 bond Oxidation by NAD + Thiol cleavage at C2-C3 Acetyl-CoA 81 27
28 Example Production And Conversion Of Amino Acids: Amination, Transamination, Deamination 82 Fitting Cellular Together 83 The Big Picture 84 28
29 Macromolecules Cellular building blocks Monosaccharides Amino acids Fatty acids Nitrogen bases Vitamins 85 Photosynthesis Free Power! 6H2O + 6CO2 C6H12O6+ 6O2 2 independent reactions in the chloroplast 86 So Humans vs Plants! Plants: 6H 2 O + 6CO 2 C 6 H 12 O 6 + 6O 2 Humans: 6O 2 + C 6 H 12 O 6 6 H 2 O + 6 CO
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