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Introduction to Aerobic Metabolism
The purpose of this lecture is to provide a general introduction to metabolic
principles as well as briefly discuss oxidative stress that results from the use of
oxygen as the final electron acceptor in aerobic catabolism.
1) We will briefly discuss an overview of catabolic and anabolic pathways.
2) We will discuss, again in brief, ATP as the universal currency of metabolic energy
and also review vitamins that are precursors for many of the coenzymes used in
metabolism.
3) The use of oxygen as the terminal electron acceptor in the oxidation of foodstuffs
permits much greater energy to be obtained from their breakdown than would be
possible in its absence. However, a byproduct of this role for oxygen is the
formation of toxic free radicals that result from incomplete reduction of oxygen.
We will discuss antioxidant defenses used to reduce toxic free radicals in the cell.
1. Overview of
metabolic pathways
At first glance, metabolism
appears to be a bewildering
array of chemical reactions.
The figure to the right
represents over 500 different
chemical intermediates and a
greater number of enzymes.
Virtually all organisms carry
out the same basic set of
metabolic pathways. Despite
these large number of
enzyme mediated reactions,
they actually represent a
highly integrated, and tightly
regulated, process. We will
only cover a very small
subset of these reactions in
the course.
From Garrett & Grisham “Biochemistry”
A more useful way to
illustrate an overview of
metabolism is shown to the
right with pathways colorcoded. This provides a first
glimpse of interrelationships
between major pathways.
For instance carbohydrate,
lipid and some amino acid
metabolism converge at the
formation of Acetyl CoA (dark
circle) prior to entering the
Krebs cycle (blue circle at the
lower center of the diagram.)
Probably most important, and
placed centrally in this
diagram, is carbohydrate
metabolism, which will be
discussed in detail in the next
three lectures.
From Berg, Tymoczko & Stryer “Biochemistry, 5th ed”
Metabolism can be divided into two major processes, termed catabolism and anabolism.
Catabolism is the process of breaking down the larger, reduced, compounds such as glucose, amino acids
or fatty acids. Energy is released as electrons are transferred from these reduced compounds ultimately to
oxygen forming to small end products such as CO2, H2O and NH3 to yield energy. These processes are
oxidative (meaning substrates are loosing electrons) and exergonic (energy releasing). In order to capture
the energy from these compounds, the oxidation reactions must be coupled with reactions that can store the
energy chemically, otherwise the energy will be released as heat. The many steps often used in catabolic
processes allow smaller packets of energy to be released and stored chemically, usually ultimately as ATP.
Anabolism is the reverse process of
building the macromolecules that
run the processes of the cell. Driving
the reductive, endergonic, reactions
is the chemical energy largely stored
in the form of ATP and reduced
NADPH. NADPH is used almost
exclusively for reductive
biosynthesis, while NADH is used in
the generation of ATP as will be
discussed in the next few lectures.
Whereas catabolic pathways
converge to only a very few end
products, anabolic pathways diverge
to synthesize a huge variety of
molecules from a small set of
building blocks.
From Garrett & Grisham “Biochemistry”
Overview of catabolism.
It is useful to classify the
process of catabolism as
comprising three stages. The
first stage involves the
breakdown of large
macromolecules into their
component building blocks.
The second stage involves the
degradation of these building
blocks into a common product,
Acetyl CoA (with some
products of amino acid
degradation producing
intermediates in the citric acid
cycle). The final stage of
catabolism is the aerobic
combustion of the acetyl
groups of acetyl CoA by the
citric acid cycle and oxidative
phosphorylation to produce
CO2 and H20. As will be
discussed in lecture 27,
oxidation of acetyl CoA
generates most of the energy
produced by the cell.
From Garrett & Grisham “Biochemistry”
A central molecule in metabolism, about which you will hear much more in the next few
lectures, is Acetyl CoA. This molecule is an activated carrier of two carbon units, acquiring
them in the oxidation of carbohydrate, fats and amino acids. Shown below is the structure of
Coenzyme A. The sulfhydryl group (left) can be linked with acyl groups by thioester bonds.
Coenzyme A is formed from ADP (with a phosphorylated 3’ hydroxyl on the ribose sugar), plus
pantothenate (a B vitamin) and a b-mercaptoethylamin unit. We will briefly discuss vitamins
slightly later in the lecture.
Coenzyme A:
From Berg, Tymoczko & Stryer “Biochemistry, 5th ed”
2. ATP, energy, coenzymes and vitamins
Life requires the continual input of energy for building macromolecules, maintaining ionic
gradients, motion and many other purposes. ATP is considered the universal currency of free
energy in biological systems. Hydrolysis of ATP to ADP (or AMP) is a highly favorable
reaction (DGº = -7.3 kcal/mol) due to the resonance bonding and electrostatic repulsion of
phosphates. By coupling its hydrolysis with otherwise unfavorable reactions it can drive such
reactions that are key to living processes (see below). ATP is continually being used in energy
requiring processes and regenerated during catabolism through processes discussed in the next
three lectures.
Favorable process (-DG )
Unfavorable process (+DG)
Coupling of a Favorable process (-DG ) with an Unfavorable (+DG )
yields an overall favorable reaction (-DG )
-DG
+DG
ATP is the universal currency of metabolic energy, but it is constantly being spent and
regenerated. It is estimated that ATP stores (~4mM) provide sufficient energy to maintain muscle
contraction for only a second. Muscle also contains creatine phosphate (~25mM) that can be
used to generate ATP and thus supply energy for a few seconds. (Creatine phosphate is the major
source for generating ATP during the first 4 seconds of a 100 meter sprint.) After these stores are
used up, ATP must be generated through metabolism. As will be discussed in Block III, glycogen
provides a readily mobilized storage of glucose, particularly in the muscle and liver. Glucose
units from glycogen can be degraded through glycolysis anaerobically to yield a small quantity of
ATP or aerobically to produce much more ATP if oxygen is sufficient.
From Berg, Tymoczko & Stryer “Biochemistry, 5th ed”
Carbon Fuels: The transient stores of ATP are constantly being replenished by the oxidation
of carbon fuels. Shown below are the free energies associated with oxidation of one-carbon
compounds to carbon dioxide. Physiological fuels are obviously more complex (bottom), but
the trends in free energy of oxidation will be similar.
Glucose is an extremely important fuel that is universally and, under well-fed circumstances,
the sole energy source for the brain. However, fats provide a more efficient long-term energy
storage since their carbon atoms are more reduced than those of sugars.
Vitamins are small organic molecules required in small amounts in the diet of higher animals,
several of which are used as precursors to coenzymes, as has already been alluded to earlier in the
course. You will be exposed to vitamins at various points throughout the course; this chart is to
provide some familiarity with them.
Water-Soluble Vitamins
Vitamin
Coenzyme
Typical reaction type
Consequences of
deficiency
Thiamine (B1)
Thiamine pyrophosphate
Aldehyde transfer
Beriberi
Riboflavin (B2)
Flavin adenine dinucleotide (FAD)
Oxidation-reduction
Pyridoxine (B6)
Pyridoxal phosphate
Group transfer to or from
amino acids
Cheliosis,
dermititis
Nicotinic acid
(niacin- B3)
Nicotinamide adenine dinucleotide
(NAD+)
Oxidation-reduction
Pellagra
Pantothenate (B5)
Coenzyme A
Acyl-group transfer
Hypertension
Biotin
Biotin-lysine complexes (biocytin)
Folic acid
Tetrahydrofolate
B12
5’ Deoxyadenosyl cobalamin
C (ascorbic acid)
Depression,
convulsions
ATP-dependent carboxylation Rash, muscle pain
and carboxyl-group transfer
Anemia, neuralTransfer of one-carbon
tube defects in
components; thymine synthesis development
Transfer of methyl groups;
Anemia
intramolecular rearrangements
Scurvy
Antioxidant
(NAD+)
(Coenzyme A)
(FAD)
The B-vitamins are
components of coenzymes.
Pyridoxal Phosphate
Involved in transferring amino groups
Coenzyme A
From Berg, Tymoczko & Stryer “Biochemistry, 5th ed”
Adenosine diphosphate (ADP) is a fundamental building block in key
metabolic compounds including ATP, NADH, FAD and Coenzyme A.
This suggests ADP is an ancient module in the evolution of metabolic
pathways.
From Berg, Tymoczko & Stryer “Biochemistry, 5th ed”
Fat-Soluble Vitamins
Vitamin
Function
Consequences of Deficiency
A
Roles in vision, growth,
reproduction
Night blindness, cornea damage, damage to
respiratory and gastrointestinal tract
D
Regulation of calcium and
phosphate metabolism
Rickets (children): skeletal deformaties, impaired
growth
Osteomalacia (adults): soft, bending bones
E
Antioxidant
Inhibition of sperm production; lesions in muscles and
nerves (rare)
K
Blood coagulation
Subdermal hemorrhaging
A hallmark of eukaryotes is the compartmentalization of different tasks. Metabolism is no
exception to such compartmentalization. Many tasks involve shuttling components between
the cytosol and mitochondria. As an example, consider glucose metabolism below. Glycolysis
takes place in the cytosol. To continue the breakdown of pyruvate under aerobic conditions, it
is transported into the mitochondria, which contains the enzymes of the citric acid cycle and
the enzymes and membrane structure used for oxidative phosphorylation and electron
transport.
From Garrett & Grisham “Biochemistry”
3. Oxidative Stress
Aerobic catabolism permits much greater energy from the breakdown
of glucose (and other compounds) than is possible under anaerobic
conditions. This high yield, however, comes at the price of potential
poisoning by intermediates in the reduction of oxygen. These
intermediates are termed reactive oxygen species (ROS). Although
most of the oxygen consumed during aerobic metabolism is fully
reduced to H20, some free radicals are produced as byproducts. In
addition, reactions of oxygen with drugs and environmental toxins can
also add to the level ROS. It is estimated that 3 to 5% of the oxygen
we consume is converted to oxygen free radicals. Cells contain
antioxidant enzymes designed to remove ROS. When the ability of
the cell to deal with these ROS is overwhelmed, oxidative stress
results.
From “Marks – Basic Medical
Biochemistry, a Clinical Approach”
Oxygen radicals, like all radicals, have a single unpaired electron
in an orbital. (A free radical is one that is capable of independent
existence.) Radicals are highly reactive because they will extract
an electron from a neighboring molecule to fill their orbital, which
can initiate a chain reaction. The superoxide anion, resulting from
a single electron transfer to oxygen, will not diffuse far from the
site of origin, but can generate other radicals. Hydrogen peroxide
is not a radical, but can participate in the generation of free
radicals (see right) and can diffuse through membranes to expand
the extent of free radical damage. The hydroxyl radical is the most
reactive species and can be produced from hydrogen peroxide and
superoxide, through reactions shown to the right. Oxidative stress
is thought to contribute to a large number of disease states (see
below).
Some disease states associated with oxidative stress
From “Marks – Basic Medical
Biochemistry, a Clinical Approach”
The first line of cellular defense against oxygen radicals is the enzyme superoxide dismutase
(SOD). There are three important isoforms of SOD, including a Cu/Zn protein in the cytosol, a
Mn protein in the mitochondria and an extracellular Cu/Zn enzyme. SOD catalyzes the
reaction of 2 superoxide molecules (O2-) to form one molecule of O2 and one of hydrogen
peroxide (H2O2). Catalase is a key enzyme that rids the cell of hydrogen peroxide and is
found largely in peroxisomes (organelles that generate a fair bit of hydrogen peroxide during
long-chain fatty acid oxidation and other reactions), with smaller amounts in the cytosol.
Superoxide dismutase converts superoxide
to molecular oxygen and hydrogen
peroxide in two steps.
From “Marks – Basic Medical
Biochemistry, a Clinical Approach”
A third important mechanism for the
cell’s defense of oxidative stress is
the use of reduced glutathione (GSH) to detoxify hydrogen peroxide
(see right). Glutathione peroxidase
catalyzes the reaction of reduced
glutathione (G-SH) and hydrogen
peroxide to form oxidized glutathione
(G-S-S-G) and water. Reduced
glutathione is then regenerated by
glutathione reductase, using electrons
donated by NADPH.
Fig. 13.6 from Lippincott
A number of exogenous antioxidant
compounds are also thought to be able to
contribute to the detoxification of reactive
oxygen species. Included among these are
vitamins C (below) and E (right). Vitamin E
may play an especially important role in
protecting membranes from lipid peroxidation
since it is hydrophobic in nature. Eating foods
rich in these antioxidants has been correlated
with reduced risk of various diseases
associated with oxidative stress. However,
clinical trials with dietary supplements have
been less convincing.
Vitamin E (atocopherol) acts to
terminate free
radical lipid
peroxidation by
donating single
electrons to lipid
peroxyl radicals to
form the more
stable lipid
peroxide (LOOH).
As a result, atocopherol is
converted to the
fully oxidized
version. From
“Marks – Basic
Medical Biochemistry,
a Clinical Approach”
L-Ascorbate (Vitamin C), in addition to the classical role it plays in formation of hydroxy
proline in collagen, can play a more general role in donating single electrons to free radicals or
disulfides as it is oxidized to dehydro-L-ascorbic acid. It may also play an important role in
regeneration of Vitamin E. From “Marks – Basic Medical Biochemistry, a Clinical Approach”
Sample questions:
Which of the following compounds contributes to the cell’s defense against
oxidative stress?
A)
B)
C)
D)
E)
Pyridoxine
Coenzyme A
Vitamin E
Biotin
Vitamin A
Which of the following is NOT considered a reactive oxygen species (ROS)?
A)
B)
C)
D)
Superoxide
Hydroxyl ion
Hydrogen peroxide
Hydroxyl radical
Study Points :
1) Understand that catabolism refers to the oxidative breakdown of reduced
compounds such as glucose, amino acids and fatty acids to form small compounds
such as CO2, H2O and NH3 with the release of energy.
2) Understand that anabolism is the reductive process of building a wide variety of
compounds using chemical energy that is largely stored in the form of ATP and
NADPH.
3) Recognize the general role of B-vitamins as components of important coenzymes
used in metabolic processes and be able to recognize key vitamins and their role
in metabolism.
4) Understand what is meant by “Oxidative Stress”.
5) Understand that reactive oxygen species (ROS) form during the incomplete
reduction of oxygen and be able to identify them.
6) Be able to recognize enzymes involved in cellular defense against oxidative stress
along with exogenous antioxidant compounds.