| |
|
Energy in
Chemical Reactions
|
|
|
| |
|
|
| |
|
Energy is a
tough thing to define - it's recognizable, but difficult to pin down
with words. The classic definition has it as "ability to do
work," but that's not terribly useful. But however you define
it, there are some rules that energy follows. |
|
Energy behaves
according to some of the Laws of Physics, in this case the Laws
of Thermodynamics. The
First Law of Thermodynamics is
often called the Conservation Law: energy can't be
created from nothing or disappear to nothing. It can, however,
change its form. This means that, as energy works through
living systems, it gets transferred, changes, and lost as random
molecular motion, but it doesn't disappear. It also came from
somewhere.
One of Einstein's Laws, the
famous E = mc2, established that energy and
matter are forms of the same stuff. Matter can be accelerated
to the form of energy (this happens in nuclear weapons and power
plants), and energy could be slowed down and become matter.
The First Law applies to matter, too: in biological systems,
matter neither appears from nowhere nor disappears to nothing. |
More on the conservation of energy.
Different energy
forms.
Background on Einstein's theory, including his own recorded
explanation. |
|
The
Second
Law of Thermodynamics often is called the Law of Entropy;
it helps explain where energy goes in living systems when it
seems to disappear. The Law applies to systems with
internal order, and says that, without energy input and usage, such
as system will eventually lose its order (entropy means disorder).
Life is a very ordered system, and without constant energy input
would stop working. We have a huge energy source that
virtually every living thing depends upon to keep the system going:
the Sun. Sunlight gets converted, through photosynthesis,
into the chemical energy that holds sugar molecules together;
that energy is shifted into an energetic but very usable molecule,
adenosine triphosphate (ATP), from which most chemical
reactions in cells get a boost. Every single reaction loses
some energy in its process, which "bleeds" out through the random
motion of the atoms and molecules involved. This random motion
is heat; temperature is a measurement of how fast the
local particles are moving.
In a food chain,
materials get moved through and eventually recycled by
decomposers, but almost every bit of the energy gets lost as
heat. This is why the chain absolutely requires the
organisms on the first link to be able to capture more energy in a
usable form. |
More on the Second Law.
Shakespeare and the 2nd Law (really!).
Energy Flow in Ecosystems.
|
|
Chemical
reactions need an energy "push" to get started. This
activation energy varies from reaction to reaction: some
need vary little, some need so much that they will likely never
happen.
Chemical reactions fall into two
broad classes based on their activation energy. Exergonic
reactions (sometimes called exothermic) release enough energy
during the reaction to give activation to more reacting: get
them started, and they keep themselves going (lighting a piece of
paper is exergonic). Endergonic reactions (or
endothermic) always require energy fed into them to happen and
continue to happen. Most synthesis reactions are endergonic,
since the energy is being stored in bonds and not released. It
is common for reactions in cells to link an exergonic reaction to an
endergonic one to "feed" it energy; these are called
coupled reactions. These reactions, moving energy around
in a living thing, are called metabolic reactions, and all of
them in a defined system (it could be an organelle, a cell, an
organ, a population, an ecosystem...) are called metabolism.
Reactions often occur in long sequences.
The product of the first step is the reactant for the second, and
its product is the reactant for the third, and so on. These
reaction sequences are called metabolic pathways. In
prokaryotes, the enzymes for the pathways often have genes in
sequence on the chromosome, since the reactions can take place right
near where the codes are. In eukaryotes, the enzymes are made
far from the codes in the nucleus, and this sequencing of genes is
rare. |
A video on activation energy.
Demonstration of the two classes of reactions.
Simple animation of a coupled reaction.
|
|
|
| |
|
|
| |
|
Enzyme Roles in
Chemical Reactions
|
|
|
| |
|
|
| |
|
Enzymes, as
catalysts, lower the activation energy needed to get a reaction
started. That's how they get stuff to happen that would
easily happen by itself.
Enzymes have spots
on their molecules where they attach to the reactants (called
substrates when they do this); these attachment spots are
called active sites. Enzymes are not the
only proteins with spots that attach to other molecules:
proteins like receptors, carriers, and antibodies attach to
ligands to do their jobs. Specificity is a term
applied to measure how particular these attachment sites are:
will they attach to just one molecule, or several similar ones?
One or more substrate molecules attach to the
active site, and something happens to them there that vastly
increases the likelihood that they will react: maybe a bond is
stressed to the breaking point, or an electron is fed in to ionize a
substrate, or two molecules are put physically where they are likely
to bond together. The substrates react and change, and the
products aren't built to stay in the active sites; they come
loose, and the enzyme is free to grab more substrates. At the
end, the reactants change but the enzymes don't. There is also
a minimum time it takes for a reaction to happen on the enzyme,
which means that how fast a cell can do something is limited by that
time and the number of enzyme molecules it has working. |
Animations showing activation energy and enzyme function, with ATP.
Enzyme in action.
Simple graphic image of enzyme action.
|
|
Many reactions
that are moved along by enzymes are not processes that need to be
running all of the time. For a very occasional reaction, a
cell may build the enzyme, use it, then break it down and reuse the
amino acids in something else. But if an enzyme is used
regularly, it's better to have some way to deactivate it and then
reactivate it later. This is typically done with control
molecules called inhibitors.
Inhibitors can work several ways. Direct inhibitors
(also called competitive inhibitors) actually attach right in
the active site so that a substrate won't fit in. They don't
have to be particularly like the substrate, or even fill the active
site up, so long as they get in the way. Getting in the way is
used by one type of indirect (noncompetitive) inhibitor:
these molecules attach to the enzyme in such a way as to keep the
substrate from being able to get at the active site. Another
type of indirect inhibitor attaches to a regulatory site on
the enzyme molecule, changing the shape of the molecule, and
changing the active site shape so the substrate won't attach there.
To turn the enzyme back "on," the inhibitors are taken back off.
This is reversible inhibition. Irreversible
inhibition sometimes happens to turn a system off permanently;
this may be done when the enzyme is going to be recycled. It
also is a common effect of toxins: a poison may
have its effect by attaching to and changing the shape of a critical
protein.
In end-product inhibition, the first enzyme
in a production pathway has a regulatory site that will loosely
attach to the eventual pathway product. As product builds up,
it shuts down the beginning of production; as it gets used,
the pathway builds more. |
More on inhibition.
Reversible direct inhibition.
Indirect inhibition.
Shape-changiug (allosteric) inhibition.
End-product inhibition.
|
|
|
| |
|
|
| |
|
Factors in
Enzyme Activity
|
|
|
| |
|
|
| |
|
Enzymes depend
upon a particular shape to be able to do what they do. Factors
that affect their shape affect their activity as well. If a
protein shape unwinds to the point that the protein loses its
function, it has denatured. Denaturation may be
reversible or not.
Temperature is a
measurement of the random motion of particles; small particles
move faster as they get warmer, and big molecules shake and twist as
well as moving faster. Any protein, including enzymes, will
have a range of temperatures where they have a good working shape:
this is called their optimal (or optimum) temperature.
For enzymes, cooler-than-optimum temperature affects their shape
slightly, and also changes the particle speeds, making it harder to
get reactants and release products, lowering their activity.
Warmer-than-optimum temperatures lead to the denaturation of the
enzyme, also lowering their activity. A curve showing the
relationship between temperature and enzyme activity follows a
bell-like shape, peaking at the optimum. The shape of the bell
has a lot to do with the evolution of the system and the conditions
the system works under: you can probably tell what the optimum
temperature is for most human cell reactions. Plants have
curves that tend to be broad and low: activity doesn't get too
high, but the enzymes stay active across a wide range of
temperatures.
In the same way that there is an optimum
temperature, enzymes each have an optimal pH. pH,
remember, is a measure of how common H+ ions or OH- ions are in a
solution; a shift will have a strong effect on the hydrogen
bonds that hold a protein in its working shape. Below the
optimum pH, too many H+ ions disrupt the shape; above, too
many OH- ions do it. |
Denaturation.
Denaturation explained.
Temperature effects.
Temperature curve.
pH optimums.
|
|
Enzymes often
work with other molecules. Sometimes ions or metal atoms are
used to help electrons move, or small helper molecules do a variety
of helpful things. Single-atom helpers are called
cofactors; small molecule helpers are called coenzymes.
Coenzymes that we can't build ourselves, that we need
to get from our food in their working form, are called vitamins.
Vitamins are important because they are critical contributors to our
many metabolic pathways. |
Some ways that one cofactor may work.
Coenzyme. |
|
|
| |
|
|
| |
|
|
| |
|
|
| |
|
Adenosine
Triphosphate, ATP, has a core structure with a string of 3
phosphates attached. The bonds that hold the phosphates on
hold a lot of energy.
Breaking off a
phosphate can release energy that can be fed into cellular
reactions. Also, transferring a phosphate to a reactant (phosphorylation)
can destabilize the reactant and get it to react. When ATP
loses a phosphate, it becomes ADP (Adenosine Diphosphate).
ADP picks a phosphate back up in systems such as respiration
and photosynthesis, covered in the next 2 chapters.
Sometimes the end phosphate of ADP can be pulled off to fuel a
reaction, leaving AMP (Adenosine Monophosphate). AMP
has some form variations that are used for other purposes than
energy. |
More on ATP.
ADP and ATP.
Some AMP variants. |
|
|