Carbon is the most versatile element. It can form rings, chains and other interesting molecules. Carbon chemistry is an entire field of chemistry.
Basically, life as we know it is based on the elements C, H, O, P, S and N: carbon, hydrogen, oxygen, phosphor, sulphur and nitrogen. There are other
elements in our body, but they are not as common or as important as these six. Because of it’s versatility, carbon can form very complex molecules.
Once you have the formation of complex molecules you can have the complex chemical pathways required for life.
3.1 Carbon forms long chains
Carbon’s number one special ability is forming long chains of itself through single covalent bonds. This chains are very stable and can easily be
hundreds of carbon atoms long. The structure of these polymers is like this (figure 3.1) and their general formula is CnH2n+2, where n can be any
These chains are the back bone of virtually all organic chemicals required for cell pathways to function. Just take a look at glucose (figure 3.2). It
has a central ring of carbon.
Other molecules vital to you that have a simple carbon backbone (as in figure 3.1) are fatty acids and phospholipides (in cellular membranes).
Figure 3.1 - Carbon polymer
Figure 3.2 - Glucose
3.2 Double and triple bonds allow rigid chains
The second important feature is that the chain can easily be made into rigid shape. Normally the chain has the structure of a chain of tetrahedrals
that are connected at the points. This structure can be rotated around every bond between two connected carbon atoms. Sometimes a certain shape is
needed for the molecule to function well, like in most enzymes. This can be easily accomplished by replacing two hydrogen atom with a double bond
between the two carbon atoms. A triple bond can also be made by replacing four hydrogen atoms with two extra bonds. You can check that every carbon
atom still has four bonds. The structure of such a rigid chain looks like a polymer similar to figure 3.1 (figure 3.3).
Figure 3.3 - A carbon chain with a double and a triple bond
3.3 Carbon supports ‘handedness’
Because carbon can form four bonds, usually in a tetrahedral, it can have a property called handedness. The molecules have different properties when
they are mirrored. An example is glycogen and cellulose (see section 3.7). The only difference between the molecules is the handedness, but the
properties are completely different: cellulose is very rigid, while glycogen is not. (3.7) You can’t even digest cellulose without the help of
specialized bacteria. Glycogen is no problem at all.
Handedness is very important to enzyme functions, because the substrates fit into the enzyme exactly. The handedness can make the difference between
fitting and not fitting. By changing the handedness of molecules with enzymes, the cell can regulate chemical processes.
Figure 3.4 A benzene ring (left) and a benzene ring with a carbon atom
replaced with a nitrogen atom
3.4 Carbon can form stable rings with itself
One the most important carbon groups is the benzene ring. Six carbon atoms and six hydrogen atoms in the following shape (figure 3.4). Benzene rings
(C6H6) are important for a lot of hormones (cortisone, progesterone and testosterone all have four rings) and a few amino acids. You can also replace
a carbon atom with a nitrogen atom. Then you get the kind of ring that is the basis of all nucleotides (see section 3.5 and section 3.8).
3.5 Carbon combines well with other elements and can form complex molecules
The third important feature carbon has is the ability to bond with other atoms very well, especially the other four elements important to life: H, O,
P, S and N. There are two reasons why carbon bonds easily:
- Carbon has a high electronegativity of 2.5. There is not much shielding of the positively charged nucleus by the negatively charged electrons.
- Carbon has a small bond length of 77∙10-12 m. This also makes its bonds stronger. (1.6 and 3.2)
This allows for various chemicals to be based on carbon chains. These different molecules have various functions within a cell based on the rest of
its chemical makeup. This ability to form complex chemicals makes it the basis for life. Just an overview of some of the different kinds of special
groups within a carbon backbone that are vital to life (also see figure 3.5):
Figure 3.5 - The structure of some carbon groups (remember that C’s for carbon
are not shown, see section 1.3), from top to bottom: ethers, alcohols, aldehydes, ketons, carbon acids, alkanoates, esters, amines and
Figure 3.6 - Histamine
- Ethers, with oxygen
- Alcohols, with oxygen and hydrogen
- Aldehydes, with oxygen and hydrogen (oxidized primary alcohol)
- Ketons, with oxygen (oxidized secondary alcohol)
- Carbon acids, with oxygen and hydrogen (e.g. asparagine-acid, an amino acid)
- Alkanoates, with oxygen (rest of carbon acids)
- Esters (e.g. acetylcholine, a very important neurotransmitter), with oxygen
- Amines (e.g. histamine), with nitrogen
- Thiols, with sulphur and hydrogen
The ability of carbon to bond with other atoms so well allows for a large variety of stable molecules, including:
3.6 The metabolic pathway
- Amino acids, which are the basis of every protein in your body. Protein is probably the most important kind of molecule in your body. They do
almost all the chemical work.
- Nucleotides, which are the information carriers in DNA and RNA (see section 3.8). There are eight different kinds and they are all based on carbon
and nitrogen: adenine (A) (see figure 3.6), guanine (G), cytosine (C), thymine (T), uracil (U), hypoxanthine (I), pseudo-uracil (Ψ and
dihydro-uracil (UH2). The first five are the most important because they appear in DNA and mRNA, the others three only occur in tRNA.
- Saccharides, you all know them as sugars. There are three different kinds of sugar, monosaccharides, disaccharides and polysaccharides. Saccharides
are broken down in the metabolic pathway to get energy, which is carried by ATP (see section 3.6). Biologists only count 1, 2 and many.
- ATP and ADP, the cells energy carriers. The names stand for adenosinetriphosphate (ATP) and adenosinediphosphate (ADP). They are a combination of a
nucleotide (adenine), a monosaccharide (D-ribose) and two or three phosphate groups.
The enormous complexity of carbon chemistry allows for the most important chemical pathway in a cell: the metabolic pathway. Life comes in two
flavours on Earth. The first one kind makes its own organic molecules from inorganic molecules: the autotrophic organisms. The second kind makes it’s
organic molecules from other organic molecules: the heterotrophic organisms.
The autotrophic organisms are the plants and some bacteria. There are two kinds of autotrophic organisms: photo-autorophs, that use light as energy
source and chemo-autotrophs, that use certain inorganic chemicals as an energy source. The only way they can use inorganic molecules to make organic
molecules is a complex metabolic pathway.
The heterotrophic organisms are all the animals, fungi and most bacteria. They also have a very complex metabolic pathway. The metabolic pathway in
animals gets energy from saccharides and stores that energy in ATP molecules. The energy stored in ATP molecules can then be used to make proteins or
it can be used by enzymes.
The pathway has three different parts: glycolysis, Kreb’s cycle (also called Citric Acid cycle) and oxidative phosphorylation. (2.2) All the parts
have a lot of steps that are all regulated by special enzymes. This would not be possible without the complexity of carbon chemistry.
3.7 Energy storage in the form of carbohydrates
Organisms also have to be able to store the energy they get from the metabolic pathway for longer periods. Carbon can form carbohydrates, which store
the energy for longer periods. The release of the energy can be controlled by enzymes. Examples of carbohydrates are glycogen in the liver and
cellulose in trees.
3.8 DNA and RNA
One thing common to all known life is DNA which, as most know, is a long chain of information. This is vital to every organism and codes for all
required proteins. The DNA is read by special enzymes and an mRNA (messenger) molecule is made.
This mRNA chain goes to the organelles that make proteins. There, special tRNA (transfer) molecules adds the right amino acids to the new protein.
The back bone of a DNA or mRNA chain is carbon, the nucleotides are based on carbon and nitrogen, the DNA or mRNA is held together by a saccharide,
deoxyribose, and a phosphate group.
Figure 3.6 - Adenine, one of the nucleotides in the DNA and RNA of every organism on
earth. Other nucleotides have a similar shape.
3.9 There is a lot of carbon, it’s stable and easily accessible
No matter how good carbon is chemically for life, if there’s only a tiny bit of it (like Technetium for example) it will never a good basis of life.
Luckily for us, carbon is created in the lifecycle of normal stars and supernovae. (5.2) There is a lot of carbon on Earth now, freely available in
the atmosphere in the form of CO2, in organisms and certain minerals.
Carbon is also a stable element. If carbon were like Plutonium, it would decay too fast to form life or kill the life with it’s own decay products.
The decay products of radioactive isotopes is either α-, β- or γ-radiation. This radiation has enough energy to destroy the bonds
between the atoms in molecules.
3.10 Photosynthesis and oxidative phosphorylation support an equilibrium
Plants and other photo-autotrophic organisms get their sugar through a process called photosynthesis2.3. The real photosynthesis is a very complicated
process with a lot of different enzymes, but we can simplify it to the following simple chemical reaction:
6CO2 (g) + 6H2O (l) + Light ŕ C6H12O6 (a) + 6O2 (g)*
The overall reaction of heterotrophic glucose metabolism is:
C6H12O6 (aq) + 36Pi + 36ADP + 6O2 (g) ŕ 6CO2 (g) + 6 H2O (l) + 36ATP
The plants use CO2 and make O2, while the heterotrophic organisms use O2 and make CO2. This makes sure neither the oxygen or the carbon dioxide runs
out and therefore these two reactions form an equilibrium.