| Bioelements |
The table above shows the abundances of the most abundant atomic elements in the Universe, the Earth's
air are given by % volume, the remainder are % mass fraction). Hydrogen and helium are the most
abundant elements in the Universe, but these are less abundant on the Earth as most of the hydrogen and
almost all of the helium escaped to outer space since these were light gases that eventually escaped the
Earth's gravitational pull. Helium gas is unreactive and so was almost totally lost. Hydrogen remained as it
reacts readily with oxygen to form water (and with other elements to form hydrides, some is present as
hydrogen sulphide gas).
Note that the most abundant element on Earth is oxygen, by a long way, and by no coincidence it is also
the most abundant element in living things on Earth. This is the first point - organisms build their bodies
primarily from the most abundant elements in their environment. Hydrogen is quite abundant on Earth as
water (hydrogen oxide) and is also a common constituent of life on Earth - living things may be as much as
90% water (the human body varies from about 30% to 70% water, depending upon fat content). The first
animals and proto-plants to appear on the Earth lived in water and it is no surprise that when they
colonised the land they took their environment with them - body fluids have a close resemblance to
sea-water. This water serves as a solvent in which many chemicals dissolve and the chemical reactions of
life occur. It may well be that other solvents could work as well, but water is the most abundant inorganic
liquid in the Universe.
Two conspicuous exceptions to the rule that organisms utilise the most abundant elements in their
environment are silicon and carbon. Carbon is not especially abundant at the surface of the Earth (though
much lies buried as fossil fuels and limestone) though it is present in small amounts as carbon dioxide in
the atmosphere. However, carbon is so useful and essential to life on Earth that organisms have learnt
how to concentrate it - plants, algae and some bacteria convert carbon dioxide gas into sugars, proteins
and oils with the help of light energy - a process called photosynthesis. Indeed, it was the ability of these
creatures to assimilate carbon so well that lead to its large-scale removal from the atmosphere - coalfields,
natural gas and oil-fields are the carbon-rich remains of ancient forests and swamps. Limestone is the
fossilised remains of the carbon-containing shells of marine organisms. Carbon forms the backbones of
fats, oils, nucleic acid (DNA and RNA), sugars and proteins. Apart from water, carbon is the most major
constituent of living things on Earth.
Silicon is the second most abundant element in the Earth's crust and yet there is so little of it in the human
body and in most other organisms. However, some microscopic creatures in the oceans, including diatoms,
use silicon to build glass shells for themselves and certain types of sponge have glass skeletons. Also,
grasses, including bamboo contain appreciable amounts of silicon, but on the whole living things use little
silicon, why? The principle reason is silicons affinity for oxygen. Carbon reacts with oxygen, but the end
results are largely gaseous - carbon monoxide and carbon dioxide gases, which are mobile and see easily
recycled into the biosphere. Silicon, however, forms unreactive solids with oxygen. Most of the rocks on
Earth contain silca (silicon oxide) or silicates (silicon compounds containing metals and oxygen). For
example, quartz is silica (silicon dioxide) and clay comprises sheet silicates that flake away in sheets.
Quartz-rich sand (which most sand is) acts as a source of silica in glass manufacture. The silicon shells of
marine organisms also gets fossilised and turned into rocks such as flint. Many animals utilise this material
by swallowing it, as many birds do, and storing it in a crop or grinding chamber where grit and stones help
grind their food before it enters the stomach (adult birds do not need teeth!). The silicon is very hard to
remove from these rocks! Eventually rocks may be weathered to sand, but most of the silicon still remains
as a solid, although small amounts of silicon dissolve as silicon acids (which still contain oxygen) which are
soluble in water and can be taken up by plant roots. Since silicon is so hard to get hold of, organisms on
Earth have used little of it, and, in any case, carbon is generally more versatile and more useful, so
organisms on Earth have found little need for silicon.
Iron and aluminium are also quite abundant in the Earth's crust, but again they react with oxygen to form
unreactive solids (iron rusts in damp air!). However, iron is essential for the manufacture of haemoglobin -
the pigment that makes your blood red and which carries oxygen and carbon dioxide around the body.
Many animals, such as certain spiders, crabs and horseshoe crabs, utilise copper for this purpose and
have light blue blood.
Metals such as calcium, sodium and potassium are quite abundant and despite being extremely reactive,
form mostly water-soluble compounds and so are easily absorbed by plant roots and are widely used by
living things. A number of other elements are incorporated in trace amounts - many of the heavier metals
are useful for enzymes, as they make good catalysts, and metals like cobalt and especially selenium are
rather toxic in even small amounts, but in even smaller amounts they are essential dietary requirements!
Phosphorus is very reactive and not very abundant, but it is an essential element (it is, for example, a
component of nucleic acids and ATP and the phospholipids that make up cell membranes) and is often
limiting for plants whose roots cannot absorb it well. However, fungi can scavenge phosphorus very
efficiently, and so most plants have entered into a symbiosis with at least one species of fungus - the
fungus transports phosphorus to the plant's roots in exchange for sugars manufactured in the plant's
leaves.
Nitrogen is an essential component of nucleic acids, ATP and proteins. It is abundant as nitrogen gas in
the Earth's atmosphere. However, nitrogen gas is extremely unreactive (which is why it remains as
unreacted nitrogen) and will normally only react with hot burning materials (to form nitrides). However,
certain bacteria, called nitrogen-fixing bacteria have an ingenious enzyme system that allows nitrogen to
react rapidly at room temperature. They incorporate the nitrogen into their own cells, but when they die
this nitrogen gets released as nitrates and nitrites which are soluble and so can be absorbed by plants.
Sulphur is also an essential component of proteins (though present in much smaller amounts than
nitrogen) where it plays an important role in stabilising the structure of proteins. Many sulphur compounds
are water soluble (sulphates and sulphides) and so are readily absorbed by plants. Only in arid regions do
sulphates occur abundantly in rocks, such as in gypsum flowers and bluestone crystals which occur in
deserts. However, some water insoluble minerals incorporate sulphur, such as fool's gold (iron pyrite which
is iron sulphide).
Organic Chemistry
Organic chemistry originally referred to the biochemistry of living things, as opposed to inorganic chemistry
which dealt with non-living things like rocks. Nowadays, the term organic chemistry has been expanded to
include the chemistry of organic chemicals and derived or related chemicals. All these chemicals have one
thing in common: they are all carbon-based, carbon forms the skeleton of the molecules. Two definitions of
organic chemistry exist (each essentially amounts to the same thing):
1. The study of carbon-containing compounds and their properties. (Usually excluding carbon oxides,
carbonates and a few other inorganic compounds).
2. The study of compounds that contain carbon and hydrogen (carbon hydrides and their derivatives)
and/or carbon and a halogen (fluorine, chlorine, bromine or iodine) (carbon halides and their derivatives).
There is an infinite number of different organic compounds!
Why Carbon?
1. Carbon (C) has an unusually strong ability to covalently bond with itself, forming C-C bonds, C=C
double bonds and C to C triple bonds. This bonding of an element to itself is called catenation. Carbon
has the strongest ability to catenate and its catenation is virtually unlimited and chains of dozens or
hundreds of carbon atoms bonded to each other occur in nature. This is because the C-C bond is very
strong.
2. Carbon has a valency of 4 (each carbon atom has four links that can attach to other atoms), meaning
that not only can carbon bonded together in a large chain, but other chemical atoms or groups of atoms
may be bonded to the sides of these chains. The chains may also be branched, or closed to form rings.
Macromolecules and polymers
Organic materials form the skeleton and working machinery of the cell and water completes the rest.
These organic molecules exist in a range of monomers or subunits which can be added together (rather
like pieces in a Lego or Mechano set) to form long chains or polymers and these chains can be
cross-linked to one another to form three-dimensional meshes. These molecules can be enormous and
are called macromolecules - the entire cell wall of a plant cell, for example, consists of cellulose fibrils
(made of cross-linked polymers of glucose sugar) and proteins and polypeptides (polymers of amino
acids) and can be seen as a collection of molecules or as a single macromolecular network (or even as a
single macromolecule).
Click here to download a pdf on macromolecules.
In the following links we shall explore this organic chemistry in much more detail:
air are given by % volume, the remainder are % mass fraction). Hydrogen and helium are the most
abundant elements in the Universe, but these are less abundant on the Earth as most of the hydrogen and
almost all of the helium escaped to outer space since these were light gases that eventually escaped the
Earth's gravitational pull. Helium gas is unreactive and so was almost totally lost. Hydrogen remained as it
reacts readily with oxygen to form water (and with other elements to form hydrides, some is present as
hydrogen sulphide gas).
Note that the most abundant element on Earth is oxygen, by a long way, and by no coincidence it is also
the most abundant element in living things on Earth. This is the first point - organisms build their bodies
primarily from the most abundant elements in their environment. Hydrogen is quite abundant on Earth as
water (hydrogen oxide) and is also a common constituent of life on Earth - living things may be as much as
90% water (the human body varies from about 30% to 70% water, depending upon fat content). The first
animals and proto-plants to appear on the Earth lived in water and it is no surprise that when they
colonised the land they took their environment with them - body fluids have a close resemblance to
sea-water. This water serves as a solvent in which many chemicals dissolve and the chemical reactions of
life occur. It may well be that other solvents could work as well, but water is the most abundant inorganic
liquid in the Universe.
Two conspicuous exceptions to the rule that organisms utilise the most abundant elements in their
environment are silicon and carbon. Carbon is not especially abundant at the surface of the Earth (though
much lies buried as fossil fuels and limestone) though it is present in small amounts as carbon dioxide in
the atmosphere. However, carbon is so useful and essential to life on Earth that organisms have learnt
how to concentrate it - plants, algae and some bacteria convert carbon dioxide gas into sugars, proteins
and oils with the help of light energy - a process called photosynthesis. Indeed, it was the ability of these
creatures to assimilate carbon so well that lead to its large-scale removal from the atmosphere - coalfields,
natural gas and oil-fields are the carbon-rich remains of ancient forests and swamps. Limestone is the
fossilised remains of the carbon-containing shells of marine organisms. Carbon forms the backbones of
fats, oils, nucleic acid (DNA and RNA), sugars and proteins. Apart from water, carbon is the most major
constituent of living things on Earth.
Silicon is the second most abundant element in the Earth's crust and yet there is so little of it in the human
body and in most other organisms. However, some microscopic creatures in the oceans, including diatoms,
use silicon to build glass shells for themselves and certain types of sponge have glass skeletons. Also,
grasses, including bamboo contain appreciable amounts of silicon, but on the whole living things use little
silicon, why? The principle reason is silicons affinity for oxygen. Carbon reacts with oxygen, but the end
results are largely gaseous - carbon monoxide and carbon dioxide gases, which are mobile and see easily
recycled into the biosphere. Silicon, however, forms unreactive solids with oxygen. Most of the rocks on
Earth contain silca (silicon oxide) or silicates (silicon compounds containing metals and oxygen). For
example, quartz is silica (silicon dioxide) and clay comprises sheet silicates that flake away in sheets.
Quartz-rich sand (which most sand is) acts as a source of silica in glass manufacture. The silicon shells of
marine organisms also gets fossilised and turned into rocks such as flint. Many animals utilise this material
by swallowing it, as many birds do, and storing it in a crop or grinding chamber where grit and stones help
grind their food before it enters the stomach (adult birds do not need teeth!). The silicon is very hard to
remove from these rocks! Eventually rocks may be weathered to sand, but most of the silicon still remains
as a solid, although small amounts of silicon dissolve as silicon acids (which still contain oxygen) which are
soluble in water and can be taken up by plant roots. Since silicon is so hard to get hold of, organisms on
Earth have used little of it, and, in any case, carbon is generally more versatile and more useful, so
organisms on Earth have found little need for silicon.
Iron and aluminium are also quite abundant in the Earth's crust, but again they react with oxygen to form
unreactive solids (iron rusts in damp air!). However, iron is essential for the manufacture of haemoglobin -
the pigment that makes your blood red and which carries oxygen and carbon dioxide around the body.
Many animals, such as certain spiders, crabs and horseshoe crabs, utilise copper for this purpose and
have light blue blood.
Metals such as calcium, sodium and potassium are quite abundant and despite being extremely reactive,
form mostly water-soluble compounds and so are easily absorbed by plant roots and are widely used by
living things. A number of other elements are incorporated in trace amounts - many of the heavier metals
are useful for enzymes, as they make good catalysts, and metals like cobalt and especially selenium are
rather toxic in even small amounts, but in even smaller amounts they are essential dietary requirements!
Phosphorus is very reactive and not very abundant, but it is an essential element (it is, for example, a
component of nucleic acids and ATP and the phospholipids that make up cell membranes) and is often
limiting for plants whose roots cannot absorb it well. However, fungi can scavenge phosphorus very
efficiently, and so most plants have entered into a symbiosis with at least one species of fungus - the
fungus transports phosphorus to the plant's roots in exchange for sugars manufactured in the plant's
leaves.
Nitrogen is an essential component of nucleic acids, ATP and proteins. It is abundant as nitrogen gas in
the Earth's atmosphere. However, nitrogen gas is extremely unreactive (which is why it remains as
unreacted nitrogen) and will normally only react with hot burning materials (to form nitrides). However,
certain bacteria, called nitrogen-fixing bacteria have an ingenious enzyme system that allows nitrogen to
react rapidly at room temperature. They incorporate the nitrogen into their own cells, but when they die
this nitrogen gets released as nitrates and nitrites which are soluble and so can be absorbed by plants.
Sulphur is also an essential component of proteins (though present in much smaller amounts than
nitrogen) where it plays an important role in stabilising the structure of proteins. Many sulphur compounds
are water soluble (sulphates and sulphides) and so are readily absorbed by plants. Only in arid regions do
sulphates occur abundantly in rocks, such as in gypsum flowers and bluestone crystals which occur in
deserts. However, some water insoluble minerals incorporate sulphur, such as fool's gold (iron pyrite which
is iron sulphide).
Organic Chemistry
Organic chemistry originally referred to the biochemistry of living things, as opposed to inorganic chemistry
which dealt with non-living things like rocks. Nowadays, the term organic chemistry has been expanded to
include the chemistry of organic chemicals and derived or related chemicals. All these chemicals have one
thing in common: they are all carbon-based, carbon forms the skeleton of the molecules. Two definitions of
organic chemistry exist (each essentially amounts to the same thing):
1. The study of carbon-containing compounds and their properties. (Usually excluding carbon oxides,
carbonates and a few other inorganic compounds).
2. The study of compounds that contain carbon and hydrogen (carbon hydrides and their derivatives)
and/or carbon and a halogen (fluorine, chlorine, bromine or iodine) (carbon halides and their derivatives).
There is an infinite number of different organic compounds!
Why Carbon?
1. Carbon (C) has an unusually strong ability to covalently bond with itself, forming C-C bonds, C=C
double bonds and C to C triple bonds. This bonding of an element to itself is called catenation. Carbon
has the strongest ability to catenate and its catenation is virtually unlimited and chains of dozens or
hundreds of carbon atoms bonded to each other occur in nature. This is because the C-C bond is very
strong.
2. Carbon has a valency of 4 (each carbon atom has four links that can attach to other atoms), meaning
that not only can carbon bonded together in a large chain, but other chemical atoms or groups of atoms
may be bonded to the sides of these chains. The chains may also be branched, or closed to form rings.
Macromolecules and polymers
Organic materials form the skeleton and working machinery of the cell and water completes the rest.
These organic molecules exist in a range of monomers or subunits which can be added together (rather
like pieces in a Lego or Mechano set) to form long chains or polymers and these chains can be
cross-linked to one another to form three-dimensional meshes. These molecules can be enormous and
are called macromolecules - the entire cell wall of a plant cell, for example, consists of cellulose fibrils
(made of cross-linked polymers of glucose sugar) and proteins and polypeptides (polymers of amino
acids) and can be seen as a collection of molecules or as a single macromolecular network (or even as a
single macromolecule).
Click here to download a pdf on macromolecules.
In the following links we shall explore this organic chemistry in much more detail:
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