Chemistry for Biologists



Proteins are naturally occurring polypeptides. They:

  • contribute to the mechanical structure of animals, including humans, e.g. keratin in hair and fingernails, and fibrous proteins such as collagen in tendons
  • enable animals to move, e.g. myosin in muscle
  • facilitate transport of smaller molecules around animals' bodies, e.g. haemoglobin
  • control the types and rates of chemical reactions in living things; then they are called enzymes, e.g. amylase
  • are important components of the human immune system, e.g. immunoglobins

See also Chemistry for Biologists logo  Enzymes

Proteins make up about 15% of our body mass. They are the most abundant 'solid' substances in our bodies.

Each protein has its own precise function under the direction of its own gene. The shapes of proteins are of key importance. These are determined by the sequence of amino acids that make them up.

Amino acids

Amino acids are the building blocks (monomers) of proteins. Twenty different amino acids are used to make the body's proteins. Of these nine are called essential (meaning they can only be obtained from the food we eat) and eleven are non-essential (they may be synthesised in the body though they are usually obtained from food).

Amino acids have the general structural molecular formula -NH2CHRCOOH. They have two important functional groups (a functional group means a group of atoms in a molecule that have characteristic chemical reactions regardless of the rest of the molecule):

carboxylic acid group -COOH
amine group -NH2

ppt logo Learn more about amino acids

The R group determines the amino acid. For example,

R group amino acid Side chain
- H glycine non-polar
- CH3 alanine non-polar
- CH2OH serine uncharged polar
- CH2SH cysteine uncharged polar
- CH2COOH aspartic acid acidic
- CH2CH2CH2CH2NH2 lysine basic

When amino acids dissolve in water they ionise. At a particular pH each amino acid exists in solution as a zwitterion. In effect a proton transfers from the carboxylic group to the amine group. The pH at which this happens is the isoelectric point for the amino acid.

ppt logo Zwitterions

ppt logo Alanine

Solutions of amino acids are buffers. This means they resist changes in pH when an acid or an alkali is added to an amino acid in solution.

When an acid is added, the -NH2 group combines with H+ ions from the acid to form -NH3+

NH2CHRCOOH (aq) + H+ (aq)  -->  NH3+CHRCOOH (aq)
(H+ is frequently used as shorthand for H3O+)

When an alkali is added, the -COOH group combines with OH- ions from the alkali by loss of H+ to form

NH2CHRCOOH (aq) + OH- (aq)  -->  NH2CHRCOO- (aq) + H2O

In both cases, the concentration of H+ ions in solution does not change greatly and so the pH remains about the same.

The shape of the amino acid molecule is also important.

ppt logo The shapes of some amino acid molecules

Peptide bond formation

Two amino acids can undergo a condensation reaction to form a dipeptide. Further condensation reactions result in a polypeptide. The amino acid units are linked by peptide bonds (sometimes called peptide links).

R1-COOH + R2-NH2  -->  R1-CO-NH-R2 + H2O

ppt logo Formation of the peptide bond

Rotation about the carbon-nitrogen bond in the peptide link is restricted. This has a huge influence on the shape and structure of proteins, which in turn determine how they behave.

Peptide bonds can be broken down by hydrolysis.

R1-CO-NH-R2+ H2O  -->  R1-COOH +R2-NH2

ppt logo Hydrolysis of the peptide bond

Protein structures

The sequence of amino acids in a protein is called its primary structure. Within a chain the atoms are held together by covalent bonds. Each protein has its own characteristic sequence of amino acids.

Three types of bonding can happen within a protein molecule (intramolecular bonding) and between protein molecules (intermolecular bonding):

  • Hydrogen bonds
  • Covalent bonds
  • Ionic bonds

ppt logo Bonding between peptide chains

Protein chains arrange themselves to maximise the intra- and intermolecular bonding. The structure when protein chains are held in place is called the secondary structure. This may be:

  • helical, e.g. keratin (the protein found in hair), or
  • pleated sheet, e.g. fibroin (the protein found in silk)

These structures are held in place by hydrogen bonds.

Protein chains may fold into a globular shape. This is the tertiary structure of a protein. These globular proteins include enzymes and immunoglobins. The structures are held in place by hydrogen bonds, disulfide bridges and ionic bonds.

The precise structure of a globular protein is the key to specificity of enzymes. Similarly proteins that act as receptor sites on the cell surface can recognise specific molecules because of their shapes.

Finally some proteins have a quaternary structure. These contain more than one protein chain. Examples are insulin and haemoglobin.

Try these websites for a good description of formation of peptides and their primary, secondary, tertiary and quaternary structures:

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