11/26/2007

Berg • Tymoczko • Stryer

Biochemistry
Sixth Edition

Chapter 15:
M t b li
Metabolism:
Basic Concepts and Design

Copyright © 2007 by W. H. Freeman and Company

Introduction
• Metabolism answers the questions
– How does a cell extract energy and reducing
power from its environment?
– How does a cell synthesize the building blocks of
its macromolecules and then the
macromolecules themselves?

• What do we mean by “reduction”?

–
–

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Introduction
• Even prokaryotic organisms like E. coli use
more than 1000 chemical reactions in
metabolism
• Many reactions display common motifs, such
as
– Use of an energy currency (typically ATP)
– Repeated appearance of a limited number of
activated intermediates (~100 molecules,
important for all organisms)
– Number of kinds of reactions is small,
mechanism used generally simple
– Pathways regulated in common ways

Coupled, Interconnecting
Reactions
• Why do organisms need energy?
– Performance of mechanical work
– Active transport off molecules and ions
– Synthesis of macromolecules and biomolecules
from simple precursors
• This energy obtained from the environment
– Phototrophs trap energy from sunlight
– Chemotrophs oxidize foodstuffs generated by
phototrophs

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Hummingbirds
• Fly 500 miles across
Gulf of Mexico
without stopping!
• Weighs only 3.0 to
4.0 grams
• Fuel for trip is 1.3
grams of fat

Coupled, Interconnecting
Reactions
• Metabolism – a linked
series of chemical
reactions that begins with a
particular molecule and
converts into some other
molecule or molecules in a
carefully defined fashion

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Coupled, Interconnecting
Reactions
• Many metabolic
pathways in the
cell often
cell,
interdependent
• Communication
between pathways
coordinated often
by allosteric
enzymes

Coupled, Interconnecting
•
Reactions
Metabolic pathways divided into 2 classes
– Those that convert energy from fuels to
biologically
g y useful forms, called catabolic
reactions or catabolism
• Fuel (carbs, fats) → CO2 + H2O + useful energy
– Those that require energy input to proceed,
called anabolic reactions or anabolism
• Useful energy + simple precursors → complex
molecules
– Some pathways can be either catabolic or
anabolic, depending on energy conditions of cell,
called amphibolic
–

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Coupled, Interconnecting
Reactions
• How do we go from single reactions to
pathways?
• Pathway needs to satisfy:
f
– Individual reactions must be specific
– Entire set of reactions in pathway must be
thermodynamically favored
• Review of thermodynamics
– If ΔG > 0, reaction is
– If ΔG < 0, reaction is
– If ΔG = 0, reaction is

Coupled, Interconnecting
Reactions
• For the reaction A + B → C + D

[C ][ D ]
• ΔG = ΔG o ' + RT ln
l
[ A][ B ]
• Overall ΔG for a series of reactions is equal to the
sum of ΔG of each individual reaction
• A↔B+C ΔGo’ = +21 kJ/mol
• B↔C+D ΔGo’ = -34 kJ/mol
•

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ATP, the Currency of Free Energy

• Adenosine triphosphate, ATP
– Part of free energy from oxidation of food or light
energy converted into ATP
– ATP acts as free energy donor in most energy
requiring processes
• Motion, active transport, biosynthesis
–

ATP, the Currency of Free Energy

• ATP hydrolysis is exergonic (ΔG < 0)
• ATP energy rich because of 2 high energy

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ATP, the Currency of Free Energy

• ATP + H2O ↔ ADP + Pi ΔGo’ = -30.5
kJ/mol
• ATP + H2O ↔ AMP + PPi ΔG Go’ = -45.6
kJ/mol
• Under cellular conditions, actual ΔG ~ -50
kJ/mol
• Reverse reactions catalyzed by NMP kinases
or NDP kinases (recall from Chap. 9)
• Formation of ATP from ADP + Pi occurs
when chemotrophs oxidize food
• Some reactions use GTP, UTP, or CTP

NMP Kinases
• Nucleoside Monophosphate Kinases (NMP
Kinases)
– Catalyze transfer of the terminal phosphoryl group from a
nucleoside triphosphosphate (NTP, usually ATP) to the
phosphoryl group on a NMP
– E.g., adenylate kinases
–

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NMP Kinases & P Loops

• NMP kinase family contain P-loop structures
– X-ray structures of free & substrate bound forms
– Purple is NTP binding domain
– P-loop interacts with phosphoryl groups of bound
nucleotide, has sequence

P-loop in
green

NMP Kinases & P Loops

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ATP, the Currency of Free Energy

• How does ATP hydrolysis make a rxn favorable?
– Recall that free energy of reactions is additive
– A ↔ B,B ΔGo’ = +16 +16.7 7 kJ/mol
The K eq = [ B]eq /[ A]eq = 10− ΔG = 1.15 x 10−3
o '/ 5.69

– '

– But, if coupled to ATP hydrolysis

– A + ATP + H2O ↔ B + ADP + Pi, ΔGo’ = -13.8 kJ/mol
– K’eq now equal to 2.67 x 102, favors products!
– Has changed g the ratio of [[B]] to [A] [ ] byy a factor of about
10 , if used the energy of ATP hydrolysis under cellular
5

conditions, ratio of [B] to [A] changes by about 108

ATP, the Currency of Free Energy

• Energetics of ATP hydrolysis
– Several ATP may be coupled to a reaction
– For n ATP, equilibrium ratio changes by 108n
8

• A & B can be more than different molecules

– A & B may be inactive & active conformations of
an enzyme, like the molecular motor myosin
– A & B may refer to active transport of a molecule
or ion into or out of the cell

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ATP, the Currency of Free Energy

• Why is ATP such a good phosphoryl donor?
– ATP + H2O ↔ ADP + Pi ΔGo’ = -30.5 kJ/mol
– Glycerol
G 3-phosphate + H2O ↔ Glycerol
G + P i,
ΔG ’ = -9.2 kJ/mol, much smaller than ATP!
o

– ATP has a higher “phosphoryl transfer potential”

– Three factors important
•

ATP, the Currency of Free Energy

• Resonance stabilization
– ADP & Pi more stabilized by resonance than
ATP
–

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ATP, the Currency of Free Energy

• Electrostatic Repulsion
– At physiological pH, charge on ATP is 4-
– Strong
S electrostatic repulsion between them
–

ATP, the Currency of Free Energy

• Stabilization due to hydration
– More H2O can surround ADP and Pi than ATP,
increasing stabilization due to solvation

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ATP, the Currency of Free Energy

• Some molecules have a
higher phosphoryl
transfer potential than
ATP
– PEP
– Creatine phosphate
– 1,3-BPG
•

ATP, the Currency of Free Energy

• ATP has intermediate phosphoryl-transfer
potential

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ATP, the Currency of Free Energy

• Muscle contraction
– ATP stored in muscle can sustain activity for < 1
sec
– Creatine phosphate also stored in muscle
– Creatine phosphate then transfers a phosphoryl
group to ADP, catalyzed by creatine kinase
– Creatine phosphate + ADP ↔ ATP + creatine
– The ΔGo’ = -12.6 kJ/mol, corresponding to Keq =
162
– Creatine phosphate major source of ATP
regeneration for next several seconds
–

ATP, the Currency of Free Energy

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Oxidation of Fuels
• ATP is an immediate donor of free energy,
not a long-term storage form of free energy
• Typically, an ATP is consumed within ~1
minute of its formation
• Total ATP in the body is ~100g, but turnover
is very high
– In 24 hours a resting human turns over 40 kg
ATP
– During exercise, may turnover up to 0.5 kg
ATP/min
•

Oxidation of Fuels
• In aerobic metabolism, ultimate electron
acceptor in metabolism is O2 and oxidation
product is CO2
• The more reduced the fuel,

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Oxidation of Fuels
• How is oxidation free energy converted to
ATP?
– E.g.,
E oxidation
id ti energy used d tto create
t a
compound with a high phosphoryl-transfer
potential
– Glyceraldehyde-3-phosphate, a metabolite of
glucose, can be further oxidized

+ Energy

Oxidation of Fuels
• Oxidation occurs in steps
– 1st, carbon oxidation generates an acyl
phosphate and
phosphate,

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Oxidation of Fuels
• Oxidation occurs in steps
– 2nd, 1,3-BPG has high phosphoryl-transfer
potential,
potential

Oxidation of Fuels
• How is oxidation free energy converted to
ATP?
– E.g.,
E oxidation
id ti energy used d tto create
t an iion
gradient that results in formation of ATP
– Electrochemical potential across membranes
created by ion gradients most common way to
form ATP
– In i l H+ gradients
I animals, di account ffor >90%
90% ATP
generation, called oxidative phosphorylation
–

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Oxidation of Fuels

Oxidation of Fuels
• Energy from food extracted in three stages
– 1st, large molecules in food broken down into
smaller units in a process called digestion
• Proteins hydrolyzed to
• Polysaccharides hydrolyzed to
• Fats hydrolyzed to
– 2nd, the small molecules are degraded to a few
simple units that play a central role in
metabolism
• Most, including sugars, fatty acids, glycerol, & many
amino acids, are converted into the acetyl unit of
acetyl-CoA
• A small amount of ATP generated

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Oxidation of Fuels
• Energy from food extracted in three stages
– 3rd, ATP produced from complete oxidation of the
acetyl unit of acetyl-CoA
acetyl CoA
• 3rd stage contains citric acid cycle and oxidative
phosphorylation, which are the final common
pathways in the oxidation of fuel molecules
• Acetyl CoA brings acetyl units into the citric acid cycle
(also called tricarboxylic acid (TCA) cycle or Krebs
cycle)
• Acetyl units then oxidized to CO2, 3 e- pairs
transferred to NAD+, 1 e- pair transferred to FAD for
each acetyl group
• Then H+ gradient is generated as e- flow from NADH
& FADH2 to O2, gradient used to make ATP

Oxidation of Fuels

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Recurring Motifs in Metabolism

• Activated Carriers, e.g., ATP an activated
carrier of a phosphoryl group
• Other
O activated carriers include
– Activated carriers of electrons for fuel oxidation
– Activated carriers of electrons for reductive
biosynthesis
–

Recurring Motifs in Metabolism

• Activated carriers of electrons for fuel
oxidation
– Ultimate
Ulti t e- acceptor t is
i O2, but
b t iintermediate
t di t
carriers of either pyridine nucleotides or flavins
used to accept e- directly from fuel molecules
– These carriers then transfer e- to O2
– E.g., nicotinamide adenine dinucleotide, NAD+, a
pyridine
idi dderivative
i i or nicotinamide
i i id adenine
d i
nucleotide phosphate, NADP +

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Recurring Motifs in Metabolism

Recurring Motifs in Metabolism

• Flavin adenine dinucleotide, FAD+

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Recurring Motifs in Metabolism

Recurring Motifs in Metabolism

• Activated carriers of electrons for reductive
biosynthesis
– Precursors
P usually
ll more oxidized
idi d th
than products
d t
–
–

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Recurring Motifs in Metabolism

• Reductive biosyntheses
– Electron donor typically NADPH (NADH used
primarily for ATP generation)
–

Recurring Motifs in Metabolism

• Activated carriers of two-carbon fragments
– Coenzyme A (CoA-SH) is a carrier of acyl groups
–

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Recurring Motifs in Metabolism

• Acetyl CoA, input for TCA cycle

– Has a large hydrolysis energy, why?

Recurring Motifs in Metabolism

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Recurring Motifs in Metabolism

• Use of activated carriers illustrates two points
– 1st, ATP, Acetyl-CoA, NADH, NADPH, & FADH2
react slowly with O2 in absence of a catalyst
• Their kinetic stability enables enzymes to control flow
of free energy and reducing power
– 2nd, most interchanges of activated groups in
metabolism accomplished by a small set of
carriers
• Illustrates the modular design of metabolism, us a
unifying motif of biochemistry

Recurring Motifs in Metabolism

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Recurring Motifs in Metabolism

• Many activated carriers derived from
vitamins
–

Recurring Motifs in Metabolism

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Recurring Motifs in Metabolism

• Humans need to ingest 12 vitamins
• Not all vitamins coenzymes, e.g., A, C, D, E,
K

Recurring Motifs in Metabolism

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Recurring Motifs in Metabolism

• The thousands of biochemical reactions can
be subdivided into just 6 types

Recurring Motifs in Metabolism

• Redox reactions
– Reactions below from TCA cycle completely
oxidize acetyl CoA to two molecules of CO2

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Recurring Motifs in Metabolism

• Ligation reactions
– Form bonds using free energy from ATP
cleavage
– Formation of carbon-carbon bonds essential to
create large molecules from small molecules

Recurring Motifs in Metabolism

• Isomerization reactions
– Rearrange particular atoms within a molecule
–

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Recurring Motifs in Metabolism

• Group transfer reactions
– E.g., in glycolysis a phosphoryl group is
transferred from ATP to glucose

Recurring Motifs in Metabolism

• Hydrolytic reactions
– Cleave bonds by addition of H2O
–

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Recurring Motifs in Metabolism

• Addition or removal of functional groups
– These reactions catalyzed by lyases
–

Recurring Motifs in Metabolism

• Addition or removal of functional groups
–

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Regulation of Metabolism
• Metabolism regulated in three principal ways
–

Regulation of Metabolism
• Controlling the amounts of enzymes
– How is the amount of enzyme controlled?
– Primarily by changing the rate off gene
transcription
• Controlling catalytic activity
– Reversible allosteric control
• E.g.,
g feedback inhibition, as in cytidine
y triphosphate
p p
• Extremely quick response
– Reversible covalent modification
• E.g., phosphorylation, ubiquitination, etc.

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Regulation of Metabolism
• Controlling catalytic activity, cont.
– Hormones coordinate metabolism between
different tissues
• Often by controlling reversible modifications of
enzymes
• E.g., epinephrine triggers a signal-transduction
cascade in muscle, leading to phosphorylation of
enzymes
– Energy status of the cell
• One measure
Energy of energy[ATP]
charge status+ is
½ the
[ADP]
energy charge
= [ATP] + [ADP] + [AMP]

Regulation of Metabolism
• Energy charge, cont.

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Regulation of Metabolism
• Phosphorylation potential, alternative
measure of a cell’s energy status

[ATP]
Phosphorylation potential
= [ADP] + [Pi]

Regulation of Metabolism
• Controlling catalytic activity, cont.
– Controlling the accessibility of substrates
• IIn eukaryotes,
k t there
th is
i compartmentalization
t t li ti off
reactions
• Segregates opposing reactions
• E.g., fatty acid synthesis occurs in cytoplasm, fatty
acid oxidation occurs in mitochondria
• Controllingg flux of substrates also form of regulation
g
• E.g., transfer of substrates from one compartment to
another, like cytoplasm to mitochondria

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Regulation of Metabolism
• Controlling flux of substrates

Summary
• Metabolism is composed of many
interconnecting reactions
– Catabolism
C t b li breaks
b k down
d molecules
l l
– Anabolism builds up molecules
• ATP is the universal free energy currency
– Energy from catabolism (eventually) converted
to ATP
– Hydrolysis of ATP under cellular conditions shifts
equilibrium of a coupled reaction by ~108!

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Summary
• Oxidation of carbon fuels an important
source of cellular energy
– ATP formation
f ti coupled l d to
t oxidation
id ti off carbon
b
fuels, directly or through ion gradients
– Energy extracted from food in three stages
• Digestion of large molecules to small molecules
• Small molecules degraded to a few simple units (e.g.,
Ac CoA)
• TCA cycle and oxidative phosphorylation, where most
ATP is generated

Summary
• Metabolic pathways contain recurring motifs
– Activated carriers (ATP, NADH, acetyl CoA, etc.)
– Six key reactions (redox,
(redox isomerization
isomerization, etc
etc.))
• Metabolism regulated in a variety of ways
– Enzyme synthesis & degradation
– Allosteric interactions
– Covalent modifications
– Compartmentalization
C li i
– Movement of substrates
– Energy charge

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