(1) Chapter title: An Introduction to Metabolism
(a)
Found at this site are additional pages of possibly related interest including:
[biochemistry] [enzymes]
(b)
[an introduction to metabolism (Google Search )] [reactions and
enzymes (Online Biology Book )] [index]
(2) Bioenergetics (see also bioenergetics )
(a)
Bioenergetics is "The study of how organisms manage their energy resources."
(b)
That is, bioenergetics is the study of how energy moves through and is employed
by organisms
(c)
(note that apparently bioenergetics has become some kind of New Age therapy -and with a name like that, is it any wonder? -- but this makes it very difficult to
find meaningful links to pages that deal with the science of bioenergetics via
searches for that term)
(d)
[bioenergetics (Google Search )] [index]
METABOLISM
(3) Metabolism (see also metabolism )
(a)
Metabolism is the sum of all of the chemical reactions that occur within an
organism
(b)
Metabolism = catabolism + anabolism
(c)
[metabolism (Google Search )] [anabolic and catabolic pathways (simple, nicely
done figure giving overview of integration of catabolism with metabolism) (BSC
Courseware )] [index]
(4) Catabolism (see also catabolism )
(a)
Catabolic reactions are those metabolic reactions
(i)
That yield energy (are involved in the "generation" of cellularly-useful
energy)
(ii)
Are involved in the breaking down of more-complex molecules to simpler
ones
(b)
[catabolism (Google Search )] [index]
(5) Anabolism (see also anabolism )
(a)
Anabolism is that aspect of metabolism involved in the net use of energy to build
more-complex molecules and structures from simpler ones
(b)
The root of the word is the same as that employed in the phrase "anabolic
steroids" which are steroid drugs employed to "build up" the body, especially in
terms of increasing muscle mass [questions and answers about anabolic
steroids (NIDA Notes )]
(c)
[anabolism , anabolic steroids (Google Search )] [index]
(6) Energy coupling (see also energy coupling )
(a)
Anabolism and catabolism are intimately linked (and thereby is all
of metabolism) by energy coupling
(b)
Energy coupling means that the energy "generated" by catabolic processes is
harnessed by cells to perform anabolic processes
(c)
"The metabolic pathways intersect in such a way that energy released from the
'downhill' reactions of catabolism can be used to drive the 'uphill' reactions of the
(d)
(e)
anabolic pathways. This transfer of energy from catabolism to anabolism is called
energy coupling."
See Figure, Disequilibrium and work in close and open systems
[energy coupling and metabolism (Google Search )] [index]
ENERGY
(7) Energy (see also energy )
(a)
Energy is found in various forms
(b)
Potential energy is energy that is stored in some manner
(c)
Most stored energy in biological systems is stored chemically, i.e.,
within chemical bonds
(d)
Organisms are energy transducers, entities that transform energy from one form
into another
(e)
For example, energy flows through organisms from the energy of photons to the
potential energy found in chemical bonds, and ultimately to the less-useful energy
of heat
(a)
FAQ: What do you mean by "Energy in bonds"? When electrons are locked
into chemical bonds, there is a certain amount of energy associated with those
electrons. This is the (chemically available) energy that exists within, for example,
the food you eat. Recall that the farther an electron is from the atomic nucleus, the
more energy it contains. This distance from an atomic nucleus can be locked into
an electron when that electron is locked into a chemical bond. Indeed, one can
think of the energy required to drive forward the endergonic dehydration synthesis
reaction as energy that becomes trapped in chemical bonds and associated with
electrons that are now farther from atomic nuclei than they otherwise might be (in
fact, were). Finally, note that all else held constant, an electron that is shared
between two atoms possessing relatively equal electronegativity will be trapped at
a further distance from the two atomic nuclei than an atom locked between two
atoms having dissimilar electronegativities. For example, an electron found
between H and O will be much closer to an atomic nuclei (i.e., that of O) than an
electron found between C and C, or even O and O.
(f)
[energy metabolism (Google Search )] [index]
(8) Thermodynamics (first law of thermodynamics, second law of thermodynamics) (see
also thermodynamics , first law of thermodynamics , and second law of
thermodynamics )
(a)
First law of thermodynamics
(i)
Energy can be neither created nor destroyed
(ii)
Energy "generated" in any system is instead energy that has been
transformed from one state to another (e.g., from chemically stored energy
to heat)
(b)
Second law
(i)
The efficiencies of energy transformation can never equal 100%
(ii)
Consequently, all processes lose energy, typically as heat, and therefore
are not reversible unless this energy lost may be supplied from the
environment
(iii)
For chemical reactions that are easily reversed at ambient temperatures, the
energy required for the reversal is simply low enough that it can be supplied
by the heat of the environment (e.g., the dissociation of water H2O <==>
OH- + H+ is driven in both directions by heat)
(iv)
"In performing various kinds of work, living cells unavoidably convert
organized forms of energy to heat . . . In machines and organisms, even
energy that performs useful work is eventually converted to heat . . .
Conversion to heat is the (ultimate) fate of . . . chemical energy."
(c)
[thermodynamics , thermodynamics first law , thermodynamics second
law , thermodynamics third law (Google Search )] [index]
(9) Organisms are energy transducers (see also energy transduction )
(a)
Organisms are transducers of energy (and thereby are less than 100% efficient)
who employ the energy they've harnessed to grow, repair, and maintain their
bodies, compete with other organisms, and to produce new organisms (babies)
(b)
In the process of doing these things, organisms generate waste chemicals
and heat
(c)
Organisms create local regions of order at the expense of using up some fraction
of the total supply of useful energy found in the universe (but don't fret too much,
the energy would have been used up anyway)
(d)
[energy transduction (Google Search )] [index]
EQUILIBRIUM CHEMISTRY
(10) Chemical disequilibrium
(a)
Left to itself, any system will degrade to its most stable state
(b)
For an organism this state represents chemical equilibrium
(c)
An organism that has attained chemical equilibrium is dead
(d)
The chemistry of life is one in which energy is obtained from the environment
and employed to prevent the attainment of chemical equilibrium
(e)
Viable organisms exist in a chemical disequilibrium that is maintained via the
harnessing of energy obtained from the organism's environment (e.g., you eat to
live)
(f)
See Figure: The relationship of free energy to stability, work capacity, and
spontaneous change
(g)
[chemical disequilibrium (Google Search )] [index]
(11) Harnessing movement toward chemical equilibrium
(a)
Catabolic processes represent a chemical movement toward equilibrium
(b)
Movement toward equilibrium occurs spontaneously
(c)
The energy lost by a system as it slides toward chemical equilibrium may be
harnessed to perform work
(d)
See Figure, Disequilibrium and work in close and open systems
(e)
[movement toward chemical equilibrium (Google Search )] [index]
(12) Harnessing energy to move toward chemical disequilibrium
(a)
Anabolic processes represent chemical movement away from equilibrium
(b)
Movement away from equilibrium does not occur spontaneously
(c)
The energy required by organisms to move away from chemical equilibrium is
harnessed from catabolic processes
(d)
[movement away from chemical equilibrium (Google Search )] [index]
(13) Coupling movement toward chemical equilibrium and disequilibrium
(a)
Energy coupling within organisms represents the linkage of anabolic processes
with catabolic processes so that the inevitable tendencies toward chemical
equilibrium may be harnessed to drive other aspects of cells away from chemical
equilibrium
(b)
In other words, the food you eat is driven, for the most part, down a path
toward chemical equilibrium so that the energy found in that food may be
harnessed to build up and maintain thechemical disequilibrium of your living
body
(c)
(in terms of the waterfall analogy for energy, catabolism is the movement of
water over the falls -- See Figure 6.2: Transformations between kinetic and
potential energy; anabolism is the energy-requiring movement of water back up
to the reservoir above the falls, and reactions that
are spontaneously reversible under physiological conditions are equivalent to the
waterfall spray that floats on a breeze back to the waterfall above -- OK, the latter
analogy is a little forced but not too terrible especially if the waterfall is very short
and the flow over it very slow such that the random movement of water molecules
either in the air or within the water results in movement upstream as well as down;
if you coupled the waterfall to a turbine, then you would have a coupling between
catabolism and anabolism, but of course no turbine/pump is 100% efficient so at
least some volume of water runs over the falls whose associated-energy is lost to
the environment as heat rather than captured by the turbine -- See Figure 6.7,
Disequilibrium and work in close and open systems)
GIBBS FREE ENERGY
(14) Exergonic reaction (see also exergonic reaction )
(a)
An exergonic reaction net-generates (gives off) energy (e.g., heat)
(b)
That is, the products of such a reaction possess less stored energy than do
the reactants
(c)
Only exergonic reactions occur spontaneously
(d)
Exergonic reactions move reactants in the direction of chemical equilibrium (or,
in some cases and more-easily visualized, towards physical equilibrium with
exergonic processes that are not chemical reactions)
(e)
See Figure: The relationship of free energy to stability, work capacity, and
spontaneous change
(f)
Approximate synonyms of exergonic include
(i)
Decrease in free energy (-G)
(ii)
Increase in stability
(iii)
Spontaneous
(iv)
Downhill
(v)
Movement towards equilibrium
(vi)
ATP producing
(vii)
Catabolism
(g)
(remember exergonic as in explosion, a very spontaneous reaction)
(h)
[exergonic , exergonic reaction , exergonic reactions (Google Search )] [index]
(15) Endergonic reaction (see also endergonic reaction )
(a)
An endergonic reaction is one that requires a net input of energy in order to
proceed
(b)
The products of endergonic reactions possess more energy than do the reactants
(c)
Endergonic reactions do not occur spontaneously
(d)
Endergonic reactions (or processes) move away from chemical equilibrium
(e)
(remember endergonic as in energy must be put into the system to drive it
forward)
(f)
Approximate synonyms of endergonic include
(i)
Increase in free energy (+G)
(ii)
Decrease in stability
(iii)
Non-spontaneous
(iv)
Uphill
(v)
Movement away from equilibrium
(vi)
ATP requiring
(vii)
Anabolism
(g)
FAQ: Exergonic, exothermic, and spontaneity? To those of you who are
having troubling dealing with the terms exergonic and endergonic because you
learned these concepts in chemistry class using the terms exothermic and
endothermic, here's an attempt at a clarification. I follow this with a restatement of
activation energy and why it is that all reactions can have an activation energy,
regardless of whether those reactions are endergonic or exergonic. First, the
various terms are not quite synonymous (i.e., neither exergonic and exothermic
are synonymous nor endergonic and endothermic). However, if you find it easier
to think of them as synonymous, then go for it. The goal is to get across the
concept of how some reactions require a net input of energy in order to go forward
(endergonic and, often, endothermic) while others net give off energy (exergonic
and, also typically, exothermic). Note that the -thermic terms tend to be limited to
describing heat energy while the -gonic terms are broader, referring to free
energy. That is, two possible things can drive a reaction spontaneously forward: A
release of energy as reactants go to products or an increase in entropy as reactants
go to products. The -thermic terms more or less only deal with the former while
the -gonic terms consider both. Second, keep in mind that even exergonic
reactions will require some input of energy. That is, the exergonic term does not
mean no input of energy. Instead it means that the reactions net generate energy.
In other words, when you sum together input energy and output energy, exergonic
reactions will have produced more energy than they have consumed. The initial
input of energy is called activation energy. See figure 6.9 of your text where the
curve first rises (indicating a requirement for an input of energy, i.e., activation
energy) then drops as this exergonic reaction goes to completion. If the drop
results in the (free) energy associated with the products being less (i.e., the curve
is lower) than that associated with reactants, then it is an exergonic reaction. If the
drop results in the (free) energy associated with the products being more than that
(h)
associated with the reactants, then it is an endergonic reaction, and clearly some
net amount of energy must have been pumped into the system: what you ended
with has more energy associated with it than what you started with! Finally, keep
in mind that the term "spontaneous" does not mean, in a chemical sense, that a
reaction will happen fast. For a chemical reaction to happen at all, it must either
be spontaneous or energy must be supplied to drive the reaction forward. The rate
at which a reaction goes forward, however, depends on the amount of activation
energy necessary to initiate the reaction. If a lot of activation energy is required,
then the reaction will tend to not go forward (all else held constant). If little
activation energy is required, then the reaction will tend to go forward very
readily. These are difficult concepts. In some ways understanding them too well
may be counter-productive to your understanding of biology at this level. Just
keep in mind that some reactions require a net input of (free) energy to be driven
forward, while other reactions net give off some amount of (free) energy as they
go forward, but all reactions require some input of (free) energy (activation
energy) before they can go forward.
[endergonic , endergonic reaction , endergonic reactions (Google Search )]
[index]
ENERGY COUPLING
(16) Coupling endergonic and exergonic reactions (see also energy coupling )
(a)
In organisms, endergonic and exergonic reactions are coupled
(b)
That is, those reactions that give off a net amount of energy are used to drive
forward those reactions that absorb a net amount of energy
(c)
[coupling endergonic exergonic (Google Search )] [index]
(17) Adenosine triphosphate (ATP) (see also ATP )
(a)
Endergonic and exergonic reactions (anabolism and catabolism) are linked by an
energy storage molecule called adenosine triphosphate (ATP)
(b)
ATP is a nucleoside, which is a nucleic acid lacking a phosphate group (this way
they can name ATP in a way that indicates the number of phosphates explicitly,
i.e.,
(i)
adenosine = no phosphates
(ii)
adenosine monophosphate (AMP) = adenosine + 1 phosphate
(iii)
adenosine diphosphate (ADP) = adenosine + 2 phosphates
(iv)
adenosine triphosphate (ATP) = adenosine + 3 phosphates)
(c)
Adenosine is also the RNA nucleoside of adenine
(d)
See Figure, The structure and hydrolysis of ATP
(e)
The most-common reaction in which ATP liberates energy to power anabolic
processes is ATP hydrolysis
(f)
See Figure: The ATP cycle
(g)
[ATP , adenosine triphosphate (Google Search )] [index]
(18) ATP catabolism (ATP hydrolysis) (see also ATP hydrolysis )
(a)
The following reaction is ATP hydrolysis:
(i)
ATP + H2O + activation energy  ADP + Pi + energy
(b)
Note that this reaction releases energy (i.e., it is exergonic) which is true in
general for hydrolysis reactions (i.e., hydrolysis is an example of a catabolic
reaction)
(c)
ADP is ATP less one phosphate group
(d)
[ATP catabolism , ATP hydrolysis (Google Search )] [index]
(19) ATP is a product of catabolism
(a)
The reverse reaction of ATP hydrolysis, that which generates ATP from ADP -i.e., ADP + Pi + energy  ATP + H2O -- is the dominant useful product
of catabolic reactions
(b)
Note that this reaction requires energy (i.e., it is endergonic) which is true in
general for dehydration synthesis (i.e., dehydration synthesis is an example of
an anabolic reaction)
(c)
(The catabolic processes that drive the production of ATP -- either directly or
indirectly -- include glycolysis, the Krebs cycle, and chemiosmosis which your
text covers in chapter 9)
(d)
[ATP synthesis (Google Search )] [chemistry of ATP synthesis (heavy-duty
chemistry) (Metabolic Pathways in Biochemistry )] [index]
(20) How ATP works
(a)
ATP is often said to possess high-energy bonds
(b)
In fact, what ATP possesses are relatively low energy bonds, but ones that are
readily broken (i.e., ATP hydrolysis has a low energy of activation) and the
breaking of those bonds (i.e., ATP hydrolysis) supplies enough energy to power
the individual steps of most anabolic reactions
(c)
See Figure, The structure and hydrolysis of ATP
(d)
One reason for ATP's instability has to do with the high charge density of all of
the linked phosphates
(e)
Enzymes are employed to harness the energy released by the loss of a phosphate
from ATP to do specific, energy-requiring (endergonic) tasks
(f)
See Figure, Energy coupling by phosphate transfer