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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Biochemistry 2/e - Garrett & Grisham
Outline
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18.1 Basic Set of Metabolic Pathways
18.2 Catabolism and Anabolism
18.3 Experimental Methods
18.4 Nutrition
SPECIAL FOCUS: Vitamins
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Biochemistry 2/e - Garrett & Grisham
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
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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
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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
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Metabolism
• Metabolism consists of catabolism and
anabolism
• Catabolism: degradative pathways
– Usually energy-yielding!
• Anabolism: biosynthetic pathways
– energy-requiring!
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Biochemistry 2/e - Garrett & Grisham
Organization in Pathways
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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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Biochemistry 2/e - Garrett & Grisham
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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Biochemistry 2/e - Garrett & Grisham
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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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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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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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
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A comparison of state of reduction of
carbon atoms in biomolecules.
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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
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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
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Biochemistry 2/e - Garrett & Grisham
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
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Vitamin B1
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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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Thiamine Pyrophosphate
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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
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Role of the Thiazolium
Nitrogen
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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!!
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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
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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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Nicotinamide Coenzymes
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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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Biochemistry 2/e - Garrett & Grisham
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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.
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Riboflavin and the Flavins
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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!
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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!
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Biochemistry 2/e - Garrett & Grisham
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
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Vitamin B6
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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
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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-ofchapter problems.
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Vitamin B12
Cyanocobalamin
• B12 is converted into two coenzymes in
the body:
– 5'-deoxyadenosylcobalamin
– methylcobalamin
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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
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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)
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Vitamin C
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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
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Roles of Vitamin C
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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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Biotin
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"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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Biotin Carboxylations
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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 Ncarboxy-biotin
The "tether" allows the carboxyl group to be
shuttled from the carboxylase subunit to the
transcarboxylase subunit of ACC-carboxylase
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Lipoic Acid
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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
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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
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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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Vitamin D
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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 (1,25dihydroxyvitamin D3) is the most active form
It functions to regulate calcium homeostasis
and plays a role in phosphorus homeostasis
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Biochemistry 2/e - Garrett & Grisham
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Vitamins E and K
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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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