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Biochemistry

Biochemistry. Chapter 27 Bioenergetics. Problem Sets. PS #1 Sections 27.1 – 27.4 # 1, 3, 4, 5, 6, 7, 9, 15, 18, 21, 22, 23, 25, 26, 29, 31, 34 PS #2 Sections 27.4 – 27.8 # 36, 37, 39, 41, 43, 44, 45, 50, 51, 52, 53, 58. 27.1 Metabolism. Metabolism

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Biochemistry

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  1. Biochemistry Chapter 27 Bioenergetics

  2. Problem Sets • PS #1 • Sections 27.1 – 27.4 • # 1, 3, 4, 5, 6, 7, 9, 15, 18, 21, 22, 23, 25, 26, 29, 31, 34 • PS #2 • Sections 27.4 – 27.8 • # 36, 37, 39, 41, 43, 44, 45, 50, 51, 52, 53, 58

  3. 27.1 Metabolism • Metabolism • All the chemical reactions involved in maintaining the dynamic state of the cell • Two groups – breaking and forming molecules • Catabolism • Breaking down molecules to provide energy • Anabolism • Synthesizing needed biomolecules

  4. 27.1 Metabolism • Biochemical pathway – a series of consecutive biochemical reactions • Common Catabolic Pathway • Food consists of carbohydrates, proteins, lipids • Each is converted to energy by a different pathway • All pathways converge in the Common Catabolic Pathway • Purpose of pathway – convert food molecules to ATP

  5. 27.2 Mitochondria • Outer membrane • permeable to small molecules / ions • Inner membrane • resistant to penetration of molecules / ions • numerous embedded transport proteins • highly corrugated and folded • Matrix – inner nonmembranous portion • Cristae - membrane baffles projecting into matrix • Intermembrane space • Between inner and outer membranes

  6. 27.2 Mitochondria • Common catabolic pathway takes place in mitochondria • Enzymes catalyze common pathway • Synthesized in cytosol, imported through outer and inner membranes • Translocator Outer Membrane (TOM) channels allow enzymes to cross outer membrane • Translocator Inner Membrane (TIM) complexes chaparone enzymes through TOM channels and insert them through inner membrane • Citric acid cycle enzymes found in matrix

  7. 27.3 Components of the Common Metabolic Pathway • Citric acid cycle • Also called tricarboxylic acid cycle • Also called Krebs cycle • Oxidative phosphorylation pathway • Two parts – • Electron transport chain • Phosphorylation • Important chemical agents for these pathways found in mitochondria

  8. 27.3 Agents for Energy Storage and Phosphate Transfer AMP, ADP, ATP First phosphate – ester bond (3.4 kcal/mol) Second & third phosphates – anhydride bond (7.3 kcal/mol) ATP is very useful for energy storage and release Lasts a short time (~1 min) before used

  9. 27.3 Agents for Electron Transfer in Biological Redox Reactions Nicotinamide adenine dinucleotide (NAD+) Coenzyme ADP core + charge on N in nicotinamide Apoenzyme holds onto NAD+ by the adenosine side Nicotinomide end carries out the chemical reaction

  10. 27.3 Agents for Electron Transfer in Biological Redox Reactions Flavin adenine dinucleotide (FAD) Coenzyme ADP core Apoenzyme holds onto FAD by the adenosine side Flavin end carries out the chemical reaction

  11. 27.3 Agents for Electron Transfer in Biological Redox Reactions NAD+ can be reduced to NADH NAD can be reduced to FADH2 These are hydrogen ion and electron transporting molecules

  12. 27.3 Agents for Acetyl Group Transfer Coenzyme A Acetyl (CH3CO–) transporting molecule Acetyl group linked to CoA by thioester bond High energy bond (7.51 kcal/mol) Forms Acetyl CoA

  13. 27.4 The Citric Acid Cycle Carbohydrates and lipids are broken into 2 carbon pieces and attached to a CoA (acetyl coA) Common metabolism begins when they are dumped into the citric acid cycle

  14. 27.4 The Citric Acid Cycle Step 1 Acetyl CoA enters cycle by combining with C4 compound oxaloacetate Thioester bond is hydrolyzed, removing CoA This is a “building up” step

  15. 27.4 The Citric Acid Cycle Step 2 Citrate ion is dehydrated to cis-aconitate, which is then hydrated to isocitrate Citrate is a tertiary alcohol, which cannot be oxidized Changing it to isocitrate makes it a secondary alcohol so it can be oxidized

  16. 27.4 The Citric Acid Cycle Step 3 Isocitrate is oxidized and decarboxylated (removal of CO2) We’re now down to a C5 compound

  17. 27.4 The Citric Acid Cycle Steps 4 and 5 Another CO2 is removed from the oxaloacetate portion Occurs in many steps, requires many cofactors We’re now down to a C4 compound (succinate)

  18. 27.4 The Citric Acid Cycle Step 6 Succinate is oxidized by FAD to fumarate Two hydrogens are removed Fumarate’s double bond is the trans isomer

  19. 27.4 The Citric Acid Cycle Step 7 Fumarate is hydrated to create the malate ion

  20. 27.4 The Citric Acid Cycle Step 8 Malate is oxidized to oxaloacetate Oxaloacetate is the final product of the CAC Fed back into step 1, where it combines with an incoming acetyl coA

  21. 27.4 The Citric Acid Cycle Net reaction: 2 C’s come in with acetyl coA, 2 C’2 go out as CO2 Advantages of doing the reaction step by step: Energy released in small packets and carried away Provides raw materials for amino acid synthesis Provides methods for regulating the speed of catabolism ATP and NADH inhibit some of the CAC enzymes Excess acetyl coA causes the cycle to accelerate

  22. 27.5 Electron and H+ Transport • NADH and FADH2 produced in CAC carry hydrogen ions and electrons • Generate energy by reaction • 4 H+ + 4 e- + O2  2 H2O + energy • Carried out in many steps • Reaction catalyzed by many enzymes • Embedded in inner membrane of mitochondria • Arranged in specific sequence (increasing e- affinity) to create an “assembly line”

  23. 27.5 Electron and H+ Transport • Complex I • Uses coenzyme Q to oxidize NADH • NADH + H+ + CoQ  NaD+ + CoQH2 • Energy used to transport 2 H+ across membrane from matrix to intermembrane space • CoQ can migrate laterally within membrane • Complex II • Catalyzes e- transfer from FADH2 to CoQ • FADH2 + CoQ  FAD + CoQH2 • Not enough energy produced to transport 2 H+

  24. 27.5 Electron and H+ Transport • Complex III • Delivers e- from CoQH2 to cytochrome c • Complex III has 2 channels through which 2 H+ are pumped from CoQH2 into intermembrane space • CoQH2 + 2cyto c (ox)  CoQ + 2H+ + 2cyto c (red) • Complex IV • e- flow from cytochrome c to cytochrome a3 • There, e- transferred to O2 molecule (cleave bond) • ½ O2 + 2 H+ + 2 e- H2O • 2H+ pumped out of matrix to intermembrane space

  25. 27.5 Electron and H+ Transport Total process is called oxidative phosphorylation

  26. 27.6 The Chemiosmotic Pump • Chemiosmotic theory explains how e- and H+ transport produces chemical energy that is stored in ATP • Energy in e- transport chain generates a proton gradient across inner membrane • Higher H+ concentration in intermembrane space • Forces H+ ions to flow back into mitochondrion through a membrane complex called proton-translocating ATPase

  27. 27.6 Proton-Translocating ATPase • Rotor engine made of 16 different proteins • Contains a proton channel that rotates every time an H+ passes through • Rotation is transferred to a polypeptide rotor that catalyzes ATP synthesis • Converts mechanical energy into chemical • Can also function in reverse • ADP + Pi ATP + H2O

  28. 27.6 The Chemiosmotic Pump • H+ that enter mitochondrion combine with e- from electron transport chain and oxygen to produce water • Oxygen has two functions: • Oxidizes NADH  NAD+ and FADH2  FAD so that they can be reused • Provides energy for conversion of ADP  ATP • Overall reactions for oxidative phosphorylation: • NADH + 3 ATP + ½ O2 + 3 Pi + H+ NAD+ + 3 ATP + H2O • FADH2 + 2 ADP + ½ O2 + 2 Pi FAD + 2 ATP + H2O

  29. 27.7 Energy Yield from e- and H+ Transport • Each pair of protons produces 1 ATP • Each NADH produces 3 pairs of protons • Each FADH2 produces 2 pairs of protons • Each turn of the CAC produces • 3 NADH  9 ATP • 1 FADH2 2 ATP • 1 GTP  1 ATP • C2 + 2O2 + 12ADP + 12Pi12ATP + 2CO2

  30. 27.8 Conversion to Other Forms of Energy • Chemical Energy • Phosphorylation (transfer of ATP’s phosphate to another molecule) activates many enzymes • Electrical Energy • ATP provides energy for membrane proteins to pump K+ into cells and Na+ out of cells • Mechanical Energy • Myocin and actin bind strongly in muscles; ATP binds to myocin, complex dissociates, muscle relaxes • Heat Energy • ATP hydrolysis yields 7.3 kcal/mol

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