Briefly explain biosynthesis of cell constituents (requires energy)

Transcription

1 3 Cell Metabolism Chapter 3 Cell Metabolism - review Student Learning Outcomes: Describe central role of enzymes as catalysts Vast array of chemical reactions Many enzymes are proteins Role of NAD + /NADH coenzyme carrying electrons Explain how metabolic energy comes from breaking/ rejoining covalent bonds: ATP is energy currency Glycolysis, fermentation or aerobic respiration What goes into reactions, what comes out Briefly explain biosynthesis of cell constituents (requires energy) Fig 3.1 Energy diagrams for catalyzed and uncatalyzed reactions Enzymes: catalysts increase rate of chemical reactions in cells (lower activation energy) not consumed in reaction not alter chemical equilibrium between reactants and products Conversion of substrate (S) to product (P): Enzymes bind substrates to form enzyme-substrate complex (ES) S binds to active site of enzyme. S converted to product, released Fig. 3.1 Fig. 3.2 Enzymatic catalysis of reaction between 2 substrates Biochemical reactions often 2 or more substrates. ex: peptide bond joins 2 amino acids Enzyme brings substrates together in proper orientation to favor transition state Active sites: clefts or grooves from tertiary structure Substrates bind active site: hydrogen bonds, ionic bonds, hydrophobic interactions. Fig 3.3 Models of enzyme-substrate interaction Lock-and-key model: substrate fits precisely active site. **Induced fit: modifies configurations of both enzyme and substrate Fig. 3.2 Specific side chains in active site may react with substrate and form bonds with reaction intermediates Fig

2 Fig 3.4 Substrate binding by serine proteases Ex. Chymotrypsin digests proteins by catalyzing hydrolysis of peptide bonds Chymotrypsin digests adjacent to hydrophobic amino acids Trypsin digests next to basic amino acids Nature of active site pocket determines substrate specificity of different proteases Fig 3.5 Catalytic mechanism of chymotrypsin Chymotrypsin: Substrate binding orients peptide bond adjacent to serine in active site; catalytic reaction involves covalent join to serine Active site amino acids are involved in reaction Fig. 3.4 The Central Role of Enzymes as Biological Catalysts Small molecules binding in active sites assist catalysis. Prosthetic groups: small molecules bound to proteins - critical functional roles. Ex: myoglobin and hemoglobin, prosthetic group is heme, which binds O 2. Ex. metal ions (zinc, iron) Fig 3.6 Role of NAD + in oxidation reduction reactions Nicotinamide adenine dinucleotide (NAD + ): REDOX: coenzyme carries electrons in oxidation: reduction reactions NAD + accepts H + and 2 e- from one substrate NADH. NADH donates these e- to second substrate, re-forming NAD +. S 1 (red) + S 2 (ox) -> S 1 (ox) + S 2 (red) Coenzymes: low-molecular-weight organic molecules that work with enzymes to enhance reaction rates. Ex. NAD + works with many enzyme (carries electrons) Fig

3 Enzymes and coenzymes Some coenzymes are related to vitamins Fig 3.7 Feedback inhibition Enzyme activity is often regulated Ex. feedback inhibition, product of pathway inhibits an enzyme involved in its synthesis. Fig. 3.7 Fig 3.8 Allosteric regulation Feedback inhibition is example of allosteric regulation: enzyme activity controlled by binding of small molecules to regulatory sites on enzyme (not at active site) changes conformation of enzyme and alters active site. Fig 3.9 Protein phosphorylation **Enzyme activity can be modified by phosphorylation: addition of phosphate can stimulate or inhibit activity of an enzyme. Kinases add Phosphate (-OH of ser, thr, tyr) Phosphatases remove Phosphate Fig. 3.8 Fig. 3.9 ex. phosphorylation activates enzyme that degrades glycogen 3

4 Metabolic Energy A large portion of cell s activities is devoted to obtaining energy from environment, and using energy to drive energy-requiring reactions Many reactions in cells are energetically unfavorable, can proceed only with energy input (especially biosynthetic reactions) ATP and NADH provide energy and reducing material (e-) for coupled reactions Fig 3.10 ATP as a store of energy Adenosine 5 -triphosphate (ATP) plays central role in storing, using free energy in the cell Energy currency. Bonds between phosphates in ATP are highenergy bonds: Hydrolysis is accompanied by large decrease in free energy: powers coupled reactions. Fig Metabolic Energy Hydrolysis of ATP drives energy-requiring reactions Ex: first step in glycolysis is unfavorable ( G = +3.3) ATP hydrolysis is energy yielding: ( G = 7.3 kcal/mol): Metabolic Energy Energy-yielding reactions - coupled to ATP synthesis Energy-requiring reactions - coupled to ATP hydrolysis. Ex. complete oxidative breakdown of glucose to CO 2 and H 2 O yields large amount of free energy: G = 686 kcal/mol. Combined (coupled) reaction : ( G = -4.0) kcal/mol) Energy-yielding reactions - coupled to ATP synthesis Energy-requiring reactions - coupled to ATP hydrolysis. To harness this energy, glucose is oxidized in a series of steps coupled to ATP synthesis Glycolysis, citric acid cycle, e- transport chain (Krebs cycle), (oxidative phosphorylation) 4

5 Metabolic Energy Glycolysis: common to all cells; does not require O 2 Anaerobic organisms, can provide all metabolic energy (ex. E. coli, Streptococcus, yeast). Aerobic cells, only 1st stage in glucose degradation Figure 3.11 Reactions of glycolysis Glycolysis: 1 glucose 2 pyruvate, net gain of 2 ATP First part of pathway consumes energy (2 ATP) Second part generates energy (4 ATP) Also converts 2 molecules of NAD + to NADH: NAD + is oxidizing agent that accepts e- NADH must be recycled by donating e- for other REDOX Glycolysis: Breakdown of glucose -> 2 pyruvate, net gain 2 ATP Enzymes that catalyze reactions are regulatory points: if adequate supply of ATP, glycolysis is inhibited Also converts 2 molecules of NAD + to NADH: NADH must be recycled by donating e- for other oxidation reduction reactions.. Fig pyruvate Metabolic Energy In eukaryotic cells, glycolysis in cytosol. NADH must be recycled, donate e- for other REDOX: Anaerobic conditions, NADH reoxidized to NAD + by conversion of pyruvate to lactate or ethanol (fermentation): Wasteful process reduces pyruvate, low ATP gain Aerobic conditions, NADH donates e- to electron transport chain (oxidative respiration) (lot of ATP) Pyruvate is transported into mitochondria, for complete oxidation (Krebs + electron transport chain) (citric acid cycle) Fig 3.12 Oxidative decarboxylation of pyruvate Pyruvate oxidative decarboxylation with coenzyme A (CoA-SH): forms acetyl CoA and more NADH. Fig

6 Fig 3.13 The citric acid cycle Acetyl CoA enters citric acid cycle (Krebs cycle) 2-C acetyl group + oxaloacetate (4-C) yields citrate (6-C). 2 C of citrate are completely oxidized to CO 2; oxaloacetate is regenerated. Citric acid cycle: completes oxidation of glucose to 6 CO 2 Each Acetyl-CoA yields: 2 CO 2, 1 GTP, 3 NADH, 1 flavin adenine dinucleotide (FADH 2 ), (another e- carrier. Fig Oxidative phosphorylation summary Oxidative phosphorylation: electrons of NADH, FADH 2 combine with O 2 ; energy released drives synthesis of ATP. Passage of e- through carriers: electron transport chain, inner mitochondrial membrane of eukaryotes (inner plasma membrane of prokaryotes) H + are pumped out electrochemical gradient H + back in through ATP synthase makes ATP (~3/NADH) Fig Lieberman & Marks, Basic Medical Biochemistry Metabolic Energy Glucose breakdown (O 2 ) to CO 2, H 2 O ~36-38 ATP Breakdown of other organic molecules yields energy: Nucleotides and polysaccharides are broken down to sugars which enter glycolytic pathway Amino acids are degraded via citric acid cycle. Fats (triacylglycerols) broken to glycerol and free fatty acids. fatty acid joins to coenzyme A, yields fatty acyl-coa fatty acids degraded stepwise process, two C at a time Yield 1 Acetyl CoA, 1 NADH, 1 FADH 2 each cycle ~130 ATPs per molecule of 16-carbon fatty acid. Fig 3.15 Oxidation of fatty acids Each round of fatty acid oxidation yields one NADH, one FADH 2. Acetyl CoA enters citric acid cycle (for complete oxidation). Net gain: ~130 ATPs per molecule of 16-carbon fatty acid (net gain of ~38 ATPs per molecule of glucose with 6 C). Fig

7 Photosynthesis brief Photosynthesis converts energy of sunlight to usable form of chemical energy. ultimate source of all metabolic energy in biological systems. Overall equation for photosynthesis: Photosynthesis Photosynthetic pigments absorb photons of light; shifts electrons into higher energy orbitals, convert energy from sunlight to chemical energy in ATP, and also NADPH In eukaryotic cells, reactions occur in chloroplasts In prokaryotic cells, reactions occur on plasma membrane Chlorophylls major pigments; other pigments absorb different wavelengths of light Process takes place in two stages: Light reactions: sunlight energy drives synthesis of ATP and NADPH, coupled to oxidation of H 2 O to O 2. Dark reactions: ATP and NADPH drive synthesis of carbohydrates from CO 2 18 ATP and 12 NADPH required for each glucose Fig Fig 3.18 The Calvin cycle Light reactions: energy from light converts H 2 O to O 2. High-energy electrons enter electron transport chain: transfer through series of carriers is coupled to synthesis of ATP. Dark reactions: ATP and NADPH drive synthesis of carbohydrates from CO 2 and H 2 O. One molecule of CO 2 added each cycle of reactions, Calvin cycle, that forms carbohydrates. Fig. 3.17,18 The Biosynthesis of Cell Constituents Biosynthesis of cell constuents **Energy derived from breakdown of organic molecules (catabolism) drives synthesis of other components of cell. Biosynthetic (anabolic) pathways use ATP and reducing power (usually NADPH) to produce new organic compounds. Animal cells: glucose synthesis (gluconeogenesis) usually starts with lactate (from anaerobic glycolysis), amino acids (breakdown of proteins), or glycerol (breakdown of lipids): pyruvate is converted to glucose: not just reversal of glycolysis; requires more energy for biosynthesis of glucose than get from breakdown 7

8 Fig 3.20 Synthesis of polysaccharides Glucose is stored as starch and glycogen. Synthesis of polysaccharides requires energy. Dehydration reaction joining sugars is unfavorable, couples to energy-yielding reaction; nucleotide sugar intermediates. Glucose phosphorylated, reacts with UTP UDP-glucose. UDP-glucose (activated intermediate) donates glucose to growing polysaccharide chain. The Biosynthesis of Cell Constituents Lipids are important energy storage molecules and major constituent of cell membranes. Fatty acids are synthesized from acetyl CoA, (from the breakdown of carbohydrates), in reactions that resemble reverse of fatty acid oxidation. Requires ATP, NADPH Fig Fig 3.22 Biosynthesis of amino acids Amino acids are derived from diet (some are essential), or formed from citric acid intermediates NH 3 is incorporated during synthesis of Glu and Gln These amino acids donate NH 3 to form other amino acids, (derived from intermediates in glycolysis, citric acid cycle) Many bacteria and plants can synthesize all 20 aa Fig Molecular Medicine 3.1 Phenylketonuria: Abnormal metabolism of phenylalanine in patients with phenylketonuria Errors in amino acid metabolism can have large impacts Ex. phenylketonuria is deficiency of phenylalanine hydroxylase, which converts phenylalanine to tyrosine. Phenylalanine and metabolites accumulate and cause mental retardation. Newborns tested, special diet 8

9 The Biosynthesis of Cell Constituents Synthesis of proteins: Amino acids are incorporated into proteins in order specified by nucleotide bases in gene mrna is template for protein synthesis on ribosome Each amino acid is attached to specific transfer RNA (trna) molecule in reaction coupled to ATP hydrolysis (charging on 3 position) Aminoacyl-tRNAs align on mrna bound on ribosome; Peptide chain joins to new trna-aa, coupled to hydrolysis of GTP Fig 3.24 Biosynthesis of purine and pyrimidine nucleotides Nucleotides can be synthesized from carbohydrates and amino acids, or reused following nucleic acid breakdown. Ribose-5-phosphate is starting point for nucleotide synthesis. Different pathways for synthesis of purine and pyrimidine. Ribonucleotides are converted to deoxyribonucleotides, building blocks of DNA Fig Fig Fig 3.25 Synthesis of polynucleotides Nucleic acid synthesis requires energy; NTPs are activated precursors. Review Review Questions: 1. Binding pocket of trypsin contains Asp residue. How would changing this aa to Lys affect enzyme s activity? 4. Many biochemical reactions (synthesis of macromolecules) are energetically unfavorable under physiological conditions. How does cell carry out these reactions? 8. Yeast can grow anaerobic or aerobic. For every molecule of glucose consumed, compare number of ATP generated in anaerobic versus aerobic conditions. Fig How do organisms growing under anaerobic conditions regenerate NAD+ from NADH produced during glycolysis? 9