Learning Outcomes: Section 7.11. Describe the relationship among metabolism, catabolism, and anabolism.2. Fully define the structure and function of enzymes.3. Differentiate between constitutive and regulated enzymes.4. Diagram some different patterns of metabolism.5. Describe how enzymes are controlled.
Metabolism and the Role of Enzymes•Metabolism: pertains to all chemical reactions and physicalworkings of the cell•Anabolism: -a building and bond-making process that forms larger macromolecules from smaller ones -requires the input of energy (ATP)•Catabolism: -breaks the bonds of larger molecules into smaller molecules -releases energy (used to form ATP)
Enzymes: Catalyzing the Chemical Reactions ofLife•Enzymes -are catalysts that increase the rate of chemical reactions without becoming part of the products or being consumed in the reaction -substrates: reactant molecules acted on by an enzyme -Have unique active site on the enzyme that fits only the substrate
Enzyme Structure•Simple enzymes consist of protein alone•Conjugated enzymes contain protein and nonproteinmolecules -sometimes referred to as a holoenzyme -apoenzyme: protein portion of a conjugated enzyme -cofactors: inorganic elements (metal ions) -coenzymes: organic cofactor molecules
Enzyme-Substrate Interactions•A temporary enzyme-substrate union must occur at theactive site -fit is so specific that it is described as a “lock- and-key” fit•Bond formed between the substrate and enzyme areweak and easily reversible•Once the enzyme-substrate complex has formed, anappropriate reaction occurs on the substrate, often withthe aid of a cofactor•Product is formed•Enzyme is free to interact with another substrate
How Enzymes WorkPlease note that due to differingoperating systems, some animationswill not appear until the presentation isviewed in Presentation Mode (SlideShow view). You may see blank slidesin the “Normal” or “Slide Sorter” views.All animations will appear after viewingin Presentation Mode and playing eachanimation. Most animations will requirethe latest version of the Flash Player,which is available athttp://get.adobe.com/flashplayer.
Cofactors: Supporting the Work of Enzymes•The need of microorganisms for trace elements arisesfrom their roles as cofactors for enzymes -iron, copper, magnesium, manganese, zinc, cobalt, selenium, etc.•Participate in precise functions between the enzymeand substrate -help bring the active site and substrate close together -participate directly in chemical reactions with the enzyme-substrate complex
Cofactors: Supporting the Work of Enzymes(cont’d)•Coenzymes -organic compounds that work in conjunction with an apoenzyme -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
Classification of Enzyme Functions•Enzymes are classified and named according tocharacteristics such as site of action, type of action, andsubstrate -prefix or stem word derived from a certain characteristic, usually the substrate acted upon or type of reaction catalyzed -ending –ase
Classification of Enzyme Functions (cont’d)•Six classes of enzymes based on general biochemicalreaction -oxidoreductases: transfer electrons from one substrate to another, dehydrogenases transfer a hydrogen from one compound to another -transferases: transfer functional groups from one substrate to another -hydrolases: cleave bonds on molecules with the addition of water
Classification of Enzyme Functions (cont’d)•Six classes of enzymes based on general biochemicalreaction (cont’d) -lyases: add groups to or remove groups from double-bonded substrates -isomerases: change a substrate into its isomeric form -ligases: catalyze the formation of bonds with the input of ATP and the removal of water
Classification of Enzyme Functions (cont’d)•Each enzyme also assigned a common name thatindicates the specific reaction it catalyzes -carbohydrase: digests a carbohydrate substrate -amylase: acts on starch -maltase: digests maltose -proteinase, protease, peptidase: hydrolyzes the peptide bonds of a protein -lipase: digests fats -deoxyribonuclease (DNase): digests DNA -synthetase or polymerase: bonds many small molecules together
Regulation of Enzyme Function (cont’d)•Activity of enzymes influenced by the cell’senvironment -natural temperature, pH, osmotic pressure -changes in the normal conditions causes enzymes to be unstable or labile•Denaturation -weak bonds that maintain the native shape of the apoenzyme are broken -this causes disruption of the enzyme’s shape -prevents the substrate from attaching to the active site
Metabolic Pathways•Often occur in a multistep series or pathway, with eachstep catalyzed by an enzyme•Product of one reaction is often the reactant(substrate) for the next, forming a linear chain orreaction•Many pathways have branches that provide alternatemethods for nutrient processing•Others have a cyclic form, in which the startingmolecule is regenerated to initiate another turn of thecycle•Do not stand alone; interconnected and merge at manysites
Biochemical PathwayPlease note that due to differingoperating systems, some animationswill not appear until the presentation isviewed in Presentation Mode (SlideShow view). You may see blank slidesin the “Normal” or “Slide Sorter” views.All animations will appear after viewingin Presentation Mode and playing eachanimation. Most animations will requirethe latest version of the Flash Player,which is available athttp://get.adobe.com/flashplayer.
Direct Controls on the Action of Enzymes•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•Noncompetitive inhibition -enzymes have two binding sites: the active site and a regulatory site -molecules bind to the regulatory site -slows down enzymatic activity once a certain concentration of product is reached
Controls on Enzyme Synthesis•Enzymes do not last indefinitely; some wear out, someare degraded deliberately, and some are diluted witheach cell division•Replacement of enzymes can be regulated according tocell demand•Enzyme repression: genetic apparatus responsible forreplacing enzymes is repressed -response time is longer than for feedback inhibition•Enzyme induction: enzymes appear (are induced) onlywhen suitable substrates are present
Enzyme Induction in E. coli•If E. coli is inoculated into a medium containing onlylactose, it will produce the enzyme lactase to hydrolyzeit into glucose and galactose•If E. coli is subsequently inoculated into a mediumcontaining only sucrose, it will cease to synthesizinglactase and begin synthesizing sucrase•Allows the organism to utilize a variety of nutrients,and prevents it from wasting energy by making enzymesfor which no substrates are present
Concept CheckWhich of the following mechanisms of enzyme controlblocks a reaction catalyzed by an enzyme, by the bindingof a product to a regulatory site on the enzyme? A. enzyme repression B. competitive inhibition C. enzyme induction D. noncompetitive inhibition E. None of the choices is correct.
Learning Outcomes: Section 7.26. Name the chemical in which energy is stored in cells.7. Create a general diagram of a redox reaction.8. Identify electron carriers used by cells.
Energy in Cells•Energy is managed in the form of chemical reactionsthat involve the making and breaking of bonds and thetransfer of electrons•Exergonic reactions release energy, making it availablefor cellular work•Endergonic reactions are driven forward with theaddition of energy•Exergonic and endergonic reactions are often coupledso that released energy is immediately put to work
Oxidation and Reduction•Oxidation: loss of electrons -when a compound loses electrons, it is oxidized•Reduction: gain of electrons -when a compound gains electrons, it is reduced•Oxidation-reduction (redox) reactions are common inthe cell and are indispensable to the required energytransformations
Oxidation and Reduction (cont’d)•Oxidoreductases: enzymes that remove electronsfrom one substrate and add them to another -their coenzyme carriers are nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD)•Redox pair: an electron donor and an electron acceptorinvolved in a redox reaction
Oxidation and Reduction (cont’d)•Energy present in the electron acceptor can becaptured to phosphorylate (add an inorganicphosphate) to ADP or to some other compound to storeenergy in ATP•The cell does not handle electrons as discrete entitiesbut rather as parts of an atom such as hydrogen(consisting of a single electron and a single proton)•Dehydrogenation: the removal of hydrogen during aredox reaction
Concept CheckIn a redox reaction, loss of electrons is A. phosphorylation. B. oxidation. C. fermentation. D. reduction. E. None of the choices is correct.
Learning Outcomes: Section 7.39. Name three basic catabolic pathways, and give an estimate of how much ATP each of them yields.10. Write a summary statement describing glycolysis.11. Describe the Krebs cycle.12. Discuss the significance of the electron transport system.13. Point out how anaerobic respiration differs from aerobic respiration.14. Provide a summary of fermentation.15. Describe how noncarbohydrate compounds are catabolized.
Catabolism•Metabolism uses enzymes to catabolize organicmolecules to precursor molecules that cells then use toanabolize larger, more complex molecules•Reducing power: electrons available in NADH andFADH2•Energy: stored in the bonds of ATP -both are needed in large quantities for anabolic metabolism -both are produced during catabolism
How the NAD+ WorksPlease note that due to differingoperating systems, some animationswill not appear until the presentation isviewed in Presentation Mode (SlideShow view). You may see blank slidesin the “Normal” or “Slide Sorter” views.All animations will appear after viewingin Presentation Mode and playing eachanimation. Most animations will requirethe latest version of the Flash Player,which is available athttp://get.adobe.com/flashplayer.
Getting Materials and Energy•Nutrient processing in bacteria is extremely varied, butin most cases the nutrient is glucose•Aerobic respiration -a series of reactions that converts glucose to CO2 and allows the cell to recover significant amounts of energy -utilizes glycolysis, the Krebs cycle, and the electron transport chain -relies on free oxygen as the final electron and hydrogen acceptor -characteristic of many bacteria, fungi, protozoa,
Getting Materials and Energy (cont’d)•Anaerobic respiration -used by strictly anaerobic organisms and those who are able to metabolize with or without oxygen -involves glycolysis, the Krebs cycle, and the electron transport chain -uses NO3-, SO42-, CO33-, and other oxidized compounds as final electron acceptors•Fermentation -incomplete oxidation of glucose -oxygen is not required -organic compounds are final electron acceptors
How Glycolysis WorksPlease note that due to differingoperating systems, some animationswill not appear until the presentation isviewed in Presentation Mode (SlideShow view). You may see blank slidesin the “Normal” or “Slide Sorter” views.All animations will appear after viewingin Presentation Mode and playing eachanimation. Most animations will requirethe latest version of the Flash Player,which is available athttp://get.adobe.com/flashplayer.
The Krebs Cycle (Citric Acid Cycle):A Carbon and Energy Wheel•After glycolysis, pyruvic acid is still energy-rich•cytoplasm of bacteria and mitochondrial matrix of eukaryotes -a cyclical metabolic pathway that begins with acetyl CoA, which joins with oxaloacetic acid, and then participates in seven other additional transformations -transfers the energy stored in acetyl CoA to NAD+ and FAD by reducing them (transferring hydrogen ions to them) -NADH and FADH2 carry electrons to the electron transport chain -2 ATPs are produced for each molecule of glucose through phosphorylation
How the Krebs Cycle Works Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at http://get.adobe.com/flashplayer.
The Respiratory Chain:Electron Transport•A chain of special redox carriers that receives reducedcarriers (NADH, FADH2) generated by glycolysis and theKrebs cycle -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
The Respiratory Chain:Electron Transport (cont’d)•Principal compounds in the electron transport chain: -NADH dehydrogenase -flavoproteins -coenzyme Q (ubiquinone) -cytochromes•Cytochromes contain a tightly bound metal ion in theircenter that is actively involved in accepting electronsand donating them to the next carrier in the series
The Electron Chain (cont’d)•Released energy from electron carriers in the electrontransport chain is channeled through ATP synthase•Oxidative phosphorylation: the coupling of ATPsynthesis to electron transport -each NADH that enters the electron transport chain can give rise to 3 ATPs -Electrons from FADH2 enter the electron transport chain at a later point and have less energy to release, so only 2 ATPs result
The Terminal Step•Aerobic respiration -catalyzed by cytochrome aa3, also known as cytochrome oxidase -adapted to receive electrons from cytochrome c, pick up hydrogens from solution, and react with oxygen to form water 2H+ + 2e- + ½ O2 H20
The Terminal Step (cont’d)•Most eukaryotes have a fully functioning cytochromesystem•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
The Terminal Step (cont’d)•A potential side reaction of the respiratory chain is theincomplete reduction of oxygen to the superoxide ion(O2-) and hydrogen peroxide (H2O2)•Aerobes produce enzymes to deal with these toxicoxygen products -superoxide dismutase -catalase -Streptococcus lacks these enzymes but still grows well in oxygen due to the production of peroxidase
Electron Transport System and ATP Synthesis Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at http://get.adobe.com/flashplayer.
The Terminal Step (cont’d)•Anaerobic Respiration -the terminal step utilizes oxygen-containing ions, rather than free oxygen, as the final electron acceptor Nitrate reductase NO3- + NADH NO2- + H2O + NAD+•Nitrate reductase catalyzes the removal of oxygen fromnitrate, leaving nitrite and water as products
Anaerobic Respiration (cont’d)•Denitrification -some species of Pseudomonas and Bacillus possess enzymes that can further reduce nitrite to nitric oxide (NO), nitrous oxide (N2O), and even nitrogen gas (N2) -important step in recycling nitrogen in the biosphere•Other oxygen-containing nutrients reducedanaerobically by various bacteria are carbonates andsulfates•None of the anaerobic pathways produce as much ATPas aerobic respiration
After Pyruvic Acid II: Fermentation•Fermentation -the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen -uses organic compounds as the terminal electron acceptors -yields a small amount of ATP -used by organisms that do not have an electron transport chain -other organisms revert to fermentation when oxygen is lacking
Fermentation (cont’d)•Only yields 2 ATPs per molecule of glucose•Many bacteria grow as fast as they would in thepresence of oxygen due to an increase in the rate ofglycolysis•Permits 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
Fermentation (cont’d)•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•Human muscle cells -undergo a form of fermentation that permits short periods of activity after the oxygen supply has been depleted -convert pyruvic acid to lactic acid, allowing anaerobic production of ATP -accumulated lactic acid causes muscle fatigue
Products of Fermentation in Microorganisms•Alcoholic beverages: ethanol and CO2•Solvents: acetone, butanol•Organic acids: lactic acid, acetic acid•Vitamins, antibiotics, and hormones•Large-scale industrial syntheses by microorganismsoften utilize entirely different fermentation mechanismsfor the production of antibiotics, hormones, vitamins,and amino acids
Catabolism of Noncarbohydrate Compounds•Complex polysaccharides broken into componentsugars, which can enter glycolysis•Lipids broken down by lipases -glycerol converted to dihydroxyacetone phosphate, which can enter midway into glycolysis -fatty acids undergo beta oxidation, whose products can enter the Krebs cycle as acetyl CoA
Catabolism of Noncarbohydrate Compounds(cont’d)•Proteins are broken down into amino acids byproteases -amino groups are removed through deamination -remaining carbon compounds are converted into Krebs cycle intermediates or decarboxylated
Concept CheckWhat is the maximum net yield of ATP per molecule ofglucose for each of the following types of respiration? A. aerobic respiration B. anaerobic respiration C. fermentation
Learning Outcomes: Section 7.416. Provide an overview of the anabolic stages of metabolism.17. Define amphibolism.
Anabolism and the Crossing Pathways ofMetabolism•The Frugality of the Cell -cells have systems for careful management of carbon compounds -catabolic pathways contain strategic molecular intermediates (metabolites) that can be diverted into anabolic pathways -a given molecule can serve multiple purposes; maximum benefit can be derived from all nutrients and metabolites of the cell pool•Amphibolism: the ability of a system to integratecatabolic and anabolic pathways to improve cellefficiency
Anabolism:Formation of Macromolecules•Two possible sources for monosaccharides, aminoacids, fatty acids, nitrogenous bases, and vitamins -enter the cell from the outside as nutrients -can be synthesized through various cellular pathways
Anabolism:Formation of Macromolecules (cont’d)•The degree to which an organism can synthesize itsown building blocks is genetically determined and variesfrom group to group -autotrophs only require CO2 as a carbon source and a few minerals to synthesize all cell substances -some heterotrophs such as E. coli can synthesize all cellular substances from a few minerals and one organic carbon source such as glucose
Carbohydrate Biosynthesis•Glucose has a crucial role in bioenergetics -major component of cellulose cell walls and certain storage molecules -an intermediary in glycolysis, glucose-6-P is used to form glycogen -peptidoglycan is a linked polymer derived from fructose-6-P from glycolysis -the carbohydrates ribose and deoxyribose are essential building blocks of nucleic acids -polysaccharides are the predominant components of capsules and glycocalyx
Amino Acids, Protein Synthesis, and NucleicAcid Synthesis•Proteins -account for a large proportion of a cell’s constituents -essential components of enzymes, cell membrane, cell wall, and cell appendages -20 amino acids needed to make these proteins -some organisms, such as E. coli, have pathways that will synthesize all 20 amino acids -others, such as animals, lack some or all of the pathways for amino acid synthesis
Amino Acids, Protein Synthesis, and NucleicAcid Synthesis (cont’d)•Nucleic acids: DNA and RNA -responsible for the hereditary continuity of cells and the direction of protein synthesis -covered in more detail in chapter 8
Assembly of the Cell•Component parts of bacteria are being synthesized on acontinuous basis•Catabolism is also taking place as long as nutrients arepresent and the cell is nondormant•Cell division takes place when -anabolism produces enough macromolecules to serve two cells -DNA replication produces duplicate copies of the cell’s genetic material -membrane and cell wall have increased in size•Catabolic processes provide all of the energy for complexbuilding reactions
Concept CheckThe ability of a cell to integrate molecule-using andmolecule-building pathways to improve cell efficiency isknown as A. anabolism. B. amphibolism. C. catabolism. D. metabolism. E. None of the choices is correct.