Chapter 18. Metabolism--an Overview. to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham. Biochemistry 2/e - Garrett & Grisham

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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

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 CO 2 ; 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 CO 2, O 2, and H 2 O are recycled See Figure 18.3

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

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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

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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

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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 on and the other off

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16 The ATP Cycle ATP is the energy currency of cells Phototrophs transform light energy into the chemical 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

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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: 14 C, 3 H, 32 P Stable heavy isotopes: 18 O, 15 N

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 B 1 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

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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 !!

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 + )

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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

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32 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.

33 Riboflavin and the Flavins Vitamin B 2 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!

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35 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 Other transfers are possible!

36 Coenzyme A Pantothenic acid (vitamin B 3 ) 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

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38 Vitamin B 6 Pyridoxine and pyridoxal phosphate Catalyzes reactions involving amino acids Transaminations, decarboxylations, eliminations, racemizations and aldol reactions See Figure This versatile chemistry is due to: formation of stable Schiff base adducts a conjugated electron sink system that stabilizes reaction intermediates

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42 Pyridoxal Phosphate Mechanisms Figure 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-ofchapter problems.

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44 Vitamin B 12 Cyanocobalamin B 12 is converted into two coenzymes in the body: 5'-deoxyadenosylcobalamin methylcobalamin

45 Vitamin B 12 Cyanocobalamin Dorothy Hodgkin determined the crystal structure of B 12 in 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 nm (2.05 A) - an essentially covalent bond

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47 B 12 Function & Mechanism See Figures B 12 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)

48 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

49 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

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51 Biotin "Chemistry on a tether" Biotin functions as a mobile carboxyl group carrier Bound covalently to a lysine The biotin-lysine conjugate is called biocytin The biotin ring system is thus tethered to the protein by a long, flexible chain

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53 Biotin Carboxylations Most use bicarbonate and ATP Whenever you see a carboxylation that requires ATP and CO 2 or HCO 3-, think biotin! Activation by ATP involves formation of carbonyl phosphate (aka carboxyl phosphate) Carboxyl group is transferred to biotin to form N- carboxy-biotin The "tether" allows the carboxyl group to be shuttled from the carboxylase subunit to the transcarboxylase subunit of ACC-carboxylase

54 Lipoic Acid Another example of "chemistry on a tether"! Lipoic acid, like biotin, is a ring on a chain and is linked to a lysine on its protein Lipoic acid is an acyl group carrier Found in pyruvate dehydrogenase and α-ketoglutarate dehydrogenase Lipoic acid functions to couple acyl-group transfer and electron transfer during oxidation and decarboxylation of α-keto acids

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56 Folic Acid Folates are donors of 1-C units for all oxidation levels of carbon except that of CO 2 Active form is tetrahydrofolate (THF) THF is formed by two successive reductions of folate by dihydrofolate reductase Know how to calculate oxidation states of C! See Table 18.6

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58 Vitamin A Retinol, retinyl esters and retinal are forms of Vitamin A Retinol-binding proteins (RBPs) help to mobilize and transport vitamin A and its derivatives Retinol is converted to retinal in the retina of the eye and is linked to opsin to form rhodopsin, a light-sensitive pigment protein in the rods and cones Vitamin A also affects growth and differentiation

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60 Vitamin D Ergocalciferol and cholecalciferol Cholecalciferol is made in the skin by the action of UV light on 7-dehydrocholesterol Major circulating form is 25-hydroxyvitamin D 1,25-dihydroxycholecalciferol (1,25- dihydroxyvitamin D 3 ) is the most active form It functions to regulate calcium homeostasis and plays a role in phosphorus homeostasis

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62 Vitamins E and K Less understood vitamins Vitamin E (α-tocopherol) is a potent antioxidant Molecular details are almost entirely unknown May prevent membrane oxidations Vitamin K is essential for blood clotting Carboxylation of 10 glutamyl residues on prothrombin (to form γ-carboxy-glu residues) is catalyzed by a vitamin K-dependent enzyme, liver microsomal glutamyl carboxylase

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