BIOLOGICAL MOLECULES: Proteins

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Primary structure: the sequence of amino acids found in a molecule

Secondary structure: the coiling or folding of an amino acid chain, which arises often as a result of hydrogen bond formation between different parts of the chains. The main forms of secondary structure are the helix and the pleated sheets.

Tertiary structure: the overall 3D shape of a protein molecule. Its shape arises due to interactions including hydrogen bonding, disulfide bridges, ionic bonds and hydrophobic interactions.

Quarternary structure: protein structure where a protein consists of more than one polypeptide chain e.g. insulin.

Primary Structure

This is the sequence of the amino acid chain. Changing one amino acid in this sequence can alter the whole protein. Most proteins are around 100 amino acids long meaning many different proteins can be formed. The function of the protein is determined by its structure. The order of amino acids in the primary structure will determine the shape of the protein molecule.

Secondary Structure

The chain of amino acids is not straight, but twist into the secondary structure. Some chains coil into an a-helix. The helix is held together by hydrogen bonds between the -NH group of one amino acid and the -CO group of another four places ahead of it in the chain. 

Other chains fold very slightly in a zig-zag structure. When one such chain folds over on itself, this produces a B-pleated sheet. Hydrogen bonds between the -NH group of one amino acid and the -CO group of another further down the strand hold the sheets together. Although hydrogen bonds are relatively weak, many are formed,making both the a-helix and b-pleated sheets stable structure at optimal temperatures and pH. Some chains don't adopt any regular structure, and some chains may have more than one secondary structure at different points in the chain.

Tertiary Structure

When the coils/pleats themselves start to fold, along with areas of straight chains of amino acids, this forms the tertiary structure. The tertiary structure is a very precise shape which is held firmly in place by bonds between amino acids which lie close to each other. The tertiary structure may adopt a supercoiled shape e.g. in fibrous proteins or a more spherical shape e.g. in globular proteins.

Quarternary Structure

Many proteins are made up of more than one polypeptide chain. The quarternary structure is multiple polypeptide chains arranged to make the complete protein molecules.

Protein Bonding

Primary structure = held together by peptide bonds (covalent bonds).

Secondary structure = primarily held by hydrogen bonds

Tertiary + quarternary structure = held by hydrogen bonds and many others.

Hydrogen Bonds

Like in water, hydrogen bonds form between hydrogen atoms with a slight positive charge and other atoms with a slight negative charge. 

Ionic Bonds

Ionic bonds can form between those carboxyl and amino groups that are part of R groups. These ionise into NH3+ and COO- groups. Positive and negative groups like this are strongly attracted to eachother to form an ionic bond.

Disulfide Links

The R group of…

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