Chapter 15 Metabolism: Basic concepts and design

1. Chapter 15 Metabolism: Basic concepts and design Part Ⅰ: the specificity and catalytic power of enzymes  the regulation of enzyme activity  the transport of molecules and ions across membranes Part Ⅱ: to extract energy and reducing power from its environment  to synthesize the building blocks of its macromolecules and then the macromolecules themselves Metabolism: a highly integrated network of chemical reactions  contain many common motifs

2. § 15.1 Metabolism is composed of many coupled, interconnecting reactions Cells transform different types of energy ¤ Phototrophs (photsynthetic organisms): light energy  chemical energy ¤ Chemotrophs: Utilize chemical energy generated by phototrophs  ion gradient: other types of chemical energy, nerve impulses, etc.  mechanical energy: muscle contraction and movement  synthesis biomolecules

3. Metabolism(or intermediary metabolism) Energy is being extracted from fuels via a linked series chemical reactions and used it to power biosynthesis processes Two broad classes: ¤Catabolism:fuels transform into cellular energy Fuels (carbohydrates, fats, etc)  CO2+H2O+useful energy ¤Anabolism: cellular energy to generate complex structures or energy-rich compounds Useful energy + small molecules  complex molecules * Amphibolic pathways: either anabolic or catabolic is depended on the energy conditions in the cell. Biosynthetic and degradative pathways are always distinct.

4. Metabolic pathways– many coupled, interconnecting reactions

5. § 15.2 Adenosine triphosphate (ATP) – the universal currency of free energy in biological systems (XTP?) Carbohydrates and fats  ATP 2 Phosphoanhydride bonds Mg2+ or Mn2+ -4 -3 -2

6. Pi: orthophosphate PPi: pyrophosphate ATP  ADP (ATP-ADP cycle) the fundamental mode of energy exchange in biological systems ATP + NDP  ADP + NTP (nucleoside diphosphate kinase) ATP + NMP  ADP + NDP (nucleoside monophosphatekinase) ATP + AMP  2 ADP (adenylate kinase, myokinse)

7. ¤ATP + H2O  ADP + Pi G0’= -7.3 kcal/mol ATP + H2O  AMP + PPi G0’= -10.9 kcal/mol Under typical cellular condition: G = -12 kcal/mol A + B  C + D G = G0’ + RT ln [C][D]/[A][B] ¤A thermodynamically unfavorable reaction can be driven by a favorable reaction  increase a factor of about 108. Keq of A B under standard condition: 1.15×10-3 Keq of A B under standard condition + ATP:2.67×102 at pH 7, G°’= -7.3 kcal/mol Keq of A B under typical cellular condition + ATP:7.7×105 G= -12 kcal/mol if nATP 108n ¤ATP hydrolysis drives metabolism by shifting the equilibrium of coupling reactions  chemical energy coupling agent  protein conformation shift, e.g., muscle contraction  the conc. of ion or molecule on the outside/inside of a cell, e.g., Na+/K+ pump

8. What makes ATP a particular efficient phosphoryl-group donor ~ P: high energy bond  The free energy of hydrolysis  Three structural factors: 1. resonance stabilization, 2. electrostatic repulsion, 3. stabilization due to hydration ADP and Pi both effectively bind to water than ATP squiggle (~P) indication

9. Phosphoryl transfer potential– an important form of cellular energy transformation An efficient carrier of phosphoryl groups

10. High phosphoryl transfer potential compounds Creatine kinase: Creatine phosphate + ADP  ATP + creatine In vertebrate muscle serves as a reservoir of high-potential phosphoryl groups C

11. Sources of ATP (energy) during exercise

12. § 15.3 The oxidation of carbon fuels  an important source of cellular energy immediate energy donor Chemotrophs Phototrophs

13. Free energy of oxidation of single-carbon compounds H2 11/20 施明哲主任

14. Two kinds of trapped energy of fuels oxidation 1. A high-energy phosphate compound GAP 1,3-BPG  3PGA 2. Ion gradient formation  acid Substrate-level phosphorylation ( p. 443)

15. Three stages of catabolism

16. §15.4 Metabolic pathways contain many recurring motifs ¤ Activated carrier of phosphoryl groups, e.g., ATP ¤ Activated carrier of electrons for fuel oxidation e.g., nicotinamide adenine dinucleotide (NAD+) flavin adenine dinucleotide (FAD) ¤ Activated carrier of electrons for reductive biosynthesis e.g., reduced form of nicotinamide adenine dinucleotide phosphate (NADPH)  NADH is used primarily for the generation of ATP ¤ Activated carrier of two-carbon fragments e.g., acetyl coenzyme A (CoA)

17. NAD(P)+: nicotinamide adenine dinucleotide (phosphate) Niacin (vit. 3) (Fig. 15.17) ADP H+ + 2e- H- (hydride ion) NADH vs. NADPH

18. FAD: flavin adenine dinucleotide isoalloxazine ring Vit B2 riboflavin FMN 5C

20. Coenzyme A: a carrier of acyl group thioester

21. Transfer acetyl group is exergonic Acetyl CoA carries an activated acetyl group, just as ATP carries an activated phosphoryl group.

22. Two key aspects of metabolism utilize activated carriers: 1. The use of specificity of enzymes to control the flow of free energy and reducing power, such as NAD(P)H, FADH2 2. The economy and elegance of metabolism underlie design Lys residue

24. Act as coenzyme: are needed in small amounts in the diets at least 12 vitamins are needed

26. react with hydroxyl radicals

27. Nelson Vitamins: essential to the health of vertebrates but cannot be synthesized, so must be obtained in the diet. fat-soluble vitamins: A, D, E, K, all of which are derived from isoprene units water-soluble vitamins: C, B, biotin, folic acid, nicotinic acid,… No biological activity

28. Nelson Regulate calcium uptake in the intestine and calcium levels in the kidney and bone Vitamin D2 (ergocalciferol): is added to milk and butter

29. Nelson Vitamin A (retinol): the visual pigment of the vertebrate eye Cure acne and wrinkled skin p. 424 From fish liver oils, liver, eggs, whole milk, butter carrots, sweet potato, and other yellow vegetables Deficiency: night blindness, dryness of the skin and eyes… β-carotenoids

30. Vitamin E: tocopherols: a substituted aromatic rings and a long isoprenoid side chain Nelson The aromatic ring reacts with and destroys the reactive oxygen species, protecting unsaturated fatty acids from oxidation. Tocopherols: in eggs, vegetable oils, and wheat germ Vit E deficiency: fragile erythrocytes for humans scaly skin, muscle weakness and wasting, sterility

31. Vitamin K: active prothrombin formation Vit. K deficiency: hemorrhagic disease of the newborn in U.S.A., newborns are injected Vit. K Vit. K1 rich in green plant leaves Vit. K2 is formed by the intestinal bacteria Nelson K2: menaquinone

32. Key reactions are reiterated throughout metabolism 15.5 p. 237 EC1 oxidoreductase ligase EC6 isomerase transferase EC5 EC2 hydrolase EC3 EC4 lyase p. 427 can proceed in either direction, depending on G and [reactants] and [products]

33. Isomerization aconitase Glucose isomerase

34. The addition of functional groups to double bonds or removal of groups to form double bonds —lyase aldolase enolase

35. The commonalties in the diverse metabolic pathway (02)

36. Metabolic processes are regulated in four principal ways 1.The amount of enzymes the rate of synthesis and degradation the rate of transcription of the genes that encoding enzymes 2. The catalytic activities of enzymes the reversible allosteric inhibition CTP inhibit asparate transcarbamoylase the reversible covalent modification phosphorylation, glycosylation, lipidation, methylation hormone coordination:epinephrine, insulin act through 2nd messengers 3. The accessibility of substrates the flux of substrates among different compartments compartmentalization (synthesis/degradation) 4. The energy state myristoylation, palmitoylation,prenylation farnesylation

37. Farnesyl transferase inhibitors are a new class of biologically active anticancer drugs. The exact mechanism of action of this class of agents is, however, currently unknown. The drugs inhibit farnesylation of a wide range of target proteins, including Ras. It is thought that these agents block Ras activation through inhibition of the enzyme farnesyl transferase, ultimately resulting in cell growth arrest. Ubiquitination: lysis protein Sumoylation: repress gene expression small ubiquitin-like modifer, SUMO KXE

38. Energy charge: [ATP] + 0.5 [ADP] / {[ATP] + [ADP] + [AMP]} catabolism The pH of a cell anabolism 0.9 Phosphorylation potential: [ATP] / [ADP] [Pi] ex. 11

39. Evolution of metabolic pathways RNA ribozymes

40. 96 T

41. 97T

42. 96 C

43. 97C

44. 98T