Lecture #9
Metabolism
Slide 1. In this lecture we will consider the general features of metabolism
in living organisms.
Slide 2. All organisms use ATP as the primary energy source.
-Almost all the energy used by living organisms originates from
photosynthesis (sunlight). Photoautotrophic cells (plants, green algae etc.)
trap sunlight to produce chemical energy (as ATP and NADPH). They then
use that energy to synthesize reduced organic compounds such as glucose.
-Heterotrophic cells (most non-phototosynthetic organisms) obtain
energy by oxidizing reduced organic material that is obtained either
directly or indirectly from consuming photosynthetic organisms.
-Most of the energy consumed by living organisms is used for motion,
signal transduction and amplification, biosynthesis and the active
transport of ions and metabolic intermediates.
Slide 3. When adenosine triphosphate (ATP) is used as a cofactor the two
terminal phosphates ( and  phosphates) release high amounts of energy
upon hydrolysis. These phosphates are linked to each other and to the 
phosphate by phosphoanydride bonds which release approximately 7.3
kcal per mole upon hydrolysis. The inner  phosphate, which is linked to a
carbon atom by a phosphoester bond, releases much less energy upon
hydrolysis and is not generally coupled to energy requiring reactions.
Slide 4. Thus, the hydrolysis of ATP results in energy output and in turn
serves as a source of energy input for other biochemical reactions.
Conversely the synthesis of ATP requires energy input and is coupled to
energy output from other catabolic reactions.
Slide 5. The three relevant forms of adenosine phosphate are adenosine
triphosphate (ATP), adenosine diphosphate (ADP), and adenosine
monophosphate (AMP).
Slide 6. A glance at a table of the standard free energies of hydrolysis
reveals some important information about metabolic reactions.
-With respect to glycolysis (the conversion of glucose to pyruvate or lactate)
it turns out that the phosphorylation of monosaccharides like glucose to form
phosphoester bonds requires the input of about 2 -5 kcal/mol.
-With respect to the dephosphorylation reactions in glycolysis, we can see
that the dephosphorylation of the trioses phosphoenolpyruvate and bisphosphoglycerate release 14.8 and 11.8 kcal/mol respectively. That is a very
high amount of energy released by these dephosphorylation reactions.
-On the other hand the conversion of ATP to ADP releases 7.3 kcal/mol.,
which is an intermediate amount of energy.
-What this all means is that ATP has a high enough phosphoryl transfer
potential so that it can donate a phosphate to the hexoses intermediates in
glycolysis in an energy releasing reaction. It also means that ADP can
accept a phosphate from the trioses phosphoenolpyruvate and bisphosphoglycerate in an energy releasing reaction (because they have an even
higher phosphoryl transfer potential than ATP). Thus the energy transfer
reactions in glycolysis all have a negative standard free energy (they
have a negative G) and are energetically favorable in the direction of
product formation.
Slide 7. The conversion of ATP to ADP and inorganic phosphate is
favored because the inorganic phosphate that is produced in the
hydrolysis of ATP has more resonance possibilities than does the 
phosphate of ATP. This means that that phosphate product of ATP
cleavage is at a lower energy level than it would be in ATP itself.
Slide 8. The diagram shows one possible resonance structure for
inorganic pyrophosphate which would creates two adjacent positive
charges. The juxtaposition of these two positive charges gives this
resonance structure a very high energy level and makes its occurrence
unlikely. This same result would apply to a similar resonance structure
between the  and  phosphates of ATP, so the occurrence of that form of
ATP is also unlikely.
Slide 9. Here is another list of standard free energies of hydrolysis.
Compounds at or near the top of the list are the better phosphoryl group
donors whereas compounds near the bottom of the list are better acceptors.
Slide 10. The figure shows three compounds, PEP, creatine phosphate,
and 1,3-BPG all of which have a higher phosphoryl transfer potential
than that of ATP, and thus these compounds can be used to
phosphorylate ADP to ATP.
Slide 11. The source of energy during exercise varies with duration and
intensity. Initial bursts of intense activity lasting seconds are fueled by
existing stocks of ATP and creatine phosphate. For exercise of longer
duration the body must rely on other metabolic activity—anaerobic
glycolysis, aerobic glycolysis, and the aerobic TCA cycle in that order.
During the earlier and often more intense stages of exercise (such as running
a mile) the metabolism of glucose is the primary source of energy. For
endurance events, such as marathons, ultramarathons or for long distance
cycling events, stored fats provide an additional major source of energy.
( nb. The green line on the figure may be taken to imply that anaerobic
metabolism supplies a high percentage of energy over a number of hours.
Although glycolysis provides energy over hours of activity, it is the aerobic
mode of glycolysis that prevails as the duration of exercise increases.)
Slide 12. This figure shows the core metabolic pathways which provide
energy in living organisms. The primary energy sources are fats,
carbohydrates and to a lesser extent proteins. There are three stages of
energy metabolism.
-During the first stage of energy production the biological polymers are
converted into their component parts.
-During stage two the component fatty acids, monosaccharides and amino
acids are oxidized to acetylCoA.
-In stage three acetylCoA is oxidized to carbon dioxide and water by the
TCA cycle and oxidative phosphorylation.
Slide 13. The production of energy by catabolic pathways in most
organisms is an oxidative process in which highly hydrogenated
compounds are oxidized in a stepwise manner into carbon dioxide. The
most reduced (highly hydrogenated) intermediates have the greatest free
energy of oxidation. This is illustrated by the oxidation of single-carbon
compound from methane to carbon dioxide.
Slide 14. Fatty acids have a greater free energy of oxidation and can
produce more energy than carbohydrates (about 2X) because the fats
are more highly reduced (they have a higher percentage of hydrogen
atoms).
Slide 15. The figure shows a network of interlocking and interdependent
biochemical reactions. For aid in comprehension we divide these into
distinct pathways. The reactions are exquisitely regulated by a variety of
mechanisms of which allosteric regulation of enzyme activity is the most
notable. The glycolysis pathway and the TCA cycle play a central role in
interconnecting with various other metabolic processes.
-Degradative (catabolic) pathways that break down complex biomolecules
often produce ATP energy. They are usually oxidative and result in the
production of NADH (or NADPH).
-Biosynthetic (anabolic) pathways that result in the production of complex
products often require the input of ATP energy. They are generally
reductive and require the participation of NADPH.
Slide 16. Next is a more detailed version of the same chart showing the
reactions in great detail—scary, isn’t it???
Slide 17. The rest of the chart—we expect that you will learn every single
intermediate and chemical reaction on these charts. Then we can retire and
one of you can teach this biochemistry course.
Slide 18. Here is another look at the three stages of catabolism.
-The first stage is often called digestion. In stage one biopolymers are
broken down into their component units—fatty acids, monosaccharides
and amino acids.
-In stage two the small biomolecules are further broken down by
various catabolic pathways that converge on acetylCoA as the common
product.
-Stage three consists of the common pathways of the TCA cycle and
oxidative phosphorylation. In this phase of catabolism acetylCoA is
converted to carbon dioxide and water coupled to the production of
ATP. The stage three pathways are oxidative and require oxygen.
Slide 19. During stage three of metabolism reduced intermediates are
oxidized to carbon dioxide and water with the concomitant formation of
ATP. The flow of electrons from the TCA intermediates through the
electron transport system energizes the transmembrane flow of protons
which creates a proton gradient across the inner mitochondrial membrane.
The proton gradient is then used to energize the formation of ATP. The
energy coupling is accomplished by the downhill flow of protons back into
the mitochondrial matrix through the proton dependent ATP synthase.
Slide 20. The energy input of 7.3 kcal/mol needed for the formation of
ATP from ADP and Pi comes from the downhill flow of protons across
the mitochondrial inner membrane through the proton dependent ATP
synthase.
Slide 21. The formation of ATP driven by a proton gradient is an
example of a coupled reaction. Such reactions are a key feature of
metabolism in living cells. In coupled reactions a thermodynamically
unfavorable reaction with a positive standard free energy (G) is coupled to
a favorable reaction with a negative G. Coupled reactions involve shared
intermediates. This sharing turns out to be a bit ephemeral in the case of
proton gradients so we will use an ATP-dependent phosphorylation reaction
as our example.
Slide 22. The diagram shows a chemical reaction that has a negative G.
The products are at a lower energy than the reactants so the overall reaction
is favorable.
Slide 23. The ATP-dependent phosphorylation of glucose exemplifies
the coupling of an unfavorable reaction to a favorable reaction. The
reaction of glucose plus Pi to form glucose-6-P is unfavorable with a positive
G of 13.9 kJ/mol. The hydrolysis of ATP to ADP has a negative G of
-30.5 kJ/mol. When the two reactions are combined, and ATP transfers its 
phosphate to glucose the overall reaction has a negative G of -16.6 kJ/mol.
Slide 24. It turns out that our coupled reaction example, the ATPdependent phosphorylation of glucose to form glucose-6-P, is the first
reaction of glycolysis. It is catalyzed by the enzyme hexokinase.
Slide 25. In order to exhibit activity many enzymes require small molecules
called cofactors in addition to the protein structure itself. Cofactors can be
inorganic ions or organic molecules. An enzyme that lacks an essential
cofactor is called an apoenzyme. The enzyme with the cofactor bound is
called a holoenzyme.
Slide 26. Nicotinamide Adenine Dinucleotide (NAD+) functions in
oxidation reactions as an acceptor of hydrogen and electrons. Its
phosphorylated variant Nicotinamide Adenine Dinucleotide Phosphate
(NADP+) functions in its reduced form as a donor of protons and electrons
in reduction reactions.
Slide 27. The Nicotinamide ring of NAD+ (and NADP+) is the site of
enzymatic activity, and it can exist in a reduced or oxidized state. The
riboses, phosphates, and the adenine base of these compounds are involved
in binding to enzyme active sites. When NAD+ acts as an oxidant, the
nicotinamide ring gains two electrons and a proton, with another proton
going into the solvent. The substrate which is being oxidized loses two
electrons and two protons.
Slide 28. The structure of NADPis the same as that of NAD only there
is a phosphate on the number two carbon of the lower ribose ring. The
extra phosphate changes the binding properties of these cofactors. Enzymes
that recognize one cofactor do not generally recognize the other. NADis
usually an oxidant for catabolic reactions, and NADPH generally functions
as a reductant for anabolic reactions.
Slide 29. Flavine adenine dinucleotide (FAD) also serves in oxidationreduction reactions. In this case it is the isoalloxazine ring that serves as
the site of activity. The remaining elements of the cofactor (ribitol,
phosphate, ribose and adenine) are involved in binding to the active site of
enzymes.
Slide 30. The isoalloxizine rings of FAD can accept two electrons and
two protons. In this reduction process two conjugated double bonds in
the rings are converted to one double bond. The FAD requiring enzymes
are often involved in reactions in which saturated carbon-carbon bonds are
converted to unsaturated double bonds.
Slide 31. Flavine mononucleotide (FMN) is an analog of FAD. It has the
same isoalloxizine ring system, but the rest of the structure is less elaborate.
Its mechanism of action in oxidation-reduction reactions is the same as that
of FAD, but it is recognized by different enzymes.
Slide 32. Thiamine pyrophosphate (TPP) is involved in the transfer of
two carbon fragments. The site of chemical activity is the carbon atom
between the nitrogen and sulfur atoms on the thiazole ring. The thiazole
ring is aromatic and, similar to a phenyl group, it can delocalize electrons
over its entire ring system. We will see this cofactor in the pyruvate
dehydrogenase reaction.
Slide 33. Coenzyme A (CoA-SH) plays an important role in the transfer
of acyl groups including acetate and other fatty acyl derivatives. CoA
has the elements of ADP in its structure plus an elaborate aliphatic chain
which is derived from the vitamin pantothenic acid plus mercaptoethylamine. At the working end of the molecule there is a
sulfhydryl. group. That sulfhydryl group of CoA is generally bonded by a
thioester linkage to acyl groups which are derived from carboxylic acids.
We will encounter AcetylCoA as the end product of stage II of catabolism
and as the substrate for the TCA cycle.
Slide 34. The figure 422a shows the generalized structure of acyl CoA’s
and the specific structure of acetyl CoA.
Slides 35-38. The next four tables give information about various organic
cofactors. You may wish to read through these from time to time because
this information is fair game for your board exams. However, I find it
excruciatingly boring to go through lists, so this is where I bail.