Important words and concepts from Chapter 6, Campbell & Reece, 2002
(1/14/2005):
by Stephen T.
Abedon (abedon.1@osu.edu)
for Biology 113 at the Ohio State University
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Course-external links are in brackets Click [index]
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text’s website Vocabulary words are found below |
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(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]
(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)] [basic energy concepts
(T. Paustian’s Microbiology
Textbook)] [index]
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]
(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)] [types of catabolic pathways
(T. Paustian’s Microbiology
Textbook)] [index]
(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)] [anabolism, summary of anabolism
(T. Paustian’s Microbiology
Textbook)] [index]
(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
anabolic pathways. This transfer of energy from catabolism to anabolism is
called energy coupling.”
(d)
See Figure 6.7, Disequilibrium and work in close and
open systems
(e)
[energy coupling and metabolism
(Google Search)] [index]
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)
(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
(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
(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 6.5: 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 6.7, 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 the chemical 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
(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 6.5: The relationship of free energy to
stability, work capacity, and spontaneous change
(f)
Approximate
synonyms of exergonic include
(i)
Decrease in free
energy (-DG)
(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]
(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 (+DG)
(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 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.
(h)
[endergonic, endergonic reaction,
endergonic reactions
(Google Search)] [index]
ENERGY COUPLING
(16) Coupling
endergonic and exergonic reactions
(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)
(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) = adnosine + 1 phosphate
(iii)
adenosine
diphosphate (ADP) = adnosine + 2 phosphates
(iv)
adenosine
triphosphate (ATP) = adnosine + 3 phosphates)
(c)
Adenosine is also
the RNA nucleoside of adenine
(d)
See figure 6.8, 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 6.10: The ATP cycle
(g)
[ATP, adenosine triphosphate
(Google Search)] [index]
(18) ATP catabolism (ATP
hydrolysis)
(a)
The following
reaction is ATP hydrolysis:
(i)
ATP
+ H2O + activation energy à 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 à ATP + H2O – is the dominant useful produc