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There is a gulf between inanimate matter and living things.
A piece of granite is very different to a plant. A granite
rock fragment was formed three billion years ago. Today its
modification requires concerted effort and significant
expenditure of energy. A plant, composed of carbon dioxide,
water and sunlight, can trace its history to a seed or
cutting planted in rather recent times. In a year a potted
plant on the window ledge will have changed dramatically.
Its leaves will have exchanged large volumes of gas with the
atmosphere, and if the plant has been cared for, it will
have absorbed several gallons of water. The granite fragment
will be exactly as it was just after it was formed. Yet the
same forces which keep the rock constant permit the living
things to change and evolve. Here we look at the molecular
basis of the molecules of life.
In the eighteenth century amid the earliest glimmerings of
the dawn of chemistry, natural organic substances, such as
the extracts of plants, bone, skin, wood and so on, the
substances produced by life, were thought to be
fundamentally different from inorganic materials such as
rocks, minerals, metals and air. The difference between the
constant minerals and the changeable organic compounds, it
was supposed, lay in the possession by the latter of a
unique vital force endowing them with unique, almost
magical, properties.
One of the essential roles of science is demystification,
replacing, where possible, vague and unverifiable concepts,
like vital force by precise, rational and demonstrable
explanations or theories. One of the extraordinary
contributions of the chemical sciences to mankind's
knowledge has been the demystification of the behavior and
nature of living matter. As we shall see, living matter can
be understood in terms of the same chemical principles as
inorganic matter. Living matter is composed of atoms, in
fact a rather restricted range of atoms, and these atoms are
bound together to form molecules. Life is undoubtedly
complex and diverse, but its molecules, its matter, do not
require any new or different fundamental theories. There is
no need for a vital force to understand the molecules of
life.
However, the thinkers who proposed the vital force were by
no means fools. They were responding to the fact that living
matter is extraordinary and manifests properties quite
different from inorganic materials. Explanation of these
facts using the intellectual tools of the time demanded a
degree of inventiveness. The rapidly expanding knowledge of
underlying chemical phenomena of the time, and the
catalogs information available on the molecules of life
meant that ingenuity was required to observation.
That the molecules of life are special is emphasized by new
structural discovery revealing their modes of action. We
shall take one initial illustrative example. The unique
architectural the lysozyme molecule (shown to the left).
This complex molecule (shown in simplified form below) is
found in human tears. Its unique shape endows it with unique
molecular properties. The complexity of the molecule makes
it special. In fact it is a solution to a complex
operational problem.
Fixed eyes are effective in simple organisms, but impose a
significant impediment to survival for animals that must
contend with the challenge of predators or agile prey. The
development of eyes able to move within an eye socket marked
a significant improvement and demanded, in turn, a lubricant
able to bathe delicate optical equipment and ease the
friction of motion. The lubricant itself needed special
properties, low viscosity so as not to entrap debris, low
production cost so as not to consume too large a portion of
the organisms food intake, and low opacity so as not to
interfere with systems original visual purpose. High on the
list of requirements too was the necessity that the
lubricant should not harbor bacteria. Tears therefore
contain a specific agent that attacks just bacteria,
destroying their cell walls. The agent which nature
developed for this purpose is lysozyme. It does not effect
the delicate membranes of the eye or the eye socket.
Instead, it is able to recognize at the molecular level a
component of a bacterium's cell wall and, having keyed onto
this element, break down the wall destroying the foreign
organism.
The structure of lysozyme showing the position of alpha helices, drawn
as red cylinders.
Lysozyme is an elegant solution to a thorny operational
problem and it is just one of the 10,000 different proteins
which make up about half the dry weight of a typical
mammalian cell. These special molecular solutions in the
form of molecules are among the molecules of life. Similar
types of molecule tackle problems in the transportation of
gases, the structure of cells and muscles and the regulation
of blood flow.
The image on the left shows the structure of lysozyme
molecule again, this time all of the atoms of the molecular
are shown, include those of hydrogen atoms both in the
molecule and in a number of water molecules (in whose
presence the molecule operates). The structure reveals the
great complexity of the molecular problem solver which
nature developed to solve a difficult problem. The
complexity is a consequence, a product and indeed a
marvelous achievement of millions of years of evolution but
it can also be understood in terms of the basic principles
of chemistry. The molecules of life achieve must efficiently
tackle a vast array of difficult activities within a living
organism. As we see in the case of lysozyme and the growing
number of structures that are being made available by modern
structural discoveries, the molecules of life realize their
effects through their complex and unique molecular
architectures. How do the molecules of life achieve this
complexity?
The structure of lysozyme.
Understanding the extraordinary diversity of function that
even the simplest living matter must exhibit provided the
root for the vital force theory. The number of elements
within living molecules is small. The image on the left
shows the periodic table and highlights those element types
that form 99% of living things. The vitalists therefore
reasoned that complexity must stem from an extra
non-elemental ingredient. We now know that nature achieves
complexity with the same efficiency that allows common basic
building blocks such as transistors and resistors to be
linked together to produce devices as varied as computers,
toasters and car ignitions from common components. The
molecules of life are often chains of atoms. Once you start
building with chains, there are so many permutations or
possible orderings, that complexity naturally emerges. The
image on the left shows some of the simpler molecules that a
living organism contains, for example in cell walls and
within fatty energy reserves. Lysozyme belongs to one of the
most important classes of molecule, the proteins. These
molecules are built from a limited number of types of
component, the amino acids shown below.
Amino acids are linked together in the manner shown below. A
water molecule is eliminated between the two aligned
molecules, forming a bond known as a peptide bridge. (A
similar reaction is responsible for the formation of the
chains of molecules which make up nylon). The reaction
between two peptides can be reversed making it possible to
assemble or disassemble the chain. This makes this class of
molecule of life highly efficient. They can be assembled to
perform a specific function and then consumed in the
production of an entirely different molecular solution.
However, to achieve important actions, such as the efficient
destruction of aberrant bacteria in lysozyme's case, the
correct chain must not only be assembled but the molecule
most coil and wrap around itself to produce a finished
product. In fact the many of the molecules of life are
firstly obliged to interact with themselves, to form the
tightly packed molecular machines which perform their
assigned functions before they can begin operation. The
image above in red shows the extended length of the lysozyme
chain in comparison to the dimensions of the coiled active
molecule. It turns out that proteins are able to perform the
requisite coiling and folding for themselves, without
molecular assistance. What is it that makes this happen?
The haemoglobin structure, the protein that is responsible for
transporting oxygen.
Uncoiled and native lysozyme molecules. The native molecule is
folded in on itself in a tightly packed bundle.
When first formed the protein is in contact with water
molecules, indeed almost 80 percent of the typical organism
is water, so this is the case for many of the molecules of
life. Different parts of the protein structure are then
interacting with water from the moment that it is formed.
Different amino acids interact with water to varying degrees
owing to their differing molecular structures. One of the
most important processes is a special type of bonding known
as hydrogen bonding. Similar bonds occur between hydrogen
atoms and oxygen atoms in water molecules in ice crystals
(on the left, for example) and, just as in ice, produce a
strong stabilizing force anchoring parts of the protein
structure. One example of such bonding is provided by an
image below, which shows the alpha helix an important
element of protein structural chemistry which was predicted
on theoretical grounds before it was seen in
nature by Linus Pauling. The patterns which real proteins
exhibit can become quite beautiful and complex. Also shown
below, is the haemoglobin structure, the protein that is
responsible for transporting oxygen through your body from
your lungs to where it is required in your muscles and
cells. Complex proteins contain an array of different
patterns which are dovetailed together to give an overall
shape which controls function. Often several separate
protein strands are entwined to produce a super complex to
achieve a given objective.
Hydrogen bonds hold
water molecules in ice together. In this image the
hydrogen bonds between water molecules are depicted as narrow
light blue cylinders linking oxygen atoms (shown in red) and
hydrogen atoms (in white).
Alpha helices (as shown on the left) and beta sheet (shown on the right)
peptide structures are held together by hydrogen bonds.
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