Chapter 18

Biochemistry 2/e - Garrett & Grisham
Chapter 18
Metabolism--an Overview
to accompany
Biochemistry, 2/e
by
Reginald Garrett and Charles Grisham
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Copyright © 1999 by Harcourt Brace & Company
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 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

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!!

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 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


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 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.


Vitamin B12
Cyanocobalamin
• B12 is converted into two coenzymes in

the body:
– 5'-deoxyadenosylcobalamin
– methylcobalamin

Vitamin B12
Cyanocobalamin
• 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 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
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 Carboxylations
Most 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 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
-ketoglutarate dehydrogenase
• Lipoic acid functions to couple acyl-group
transfer and electron transfer during oxidation
and decarboxylation of -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 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


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 (-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



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Biochemistry 2/e - Garrett & Grisham

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A Common Set of Pathways

The Sun is Energy for Life

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Catabolism and Anabolism

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The ATP Cycle

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A comparison of state of reduction of

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Isotope Tracers as Probes

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Role of the Thiazolium

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Nicotinic Acid and the

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Last Notes on Nicotinamides

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Riboflavin and the Flavins

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• B12 is converted into two coenzymes in

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• Dorothy Hodgkin determined the crystal

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B12 Function & Mechanism

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