Introduction to Biochemistry

Elements in Biochemistry

Out of the 92 naturally occurring elements of the chemical periodic table, only 6 chemical elements are of primary interest in biochemistry:

C carbon    H hydrogen    O oxygen
N nitrogen    P phosphorus    S sulphur

Covalent bonds and valency
The covalent bond ( a pair of shared electrons) is the most common form of linkage between atoms in organic chemistry and biochemistry.

Each element has its own characteristic number of bonds : its valency.
Carbon has 4 bonds, hydrogen 1 bond, and oxygen and sulphur both have 2 bonds, Nitrogen and phosphorus are variable
usually 3 or 5 bonds. So these atoms can be denoted on the printed page (or the computer screen) as follows:

Elsewhere on this site a number of biological molecules are shown in 3 dimensions in an interactive format
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carbon atom & bondsoxygen atom & bondshydrogen atom - single bond

Each line represents a covalent bond, to be used to combine with other atoms.

Carbon atom inside a tetrahedron
Actually this is an over-simplification because these are only 2-dimensional. In fact, the 4 bonds of carbon are at about 109º to each other but in 3 dimensions. Another way of saying this is that the 4 bonds are each directed towards the corners of a regular tetrahedron (formed from 4 equilateral triangles), with the carbon atom in the centre!

Carbon is special, because of its four bonds which enable it to combine with other carbon atoms and form a chain. The other elements H, O, N etc are unable to form giant structures on their own.
Organic compounds
The term organic has several connotations. Originally it meant something derived from a living organism plant or animal, rather than of mineral origin: inorganic.
Then it became used by chemists to cover compounds of natural origin which were found to be based on carbon, and the term was extended to cover similar and more complex compounds produced artificially, and often containing other elements.
With this proviso, the term organic may be used without much confusion between biologists and chemists (and, indeed biochemists)!

More recently, it has been used in a more general way to describe consumer products and production processes which are not based on chemical fertilisers or other artificial chemicals. In this sense, there is scope for confusion: Artificial fertilisers are seen by chemists as inorganic compounds, and synthetic pesticides are defined as organic compounds, although banned in organic culture systems!

Methane (CH4) is the first in a family or series of similar compounds alkanes (also known as paraffins). It is also known as marsh gas, produced by decomposition of organic matter in water. As a component of natural gas, its origins are definitely biological, even if the time scale of its production is geological! 15% of atmospheric methane comes from the digestion of ruminants such as cows. Methane is a potent greenhouse gas, and may be responsible for 38% of global warming.

ethane.png propane.png

Ethane (C2H6) propane (C3H8) and butane (C4H10) are the next alkanes, each differing by CH2 . The general formula for alkanes is CnH2n+2.
The number of atoms in the molecule affects the state (solid/liquid/gas) of the compound produced. The first few mentioned above are gases, but alkanes with about 8 carbon atoms are liquid at room temperature (petrol has an “octane” rating) and molecules with larger numbers of carbon atoms are solid
like candle wax. Interestingly these compounds are used as fuels. The energy released when they are burned effectively comes from breaking covalent carbon-to-hydrogen bonds in the molecular structure, so energy must have been taken in when these bonds were formed in the first place.

Being composed of only two elements (hydrogen and carbon), these are often known as hydrocarbons. Alkanes have only single (-C-C-) bonds. Other series of hydrocarbons are alkenes, with one or more double bonds (-C=C-), and alkynes, with triple bonds. Double bonds are found in unsaturated fats.

Aromatic compounds
benzene ring.png
Organic compounds containing ring-shaped sections of carbon atoms are described as aromatic. This term is not used to describe the smell of the compound, but rather it is more concerned with the molecular similarity with benzene, C6H6, often written in chemical shorthand as a simple hexagon, usually drawn with alternating double bonds.

It is a general principle in chemistry that like dissolves like. Hydrocarbons have little in common with water, so do not dissolve in it. Indeed many similar organic compounds do not mix with or dissolve in water. This is mainly because hydrocarbons consist of a chain of carbon atoms surrounded by covalently bonded hydrogen atoms.
However, organic compounds containing different elements in addition to carbon and hydrogen may dissolve in water.

Naming organic compounds
Names of organic compounds follow a standard system: the first part of the name is usually based on the number of carbon atoms in the main chain. The first four in a series are based on the alkane names above, then they are based on Greek numbers:

Number of C atoms 1 2 3 4 5 6 7 8 9 10
Prefix Meth- Eth- Prop- But- Pent- Hex- Hept- Oct- Non- Dec-
These prefixes are applied in a systematic way to members of several series of organic compounds.

It should be borne in mind that there are two ways of naming some organic compounds, and that biochemistry has stuck with some of the older terminology, abandoned by modern chemists. In this article, both systems will be used (older terms in brackets).

It is often useful to think of organic molecules in a modular way, chemically combining subunits in a predictable manner.

Carbon based groups

Alkyl groups
These are effectively an alkane lacking a hydrogen atom:

CH3-        methyl        sometimes written as Me
C2H5 -     ethyl        sometimes written as Et
C3H7 -      propyl
In these examples, the name is based on the alkane plus “yl”.
The general formula is Cn H 2n+1 - .

These contain the OH group, directly attached to a carbon atom, usually in a group such as those above.
MeOH.png EtOH.png PrOH.png

CH3OH      methanol (methyl alcohol)
C2H5OH     ethanol (ethyl alcohol)
C3H7OH    propanol (propyl alcohol)
In these examples, the name is based on the alkane (minus “e”) plus “ol”.
The general formula is Cn H 2n+1 OH.

“Alcohol”- the active ingredient in beers and spirits - is in fact ethanol. This is produced by many biological fermentation processes involving anaerobic respiration by the fungus yeast
Saccharomyces cereviseae. Distillation, which is a physical process to concentrate the ethanol, produces liquids called spirits. Partially in view of its biological effects on the human mind and body, alcohol is taxed. Spirits not intended for consumption (industrial solvents, fuels etc) are deliberately made unpalatable through the addition of methanol - methylated spirits.

glycerol.pngGlycerol is another example of an alcohol, containing 3 -OH groups.
It is the basis for a number of 3-carbon compounds in respiration and photosynthesis.
It is also the basis for neutral fats (triglycerides) and phospholipids.
Although glycerol has only 3 carbon atoms, it is a fairly viscous liquid because of interactions between -OH groups. It is also known as glycerine, used in cough mixtures etc

Perhaps it might be useful to consider these (alcohol) compounds in relation to H.OH - water -
which explains why water and alcohols are miscible (i.e. they mix) and they dissolve (i.e. they are soluble) in one another. In this case the OH (hydroxyl) groups are the common feature.

Do not confuse this organic -OH group with OH
- (the hydroxide ion ) which is produced by alkalies and found in small quantities in water due to its dissociation into hydrogen ions (H+ ) and hydroxide ions. Both of these ions belong in the realms of inorganic chemistry, and do not interact much with organic compounds. However H+ ions (protons) are important in the biochemistry of respiration and photosynthesis!

The -CHO group makes an organic molecule somewhat more reactive than those previously mentioned.
e.g. methanal.png

HCHO     Methanal (formaldehyde)
CH3CHO    Ethanal (acetaldehyde)
Formalin is a solution of methanal. It interacts with proteins (a tanning reaction) and hence hardens and preserves biological specimens. Many preserved specimens are firstly fixed in formalin, then transferred to a more user-friendly solution.
The >C=O group is also quite reactive, sandwiched between 2 alkyl groups..

CH3COCH3    propanone (acetone)

Propanone is often used as a solvent in biochemistry, and also in nail varnish!

Many sugars have aldehyde or ketone groups in their structure, even though this may be hidden in the ring forms. There are 2 main groups aldoses and ketoses.

Aldehyde and ketone groups in reducing sugars are involved in reacting with (reducing) test reagents such as Benedict’s solution.
Carboxylic acids
The COOH grouping provides weakly acidic properties, as it can dissociate to give rise to hydrogen ions H+ , leaving a negatively charged ion COO- . The COOH group is found in a large number of biologically important compounds:
short chain carboxylic acids:
methanoic.pngmethanoate.png ethanoic.pngethanoate.png

HCOOH    methanoic acid (formic acid), an acid given out by ants
CH3COOH    ethanoic acid (acetic acid), the main component in vinegar

hydroxypropanoic acid (lactic acid), produced as a result of anaerobic respiration in muscles, and by Lactobacilli in milk.

fatty acids, usually attached to a large CH chain.
stearic acid molecule

C17H35.COOH stearic acid, a saturated fatty acid found in animal fat.


C17H33.COOH oleic acid, an unsaturated fatty acid found in plant oils.

amino acids, 20 commonly found in proteins and therefore in the diet, but many more with metabolic functions

H2N.CH2 .COOH    glycine (simplest dietary amino acid)

H2 N.(CH2)3 .COOH    gamma-amino butyric acid (neurotransmitter)

tricarboxylic acids, with 3 -COOH groups

In solution, the carbonyl group >C=O influences the OH group so that it can act as an acid by the loss of a hydrogen ion, H+

The COOH group can also form covalent linkages, e.g. peptide bonds between amino-acids in proteins, and ester linkage in lipids.

COOH groups in the side chains (“R groups”) of amino acids e.g. glutamic acid, aspartic acid, make them more acidic, even when joined by peptide links to form polypeptide chains, and these groups are able to interact with other side chains and ionise in alkaline conditions.

A derivative form of ethanoic acid, the ethanoyl (acetyl) group CH3CO- , has a function in transporting (pairs of) carbon atoms into the tricarboxylic acid cycle.

Note that in several cases, the more modern names have not been fully adopted by biochemists.

Nitrogen based groups
Amino groups
The NH2- group may give basic (alkaline) properties to a compound containing it.

The amino group thus inherits similar properties to ammonia, NH3


H2N.CH2 .COOH    glycine (simplest dietary amino acid)

Extra NH2 groups in the side chains (“R groups”) of amino acids e.g. arginine, glutamine, asparagine, make them more basic, even when joined by peptide links to form polypeptide chains, and these groups are able to interact with other side chains and ionise in acidic conditions.
Purines and pyrimidines
These are two categories of nitrogen-containing basic molecules with 2 rings and 1 ring respectively.
In the diagrams below, carbon atoms at the intersections of bonds are not labelled.
Purines adenine molecule
Guanine molecule
Thymine molecule
Cytosine molecule
Uracil molecule
Combined with sugars and phosphates, these purine and pyrimidine bases form nucleotides which are then built up into nucleic acids DNA and RNA. ATP is a single nucleotide based on adenine, with other phosphate groups (see below), which is used to store and convert chemical energy within the cell. There are several double adenine-based nucleotides such as NAD, FAD, and NADP, which act as hydrogen carriers, co-enzymes to the main enzymes involved in respiration and photosynthesis.

Sulphur based groups
Sulphydryl group
The -SH group (also known as a thiol group, from its similarity with alcohol) is found in the side chains of only one amino acid: cysteine. With the removal of 2 hydrogen atoms, it is able to form a disulphide bridge -S-S- with neighbouring cysteine side chains, which contributes to stabilising the tertiary structure level of the protein containing it.
Insulin is an example of this.

-SH + HS- arrow -S-S- (+ 2H)

Coenzyme A has a thiol group through which it may attach to groups such as acetyl or succinyl and thus function as a shuttle for 2 or 4 carbon atoms into and around the citric acid cycle.

Phosphorus based groups
Phosphate groups

Phosphoric acid, H3PO4, forms a number of inorganic salts (phosphates) which are often used as components of pH buffers.

When inorganic phosphate (often written as Pi) is combined covalently with organic compounds, energy is effectively stored within the bond so formed. Such organic phosphate compounds may be considered as more reactive. The process of adding phosphate groups is called phosphorylation.

Adenosine diphosphate + Pi reversible reaction Adenosine triphosphate

ADP + Pi reversible reaction ATP

the ATP molecule

The ATP molecule

Phosphate groups are sometimes attached to sugars, e.g. glucose, fructose or ribose. They are thus subsections within nucleotides, which form nucleic acids (DNA and RNA).

Phosphate groups also form part of phospholipids, which are the main component of cell membranes. Because they retain the ability to ionise, phosphate groups enable (one end of) these molecules to interact with water, a property known as hydrophilic.

Abbreviations are often used in biochemistry, especially for large molecules. In these cases, phosphate groups are sometimes written as P, e.g. ATP, NADP etc. This should not be confused with single atoms of phosphorus.

In fact some of the attraction of biochemistry lies in the amount of detail that is ignored in giving a simple name to a complex biochemical molecule such as DNA (only a small section of which is shown below!).

a section of theDNA molecule