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7 Strategy for learning the details of a pathway: ‘active learning’ is essential
STRATEGY FOR LEARNING THE DETAILS OF A PATHWAY: ‘ACTIVE LEARNING’ IS ESSENTIAL 21
WHERE are the control points within the pathway?
WHEN does the pathway operate? Is it always active or is it an ‘adaptive’ pathway?
The answers to all of these questions may not be evident immediately, but are usually to
be found by diligent study active learning.
Once the overview is clear, begin to look in more detail at the chemistry and
mechanisms of process. Here are some more suggestions of points to look for when
studying an unfamiliar pathway in more detail.
Chemistry of the
intermediates and the
Learn the names of the
enzymes in sequence.
Learn the structures of the
Redraw the pathway in a
What are the first and last substrates?
Is the pathway linear, branched or cyclical?
How many intermediate substrates are present?
Learn the names of the intermediates.
Which coenzymes are involved and where?
Look at them as organic chemicals;
How many carbon atoms are present and what types
of functional groups are present?
What structural similarities and differences are there
between the intermediates?
What sort of chemical reactions are occurring, for
example, oxidation, condensation, hydrolysis.
Don’t worry about getting the right sequence at this stage
Use of the EC naming system will help you deduce the
name of the substrate and the chemical change
Use cue cards with the structure of an intermediate on one
side and its name on the other;
Test yourself by selecting at random the name of an
intermediate substrate and then draw from memory its
Include structures and all names in a different way;
Design a different image thus avoiding merely
reproducing diagram from a book or the one given
during a lecture.
Be creative; make the diagram as vivid and memorable as
CH 1 INTRODUCTION TO METABOLISM
1.7.1 An Example: glycolysis as a model pathway
You will probably be familiar with glycolysis (the Embden–Meyerhof pathway,
Figure 1.20) from previous studies at school perhaps, so let’s use this important
pathway to illustrate some points in the recommended strategy.
Universal, occurs in all cell types.
To begin the oxidative catabolism of glucose. The
production of ATP is small so this is not a prime role in
most tissues. The end products pyruvate (or lactate)
are important compounds for other pathways.
What are the links to other
Pentose phosphate pathway and glycogen metabolism
(both are linked via glucose-6-P);
glycerol from lipids may enter at the level of triose
Where are the control points?
Reactions catalysed by . . ..
When does the pathway operate?
All of the time (constitutive).
glucose ! 2 Â pyruvateðC3 H3 O3 Þif operating aerobically
ðor 2 Â lactate; C3 H5 O3 ; if anaerobicÞ
C6 H12 O6 ! 2 Â C3 H3 O3 compounds
ðor 2 Â C3 H5 O3 if anaerobicÞ
number of intermediates ¼ 11 including glucose and pyruvate
10 enzyme-catalysed reactions
2 molecules of NADH ỵ Hỵ are generated per molecule
of glucose oxidized;
net gain of 2 molecules of ATP per molecule of glucose oxidized,
that is, 2 molecules ATP consumed and 4 molecules produced
per molecule of glucose.
STRATEGY FOR LEARNING THE DETAILS OF A PATHWAY: ‘ACTIVE LEARNING’ IS ESSENTIAL 23
Chemistry of the
4 hexoses 3 of which are phosphorylated, one of which is bis-P
i.e. two phosphates on different carbons within the
one aldehyde/ketone combination, both phosphorylated
5 organic acids (all have 3 carbon atoms) 4 of these
2 phosphorylations directly from ATP ỵ 1 oxidative
phosphorylation when Pi is added
Names of the enzymes
Triose phosphate isomerase
Let’s try applying the active learning model approach. The chemical structure of each
glycolytic intermediate substrate is shown in Figure 1.19. Remembering that each
individual reaction in any pathway brings about a small chemical change, arrange the
structures in a logical sequence. The names of the intermediates are given in Figure 1.20.
Hint: think back to the word puzzle in which you changed the word ‘went’ into ‘come’.
The same process of small discrete changes of chemical structure can be seen to apply here.
First, name the intermediates using knowledge of simple organic chemistry and
Start with the easy ones! Glucose [compound (iv)] should be familiar to you and it is
one of only two substrates in glycolysis which is not phosphorylated; the other one
being pyruvate [compound (i)].
From glucose, we can easily identify glucose-6-P (Glc-6-P) [compound (v)].
Similarly, fructose-6-P, one of the five-sided furan ring sugars we meet in metabolism. [Compound (x)] and fructose,-1,6-bis P [compound (xi)] should be obvious
from their structures.
There is only one compound which carries an aldehyde group, so glyceraldehyde-3P must be compound (viii) and acetone you may already know as a ketone, so
compound (ii) is dihydroxyacetone phosphate, DHAP.
CH 1 INTRODUCTION TO METABOLISM
Figure 1.19 The chemical intermediates of glycolysis
Now for the glycerates. 1,3 bis-phosphoglycerate [compound (iii)] is the only
molecule with two attached P groups. When we number the carbon atoms in an
aliphatic organic compound we invariably start at the most oxidized carbon (drawn at
the top of the chain), so carbon 2 of the glyceric acid derivatives must be the middle
STRATEGY FOR LEARNING THE DETAILS OF A PATHWAY: ‘ACTIVE LEARNING’ IS ESSENTIAL 25
Pi + NAD +
NADH + H +
1,3 bis phosphoglycerate
Figure 1.20 Glycolysis
one, so 2-phosphoglycerate is compound (ix), and so 3-phosphoglycerate must be
This leaves only one compound which must be phospho enol pyruvate (PEP) as
Metabolic pathways are better learnt as an exercise in logic than pure memory
work!! Working from first principles with a firm underpinning knowledge will seldom
CH 1 INTRODUCTION TO METABOLISM
let you down, whereas rote learning is superficial. We all suffer from ‘memory blank’
at various times!
Metabolism describes the processes which allow energy to be utilized to maintain the
integrity of an organism. Catabolic reactions usually liberate energy which the cell uses
to drive forward anabolic reactions. Energy changes are associated with chemical
changes which would normally occur far too slowly to be of biological use to an
organism, so enzymes are used to accelerate reactions. Enzymes are catalysts but share
few characteristics with inorganic catalysts such as platinum. The relative specificity of
each enzyme for its substrate(s) means that each cell of the body requires hundreds of
different types of enzyme and each type must be present in multiple copies. Enzymecatalysed reactions are arranged into pathways; sequences of individual reactions in
which each enzyme brings about a small chemical change. Keep in mind the road traffic
analogy. Pathways are controllable and adaptable.
Learning metabolism requires a step back to focus, initially at least, not on the
minute details but on the biological purpose(s) of a pathway. Look for patterns and
similarities between pathways and always ask the questions ‘what does this pathway do
for me?’ and ‘how does this pathway adapt to changing physiological situations?’ Be an
active learner and make it personal!
The word puzzle. There are probably several ways to do this, here is one way:
went ! want ! wane ! cane ! came ! come
Notice that apart from the number of letters, the first and last words are structurally
very different and indeed have opposite meanings yet there is a logical progression.
Problems and challenges
Distinguish between . . . free energy, entropy and enthalpy
Define the terms endergonic and exergonic
What information is given by the sign ( ỵ or ) of the free energy value?
Why does metabolism not grind to a resounding halt when an endergonic reaction occurs
within a pathway?
Without performing any calculation, state with reasons if the following reactions are likely
to be strongly exergonic, weakly exergonic, strongly endergonic or weakly endergonic:
R ! P Keq ¼ 0.005
R ! P Keq ¼ 127
R ! P Keq ¼ 2.5 Â 10À4
R ! P Keq ¼ 0.79
R ! P Keq ¼ 1.27
Like glucose-6-P, pyruvate and acetyl-CoA are at metabolic cross-roads. Consult a
metabolic map and identify these important compounds and note the ways in which
they may be formed and metabolized.
Refer to Section 1.4. What type of enzyme-catalysed reaction is occurring in each of the
Glucose-6-phosphate ! Fructose-6-phosphate
Fructose-6-P ỵ ATP ! Fructose-1,6 bisphosphate ỵ ADP
pyruvate ỵ CO2 ! oxaloacetate
Fructose-1,6-bisphosphate ỵ H2O ! Fructose-6-phosphate ỵ Pi
(NB: Pi is an abbreviation for inorganic phosphate)
Dynamic and quantitative
aspects of metabolism:
bioenergetics and enzyme
Overview of the chapter
An understanding of the mathematical basis of enzyme activity and of the energy changes
which occur during biochemical reactions is important to appreciate fully the control of
metabolism. This chapter provides definitions and explanations of key concepts such as free
energy, entropy, KmKi, and Vmax. Worked examples of calculations and graphical derivations
are provided and the results interpreted. The chapter ends with an overview of energy
Bioenergetics: free energy (symbol G); entropy (symbol S); standard and physiological
conditions; equilibrium constant for a reaction under physiological conditions, symbol K0 eq;
calculation of free energy from equilibrium and redox data; endergonic and exergonic reactions.
High energy compounds, substrate level phosphorylation and oxidative phosphorylation.
Enzyme kinetics: Michaelis constant, symbol Km; maximum velocity of an enzyme catalysed
reaction, Vmax; inhibitor constant, symbol Ki; Michaelis–Menten equation and graph in the
absence and the presence of inhibitors. Lineweaver–Burke and Eadie–Hofstee plots.
To the non-mathematically minded, the essentially qualitative nature of biology as
compared with pure chemistry or physics is an attraction. It is a common fallacy to
believe that biology is a nothing more than a descriptive subject. As outlined in
Chapter 1, there are facets of metabolism which can only really be appreciated when
Essential Physiological Biochemistry: An organ-based approach Stephen Reed
Ó 2009 John Wiley & Sons, Ltd
CH 2 DYNAMIC AND QUANTITATIVE ASPECTS OF METABOLISM
analysed quantitatively. Fortunately, the mathematical knowledge required to understand metabolic processes is fairly straightforward and the skills we will use in this
chapter are little more than those of basic arithmetic, the occasional use of logarithms
and the confidence to rearrange a formula. The commonest failing is not with the
computation, but a failure to take appropriate care with use of units. The most
important understanding to be gained from this chapter is how to interpret the data
rather than how to generate them.
2.2 Bioenergetics: the application of thermodynamic
principles to biological systems
The study of energy changes occurring in cells is fundamental to a sound understanding
of metabolism, but it is also one which students often find the most challenging. The
difficulties arise due to the conceptual nature of the topic and of the terms used to
describe it. Whilst it is easy to picture in one’s mind eye the basic structure of a
metabolic intermediate such as glucose or cholesterol and one can easily imagine a
small amount of, say, the amino acid alanine in the palm of the hand, to conjure up an
image of energy is not so easy.
By virtue of their very existence, all substances are considered to possess energy.
The amount of energy will however vary from one compound to another due to the
nature and number and type of atoms within a molecule and the chemical bonds
which hold those atoms together. During any chemical reaction, the total energies of
the individual reactants will become redistributed: some part of the total is used, for
instance, to make and break chemical bonds; some of the overall energy may be ‘lost’
(transferred) to the environment. Occasionally we encounter reactions in which the
total energy of the reactants is insufficient to initiate the reaction. To overcome this
situation, energy usually from the hydrolysis of ATP may be used to drive the
reaction forward or one of the reactants will need to be ‘activated’, often with
coenzyme A, often referred to as ‘active acetate’. To continue our road traffic analogy
from Chapter 1, both situations are somewhat like a vehicle taking on fuel at a filling
A measure of the overall energy change which occurs during a reaction is given by the
enthalpy, symbol H which is a function of the entropy (S) and free energy (G) of that
reaction. Entropy is ‘wasted’ energy, associated with disorder and randomness; free
energy is that energy which can be utilized to perform useful biological work, such as
driving metabolism in the right direction, transporting molecules across membranes or
causing muscles to contract. Knowledge of the change in free energy of a reaction allows
biochemists to make predictions about that reaction and its significance in a metabolic
In practice, the actual values for the free energy of a given reaction are difficult to
measure experimentally. However, during a chemical reaction when one compound
BIOENERGETICS: THE APPLICATION OF THERMODYNAMIC PRINCIPLES
–ΔG ; exergonic
Figure 2.1 Reaction progress graph: exergonic reaction
(reactant, r) is converted to another (product, p), the difference in free energy (DG)
between the reactant and the product can be measured. Thus, the change in free energy
(DG) for the reaction r ! p is simply;
DG ¼ Gp À Gr
GP is the free energy of the product(s) of the reaction
Gr is the free energy of the reactant(s) of the reaction.
Energy can be neither created not destroyed, but the total energy of the compounds
at the end of the reaction (Gp) will be less than that at the start (Gr) as energy is ‘lost’
(transferred) to the environment DG is negative). Such reactions are termed exergonic
and occur relatively easily (‘spontaneous’). See Figure 2.1.
Alternatively, sometimes the products have more free energy than the reactants so
the DG value is positive and the reaction is said to be endergonic and the reaction does
not occur spontaneously (Figure 2.2).
+ΔG ; endergonic
Figure 2.2 Reaction progress graph: endergonic reaction