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Bioc 460 - Dr. Miesfeld Spring 2008
Bioenergetics and Metabolism Supplemental Reading
Key Concepts
- Energy Conversion in Biological Systems
• Review of thermodynamic principles
• The adenylate system is used for short term energy storage
- Overview of Metabolic Pathways
• Metabolic pathways consist of linked enzymatic reactions
• The six major groups of metabolic pathways in nature
KEY CONCEPT QUESTIONS IN BIOENERGETICS AND METABOLISM:
How is energy from the sun converted to chemical energy?
What is reaction coupling and why is it important in metabolic pathways?
Biochemical Applications of Bioenergetics and Metabolism:
Under anaerobic conditions, many microorganisms can
metabolize pyruvate to lactate or to ethanol and CO2. The
bacterial strain Streptococcus cremoris is used commercially to
make cheese by producing large amounts of lactate from
pyruvate, whereas the brewers yeast Saccharomyces cerevisea,
is used to produce carbonated beer from germinated barley
seeds.
ENERGY CONVERSION IN BIOLOGICAL SYSTEMS
Figure 1.
Biochemically speaking, an organism at equilibrium with the
environment is no longer alive. For example, the concentration
of glucose is much higher inside cells of a saguaro cactus than
it is in the surrounding desert (figure 1). Similarly, the
concentration of cellular sodium chloride is lower inside a
humpback whale than it is in the surrounding ocean. However,
when an organism dies, the intracellular concentration of water,
essential ions, and macromolecules, quickly become
equilibrated with the surroundings. To put off this inevitable
event as long as possible, a living organism must be able to
extract energy from the surroundings to maintain a steadystate condition (homeostasis) that is far from equilibrium. To
accomplish this task, organisms utilize sunlight and materials
from the environment to interconvert energy in the forms of
work and heat.
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We can think of this energy conversion or
transduction in terms of 1) chemical work in
the form of macromolecular biosynthesis of
organic molecules, 2) osmotic work to
maintain a concentration of intracellular salts
and organic molecules that is different than the
extracellular milieu, and 3) mechanical work
in the form of flagellar rotation or muscle
contraction. Indeed the cycling of resources
and waste between the environment and a
living cell provides the necessary materials for
this energy conversion. As shown in figure 2,
solar energy ultimately provides the energy
source for life on earth through a three step
process.
Figure 2.
• Review of thermodynamic principles
Bioenergetics is a term that is used to describe energy conversion in biological systems and it
incorporates the idea that cells represent an open system that freely exchange energy and matter
with the surroundings. To better understand bioenergetics in quantitative terms we need to review
three thermodynamic principles; 1) First Law of Thermodynamics, 2) Second Law of
Thermodynamics, and 3) Gibbs Free Energy.
First Law of Thermodynamics
The First Law of Thermodynamics states that energy
cannot be created or destroyed, only converted from one
form to another. As a demonstration of this principle, the
French scientist Antoine Laurent Lavoisier in 1783 used a
small chamber holding a guinea pig to measure the heat
production of metabolism by determining how much ice melted
as a result of respiration (figure 3).
Figure 3.
The energy potential of a compound can be determined using a "bomb" calorimeter to measure
heat transfer as a result of combustion in pure oxygen (O2). For example, the combustion of 1
gram of glucose (C6H12O6) produces carbon dioxide (CO2), H2O and heat. The temperature
increase of the surrounding water is a measurement of the amount of energy stored in the glucose.
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We can write this equation as:
C6H12O6 + 6 O2  6 CO2 + 6 H2O + heat
Where heat = q = ΔE = 3.75 ºC/kilogram of water
Figure 4.
The unit of energy in this example is called a
Calorie (kcal) which was originally defined by
the amount of heat energy required to raise 1
kilogram of water from 14.5 ºC to 15.5 ºC. This
can also be expressed in the international unit
of measurement the Joule (J) in which 1
Calorie = 1 kcal = 4.184 kJ. Note that in
nutritional sciences calorie with a capital "C"
actually refers to a kcal. As first demonstrated
by Lavoisier, and consistent with the First Law
of Thermodynamics, the total energy potential of
this 1 gram of glucose is the same regardless of
the metabolic path taken. As illustrated in figure
4, the same amount of energy (15.7 kJ) can be
extracted from 1 gram of glucose independent
of the path taken. In the case of metabolism, a
portion of the energy content of glucose is
captured in the form of ATP and the rest is lost
as heat. In a steady state condition, there is no
net gain or loss of ATP, so all of the energy
derived from glucose is eventually lost as heat.
It is this metabolic heat that Lavoisier measured
in his experiment with the guinea pig.
Figure 5.
Second Law of Thermodynamics
The Second Law of Thermodynamics states
that all natural processes in the Universe
tend towards disorder (randomness) in the
absence of energy input. A live cell is highly
ordered as compared to the surroundings and
thus energy is required to restrain the natural
tendency toward disorder. This concept of
disorder is defined by the term entropy (S). Ice
melting at room temperature cannot be
reversed without the input of energy in the form
of electricity to lower the temperature. Once the
water is frozen the continued input of electricity
restrains the ice crystals from melting (figure 5).
Similarly, the metabolic energy required for
sustaining life restrains the natural tendency of
the molecules to become disordered. Cellular
life requires solar energy and conversion of
chemical energy into work to restrain entropy.
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Gibbs Free Energy
The change in free energy (ΔG) between a reacting system under standard conditions (reactants
initially at 1.0 M, the pressure is 1 atmosphere and the temperature is 298 K = 25ºC), and the
same system once the reaction reaches equilibrium, is defined as the change in standard free
energy, ΔGº. The ΔGº value is a measure of the spontaneity of a reaction A  B as
determined empirically by measuring the concentration of reactants at equilibrium using the
equation:
ΔG° = - RT • lnKeq (where Keq = [B]b / [A]a as described in lecture 2; "a" and "b" are moles)
A reaction where ΔGº = 0 is reversible, and by definition, at equilibrium with the surroundings. A
reaction with ΔGº < 0 is highly favorable and referred to as exergonic, or work producing, whereas,
a reaction with a ΔGº > 0 is less favorable or endergonic. Biochemists use a slightly different term
for the change in standard free energy of a reaction as denoted by, ΔGº’. The standard reaction
conditions needed to determine ΔGº’ are the same as those described above for ΔGº except that
the pH of the reaction is 7.0 ([H+] is 10-7M) and the concentration of water is 55.5 M. In
metabolism, ΔGº’ values come into play in three important ways:
1. Reactions with ΔGº’ << 0 are a driving force to make unfavorable reactions more favorable
through the use of shared intermediates (product of reaction 1 is the substrate for reaction 2).
Importantly, the ΔGº’ of a coupled reaction is the sum of the ΔGº’ values for each individual
reaction. If the conversion of A to B is unfavorable (ΔGº’ > 0), but B is quickly converted to C (ΔGº’
<< 0), then the conversion of A to B occurs because the net reaction is favorable as shown below:
A  B
B  C
A  C
ΔGº’ = +4 kJ/mol
ΔGº’ = -10 kJ/mol
ΔGº’ = -6 kJ/mol
2. The free energy released from ATP hydrolysis, which is relatively large (ΔGº’ = - 30.5
kJ/mol), can also be used drive unfavorable reactions. In fact, the first step in glycolysis is
catalyzed by the enzyme hexokinase which utilizes ATP hydrolysis to drive the unfavorable
reaction of glucose phosphorylation in a coupled reaction as shown below:
Glucose + Pi  glucose 6-phosphate + H2O
ATP + H2O  ADP + Pi
Glucose + ATP  glucose 6-phosphate + ADP
ΔGº’ = +13.8 kJ/mol
ΔGº’ = -30.5 kJ/mol
ΔGº’ = -16.7 kJ/mol
3. The actual change in free energy (ΔG) of the reaction A  B is the sum of the change in
standard free energy ΔGº’ and the term RT • ln[B]actual/[A]actual, in which the concentration values of
A and B are those present in the cell under steady-state conditions:
ΔG = ΔGº’+ RT • ln [B]actual / [A]actual
The ratio of the product and reactant concentrations under actual conditions in the cell is called the
mass action ratio = [B]actual/[A]actual, and needs to be distinguished from the equilibrium constant,
Keq = [B]equilibrium/[A]equilibrium, which is the ratio of product and substrate concentrations at
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equilibrium. Remember, you don’t want metabolic reactions to reach equilibrium with the
surroundings, because once they do, you are no longer alive.
• The adenylate system is used for short term energy storage
Energy obtained from photosynthesis and oxidation of metabolic fuels drives an ATP synthesis
reaction that captures redox energy in the form of phosphoanhydride bond energy. Importantly,
this bond energy can be readily recovered by ATP cleavage and used to drive chemical, osmotic
and mechanical work. The highest energy form is ATP which contains two phosphoanhydride
bonds as shown in figure 6.
Figure 6.
As shown in figure 7, the breakdown of
macromolecules through catabolic pathways yields
ATP, whereas, anabolic pathways used to synthesize
macromolecules in the cell require ATP hydrolysis to
drive unfavorable reactions.
The term adenylate system refers to the
interconversion of low and high energy forms of
adenylate between ATP, ADP, and AMP. To see why
the adenylate system is important consider that a 70 kg
person requires ~100 moles of ATP every day based
on the energy content of food, assuming that ~40% of
the potential energy released from metabolism is
converted to ATP. The molecular weight of ATP is 507
g/mol, which means we hydrolyze as much as 50 kg of
ATP every day! Rather than synthesizing our own
weight in ATP on a daily basis, it is much more efficient
to recycle adenylate forms by reforming ATP from ADP
+ Pi. This is done in two ways.
Figure 7.
Since ATP is the high energy form of the adenylate system, then the ratio of the concentration of
ATP to the concentration of ADP and AMP in the cell at any given time can be used as a measure
of the energy state of the cell. This relationship can be expressed in terms of the Energy Charge
(EC) of the cell which takes into account the number of phosphoanhydride bonds available for
work:
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Most cells are found to have an EC in the range of 0.7 to 0.9 which means that the [ATP] is
higher than [ADP] or [AMP]. This can be represented schematically by the graph in figure 8.
Energy charge is a useful concept when thinking about metabolism. As shown in figure 9, when
EC<0.8, then the activity of phosphorylating systems (catabolism) increases to replenish ATP
levels (battery power is low, time to recharge). Conversely, when EC > 0.8, then biosynthetic
pathways (anabolism) are more active to take advantage of the high [ATP].
Figure 8.
Figure 9.
OVERVIEW OF METABOLISM
Metabolic pathways consist of a series of reactions that are coupled together through the
metabolism of shared intermediates (figure 10). Metabolic pathways can be linked together to form
linear pathways, cyclic pathways and branched pathways (figure 11).
Figure 10.
Figure 11.
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The term metabolic flux refers to the rate at which metabolites are degraded and synthesized by
a series of linked reactions. For example the metabolic flux through glycolysis is higher than
metabolic flux through gluconeogenesis when more glucose is converted to pyruvate (glycolysis)
than pyruvate is converted to glucose (gluconeogenesis). Three primary mechanisms control
metabolic flux, 1) the amount of rate-limiting enzyme (changes in gene transcription or protein
synthesis), 2) tha catalytic activity of rate-limiting enzymes (covalent modifications or allosteric
regulation) and 3) bioavailability of substrates (nutritional supplies or cell comparmentalization).
One of the best ways to understand how flux through various catabolic and anabolic pathways
changes in response to substrate concentration and enzyme activity levels, is to look at glucose
metabolism in the liver before and after breakfast as illustrated in figures 12 and 13. Early in the
morning before your first meal, blood glucose levels begin to decline after a night of “fasting” which
triggers glucagon release from the pancreas. Glucagon signaling in liver cells activates both a
catabolic pathway (glycogen degradation) and an anabolic pathway (gluconeogenesis), while at
the same time inhibiting the catabolism of glucose by the glycolytic pathway. After breakfast,
insulin levels increase due to high blood glucose which stimulates glucose uptake, glycogen
synthesis, and glucose catabolism via the glycolytic pathway.
Figure 12.
Figure 13.
The six major groups of metabolic pathways in nature
The breakfast scenario gives the take-home message for the rest of the lectures in this course;
metabolic pathways are highly interdependent and exquisitely controlled by substrate availability
and enzyme activity levels. Even though we examine one pathway at a time for pedagogical
purposes, the key to understanding metabolic integration in terms of nutrition, exercise, and
disease (e.g., diabetes and obesity) is learning how metabolic flux between pathways is controlled.
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Figure 14.
To try and keep things interesting (and
organized), we will approach the next 16
lectures as a journey through a metabolic
forest (i.e., the proverbial don't lose sight
of the forest through the trees). As with
any extended trip, we need three items
for our journey, 1) a good map to figure
out where we are, 2) an itinerary to keep
on schedule, and 3) a guidebook to
point out the important landmarks.
Figure 14 shows the metabolic map we
will use to keep track of the pathways
(download a full page copy from the
study guide page on the website). This
metabolic map illustrates the hierarchical
nature of metabolism which includes four
classes of macromolecules (proteins,
nucleic acids, carbohydrates, and lipids),
six primary metabolites (amino acids,
nucleotides, fatty acids, glucose,
pyruvate, acetyl CoA) and six small
biomolecules (NH4+, CO2, NADH, O2,
ATP, H2O). This metabolic map will be
used as a template each time a pathway
is introduced using the “divide and
conquer” strategy illustrated in figures 15
and 16.
Figure 15.
Figure 16.
The first group of pathways we will discuss are those involved with the oxidation of
monsaccharides through a series of redox reactions culminating in ATP synthesis (glycolysis,
citrate cycle, electron transport chain, oxidative phosphorylation, photosynthesis). Lectures 32-40
cover three of the groups of pathways shown in blue that together control the synthesis and
degradation of 1) carbohydrates (carbon fixation, pentose phosphate pathway, gluconeogenesis,
glycogen synthesis and degradation), 2) lipids (fatty acid synthesis and degradation, lipid
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transport, cholesterol and steroid synthesis) and 3) amino acids (including nitrogen metabolism).
Nucleotide metabolism is covered in Bioc 461 (or Bioc 411). Finally, in lectures 41 and 42, we will
tie the various pathways together by looking at how metabolic integration in humans explains
normal (nutrition and exercise) and abnormal (diabetes and obesity) physiological states.
We will start off the discussion of each new pathway by answering the following four questions
about the pathway:
1. What does the pathway accomplish for the cell?
2. What is the overall net reaction of the pathway?
3. What are the key enzymes in the pathway?
4. What are examples of this pathway in real life?
These questions (and more importantly, the answers) function as our “guidebook” by highlighting
the contributions of each pathway to the overall metabolism of the cell. Moreover, they will help
you review your trip through the various pathways in preparation for exams 3 and 4.
ANSWERS TO KEY CONCEPT QUESTIONS:
Life on earth is made possible by the biochemical reactions of photosynthesis, carbon fixation and
aerobic respiration which together convert solar energy into ATP (and NADPH) which is used to
synthesize carbohydrates from CO2 and H2O. Aerobic organisms, such as ourselves, consume
carbohydrates as a chemical source of energy and metabolize them in the presence of O2 to from
CO2 and H2O. All organisms depend directly or indirectly on energy derived from thermonuclear
fusion reactions on the sun to prevent (for as long as possible) reaching equilibrium with the
environment; a high entropy state called death.
Reaction coupling permits energetically unfavorable reactions to be more favorable in the context
of a pathway. Coupling ATP hydrolysis to a phosphoryl transfer reaction is one example of reaction
coupling that takes place in the same enzyme active site. The net ΔGº’ for an ATP coupled
reaction is often highly negative, for example, the phosphorylation of glucose by the enzyme
hexokinase. Another type of reaction coupling is when two enzymes in pathway are energetically
linked through a shared common intermediate. Since the actual change in free energy, ΔG, is the
sum of the change in standard free energy, ΔGº’, and RT•ln(mass action ratio), in which the mass
action ratio is [product]actual/[substrate]actual , depletion of a reaction product by its metabolism as a
substrate in the coupled reaction, results in a reduction in ΔG since ln of a mass action ratio <1 is a
negative number. Therefore, even though the ΔGº’ for a reaction is a positive number (based on
the reaction reaching equilibrium in a test tube under ideal conditions), the actual ΔG is a negative
number because RT•ln(mass action ratio) is a negative number due to lower than "expected"
[product] in the cell due to its function as a substrate in a linked reaction of the pathway.
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