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Biochemistry 2/e - Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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



Outline

• 18.1 Basic Set of Metabolic Pathways

• 18.2 Catabolism and Anabolism

• 18.3 Experimental Methods

• 18.4 Nutrition

• SPECIAL FOCUS: Vitamins



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



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



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



Metabolism

• Metabolism consists of catabolism and

anabolism

• Catabolism: degradative pathways

– Usually energy-yielding!

• Anabolism: biosynthetic pathways

– energy-requiring!



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



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



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



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



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



A comparison of state of reduction of

carbon atoms in biomolecules.



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, 32P

• Stable ‘heavy’ isotopes: 18O, 15N



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



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



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



Thiamine 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 group



Role 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

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



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+)



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



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.



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!



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!



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

thioesters



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



Pyridoxal 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 B12Cyanocobalamin

• B12 is converted into two coenzymes in

the body:

– 5'-deoxyadenosylcobalamin

– methylcobalamin



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



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)



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 carrier



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



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



Biotin 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-carboxylase



Lipoic 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

α-ketoglutarate dehydrogenase

• Lipoic acid functions to couple acyl-group

transfer and electron transfer during oxidation

and decarboxylation of α-keto acids



Folic Acid

Folates 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 18.6



Vitamin 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

differentiation



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 D3) is the most active form

• It functions to regulate calcium homeostasis

• and plays a role in phosphorus homeostasis



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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