Metabolism: An Overview of Cellular Energy Transformation

1. Chapter 18 Metabolism--an Overview to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777

2. Outline • 18.1 Basic Set of Metabolic Pathways • 18.2 Catabolism and Anabolism • 18.3 Experimental Methods • 18.4 Nutrition • SPECIAL FOCUS: Vitamins

3. Metabolism • The sum of the chemical changes that convert nutrients into energy and the chemically complex products of cells • Hundreds of enzyme reactions organized into discrete pathways • Substrates are transformed to products via many specific intermediates • Metabolic maps portray the reactions

4. A Common Set of Pathways • Organisms show a marked similarity in their major metabolic pathways • Evidence that all life descended from a common ancestral form • There is also significant diversity • Autotrophs use CO2; Heterotrophs use organic carbon; Phototrophs use light; Chemotrophs use Glc, inorganics & S

5. The Sun is Energy for Life • Phototrophs use light to drive synthesis of organic molecules • Heterotrophs use these as building blocks • CO2, O2, and H2O are recycled • See Figure 18.3

7. Metabolism • Metabolism consists of catabolism and anabolism • Catabolism: degradative pathways • Usually energy-yielding! • Anabolism: biosynthetic pathways • energy-requiring!

9. Organization in Pathways • Pathways consist of sequential steps • The enzymes may be separate • Or may form a multienzyme complex • Or may be a membrane-bound system • New research indicates that multienzyme complexes are more common than once thought

11. Catabolism and Anabolism • Catabolic pathways converge to a few end products • Anabolic pathways diverge to synthesize many biomolecules • Some pathways serve both in catabolism and anabolism • Such pathways are amphibolic

13. Comparing Pathways • Anabolic & catabolic pathways involving the same product are not the same • Some steps may be common to both • Others must be different - to ensure that each pathway is spontaneous • This also allows regulation mechanisms to turn one pathway and the other off

16. The ATP Cycle • ATP is the energy currency of cells • In phototrophs, light energy is transformed into the light energy of ATP • In heterotrophs, catabolism produces ATP, which drives activities of cells • ATP cycle carries energy from photosynthesis or catabolism to the energy-requiring processes of cells

18. Redox in Metabolism • NAD+ collects electrons released in catabolism • Catabolism is oxidative - substrates lose reducing equivalents, usually H- ions • Anabolism is reductive - NADPH provides the reducing power (electrons) for anabolic processes

19. A comparison of state of reduction of carbon atoms in biomolecules.

20. Isotope Tracers as Probes • Substrates labeled with an isotopic form of some element can be fed to cells and used to elucidate metabolic sequences • Radioactive isotopes: 14C, 3H, 31P • Stable ‘heavy’ isotopes: 18O, 15N

21. Nutrition • Protein is a rich source of nitrogen and also provides essential amino acids • Carbohydrates provide needed energy and essential components for nucleotides and nucleic acids • Lipids provide essential fatty acids that are key components of membranes and also important signal molecules

22. Vitamins • Many vitamins are "coenzymes" - molecules that bring unusual chemistry to the enzyme active site • Vitamins and coenzymes are classified as "water-soluble" and "fat-soluble" • The water-soluble coenzymes exhibit the most interesting chemistry

23. Vitamin B1 Thiamine pyrophosphate (TPP) • Thiamine - a thiazole ring joined to a substituted pyrimidine by a methylene bridge • Thiamine-PP is the active form • TPP is involved in carbohydrate metabolism • It catalyzes decarboxylations of alpha-keto acids and the formation and cleavage of alpha-hydroxyketones

25. Thiamine Pyrophosphate Reactions and rationale • Yeast pyruvate decarboxylase, acetolactate synthase, transketolase, phosphoketolase • All these reactions depend on accumulation of negative charge on the carbonyl carbon at which cleavage occurs! • Thiamine pyrophosphate facilitates these reactions by stabilizing this negative charge • The key is the quaternary nitrogen of the thiazolium group

26. Role of the Thiazolium Nitrogen Key points: • It provides electrostatic stabilization of the carbanion formed by removal of the C-2 proton • It acts as an electron sink via resonance interactions • The resonance-stabilized intermediate can be protonated to give hydroxyethyl-TPP, an isolatable intermediate! • Study Figures 18.17-18.18!!

27. Adenine Nucleotide Coenzymes All use the adenine nucleotide group solely for binding to the enzyme! • Several classes of coenzymes: • pyridine dinucleotides • flavin mono- and dinucleotides • coenzyme A

28. Nicotinic Acid and the Nicotinamide Coenzymes aka pyridine nucleotides • These coenzymes are two-electron carriers • They transfer hydride anion (H-) to and from substrates • Two important coenzymes in this class: • Nicotinamide adenine dinucleotide (NAD+) • Nicotinamide adenine dinucleotide phosphate (NADP+)

30. Nicotinamide Coenzymes Structural and mechanistic features • The quaternary nitrogen of the nicotinamide ring acts as an electron sink to facilitate hydride transfer • The site (on the nicotinamide ring) of hydride transfer is a pro-chiral center! • Hydride transfer is always stereospecific! • Be sure you understand the pro-R, pro-S designations

31. Nicotinamide Coenzymes Structural and mechanistic features • The quaternary nitrogen of the nicotinamide ring acts as an electron sink to facilitate hydride transfer • The site (on the nicotinamide ring) of hydride transfer is a pro-chiral center! • Hydride transfer is always stereospecific! • Be sure you understand the pro-R, pro-S designations

33. Last Notes on Nicotinamides See box on page 590 • Nicotinamide was first isolated in 1937 by Elvehjem at the University of Wisconsin • Note similarities between structures of nicotinic acid, nicotinamide and nicotine • To avoid confusion of names (and functions!), the name niacin (for nicotinic acid vitamin) was suggested by Cowgill at Yale.

34. Riboflavin and the Flavins Vitamin B2 • All these substances contain ribitol and a flavin or isoalloxazine ring • Active forms are flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) • FMN is not a true nucleotide • FAD is not a dinucleotide • But the names are traditional and they persist!

36. Flavin Mechanisms Flavins are one- or two-electron transfer agents • Name "flavin" comes from Latin flavius for "yellow" • The oxidized form is yellow, semiquinones are blue or red and the reduced form is colorless • Study the electron and proton transfers in Figure 18.22 • Other transfers are possible!

37. Coenzyme A Pantothenic acid (vitamin B3) is a component of Coenzyme A • Functions: • Activation of acyl groups for transfer by nucleophilic attack • activation of the alpha-hydrogen of the acyl group for abstraction as a proton • Both these functions are mediated by the reactive -SH group on CoA, which forms thioesters

39. Vitamin B6 Pyridoxine and pyridoxal phosphate • Catalyzes reactions involving amino acids • Transaminations, decarboxylations, eliminations, racemizations and aldol reactions • See Figure 18.26 • This versatile chemistry is due to: • formation of stable Schiff base adducts • a conjugated electron sink system that stabilizes reaction intermediates

43. Pyridoxal Phosphate Mechanisms • Figure 18.27 is a key figure - relate each intermediate to subsequent mechanisms • Appreciate the fundamental difference between intermediates 2-5 and 6,7 • It would be a good idea to devote some time to the mechanisms in the end-of-chapter problems.

45. Vitamin B12Cyanocobalamin • B12 is converted into two coenzymes in the body: • 5'-deoxyadenosylcobalamin • methylcobalamin

46. Vitamin B12Cyanocobalamin • Dorothy Hodgkin determined the crystal structure of B12 in 1961 - at the time it was the most complicated structure ever elucidated by X-ray diffraction and she won a Nobel prize • Most striking feature - the C-Co bond length of 0.205 nm (2.05 A) - an essentially covalent bond

48. B12 Function & Mechanism See Figures 18.28-18.29 • B12 catalyzes 3 kinds of reactions: • Intramolecular rearrangements • Reductions of ribonucleotides to deoxyribonucleotides • Methyl group transfers (assisted by tetrahydrofolate - which is covered in a later section of this chapter)

49. Vitamin C Ascorbic acid • Most plants and animals make ascorbic acid - for them it is not a vitamin • Only a few vertebrates - man, primates, guinea pigs, fruit-eating bats and some fish (rainbow trout, carp and Coho salmon) cannot make it! • Vitamin C is a reasonably strong reducing agent • It functions as an electron carrier

50. Roles of Vitamin C Many functions in the body • Hydroxylations of proline and lysine (essential for collagen) are Vitamin C-dependent • Metabolism of Tyr in brain depends on C • Fe mobilization from spleen depends on C • C may prevent the toxic effects of some metals • C ameliorates allergic responses • C can stimulate the immune system