Anabolism: - synthesis of molecules, requires the input of energy. Catabolism: - breaks the bonds of larger molecules, releases energy

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Oswin Freeman
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Metabolism Metabolism in bacteria is similar to that in eukaryotes.

owever, bacteria also have unique enzymes that allow them to adapt to many niches. ow do horses and cows digest cellulose? ow do bacteria live at the depths of the ocean?

Metabolism Metabolism: pertains to all chemical reactions and physical workings of the cell Anabolism: - synthesis of molecules, requires the input of energy Catabolism: - breaks the bonds of larger

Directly related to oxidation & reduction (remember those redox reactions from chemistry?

1 Metabolism Metabolism in bacteria is similar to that in eukaryotes. Some bacterial enzymes (especially metabolic enzymes, like oxidase) can be interchanged with human enzymes in laboratory experiments. owever, bacteria also have unique enzymes that allow them to adapt to many niches. ow do horses and cows digest cellulose? ow do bacteria live at the depths of the ocean? They have special enzymes which have been adapted for specific environments. Metabolism Metabolism: pertains to all chemical reactions and physical workings of the cell Anabolism: - synthesis of molecules, requires the input of energy Catabolism: - breaks the bonds of larger molecules, releases energy All Catabolic reactions involve electron transfer Electron transfer: allows energy to be captured in high energy bonds in and similar molceules. Directly related to oxidation & reduction (remember those redox reactions from chemistry?) xidation=loss of electrons Reduction=gain of electrons Imagine A=organic molecule like glucose Imagine B=AD+ coenzyme, an electron carrier 3 Relative complexity of molecules Simplified Model of Metabolism Copyright The McGraw-ill Companies, Inc. ermission required for reproduction or display. AABLISM Bacterial Glu cell AABLISM Macromolecules CATABLISM AABLISM roteins Building blocks eptidoglycan utrients from recursor RA + DA outside molecules Amino acids or from Complex lipids Sugars internal pathways cycle ucleotides Respiratory Acetyl CoA chain Fatty acids Glyceraldehyde-3- Some assembly reactions occur spontaneously Yields energy Uses energy Uses energy Uses energy ow do chemical reactions take place? In order for bonds to be FRMED or BRKE, there has to be a minimal amount of energy available. This minimal amount of energy is termed activation energy. ow do chemical reactions take place? Activation energy can be in the form of temperature or pressure, etc. to increase the number of particle collisions. aradoxically, the temperature and pressure that humans and bacteria would require for their chemical reactions would KILL them! 5 ow do we solve this problem? EZYMES!! Enzymes reduce the amount of activation energy needed for chemical reactions and speed them up so that life can continue. 1

Enzymes Specific active sites arise due to the folding of the protein Enzymes have specific active sites that bind to specific substrates.

- the number of substrate molecules converted per enzyme per second - Catalase reacts several million times per second - lactate dehydrogenase reacts a thousand times per

released and the enzyme reused Lock-andkey model Induced fit model Enzyme Substrate Reactions 9 Cofactors Coenzymes The need of microorganisms for trace elements arises

articipate in precise functions between the enzyme and substrate - help bring the active site and substrate close together - participate directly in chemical reactions

2 Enzymes Specific active sites arise due to the folding of the protein Enzymes have specific active sites that bind to specific substrates. Bond formed between the substrate and enzyme are weak and easily reversible Enzyme are fast! - the number of substrate molecules converted per enzyme per second - Catalase reacts several million times per second - lactate dehydrogenase reacts a thousand times per second Enzyme substrate interactions Substrates specifically bind to the active sites on the enzyme lock and key Induced fit nce the reaction is complete, the product is released and the enzyme reused Lock-andkey model Induced fit model Enzyme Substrate Reactions 9 Cofactors Coenzymes The need of microorganisms for trace elements arises from their roles as cofactors for enzymes - iron, copper, magnesium, manganese, zinc, cobalt, selenium, etc. articipate in precise functions between the enzyme and substrate - help bring the active site and substrate close together - participate directly in chemical reactions with the enzyme substrate complex Metallic cofactor - organic compounds that work in conjunction with an enzyme - general function is to remove a chemical group from one substrate molecule and add it to another substrate molecule - carry and transfer hydrogen atoms, electrons, carbon dioxide, and amino groups - many derived from vitamins Coenzyme 2

Apoenzyme The main enzyme portion is a globular protein called an apoenzyme Example of how a

Regulation of Enzymes Constitutive enzymes: always present in relatively constant amounts

or turned off (repressed) in responses to changes in concentration of the substrate

lactose into glucose and galactose If E.

3 Apoenzyme The main enzyme portion is a globular protein called an apoenzyme Example of how a coenzyme transfers chemical groups from one substrate to another Regulation of Enzymes Regulation of Enzymes Constitutive enzymes: always present in relatively constant amounts regardless of the amount of substrate Regulated enzymes: production is turned on (induced) or turned off (repressed) in responses to changes in concentration of the substrate Regulation of Enzymes ne type of genetic control of enzyme synthesis Enzyme Induction in E. coli If E. coli is inoculated with only lactose, it will produce the enzyme lactase to hydrolyze the lactose into glucose and galactose If E. coli is inoculated with only sucrose, it will cease to synthesizing lactase and begin synthesizing sucrase Benefits: Allows the organism to utilize a variety of nutrients revents wasting energy by making enzymes for a substrate that is not present 3

Regulation of Enzyme Function Inhibition of Enzymes Activity of enzymes influenced by the cell s environment atural

Competitive inhibition - inhibits enzyme activity by supplying a molecule that resembles the enzyme s normal

Metabolic athways oncompetitive inhibition oncompetitive inhibitors bind to an allosteric or other site on the

ften occur in a multistep series or pathway, with each step catalyzed by an enzyme roduct of one reaction is often

athways Metabolic athways Many pathways have braches that provide alternate methods for nutrient processing Branched

4 Regulation of Enzyme Function Inhibition of Enzymes Activity of enzymes influenced by the cell s environment atural temperature, p, osmotic pressure Denaturation: weak bonds that maintain the native shape of the enzyme are broken Competitive inhibition - inhibits enzyme activity by supplying a molecule that resembles the enzyme s normal substrate - mimic occupies the active site, preventing the actual substrate from binding Inhibition of Enzymes Metabolic athways oncompetitive inhibition oncompetitive inhibitors bind to an allosteric or other site on the enzyme, not the active site. ften occur in a multistep series or pathway, with each step catalyzed by an enzyme roduct of one reaction is often the reactant (substrate) for the next, forming a linear chain or reaction Linear A B C D E Example: Metabolic athways Metabolic athways Many pathways have braches that provide alternate methods for nutrient processing Branched Divergent Convergent 1 2 M Q R A B C M X Y Z Example: Amino acid synthesis ther pathways have a cyclic form, in which the starting molecule is regenerated to initiate another turn of the cycle Cyclic V T input S product Z W Y X U 4

Metabolic athways xidation and Reduction Chromosomes Enzymes/ Membranes Cell wall storage Membranes storage Cell structure xidation: loss of electrons Metabolic pathways do not stand alone; they are

acid Acetyl coenzymea Macromolecule Building block Metabolic pathways Simple pathways Reduction: gain of electrons xidoreductases: enzymes that remove electrons from one substrate and add them to

5 Metabolic athways xidation and Reduction Chromosomes Enzymes/ Membranes Cell wall storage Membranes storage Cell structure xidation: loss of electrons Metabolic pathways do not stand alone; they are interconnected and merge at many sites CATABLISM AABLISM ucleic acids ucleotides roteins Amino acids Deamination Starch/ Lipids/ Cellulose Fats Carbohydrates Fatty acids Beta oxidation GLUCSE yruvic acid Acetyl coenzymea Macromolecule Building block Metabolic pathways Simple pathways Reduction: gain of electrons xidoreductases: enzymes that remove electrons from one substrate and add them to another - their coenzyme carriers are nicotinamide adenine dinucleotide (AD) and flavin adenine dinucleotide (FAD) a Cl Reducing agent gives up electrons. + xidizing agent accepts electrons. a 2 8 Cl xidized cation Reduced anion xidation and Reduction Adenosine Triphosphate Energy present in the electron acceptor can be captured to phosphorylate to AD to store energy in Three part molecule - nitrogen base (adenine) - 5 carbon sugar (ribose) - chain of three phosphate groups bonded to ribose - phosphate groups are bulky and carry negative charges, causing a strain between the last two phosphates making it very volatile Adenosine Adenosine Triphosphate Diphosphate () (AD) Bond that releases energy when broken Adenosine Ribose Adenine and hosphorylation can be used to phosphorylate an organic molecule Ex. hosphorylation of glucose to activate its catabolism Electron Carriers: Cell s Reducing ower Electron carriers resemble shuttles that load and unload, electrons and hydrogens to facilitate transfer of redox energy electrons available in AD and FAD 2 Copyright The McGraw-ill Companies, Inc. ermission required for reproduction or display. AD+ xidized icotinamide C C C C 2 C C Adenine Ribose From substrate 2 2e: + Reduced icotinamide C C C C 2 C C 5

Yields 2 s Yields 2 GTs Yields variable amount of energy Maximum net yield verview of the Three Main Aerobic Respiration: verview - a series of reactions that Catabolic athways converts glucose to

36 s FERMETATI Using organic compounds as electron acceptor Alcohols, acids 2 s allows the cell to recover significant amounts of energy - Complete breakdown of pyruvic acid into inorganic molecules

6 Yields 2 s Yields 2 GTs Yields variable amount of energy Maximum net yield verview of the Three Main Aerobic Respiration: verview - a series of reactions that Catabolic athways converts glucose to and AERBIC RESIRATI FAD 2 Electron Transport System s AAERBIC RESIRATI FAD 2 Electron Transport System Using 2 as electron acceptor Using non- 2 compound as electron acceptor (So 2 4, 3, 3 ) 2 36 s FERMETATI Using organic compounds as electron acceptor Alcohols, acids 2 s allows the cell to recover significant amounts of energy - Complete breakdown of pyruvic acid into inorganic molecules - relies on free oxygen as the final electron - characteristic of many bacteria, fungi, protozoa, and animals Maximum net yield FAD 2 Electron Transport System s Using 2 as electron acceptor Anaerobic Respiration: verview - uses 3, S 2 4, C 3 3, and other oxidized compounds as final electron acceptors - Like aerobic respiration there is a complete breakdown of pyruvic acid into inorganicmolecules - Unlike aerobic respiration, anaerobic respiration does not use all of the steps in the Kreb s cycle. - characteristic of bacteria that require or tolerate anaerobic conditions Maximum net yield FAD 2 Electron Transport System Using non- 2 compound as electron acceptor (So 2 4, 3, 3 ) 2 36 s : verview Unlike aerobic and anaerobic respiration pyruvic acid is not a completely broken down into inorganic molecules yruvic acid is partially broken down into organic compounds that are the final electron acceptors. Ex. lactic acid, ethanol oxygen is not required Maximum net yield Using organic compounds as electron acceptor Alcohols, acids 2 s xidation of glucose into pyruvate, which yields energy in the pathways that follow ccurs in cytoplasm of both eukaryotes and prokaryotes Does this go against the Endosymbiotic theory? The roduces 2 for each molecule of glucose urpose is to produce AD and FAD 2 to be fed into the ETC ccurs in the cytoplasm of bacteria and in the mitochondrial matrix of eukaryotes Table 7.2 Energy Lost or Gained verview Details Table 7.3 The Uses 2 s Energy Lost or Gained verview Details Fructose-1, 6-diphosphate Three reactions alter and rearrange the 6-C glucose molecule into 6-C fructose-1,6 diphosphate. ne is liberated and one AD is formed. C C C C C C The 3C pyruvate is converted to 2C acetyl CoA in one reaction. Yields 4 s and 2 ADs Total Energy Yield: 2 s and 2 ADs is a molecule that is uniquely suited for chemical reactions that will produce reducing power (which will eventually produce ). ne reaction breaks fructose-1,6-diphosphate into two 3-carbon molecules. Five reactions convert each 3 carbon molecule into the 3C pyruvate. Each acetyl CoA yields 1 GT, 3 ADs, 1 FAD, and 2 molecules. Total Yield per 2 acetyl CoAs: : 4 Energy: 2 GTs, 6 ADs, 2 FADs Acetyl CoA xaloacetate C C C C C C Yields: 3 ADs 1 FAD 2 ther intermediates Remember: This happens twice for each glucose molecule that enters glycolysis. Citrate GT In the first reaction, acetyl CoA donates 2Cs to the 4C molecule oxaloacetate to form 6C citrate. In the course of seven more reactions, citrate is manipulated to yield energy and and oxaloacetate is regenerated. Intermediate molecules on the wheel can be shunted into other metabolic pathways as well. 6

and the cycle Cell wall Cell membrane With ETS Cytochromes Cytoplasm + synthase AD 2 S 2 4 3 2 2 S - passes them in a sequential and orderly fashion from one to the next - highly energetic - allows

in the cell membrane in prokaryotes and on the inner mitochondrial membrane in eukaryotes Aerobic respirers Anaerobic respirers Electron Transport Chain Released energy from electron carriers in the

7 Table 7.4 Electron Transport Chain The Respiratory (Electron Transport) Chain Electron Transport Chain A chain of special redox carriers that receives reduced carriers (AD, FAD 2 ) generated by glycolysis and the cycle Cell wall Cell membrane With ETS Cytochromes Cytoplasm + synthase AD 2 S S - passes them in a sequential and orderly fashion from one to the next - highly energetic - allows the transport of hydrogen ions outside of the membrane - in the final step of the process, oxygen accepts electrons and hydrogen, forming water - Electron transport carriers and enzymes are embedded in the cell membrane in prokaryotes and on the inner mitochondrial membrane in eukaryotes Aerobic respirers Anaerobic respirers Electron Transport Chain Released energy from electron carriers in the electron transport chain is channeled through synthase xidative phosphorylation: the coupling of synthesis to electron transport - each AD that enters the electron transport chain can give rise to 3 s Final Electron Acceptor: Aerobic Respiration - electrons from cytochrome c, and from solution react with oxygen to form water 2 + 2e + ½ Electrons from FAD 2 enter the electron transport chain at a later point and have less energy to release, so only 2 s result Final Electron Acceptor: Aerobic Respiration Most eukaryotes have a fully functioning cytochrome system Bacteria exhibit wide ranging variations in this system - some lack one or more redox steps - several have alternative electron transport schemes - lack of cytochrome c oxidase is useful in differentiating among certain genera of bacteria (we will do this with MM) Final Electron Acceptor: Anaerobic Respiration Utilizes oxygen containing ions, rather than free oxygen, as the final electron acceptor Ex. itrate reductase 3 + AD AD + itrate reductase catalyzes the removal of oxygen from nitrate, leaving nitrite and water as products 7

- the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen Table 7.

production of electron transport chain proteins when oxygen is lacking in their environment to revert to fermentation C C C yruvic acid C C Acetaldehyde AD + C C Ethyl alcohol Remember: This happens

8 - the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen Table uses organic compounds as the terminal electron acceptors - Yields 2 s per molecule of glucose - Used by organisms that do not have an electron transport chain - ther organisms repress the production of electron transport chain proteins when oxygen is lacking in their environment to revert to fermentation C C C yruvic acid C C Acetaldehyde AD + C C Ethyl alcohol Remember: This happens twice for each glucose molecule that enters glycolysis. C C C Lactic acid yruvic acid from glycolysis can itself become the electron acceptor. yruvic acid can also be enzymatically altered and then serve as the electron acceptor. The ADs are recycled to reenter glycolysis. The organic molecules that became reduced in their role as electron acceptors are extremely varied, and often yield useful products such as ethyl alcohol, lactic acid, propionic acid, butanol, and others. - Many bacteria grow as fast as they would in the presence of oxygen due to an increase in the rate of glycolysis ermits independence from molecular oxygen - allows colonization of anaerobic environments - enables adaptation to variations in oxygen availability - provides a means for growth when oxygen levels are too low for aerobic respiration Bacteria and ruminant cattle - digest cellulose through fermentation - hydrolyze cellulose to glucose - ferment glucose to organic acids which are absorbed as the bovine s principal energy source Final Electron Acceptor: - Uses organic compounds as the terminal electron acceptors roducts: Alcoholic beverages: ethanol and Solvents: acetone, butanol rganic acids: lactic acid, acetic acid Vitamins, antibiotics, and hormones The Crossing athways of Metabolism The Frugality of the Cell - cells have systems for careful management of carbon compounds Chromosomes ucleic acids Enzymes/ Membranes roteins Cell wall storage Starch/ Cellulose Membranes storage Lipids/ Fats Cell structure Macromolecule - catabolic pathways contain strategic molecular intermediates (metabolites) that can be diverted into anabolic pathways ucleotides Amino acids Deamination Carbohydrates GLUCSE Fatty acids Beta oxidation Building block Metabolic pathways - a given molecule can serve multiple purposes; maximum benefit can be derived from all nutrients and metabolites of the cell pool yruvic acid Acetyl coenzymea 3 2 Simple pathways 8

Anabolism: - synthesis of molecules, requires the input of energy. Catabolism: - breaks the bonds of larger molecules, releases energy

Anabolism: - synthesis of molecules, requires the input of energy. Catabolism: - breaks the bonds of larger molecules, releases energy Metabolism Metabolism in bacteria is similar to that in eukaryotes. Some bacterial enzymes (especially metabolic enzymes, like oxidase) can be interchanged with human enzymes in laboratory experiments.