Bài giảng Biochemistry 2/e - Chapter 18: Metabolism--an Overview

Chapter 18Metabolism--an Overviewto accompanyBiochemistry, 2/ebyReginald Garrett and Charles GrishamAll 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 Outline18.1 Basic Set of Metabolic Pathways18.2 Catabolism and Anabolism18.3 Experimental Methods 18.4 NutritionSPECIAL FOCUS: VitaminsMetabolismThe sum of the chemical changes that convert nutrients into energy and the chemically complex products of cellsHundreds of enzyme reactions organized into discrete pathwaysSubstrates are transformed to products via many specific intermediatesMetabolic maps portray the reactionsA Common Set of PathwaysOrganisms show a marked similarity in their major metabolic pathwaysEvidence that all life descended from a common ancestral formThere is also significant diversityAutotrophs use CO2; Heterotrophs use organic carbon; Phototrophs use light; Chemotrophs use Glc, inorganics & SThe Sun is Energy for LifePhototrophs use light to drive synthesis of organic moleculesHeterotrophs use these as building blocksCO2, O2, and H2O are recycledSee Figure 18.3MetabolismMetabolism consists of catabolism and anabolismCatabolism: degradative pathwaysUsually energy-yielding!Anabolism: biosynthetic pathwaysenergy-requiring!Organization in PathwaysPathways consist of sequential stepsThe enzymes may be separateOr may form a multienzyme complexOr may be a membrane-bound systemNew research indicates that multienzyme complexes are more common than once thoughtCatabolism and AnabolismCatabolic pathways converge to a few end productsAnabolic pathways diverge to synthesize many biomoleculesSome pathways serve both in catabolism and anabolismSuch pathways are amphibolicComparing PathwaysAnabolic & catabolic pathways involving the same product are not the sameSome steps may be common to bothOthers must be different - to ensure that each pathway is spontaneousThis also allows regulation mechanisms to turn one pathway on and the other offThe ATP CycleATP is the energy currency of cellsPhototrophs transform light energy into the chemical energy of ATPIn heterotrophs, catabolism produces ATP, which drives activities of cellsATP cycle carries energy from photosynthesis or catabolism to the energy-requiring processes of cellsRedox in MetabolismNAD+ collects electrons released in catabolismCatabolism is oxidative - substrates lose reducing equivalents, usually H- ionsAnabolism is reductive - NADPH provides the reducing power (electrons) for anabolic processesA comparison of state of reduction of carbon atoms in biomolecules.Isotope Tracers as ProbesSubstrates labeled with an isotopic form of some element can be fed to cells and used to elucidate metabolic sequencesRadioactive isotopes: 14C, 3H, 32PStable ‘heavy’ isotopes: 18O, 15NNutritionProtein is a rich source of nitrogen and also provides essential amino acidsCarbohydrates provide needed energy and essential components for nucleotides and nucleic acidsLipids provide essential fatty acids that are key components of membranes and also important signal moleculesVitaminsMany 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 chemistryVitamin B1Thiamine 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-hydroxyketonesThiamine PyrophosphateReactions 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 groupRole of the Thiazolium NitrogenKey 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!!Adenine Nucleotide CoenzymesAll use the adenine nucleotide group solely for binding to the enzyme! Several classes of coenzymes: pyridine dinucleotides flavin mono- and dinucleotides coenzyme A Nicotinic Acid and the Nicotinamide Coenzymesaka 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+) Nicotinamide CoenzymesStructural 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 designationsLast Notes on NicotinamidesSee 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.Riboflavin and the FlavinsVitamin 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!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 18.22Other transfers are possible!Coenzyme APantothenic 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 thioestersVitamin B6Pyridoxine and pyridoxal phosphate Catalyzes reactions involving amino acids Transaminations, decarboxylations, eliminations, racemizations and aldol reactions See Figure 18.26This versatile chemistry is due to: formation of stable Schiff base adducts a conjugated electron sink system that stabilizes reaction intermediatesPyridoxal PhosphateMechanisms 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.Vitamin B12 CyanocobalaminB12 is converted into two coenzymes in the body: 5'-deoxyadenosylcobalamin methylcobalamin Vitamin B12 CyanocobalaminDorothy 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 bondB12 Function & MechanismSee 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)Vitamin CAscorbic 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 carrierRoles of Vitamin CMany 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 systemBiotin"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 chainBiotin CarboxylationsMost use bicarbonate and ATP Whenever you see a carboxylation that requires ATP and CO2 or HCO3-, 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-carboxylaseLipoic AcidAnother 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 -ketoglutarate dehydrogenase Lipoic acid functions to couple acyl-group transfer and electron transfer during oxidation and decarboxylation of -keto acidsFolic AcidFolates are donors of 1-C units for all oxidation levels of carbon except that of CO2 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 18.6Vitamin ARetinol, 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 differentiationVitamin DErgocalciferol 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 D3) is the most active form It functions to regulate calcium homeostasis and plays a role in phosphorus homeostasisVitamins E and KLess understood vitamins Vitamin E (-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 -carboxy-Glu residues) is catalyzed by a vitamin K-dependent enzyme, liver microsomal glutamyl carboxylase