Module on Catabolism

CHEM41 and 43 Lecture Course Guide

Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Catabolism
Introduction
The degradation of carbohydrates, lipids, proteins and other macromolecules into simpler
molecules or small precursor molecules with concomitant release of energy is called
catabolism. The released energy is stored by the production of adenosine triphosphate (ATP)
which is used to power most cellular functions.

In order to utilize carbohydrates, fats and proteins as energy sources they are digested and
their digestion products are made to undergo series of enzymatic reactions. Starch, the
principal dietary carbohydrate, for instance is broken down into glucose, which through the
action of several enzymes found inside cells is oxidized to CO2 and H2O. Fats or triglycerides,
the major dietary lipids are hydrolyzed into fatty acids and glycerol and like glucose are
oxidized to carbon dioxide and water, though they follow different pathways. The amino acids
obtained from proteins are also utilized as sources of energy when taken in excess and during
starvation. The energy liberated from oxidations of the digestion products is stored mainly in
the phosphate bonds of ATP.

The utilization of carbohydrates, fats and proteins as energy sources can be divided into
three stages: stage 1: hydrolysis of dietary molecules into small monomers; stage 2: conversion
of monomers into acetyl CoA; stage 3: oxidation of acetyl CoA and production of ATP.

The purpose of the first stage of catabolism is to degrade large food molecules into their
small subunits so that they can be absorbed by the body. Simple sugars, amino acids, fatty
acids, and glycerol, obtained from hydrolysis of carbohydrates, proteins and fats, respectively
are taken into the cells of the body and are used as energy sources.

In the second stage, the monosaccharides, amino acids, fatty acids and glycerol obtained
in stage 1, are converted to acetyl CoA, the form that can be completely oxidized in the
tricarboxylic acid cycle (TCA cycle). Glucose and fructose enter first the glycolytic pathway
where a series of reactions convert them into pyruvate, which is eventually converted to acetyl
CoA. Fatty acids and certain amino acids are also converted to acetyl CoA, but in different
paths.

The third stage consists of the energy production mainly associated with TCA cycle and
oxidative phosphorylation. Acetyl CoA formed from pyruvate or from oxidation of fatty acid in
stage 2, enters the TCA cycle and the electrons and hydrogen are passed on to the ETC. The
energy released from the movement of electrons in the electron transport chain is used in the
process of oxidative phosphorylation to produce ATP.

Learning Objectives:
The students should be able to:

1. Discuss cellular respiration as the major catabolic and energy-producing pathway of all
cells

2. Illustrate various catabolic pathways for carbohydrates

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

3. Discuss the role of lipids as alternative sources of energy and the different reactions in the
catabolism of fatty acids and glycerol

4. Discuss the role of amino acids as primary or alternative sources of energy

5. Trace the fates of the amino group and carbon skeleton of amino acids

6. Calculate and compare the ATP generated from various sources

7. Explain nucleic acid catabolism

Reference Textbooks:
1. Nelson, D., Cox, M. (2008). Lehninger Principles of Biochemistry, 5th Ed. New York:
W.H. Freeman and Company.

2. Berg, J., Tymoczko, J., Stryer, L., Gatto, G. (2012). Biochemistry, 7th Ed. New York:
W.H. Freeman and Company.

3. Voet, D. & Voet, J. (2011). Biochemistry. (4th ed). United States of America: John Wiley
& Sons, Inc.

4. Campbell, M.K. & Farrell, S.O. (2012). Biochemistry. (7th ed). Belmont, CA, USA:
Brooks/Cole Cengage Learning.

I. Catabolism of Glucose
Glucose is a very important molecule for most organisms. It is used as energy source of the
cells, and the energy is released when glucose enters glycolysis. Glycolysis is a pathway that
converts glucose into pyruvate, which under aerobic condition can be further oxidized to acetyl
CoA, then to carbon dioxide via the TCA cycle. Aside from glycolysis, glucose is also the
source of ribose-5-phosphate needed in the synthesis of nucleotides and nucleic acids. Below
is an overview of metabolism of glucose.

Figure 1. Overview of Metabolism of Glucose. (a) storage, (b) glycolysis, (c) oxidation
via pentose phosphate pathway, (d) synthesis of structural polymers

To produce ribose-5-phosphate, glucose is oxidized via pentose phosphate pathway.

Glucose also serves as the precursor of monosaccharide monomers found in proteoglycans in
extracellular matrix and peptidoglycans in bacterial cell wall. In high glucose intake, excess
glucose is stored as glycogen in animals, and starch and sucrose in plants. The oxidation of
glucose via glycolysis, pyruvate dehydrogenase reaction and TCA cycle will be discussed in
this chapter.

Cellular Respiration
Cellular respiration is the central catabolic pathway for all organisms. It functions to convert
biochemical energy through redox reactions to ATP and waste products.

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

About 686 kcal of solar energy is converted into chemical energy when one mole of glucose
is synthesized from CO2 and H2O during photosynthesis. The same amount is released when
glucose is completely oxidized to CO2 and H2O. However, when not conserved, all the potential
energy of glucose will be lost as heat and light.

To be able to utilize the energy stored in glucose, it undergoes series of enzyme-catalyzed

reactions, called biochemical pathway. The multi-step oxidation allows small amounts of
energy to be released at several points in the pathway, and saved in the bonds of ATP.

Most cells obtain energy from one or two major catabolic reactions, namely cellular
respiration and β-oxidation. Cellular respiration is the central catabolic pathway for all
organisms. It is divided into 3 phases: glycolysis or anaerobic phase; an intermediate phase
where pyruvate is converted to acetyl CoA ; and the aerobic phase where acetyl CoA is
completely oxidized in the Krebs cycle. In all these phases, ATP is produced.

All organisms metabolize substances by breaking them down or synthesizing

macromolecules from precursors. However, organisms differ in the pathways they undergo. The
difference is dependent on the functions of the cell, as well as the requirements of the
pathways. Anaerobes do not require O2 for all the pathways they undergo while aerobes
require O2 and are equipped with a respiratory process.

Phase 1: The Anaerobic phase (Glycolysis)

Supplemental Video (Glycolysis): https://www.youtube.com/watch?v=A1nJRoPGkRs

All organisms and cells undergo the anaerobic phase. This phase called glycolysis or the
Embden-Meyerhof-Parnas Pathway (EMP Pathway), is the breakdown of glucose to 2 pyruvate,
a 3 carbon-containing compound (Figure 2 in the next page). Although there is no net oxidation
in this process, it is significant in that it breaks down glucose into smaller molecules that can
pass through the mitochondrial membrane to allow for its complete oxidation. It also provides
precursor substances for other processes or pathways, for example pyruvate gives rise to
acetyl CoA which serves as the precursor molecule in the synthesis of fatty acid. Glycolysis is
also the pathway that serves to provide energy for completely anaerobic processes.

Glycolysis is the sole source of metabolic energy by the erythrocytes, renal medulla and
sperm cells; and main source of energy by the brain. Many anaerobes are entirely dependent
on glycolysis. Glycolysis takes place in the cytosol. It is composed of ten enzyme-catalyzed
steps. The enzymes are soluble cytosolic proteins (Figure 2).

The anaerobic phase has two phases: phase 1 (preparatory phase): involves
phosphorylation of glucose and its conversion to glyceraldehyde-3-phosphate; phase 2 (payoff
phase): oxidative conversion of glyceraldehydes-3-phosphate to pyruvate and the coupled
formation of ATP and NADH.

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Figure 2. Overview of Glycolysis: Preparatory Phase (left) and Payoff Phase (right).

Preparatory Phase of Glycolysis

Reaction 1: Phosphorylation of Glucose
The initial reaction in glycolysis is the phosphorylation of glucose to its active form
glucose-6-P. Without such a reaction, glucose cannot be metabolized. In the liver, the reaction
is mediated by the hormone insulin which causes a kinase (glucokinase) to phosphorylate
glucose. Thus, in diabetics (insulin deficient) there is no glucokinase that can convert glucose
into glucose-6-phosphate in the liver, and this results in increased blood glucose level while the
cells are starved.

It is also the conversion to glucose-6-phosphate which drives the absorption of glucose

into liver as well as adipose cells. The addition of phosphate to glucose is a way of trapping it
inside the cytoplasm where it can be acted upon by the glycolytic enzymes, converting it into 2
pyruvate molecules. The high concentration of negative charges with addition of phosphate
makes it difficult to pass through the nonpolar membrane.

The phosphorylation of glucose to glucose-6-phosphate with inorganic phosphate is not

favorable. To make it happen, the reaction is coupled with the hydrolysis of ATP for a negative
free energy.

Reaction 2: Isomerization

The conversion of glucose-6-phosphate to fructose-6-phosphate is a reversible reaction

catalyzed by isomerase. Glucose-6-P and fructose-6-P are aldose-ketose pair. The change
from a six-membered ring glucose-6-P to five-membered ring fructose-6-P results in increase
instability for the molecule. This is because a five membered ring has more compressed

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

orbitals and with an instability value of 0.6. This change into five-membered ring is necessary
to prime the hexose for subsequent lysis.

Reaction 3: Phosphorylation of Fructose-6-phosphate (Committed Step in Glycolysis)

The next reaction converts fructose-6-phosphate to fructose-1,6-diphosphate (or

fructose-1,6-bisphosphate). This addition of another phosphate is non-spontaneous and does
not normally proceed under standard conditions. Hence, it is coupled to another ATP
hydrolysis. With 2 phosphate groups in fructose, the negative charge increases and this makes
the molecule even more unstable and easily breaks into dihydroxyacetone-phosphate and
glyceraldehyde-3-P. The formation of fructose-1,6-diP is the committed step in glycolysis.
Once fructose-6-P is converted into fructose-1,6-diP, there is no turning back in the pathway.
Fructose-1,6-diP is thus an important intermediate and its formation is subject to regulation.

Reaction 4: Split of fructose-1,6-diP into DHAP and glyceraldehydes-3-P

The highly unstable fructose-1,6-diP divides into two 3-carbon-containing compounds,

dihydroxyacetone-phosphate (DHAP) and glyceraldehyde-3-phosphate which are aldose-
ketose pair. They are readily convertible to each other with the action of triosephosphate
isomerase.

Payoff Phase of Glycolysis:

The phase 2 of glycolysis involves series of reactions converting glyceraldehyde-3-P into
pyruvate molecules. The first reaction is the formation of 1.3-diP-glycerate. This redox reaction
catalyzed by the enzyme glyceraldehyde-3-P dehydrogenase requires NAD+ which in turn is
reduced to NADH. The 1,3-diP-glycerate is also an unstable compound that can readily be
hydrolyzed to 3-P-glycerate, releasing a very large amount of energy. The energy released can
be trapped and utilized for the formation of ATP.

The product, 3-P-glycerate is then isomerized to 2-P-glycerate, then dehydrated to

phosphoenolpyruvate, another very unstable product which is readily converted to pyruvate
with the removal of phosphate group. This reaction releases a very high free energy that can
be used to phosphorylate ADP forming ATP. The end product of this anaerobic phase of cellular
respiration (or glycolysis) is pyruvate, which in the absence of oxygen can be converted into
lactate.

Fates of Pyruvate and NADH

As discussed earlier, the oxidation of glyceraldehyde-3-P to 1,3-diphosphoglyerate requires
NAD+. Therefore, in order for glycolysis to continue to function, there should be enough supply
of NAD+. Its products, pyruvate and NADH must therefore be allowed to react further to
regenerate NAD+ from NADH. The fates of pyruvate depend on the organisms and conditions of
the surroundings (Figure 3 see the next page).

In animals, plants and many microbial cells under aerobic conditions, pyruvate is oxidized
to acetyl CoA in the mitochondrion with concomitant production of NADH. The acetyl CoA is
further oxidized via the TCA cycle, and the oxidation also produced NADH. Each NADH is
reoxidized to NAD+ by transferring its electrons as hydride ions to the electron transport chain

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

a) Glycolysis
b) Reduction of pyruvate to lactate
(anaerobic condition); in
vigorously contracting muscles,
in erythrocytes, in some other
cells and in some
microorganisms
c) Reduction of pyruvate to
ethanol (anaerobic condition);
in yeast
d) Oxidative decarboxylation ot
pyruvate (aerobic condition)
e) Oxidation of acetyl CoA in the
Krebs cycle

Figure 3. Fates of Pyruvate.

(ETC). The energy liberated from the flow of electrons is coupled to the synthesis of ATP from
ADP and Pi via oxidative phosphorylation.

Under anaerobic conditions, different types of fermentation reactions are used to oxidize
NADH. In lactic acid fermentation, pyruvate is used to oxidize the NADH produced in glycolysis
by accepting electrons from NADH and becomes lactic acid. In yeasts, pyruvate is
decarboxylated to acetaldehyde and the acetaldehyde is reduced to ethanol by accepting
electrons from NADH.

In animals, pyruvate can also be converted into alanine by accepting amino group from an
amino acid via transamination.. Alanine is the storage form of pyruvate in the blood.
Carboxylation of pyruvate produces oxaloacetate, the molecule that condenses with acetyl
CoA to become citric acid. Citric acid is oxidized in the tricarboxylic acid (TCA) cycle.

Lactic Acid Fermentation

Fermentation of glucose to lactate occurs in vigorously contracting muscle, in erythrocytes

and in some other cells, and in some microorganisms. Too much physical exertion depletes the
muscle with oxygen. Without oxygen, the aerobic (oxygen-requiring) energy harvesting
pathways are not able to supply enough ATP to muscles. Since the muscles are in demand of
energy, this depletion causes the utilization of anaerobic glycolysis as the source of ATPs.

The lactate produced in muscle cell passes into

the blood, and if strenuous exercise is
continued, the concentration of lactate becomes
so high that its synthesis stops. Glycolysis, and
thus ATP production ceases, depriving the
muscle with energy, causing it to stop
functioning. The point of exhaustion is called
anaerobic threshold.

Figure 4. Reduction of pyruvate to lactate.

Glucose + 2 Pi + 2 ADP ⟶ 2 lactate + 2 ATP + 2 H2 O
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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Pyruvate is reduced to lactate by the enzyme lactate dehydrogenase with NADH as the
reducing agent. The series of reactions that convert glucose to lactic acid is called lactic acid
fermentation. Figure 4 (previous page) shows the reaction that converts pyruvate to lactate.

After exercise, when the supply of oxygen becomes available, the body begins the process
of recovering all of the potential energy that was lost in the form of lactate (Figure 5).

Figure 5. The Cori cycle.

The liver takes up the lactate from the blood and converts it back to pyruvate. The pyruvate
is converted back to glucose and sent back to the muscle where it can be oxidized again to
pyruvate. This process is called Cori Cycle.

Alcoholic Fermentation

Under anaerobic conditions, yeasts ferment the sugars in fruits and grains into alcohol
(Figure 6). The sugars are broken down to pyruvate by glycolysis, then CO2 is removed from
pyruvate by pyruvate decarboxylase to form acetaldehyde. Acetaldehyde is reduced to
ethanol with NADH by alcohol dehydrogenase and the NADH is oxidized to NAD+. With the
regeneration of NAD+, glycolysis is allowed to continue.

Figure 6. Alcoholic fermentation.

Alcoholic fermentation finds application in wine making and baking. Ethanol, the product of
fermentation is the alcohol in beverages. The product carbon dioxide, on the other hand,
serves as leavening agent in bread.

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Laboratory Activity: Experiment 10: Yeast Metabolism

ATPs from Anaerobic Glycolysis

The net energy produced in glycolysis is 2 ATPs. These come from two substrate-level
phosphorylation involving 1,3-diPglycerate and phosphoenolpyruvate. The pathway also
produces 2 NADH from the reaction converting two glyceraldehyde-3-phosphate to two 1,3-
diPglycerate. In a purely anaerobic process, the NADH is reconverted to NAD+ by the reduction
of pyruvate to lactate. The enzyme, lactate dehydrogenase is an NADH-requiring enzyme,
where the hydride added to lactate comes from NADH.

Glucose + 2 ATP + 2 NAD+ + 4 ADP + 2 Pi ⟶ 2 pyruvate + 2 ADP + 2 NADH + 2 H+ + 4 ATP + 2 H2O

Although 4 ATPs are produced, the net gain of ATP in anaerobic glycolysis of glucose is
only two. This is because the two ATPs are used early in glycolysis. The net equation is shown
below:

Glucose + 2 NAD+ + 2 ADP + 2 Pi ⟶ 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O

Sample Computation of ATP: How much energy is produced by an obligate anaerobe from
the catabolism of one mole of sucrose?

Answer: Sucrose is made up of glucose and fructose. Both hexoses will be phosphorylated by
a coupled reaction with ATP hydrolysis and eventually converted to fructose-1,6-diphosphate.
The end product of this catabolism (fermentation) is lactate which can be converted to other
fermentation products such as propionic acid, butyric acid, or ethanol. Glycolysis yields 2 ATP
units per fructose-1,6-diphosphate catabolized. Since sucrose will give 2 fructose-1,6-
diphosphate, 4 ATP units will be produced.

Phase 2: The Intermediate Phase : Oxidative Decarboxylation of Pyruvate

Supplemental Video:

Pyruvate dehydrogenase complex: https://www.youtube.com/watch?v=NjQSxcxOVQI

In order for pyruvate to be oxidized further, it must be able to enter the TCA cycle To
enter, it is converted to a two-carbon acetyl group, activated to acetyl CoA. Under aerobic
conditions, pyruvate enters the mitochondria where it is converted to acetyl CoA. The reaction
is catalyzed by pyruvate dehydrogenase complex, a multi-enzyme complex made up of
decarboxylase, a transacetylase and a dehydrogenase.

Figure 7. General mechanism for the oxidative decarboxylation of pyruvate Page 8 of 33

to acetyl-CoA.
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Figure 8. Oxidative decarboxylation of pyruvate to acetyl-CoA by the action of the pyruvate

dehydrogenase complex. Adapted from Nelson, D., Cox, M. (2008). Lehninger Principles of
Biochemistry, 5th Ed. New York: W.H. Freeman and Company.

Table 1. Enzymes in oxidative decarboxylation.

Enzyme Abbreviation Coenzyme Reaction catalyzed

Pyruvate dehydrogenase E1 TPP Decarboxylation of pyruvate

Dihydrolipoyl transacetylase E2 Lipoamide Transfer of the acetyl group to CoA

Dihydrolipoyl dehydrogenase E3 FAD Reoxidation of lipoamide

The reaction of oxidative decarboxylation catalyzed by pyruvate dehydrogenase complex is

as follows:

Pyruvate + CoA-SH + NAD+ ⟶ acetyl-CoA + CO2 + NADH + H+

This phase 2 or the intermediate phase of cellular respiration is the first oxidation reaction
releasing a carbon as CO2 from pyruvate. The product, an acetyl group is condensed with a
carrier molecule, coenzyme A to become acetyl CoA. This phase in cellular respiration commits
pyruvate to complete oxidation in the aerobic phase of cellular respiration as it is trapped in the
mitochondria. The mitochondrial membrane is permeable to pyruvate, but the addition of
CoASH, a large molecule ensures that the remaining two carbons of pyruvate are completely
oxidized in the Krebs cycle. This is also a reaction subject to allosteric regulation for the control
of ATP production and conservation of essential metabolites. The reaction is shown below:

Activation of acetyl group requires coenzyme A, a large thiol derived from pantothenic acid.
The structure of acetyl CoA is given in Figure 9.

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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

This is the acetyl group, the rest is CoA!

β-mercapto-
ethylamine Panthothenic acid 3’-phosphoADP

Figure 9. Structure of Acetyl CoA

Phase 3: The Citric Acid Cycle (Kreb’s Cycle or Tricarboxylic acid (TCA) Cycle)
Supplemental Video (Kreb’s Cycle): https://www.youtube.com/watch?v=o2h7XsNQ1kI

The TCA cycle, also known as Citric Acid Cycle (CAC) and Krebs Cycle is the final stage of
the breakdown of carbohydrates, fats and amino acids released from dietary proteins. It is also
the central hub in the metabolism of these substances (Figure 10). Glucose, fatty acids and
certain amino acids can all produce acetyl CoA in stage 1 of catabolism. In stage 2, acetyl CoA
enters the citric acid cycle. Stages 1 and 2 produce reduced electron carriers, e.g. NADH
(shown in the above diagram as electrons). The electrons enter the electron transport chain,
which then produces ATP when coupled to the phosphorylation of ADP.

Figure 10. The Central Relationship of the Citric Acid Cycle to Catabolism. Adapted from Campbell, M.K. & Farrell, S.O.
(2012). Biochemistry. (7th ed). Belmont, CA, USA: Brooks/Cole Cengage Learning.

The TCA cycle which is composed of eight enzyme-catalyzed steps takes place in the
mitochondria. It involves oxidation of the two carbons of acetyl CoA to two CO2 to further
harness the energy from glycolytic product (pyruvate), by generating reduced coenzymes
NADH and FADH2 which can be oxidized in the electron transport chain to produce ATPs. The

Page 10 of 33
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

oxidation of NADH and FADH2 in the ETC can be coupled to the synthesis of 2.5 ATPs and 1.5
ATPs, respectively.

The TCA cycle (Figure 11) starts with condensation of the two-carbon compound, acetyl
CoA with a four-carbon compound, oxaloacetate. The reaction is catalyzed by citrate synthase
producing a six-carbon compound, citrate. Citrate undergoes a series of reaction, producing 5-
carbon, then 4-carbon compounds with the release of the two carbons as carbon dioxide. In
the final reaction, the four-carbon oxaloacetate is regenerated.

Figure 11. The tricarboxylic acid (TCA) cycle, also known as citric acid cycle or the Kreb’s cycle. Adapted
from Nelson, D., Cox, M. (2008). Lehninger Principles of Biochemistry, 5th Ed. New York: W.H. Freeman
and Company.

Citrate undergoes dehydration and hydration to become isocitrate. Isocitrate is oxidized to

⍺-ketoglutarate accompanied by the release of one CO2. The ⍺-ketoglutarate is oxidized into
succinyl CoA, with the release of another carbon as CO2. The succeeding reactions,
conversion of succinyl CoA to succinate, then to fumarate, then malate are simply reactions
Page 11 of 33
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

that will eventually regenerate oxaloacetate. These reactions ensure the continuity of the
aerobic phase of cellular respiration while minimizing production of metabolic intermediates.

The TCA cycle will operate as long as two carbon compounds are fed to it and allowed to
condense with oxaloacetate. In the cells, the two carbons can come from pyruvate, a product
of glycolysis, from fatty acid breakdown and/or from amino acids. During starvation, however,
the level of oxaloacetate (produced by carboxylation of pyruvate derived from glucose) is low,
and this limits the number of acetyl-CoA produced from the β-oxidation of fatty acids that can
be oxidized in the TCA cycle.

ATPs from the oxidation of Acetyl CoA in the TCA cycle

The net yield of ATP from oxidation of acetyl-CoA in the TCA cycle is 10. Since the
glycolytic process produces two pyruvate which becomes two acetyl CoAs, 20 ATP units will
be produced in the Kreb’s cycle for every glucose that undergoes cellular respiration. Three
NADH, 1 FADH2, 1 ATP and 2 CO2 molecules are produced in the oxidation of acetyl-CoA in the
Krebs cycle (Figure 12). Three NADH will produce 7.5 ATPs, and 1 FADH2 will produce 1.5
ATPs. One ATP is produced via substrate-level phosphorylation. Hence, total ATPs is 10 per
acetyl-CoA oxidized.

Figure 12. Reduced Coenzymes and ATP generated in the

Kreb’s cycle.

Shuttle Systems
When pyruvate is converted to acetyl CoA, the cytoplasmic NADH produced in glycolysis is
not reconverted to NAD+ by converting pyruvate to lactate. This is because the hydride carried
by NADH does not have pyruvate to receive it. Hence, to regenerate NAD+, the electrons must
be transported to the mitochondria where receiver substances in the electron transport chain
will accept these electrons. However, the mitochondrial membrane is not permeable to NADH,
NAD+ or electrons. Thus, the electrons must be passed on to the electron transport chain and
this is done via shuttle systems.

There are two shuttle systems that bring electrons from cytoplasmic NADH to the electron
carrier in the electron transport chain (ETC). These are glycerol phosphate shuttle and malate-

Page 12 of 33
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

aspartate shuttle. The glycerol phosphate shuttle is active in muscle and brain cells while the
malate-aspartate shuttle is operational in liver, heart and kidney.

Glycerol Phosphate Shuttle

In the glycerol-3-phosphate shuttle (Figure 13), the electrons of cytoplasmic NADH are
transferred to dihydroxyacetone phosphate to become glycerol-3-phosphate. Glycerol-3-P
floats until it encounters inner membrane bound glycerol 3-phosphate dehydrogenase which
transfers the electrons to its prosthetic group FAD, reducing it to FADH2. From the reduced
FADH2, the electrons are transferred to ubiquinone, then to other components of the electron
transport chain, and finally to oxygen.

Occurs in muscle cells.

FAD - acceptor of electrons

1.5 ATPs formed / FADH2 oxidized

Figure 13. Glycerol-3-phosphate shuttle. Adapted from Voet, D. & Voet, J. (2011). Biochemistry. (4th ed). United
States of America: John Wiley & Sons, Inc.

Malate-Aspartate Shuttle
In the malate-aspartate shuttle, the electrons of cytoplasmic NADH are transported to the
mitochondrial matrix via malate as shown in Figure 14 (see next page).

First, the NADH electrons are transferred to oxaloacetate which reduce it to malate. Malate
then goes into the matrix through a malate-ketoglutarate transporter, where it is oxidized by
NAD+ back into oxaloacetate, and thereby reducing NAD+ to NADH. Oxaloacetate returns to
the cytosol as aspartate via glutamate-aspartate transporter, and the reduced NADH is oxidized
by passing the received electrons (as hydride) to the electron transport chain (ETC).

Comparison of ATP Yield from the Two Shuttle Systems:

In the malate-aspartate shuttle, the receiver of cytoplasmic NADH electrons in the
mitochondrion is NAD+, which is reduced to NADH. The two electrons and one proton (hydride)
from NADH + H+ are then transferred to the electron transport chain, to produce a net of 2.5

Page 13 of 33
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Figure 14. Malate-aspartate shuttle. Adapted from Voet, D. & Voet, J. (2011). Biochemistry.
(4th ed). United States of America: John Wiley & Sons, Inc.

ATPs. In the glycerol-3-P shuttle, the receiver of the two electrons is FAD, which is reduced to
FADH2. FADH2 is then oxidized in the electron transport chain to generate 1.5 ATPs. Therefore,
whether the cytoplasmic NADH will generate 1.5 or 2.5 ATPs when oxidized, will depend on
how the cytoplasmic NADH electrons are transported to the mitochondria where they are pass
on to the electron transport chain.

Table 2. Total ATPs from Complete Oxidation of Glucose.

Pathway Muscle and Brain Liver, Heart and Kidney

Glycolysis 2 ATPs
2 ATPs

2 NADH → 2 x 1.5 = 3 ATPs

2 NADH → 2 x 2.5 = 5 ATPs

Total = 5 ATPs Total = 7 ATPs

Oxidative Decarboxylation
2 NADH → 2 x 2.5 = 5 ATPs 2 NADH → 2 x 2.5 = 5 ATPs
(2 pyruvate → 2 acetyl CoA)

TCA cycle 6 NADH → 6 x 2.5 = 15 ATPs

6 NADH → 6 x 2.5 = 15 ATPs

2 FADH2 → 2 x 1.5 = 3 ATPs

2 FADH2 → 2 x 1.5 = 3 ATPs

1 ATP x 2 = 2 ATPs 1 ATP x 2 = 2 ATPs

Total 30 ATPs 32 ATPs

Total ATPs From Complete Oxidation Of Glucose

The total ATP yield in the complete oxidation of glucose is 30 in muscle cells and 32 in liver
and heart cells. Above is a summary of number of ATPs and reduced coenzymes formed in the
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Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

aerobic degradation of glucose via glycolysis, the pyruvate dehydrogenase complex reaction,
the TCA cycle and oxidative phosphorylation.

Alternative Pathways For Generating ATP

Glycogenolysis
Glycogen Degradation (Glycogenolysis):

https://www.slideshare.net/namarta28/glycogen-metabolism-part2

Glucose is the sole source of energy of mammalian red blood cells and the major source of
energy for the brain. Because both the red blood cells and the brain cannot store glucose, a
constant supply of glucose must be provided to them. The breakdown of glycogen
(glycogenolysis) is one of the sources of glucose especially when the concentration of glucose
in the blood begins to go down. Breakdown of glycogen is facilitated by three enzymes:
glycogen phosphorylase which releases glucose-1-P; debranching enzyme which rearranges
the remaining glycogen to permit continued breakdown; and phosphoglucomutase which
converts glucose-1-P to glucose-6-P for further metabolism.

Glycogenolysis is primarily a phosphorolysis reaction which involves insertion of inorganic

phosphate to carbon 1 of the glucose residue in the non-reducing end of glycogen, breaking
⍺(1→4) glycosidic bonds in glycogen. This reaction, catalyzed by glycogen phosphorylase
releases glucose as glucose-1-phosphate. The phosphorolysis reaction is shown below.

Figure 15. Action of glycogen phosphorylase. Adapted from Berg, J., Tymoczko, J., Stryer, L.,
Gatto, G. (2012). Biochemistry, 7th Ed. New York: W.H. Freeman and Company.

Phosphorylation continues until about 4 residues remain near an ⍺(1→6) branch. Then a
debranching enzyme transfers three of the residues to the non-reducing and cleaves the
remaining ⍺(1→6)-linked glucose (Figure 16, see next page). Hence, the debranching enzyme is
both an ⍺(1→4) to ⍺(1→4) glucan transferase and an amylo-⍺(1→6) glucosidase. Shown in
Figure 16 (see next page) is a pictorial presentation of debranching in glycogenolysis. You can
check the link below for more details: http:// themedicabio.lchemistrypage.org.

The products of glycogenolysis are glucose-1-P and glucose. Glucose-1-phosphate is

converted to glucose-6-phosphate by phosphoglucomutase as shown in Figure 17.

In liver cells, glucose-6-phosphate is dephosphorylated by glucose-6-phosphatase into

glucose (Figure 18), then released into the blood for utilization of other tissues. In muscle cells,
there is no glucose-6-phosphatase, hence glucose-6-phosphate is not dephosphorylated. This

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prevents glucose-6-phosphate from leaving muscle cells, and allows the muscle cells to have
greater amount of it that can enter glycolytic pathway to generate ATPs, which are very much
needed by active muscles.

Figure 16. Pictorial representation of debranching of Figure 17. Conversion of glucose-1-phosphate to glucose-6-phosphate.
glycogen. Adapted from Berg, J., Tymoczko, J., Stryer, L., Adapted from Berg, J., Tymoczko, J., Stryer, L., Gatto, G. (2012).
Gatto, G. (2012). Biochemistry, 7th Ed. New York: W.H. Biochemistry, 7th Ed. New York: W.H. Freeman and Company.
Freeman and Company.

Figure 18. Fates of glucose 6-phosphate from glycogenolysis.

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CHEM41 and 43 Lecture Course Guide
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II. Utilization Of Fatty Acids As Energy Sources

Supplemental Powerpoint Presentation:

1.Lipid Metabolism: Fatty Acid Oxidation

https://www.slideshare.net/shainamavreenvillaroza/chem-45-biochemistry-stoker-
chapter-25-lipid-metabolism

Fats are long term storage form of energy. About one third of our energy needs comes from
dietary triacylglycerols, and about 80% of energy needs of mammalian heart and liver are met
by oxidation of fatty acids.

Fatty acids represent the principal form of stored energy for many organisms. The carbon in
fatty acids which is mostly –CH2- groups, is almost completely reduced compared to those in
sugars and amino acids. Furthermore, fatty acids generally are not as hydrated as
monosaccharides and polysaccharides; thus can pack more closely in storage tissues.

Being more reduced, fatty acids when oxidized will yield more energy in the form of ATP,
than any other forms of carbon. Fatty acids are acquired readily in the diet and can also be
made from carbohydrates and the carbon skeletons of amino acids. In the diet, the triglycerides
are a major source of fatty acids. During starvation, the source of fatty acids are the stored fats
in the adipocytes or adipose cells.

Mobilization of Triacylglycerols Stored In The Adipose Tissue

When ATP level in the cells (e.g. liver) goes down, the fat reserves in the adipose tissues are
mobilized by the action of lipase to release fatty acids and glycerol. The fat mobilization is
illustrated below.

Figure 19. Fat mobilization in the adipose tissues.

The activity of lipase is mediated by cAMP, a second messenger synthesized when ATP
level in the cell is low. Cyclic AMP (cAMP) which is synthesized by adenyl (or adenylate)
cyclase activates protein kinase (PKA), which phosphorylates and activates a triacylglycerol
(TG) lipase, a hormone-sensitive lipase. Fatty acids are mobilized from adipocytes in response
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to hormone messengers such as adrenaline, glucagon and adrenocorticotropic hormone

(ACTH).

The glycerol released by lipase action is converted to glycerol phosphate then to

glyceraldehydes-3-phosphate, an intermediate in glycolysis. This, subsequently is converted to
pyruvate which can either be reduced to lactate, or converted to acetyl CoA or to glucose in
gluconeogenesis. The reactions that convert glycerol to metabolites of glycolysis are shown
below.

Figure 20. Conversion of glycerol to metabolites of glycolysis.

Transport of Fatty Acids Into The Mitochondria

Supplemental Video:

Transport of Fatty acid:

https://www.youtube.com/watch?v=ueQqdrqBGiU

Fatty acids are oxidized to provide the cells with energy. Since the enzymes in the oxidation
of fatty acids are located in the mitochondrial matrix, the fatty acids in the cytoplasm must be
transported to it. Short chain fatty acids are transported into the matrix as free acids, whereas
the long-chain fatty acids are activated first to fatty acyl CoA, then transported as fatty
acylcarnitine.

The activation (Figure 21) involves formation of a thiol ester bond between the fatty acid
and the thiol group of coenzyme A. This is catalyzed by acyl-CoA synthetase, also called acyl-
CoA ligase or fatty acid thiokinase. Since two phosphate bonds are cleaved in the hydrolysis of
ATP during activation of fatty acid, the amount of energy used is equivalent to 2 ATP units. The
activation of fatty acids occurs in the following sites: a) outer mitochondrial membrane (higher
eukaryotes) – for long chain fatty acids before entry of the fatty acid into the mitochondrion, b)
surface of endoplasmic reticulum and c) mitochondria – for short- and medium-chain fatty
acids.

Figure 21. Activation of fatty acid to fatty acyl-CoA.

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After activation of long chain fatty acid to fatty acyl-CoA, the fatty acyl group is transferred
from CoA to carnitine by carnitine acyltransferase 1 (carnitine palmitoyl transferase 1 in the
illustration meaning the fatty acyl group to be transferred is palmitoyl), associated with the
outer mitochondrial membrane. The acylcarnitine, is transported across the inner membrane by
a translocase (carnitine carrier protein). The acylcarnitine is then passed to carnitine
acyltransferase II on the matrix side of the inner membrane, which transfers the fatty acyl group
back to CoA to reform the fatty acyl-CoA. The free carnitine is transported back via the
translocase to carry another fatty acyl group to the mitochondrion. The fatty acyl-CoA in the
matrix undergoes beta-oxidation to produce acetyl-CoA.

Figure 22. Transport of fatty acids into the mitochondrion. Adapted from Voet, D. & Voet, J.
(2011). Biochemistry. (4th ed). United States of America: John Wiley & Sons, Inc.

β-oxidation of Fatty Acids

Supplemental Video:

Beta Oxidation: https://www.youtube.com/watch?v=uYutpPY7xcw

Beta-oxidation of fatty acids provides energy to organisms. Franz Knoop’s experiment in

early 1900, where he fed dogs with fatty acids showed that fatty acids are degraded by
oxidation of the β-carbon, followed by cleavage of the C⍺-Cβ bond. A two-carbon unit is
released as acetyl CoA per turn or repetition of the process. Complete oxidation of fatty acid is
divided into three stages: β-oxidation, Kreb’s cycle, Oxidative phosphorylation.

In mammalian cells, β-oxidation takes place primarily in mitochondria. The saturated

fatty acyl CoA undergoes the reactions below, and repeat the steps (cycles) until fatty acyl
group is completely degraded into acetyl CoA molecules.

Steps in the β-oxidation of Saturated Fatty Acid:

Step 1: Dehydrogenation of Fatty acyl CoA; formation of double bond between ⍺- and β-
carbons (oxidation); yields 1 FADH2 equivalent to 1.5 ATPs

Step 2: Hydration of double bond: addition of H to ⍺-carbon and OH to β-carbon

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Figure 23. β-oxidation of a saturated fatty acid.

Step 3: Dehydrogenation at β-carbon: Cβ-OH becomes carbonyl carbon (oxidation); yields 1

NADH, equivalent to 2.5 ATPs

Step 4: Thiolysis; yields 1 acetyl CoA plus acyl CoA (n-2)

Summary:

• Every other carbon is converted to a C=O

• Allows nucleophilic attack by CoA-SH on remaining chain

• 1 CoA-SH is used for every 2 carbon segment to release acetyl CoA

• Each round produces: 1 FADH2, 1 NADH, 1 Acetyl-CoA (2 in the last round)

How are odd-carbon fatty acids oxidized?

The saturated fatty acids with an odd number of carbon atoms follow the β-oxidation
pathway for even-numbered saturated fatty acids, except that the last fragment is propionyl
CoA instead of acetyl CoA. Although rare in mammals, these odd-numbered fatty acids can be
obtained from plants and marine organisms. Propionyl CoA enters the TCA cycle via succinyl
CoA to produce 1 GTP (equivalent to 1 ATP), 1 FADH2 and 1 NADH. The entry of propionyl CoA
to the TCA cycle is shown below:

Figure 24. Conversion of propionyl-CoA to succinyl-CoA, where succinyl-CoA directly enters the Krebs cycle.

Since β-oxidation occurs in the mitochondrial matrix, acetyl CoA produced from odd-
carbon fatty acids can condense with oxaloacetate and oxidize in the TCA cycle. The reduced

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coenzymes NADH and FADH2 from the oxidation can pass their electrons to the electron
transport chain, thereby re-oxidizing them to NAD+ and FAD, respectively. The propionyl CoA,
on the other hand, can be converted to succinyl CoA, a TCA cycle intermediate. Three enzymes
carry out the reactions that convert propionyl CoA to succinyl CoA.

The conversion of propionyl CoA to succinyl CoA involves an initial carboxylation at the ⍺-
carbon of propionyl CoA to produce D-methylmalonyl-CoA. The reaction is catalyzed by biotin-
dependent enzyme, propionyl-CoA carboxylase, which requires 1 ATP. This is followed by
nucleophilic attack by the ⍺-carbanion of propionyl CoA in a stereospecific manner. Two more
enzymes, methylmalonyl-CoA epimerase and methylmalonyl-CoA mutase act to complete
conversion to succinyl-CoA.

Sample Computations of ATPs from Beta-Oxidation of Fatty Acids

1. What are the products of β-oxidation of palmitic acid?

Answer: Palmitic acid is a 16:0 fatty acid. Therefore, it will produce 8 acetyl-CoA. In
addition, 7 β-oxidation cycles are needed to hydrolyze palmitic acid, thereby producing 7
FADH2 and 7 NADH. The number of cycles or turns of β-oxidation equals the number of
these reduced coenzymes.

2. How many ATPs will be produced from the complete oxidation of palmitic acid?

Answer: 108 ATPs are produced from complete oxidation of palmitic. However, prior to
oxidation, palmitic acid is activated to palmitoyl CoA, which utilizes 2 ATP units. The net ATP
units, therefore, is 108-2 =106.

Palmitoyl CoA + 7 CoA + 7FAD + 7NAD+ + 7 H2O → 8acetyl-CoA +7FADH2 + 7NADH + 7H+

8 acetyl CoA + 16O2 + 80Pi + 80ADP → 8CoA + 80ATP +16CO2 + 16H2O

Palmitoyl CoA +23O2 + 108Pi + 108ADP →CoA +108ATP + 16CO2 + 23H2O

Table 3. ATPs from complete oxidation of one molecule of palmitoyl CoA.

Enzyme catalyzing the Number of NADH or

Number of ATP formed
oxidation step FADH2 formed

Acyl-CoA dehydrogenase 7 FADH2 10.5

β-Hydroxyacyl-CoA
7 NADH 17.5
dehydrogenase

Isocitrate dehydrogenase 8 NADH 20

Α-ketoglutarate dehydrogenase 8 NADH 20

Succinyl-CoA synthetase - 8*

Succinate dehydrogenase 8 FADH2 12

Malate dehydrogenase 8 NADH 20

Total 108

*ATP is produced via substrate level phosphorylation. GTP produced directly in this step yield ATP in
the reaction catalyzed by nucleoside diphosphate kinase.
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3. What are the products of β-oxidation of a 15-C fatty acid?

Answer: 1 propionyl CoA, 6 Acetyl CoA, 6 FADH2, 6 NADH + 6H+

4. How many ATPs can be formed from complete oxidation of a 15-C fatty acid?

Answer: Beta-oxidation: (6 turns x 4 ATPs/turn) – 2 ATPs for activation = 22 ATPs

Kreb’s Cycle: 1 propionyl CoA = 5 - 1 = 4 ATPs

6 acetyl CoA = 6 x 10 = 60 ATPs

Total = 86 ATPs

How are unsaturated fatty acids oxidized?

Like saturated fatty acids, unsaturated fatty acids are also catabolized by β-oxidation.
However, two additional mitochondrial enzymes – an isomerase and a reductase are required to
handle the cis double bonds of naturally occurring fatty acids. For example, during oxidation of
oleic acid, C18:1, with a double bond at 9,10 position, an intermediate ∆9-dodecenoyl-CoA is
formed. This intermediate with a double bond at 3,4-position will not be acted upon by acyl-
CoA dehydrogenase to form another double bond at the 2,3- (or β-position) which is the one
acted upon by the next enzyme enoyl CoA hydratase. To remedy, enoyl-CoA isomerase
rearranges this cis-∆3 double bond to a trans-∆2 double bond. This latter intermediate can
proceed through the normal route of β-oxidation.

Figure 25. β-oxidation of a monounsaturated fatty acid. Adapted from Berg, J., Tymoczko, J., Stryer, L.,
Gatto, G. (2012). Biochemistry, 7th Ed. New York: W.H. Freeman and Company.

The presence of double bond in unsaturated fatty acids eliminate the first dehydrogenation
reaction. As a result, FADH2 is not produced. The ATP produced therefore will decrease by 1.5
ATP. Consider β-oxidation of oleic acid (C18:1) compared with that of stearic acid (C18:0). β-
oxidation of stearic acid produces 30 ATPs whereas, oleic acid only 28.5 ATPs. Complete

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CHEM41 and 43 Lecture Course Guide
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College of Arts and Sciences, University of the Philippines Manila

oxidation, on the other hand, produces 120 ATPs and 118.5 ATPs for stearic acid and oleic
acid, respectively.

Beta-oxidation of a Polyunsaturated Fatty acid (linoleic acid):

Supplemental Videos: Oxidation of Polyunsaturated Fatty Acids (linoleic acid)

https://www.youtube.com/watch?v=zCLC9PV5ZUo https://www.youtube.com/watch?
v=mZCSUP0pq_w

The oxidation of linoleic acid, as linoleoyl CoA requires a secondary auxiliary enzyme in
addition to enoyl-CoA isomerase: NADPH-dependent 2,4-dienoyl-CoA reductase. Together,
these two enzymes convert a trans-2, cis-4-dienoyl-CoA intermediate to the trans-2-enoyl-CoA
substrate necessary for oxidation. Linoleoyl-CoA undergoes three cycles in the oxidation of
saturated fatty acids to yield three molecules of acetyl CoA and the coenzyme A ester of the
remaining 12-carbon unsaturated fatty acid with cis-3, cis-6 configuration. This intermediate
cannot be used by the enzymes of the β-oxidation pathway because the double bonds are in
the wrong position and have the wrong configuration (cis, not trans). However, the combined
action of enoyl-CoA isomerase and 2,4-dienoyl- CoA reductase, as shown in Figure 26, allows
the remaining 12-carbon fatty acyl CoA to be oxidized in the β-oxidation pathway.

Figure 26. β-oxidation of a polyunsaturated fatty acid. Adapted from Berg, J., Tymoczko, J., Stryer, L., Gatto, G. (2012).
Biochemistry, 7th Ed. New York: W.H. Freeman and Company.

III. Utilization of Amino Acids As Alternative Sources Of Energy

Amino acids do not only serve as precursors of proteins in organisms, they also provide
nitrogen for the synthesis of other nitrogen-containing molecules like neurotransmitters,
purines, pyrimidines and nucleic acids. Excess amino acids in the diet can be converted into ⍺-
keto acids and used for energy production.

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CHEM41 and 43 Lecture Course Guide
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Below is an overview of catabolism of amino acids:

Figure 27. Overview of Catabolism of Amino Acids.

In excess protein intake, amino acids are not stored, and those not utilized for the different
synthetic processes are preferentially degraded and utilized as energy sources over
carbohydrates. Moreover, during starvation, when carbohydrates and triglyceride stores are
already depleted, amino acids are also used as alternative energy sources.

The major site of amino acid degradation in mammals is the liver. The initial step in the
utilization of amino acids as energy sources is the removal of the amino group via oxidative
deamination or transamination. Both processes convert an amino acid to an ⍺-keto acid that
can be oxidized by the citric acid cycle to generate metabolic energy or used to synthesize
glucose or fatty acids for energy storage. It should be noted however, that only a few amino
acids are deaminated directly.

Transamination involves transfer of an ⍺-amino group from an amino acid to the ⍺-keto
position of an ⍺-keto acid. In the process, the amino donor becomes an ⍺-keto acid while the
⍺-keto acid acceptor becomes an ⍺-amino acid. The general equation is shown below.
Transaminase (amino transferase) – catalyzes the reversible reaction shown below. There are
multiple transaminase enzymes which vary in substrate specificity. Some show preference for
particular amino acids or classes of amino acids as amino group donors, and/or for particular
a-keto acid acceptors.

Figure 28. Transamination reaction.

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CHEM41 and 43 Lecture Course Guide
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College of Arts and Sciences, University of the Philippines Manila

Examples of
Transamination reactions:

(Top) Aspartate donates its amino

group, and becomes ⍺-keto acid
oxaloacetate. ⍺-Ketoglutarate
accepts the amino group, and
becomes the amino acid glutamate.

(Bottom)Alanine transfers its

amino group to ⍺-ketoglutarate.
Alanine becomes pyruvate as the
amino group is transferred to ⍺-
ketoglutarate.

Figure 29. Examples of transamination reactions.

Transaminases equilibrate amino groups among available ⍺-keto acids. This permits
synthesis of non-essential amino acids, using amino groups from other amino acids & carbon
skeletons synthesized in a cell. Thus, a balance of different amino acids is maintained, as
proteins of varied amino acid contents are synthesized. The predominant amino acid/⍺-keto
pair in transamination reactions is glutamate/⍺-ketoglutarate. Glutamate is the primary amino
donor for the synthesis of amino acids.

The enzymes aminotransferases (or transaminases), are named according to their amino
acid substrates, e.g. glutamate aminotransferase (or glutamate-aspartate aminotransferase for
the enzyme that transfers amino group from glutamate to oxaloacetate to form aspartate).
Aspartate aminotransferase (or aspartate-glutamate transaminase), one of the most important
of transaminases, catalyzes the transfer of the amino group of aspartate to ⍺-ketoglutarate.

The transaminases require pyridoxal phosphate (PLP), derived from vitamin B6.

Figure 30. The prosthetic group of transaminase

is pyridoxal phosphate (PLP), a derivative of
vitamin B6.
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CHEM41 and 43 Lecture Course Guide
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College of Arts and Sciences, University of the Philippines Manila

Supplemental Videos:

1. Amino acid metabolism: https://www.youtube.com/watch?v=TV1gzWHov8Y

2. Deamination of Amino Acids: https://www.youtube.com/watch?v=c_-lwMgBsDE

Oxidative Deamination of Amino Acids

The ⍺-amino group of many amino acids is transferred to ⍺-ketoglutarate to form

glutamate, which is oxidatively deaminated to yield NH4+. Ammonium ion is formed from
glutamate by oxidative deamination. The reaction is catalyzed by glutamate dehydrogenase
(GDH). The enzymatic reaction is shown in Figure 31. The ⍺-ketoglutarate formed is a citric acid
cycle intermediate.

Three enzymes/pathway are responsible for most of the ammonium assimilation into
organic molecules. These are glutamate dehydrogenase, glutamine synthetase and carbamoyl-
phosphate synthetase I.

Glutamate dehydrogenase is one

of the few enzymes that can use
NAD+ or NADP+ as e- acceptor.

Oxidation at the ⍺-carbon is

followed by hydrolysis, releasing
NH4+.

Figure 31. Glutamate dehydrogenase catalyzes a major reaction that effects net removal of N from the amino acid pool.

Glutamate dehydrogenase catalyzes the reductive amination of ⍺-ketoglutarate to yield

glutamate. Reduced pyridine nucleotides (NADH of NADPH) provide the reducing power.

NH4+ + ⍺-ketoglutarate + NADPH + H+ ⟶ glutamate + NADP+ + H2O

Glutamate dehydrogenase also catalyzes the conversion of glutamate to ⍺-ketoglutarate

with NAD+, as the electron acceptor.

Glutamine synthetase (GS) catalyzes the ATP-dependent amination of the gamma-

carboxyl group of glutamate to form glutamine. Glutamine is a major N donor in the
biosynthesis of many organic N compounds such as purines, pyrimidines and other amino
acids.

Carbamoyl-phosphate synthetase is the third enzyme capable of assimilating ammonium

into organic compound. This enzyme catalyzes the first step in the urea cycle that converts
ammonium into urea.

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Most terrestrial land animals

convert excess nitrogen to urea,
prior to excreting it.
Urea is less toxic than ammonia.

Figure 32. Structure of urea.

Urea Cycle
Supplementary Video: Urea cycle: https://www.youtube.com/watch?v=VtDtG58ETLQ

In terrestrial vertebrates, excess nitrogen is generated with increased amino acid

catabolism following high protein intake. Urea cycle which is confined in the liver is used by
cells to remove excess nitrogen as ammonium ion, NH4+. The ammonium (as NH3) combines
with CO2 and ATP to form carbamoyl phosphate, and the reaction is catalyzed by carbamoyl
phosphate synthase.

Figure 33. Synthesis of Carbamoyl Phosphate

Carbamoyl Phosphate Synthase (Type I) catalyzes a 3-step reaction, with carbonyl

phosphate and carbamate intermediates. Ammonia is the N input. The reaction, which involves
cleavage of 2 ~P bonds of ATP, is essentially irreversible. Carbamoyl phosphate synthase
reaction is the committed step of the Urea cycle, and is subject to regulation. The HCO3- used
is a by-product of mitochondrial respiration.

The carbamoyl phosphate condenses with L-ornithine, a rare amino acid forming L-
citrulline. Citrulline condenses with aspartate to form argininosuccinate that breaks up to
fumarate and arginine. Arginine in turn is hydrolyzed to ornithine and urea, the detoxified form
of ammonia. Note that the N atoms in urea came from NH4+ and aspartate amino group.

The urea cycle is compartmentalized (see Figure 34 in the next page). The condensation of
carbamoyl phosphate and ornithine to form citrulline occurs in the mitochondrion. Other
reactions occur in the cytosol. The urea cycle is almost exclusive to hepatocytes.

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College of Arts and Sciences, University of the Philippines Manila

Argininosuccinate
Ornithine transcarbamoylase synthetase

Argininosuccinate
Arginase synthetase

Argininosuccinase

Figure 34. The urea cycle with its associated enzymes and its compartmentalization in the cell.
Adapted from Campbell, M.K. & Farrell, S.O. (2012). Biochemistry. (7th ed). Belmont, CA, USA:
Brooks/Cole Cengage Learning.

Fates of the Carbon Skeleton Of Amino Acids After Removal of Their Amino Group
Supplemental Videos:

Amino acid catabolism 1. https://www.youtube.com/watch?v=M7-J6V8YXiwu

2. https://www.youtube.com/watch?v=6iq0klfZMo8

With the removal of amino group from amino acids, they are converted to intermediates of
the TCA cycle and oxidized to CO2 and oxaloacetate. The entry points of the various carbon
skeletons of amino acids are shown in Figure 35 (see next page).

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College of Arts and Sciences, University of the Philippines Manila

Figure 35. Fates of the carbon skeletons of amino acids. Amino

acids in red are called glucogenic amino acids, whlle amino
acids in green are call ketogenic amino acids. Adapted from
Voet, D. & Voet, J. (2011). Biochemistry. (4th ed). United States
of America: John Wiley & Sons, Inc.

On the average, the ATP yield of amino acids is lower, hence they are not the primary
energy source. However, the utilization of amino acids as sources during starvation will be at
the expense of tissue build-up and repair. Thus, while amino acids are initially used as
alternative energy sources during starvation, at a later stage, the cells provide a protein sparing
mechanism to reduce the risk of degradation of essential tissues. In addition, amino acids can
also provide carbons for the synthesis of glucose.

Sample Computation of ATP Yield:

Compare the amount of energy that can be produced from the complete oxidation of the
following compounds in muscle and liver tissues.

1. Maltose

2. Myristic acid

3. Ile-tyr-met-asp (only ATPs generated from the TCA cycle)

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CHEM41 and 43 Lecture Course Guide
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College of Arts and Sciences, University of the Philippines Manila

Answers: Maltose

The complete oxidation of glucose produces 30 ATPs in muscle and 32 ATPs in liver cells.
Since maltose is made up of two glucose units, 60 and 64 ATP units will be produced from
complete oxidation of maltose in muscle and liver cells, respectively

Answers: Myristic acid

The β-oxidation of myristic acid produces 7 acetyl CoA molecules. When completely
oxidized, each acetyl CoA produced 10 ATP units.

Total ATPs = [(6 turns x 4 ATPs/turn) – 2 ATPs] + [7 acetyl CoA x 10 ATPs/acetyl CoA] = 82

Answers: Ile-tyr-met-asp

Ile = 10 + 5 ; tyr = 20 + 2.5; met = 5; asp = 0

Total ATPs = 42.5

IV. Catabolism Of Nucleic Acids

Nucleic acids are ubiquitous molecules in the cells. Significant amounts are ingested in the
diet, and are degraded in the digestive tract to nucleotides by pancreatic nucleases and
intestinal phosphodiesterases. Group-specific nucleotidases and non-specific phosphatases
degrade nucleotides into nucleosides. The nucleoside is further hydrolyzed by nucleosidase
into base and ribose or phosphorylated by inorganic phosphate by phosphorylase to base and
ribose-1-phosphate. Most ingested nucleic acids are degraded and excreted. Both DNA and
RNA are degraded by nucleases to oligonucleotides which can further be hydrolyzed to
nucleotides.

Supplemental Videos:

1. Nucleic Acid Catabolism: https://www.youtube.com/watch?v=flAWh9XsMQk

2. Purine and Pyrimidine Catabolic Pathways - Nucleotide Breakdown: https://

www.youtube.com/watch?v=oBMKSFGj_2E

Catabolism of Purine Nucleotides

Purine nucleotides are dephosphorylated by the action of 5’-nucleotidases to become
nucleosides. For example, adenylate, is dephosphorylated into adenosine which is
subsequently deaminated into inosine by adenosine deaminase. Inosine is hydrolyzed to
hypoxanthine and D-ribose, then hypoxanthine is oxidized successively into xanthine, and to
uric acid by xanthine oxidase (Figure 36).

Guanosine monophosphate (GMP) catabolism also yields uric acid as end product. GMP is
first hydrolyzed to guanosine, which is cleaved to free guanine. Guanine undergoes hydrolytic
removal of its amino group to yield xanthine, which is converted to uric acid by xanthine
oxidase. Thus, adenosine phosphate and guanosine phosphate are both degraded into uric
acid.

Uric acid is the excreted end product of purine catabolism in primates, birds, and some
other animals. About 0.6 g of uric acid is excreted by a healthy adult human in 24 hours; Uric
acid arises from ingested purines and in part from turnover of the purine nucleotides of nucleic
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acids. In most mammals and many other vertebrates, uric acid is further degraded to allantoin
by the action of urate oxidase.

Figure 36. Purine Catabolism.

GMP ⟶ Guanosine ⟶ Guanine ⟶ xanthine ⟶ uric acid

AMP ⟶ Inosine monophosphate ⟶ hypoxanthine ⟶ xanthine ⟶ uric acid

Uric acid – excreted by primates, birds, reptiles and insects

Catabolism of Pyrimidine Nucleotides

The nucleosides formed from dephosphorylation of pyrimidine nucleotides can be cleaved
into base and ribose-5-phosphate by addition of inorganic phosphate (Pi). Uridine is cleaved by
inorganic phosphate to uracil with formation of ribose-1-phosphate. Cytidine and cytosine are
also converted to uracil. Uracil is reduced to deoxyuracil by NADPH + H+ and deoxyuracil is
hydrolyzed subsequently into β- ureidopropionic and then into alanine. Thymine, on the other
hand, is reduced to dihydrothymine by NADPH, then hydrolyzed into ureodoisobutyrate, which
is further hydrolyzed into β-aminoisobutyrate. β-aminoisobutyrate is deaminated into
methylmalonylsemialdehyde which is degraded through propionyl CoA and methylmalonyl CoA
to succinyl CoA. The pathways for degradation of pyrimidines generally lead to NH4+
production and thus to urea synthesis (Figure 37).

Thymine ⟶ ⟶ ⟶ β-aminoisobutyrate ⟶ methymalonylsemialdehyde ⟶ succinyl CoA

Cytosine/Uracil ⟶ ⟶ ⟶ alanine (metabolized as amino acid)

Page 31 of 33
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

Figure 37. Pyrimidine Catabolism.

Problems
1. How many acetyl CoA(s) can be produced from the following?

Pyruvate
Glycerol
Fructose-1,6-diP

Succinate
Pentadecanoic acid
Sucrose

Sucrose from individual with defective triosephosphate isomerase

2. How many ATP units can be produced from the complete oxidation of the molecules in
number 1 problem?

3. Identify the committed step in each of the following pathways:


Glycolysis
Glycogenolysis

β-oxidation
TCA cycle


4. In which of the following tissues/cells is glucose absorption dependent on insulin? 


Liver
Kidneys
Erythrocytes

Brain
Adipose tissue

5. What is the implication of number 4 in the function of the tissues indicated?

6. A boy has an impairment in the enzyme pyruvate dehydrogenase. What will be the amount
of energy that can be produced in the oxidation of dextrin, a trisaccharide in the liver of this
boy?

Page 32 of 33
Module on Catabolism
CHEM41 and 43 Lecture Course Guide
Department of Physical Sciences and Mathematics

College of Arts and Sciences, University of the Philippines Manila

7. How do the committed steps in cellular respiration function as regulatory control in

metabolism?

8. It was observed that O2 can decrease glycolysis. This phenomenon is known as Pasteur
effect. Explain.

9. Compare the utilization of foodstuffs and production of energy of aerobes and anaerobes.

10. Despite a high energy yield from the oxidation of fats, why are fats not the primary source of
energy?

11. What is the role of fermentation in aerobic organisms?

References:
1. Principles of Biochemistry, Lehninger

2. Biochemistry, Stryer

3. Biochemistry, Campbell and Farrell

Supplemental Videos

4. https://www.youtube.com/watch?v=A1nJRoPGkRs

5. https://www.youtube.com/watch?v=NjQSxcxOVQI

6. https://www.youtube.com/watch?v=o2h7XsNQ1kI

7. https://www.slideshare.net/namarta28/glycogen-metabolism-part2

8. https://www.youtube.com/watch?v=ueQqdrqBGiU

9. https://www.youtube.com/watch?v=uYutpPY7xcw

10. https://www.youtube.com/watch?v=zCLC9PV5ZUo

11. https://www.youtube.com/watch?v=mZCSUP0pq_w

12. https://www.youtube.com/watch?v=TV1gzWHov8Y

13. https://www.youtube.com/watch?v=c_-lwMgBsDE

14. https://www.youtube.com/watch?v=VtDtG58ETLQ

15. https://www.youtube.com/watch?v=M7-J6V8YXiwu

16. https://www.youtube.com/watch?v=6iq0klfZMo8

17. https://www.youtube.com/watch?v=flAWh9XsMQk

18. https://www.youtube.com/watch?v=oBMKSFGj_2E

19. https://library.med.utah.edu/NetBiochem/pupyr/pupy11.gif

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