1.4 Proteins

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Aims:

•What an amino acid is

•What a peptide, dipeptide and a polypeptide are

•How you make a peptide bond

•That the protein’s shape and order of amino acids defines its function

•What primary, secondary, tertiary and quarternary

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Examples:

• Enzymes are proteins

• Antibodies are proteins

• Proteins are involved in the transport of substances across cell membranes

• Muscle is made out of proteins

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Properties of proteins

• 1. They are polymers – they are made up of lots of

repeating units (monomers). The monomers of proteins are AMINO ACIDS.

• 2. There are 20 different amino acids that proteins can be made up from

• 3. The long amino acid chain is folded up in a very precise way so that the protein forms a particular shape.

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An amino acid

Carboxyl group (COOH)

Amino group

(NH2)

R- group

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Forming a dipeptide

First and second amino

acids line up together – the carboxyl group of the first next to the amine group of the second.

•Water is eliminated (= condensation reaction)

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Forming a polypeptide

•Hundreds or thousands of amino acids join together

•Proteins are synthesized at the ribosomes – that is the place where amino acids get joined together

•The order of the amino acids in a polypeptide is known as PRIMARY

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Protein structure

• The topic of protein structure refers to the way polypeptide chains are folded up to make specific 3D shapes.

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There are four levels of protein

structure:

• Primary – the most simple. Simply describes the

order of amino acids in the polypeptide chain.

• Secondary – the most simple way polypeptides can

be folded is into either an α-helix (alpha helix) or a

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• _Tertiary_{– further folding of the polypeptide to}

make it into its precise 3D shape. Four types of

intermolecular bonds are involved in holding its shape together.

• Quaternary – some proteins are made up of

more than one polypeptide chain. The chains

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Primary structure

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Secondary Protein Structure

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Beta (β) pleated sheets

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The Alpha (α) helix and β-pleated sheet keep their shape because of H-bonds

• The H on the amino group is attracted to the O on the carboxyl group

• The H is slightly positive and the O is slightly negative

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Tertiary structure

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Tertiary structure is held together by 4

types of intermolecular bonds:

1. Disulphide bonds – bond occurring between adjacent sulphur containing amino acids

2. Hydrophobic Interactions – the tendency for

nonpolar R groups to be attracted to one another

3. Ionic bonds – Forming between ionised amine & carboxylic groups

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Tertiary structure

• The four types of intermolecular bonds listed on the previous slide help the

polypeptide chain fold up into its precise shape.

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QUATERNARY PROTEIN STRUCTURE

• Quaternary structure refers proteins that are made up of more than one polypeptide chain

• For example, Haemoglobin (Hb) is made up of four polypeptide chains and collagen is made up of three.

• The polypeptide chains are held together by the same intermolecular bonds that are involved in tertiary structure – namely disulphide bridges, hydrophobic interactions, ionic bonds and

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Fibrous and Globular Proteins

• Globular proteins are soluble molecules made of chains that are folded into a compact structure.

• They play an important role in metabolic reactions – such as enzymes and haemoglobin (Hb)

• Fibrous proteins are made up of long molecules to

form fibres. Several helices may be wound around each other to form very strong fibres.

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Haemoglobin

• A globular protein

• Made up of four subunits (polypeptide chains) consisting of two parts – haem and globin

• Haemoglobin combines with oxygen in the lungs to form oxyhaemoglobin

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HAEMOGLOBIN (Hb)

• Of the 4 polypeptide chains - two are α-chains and two are β-chains

• Hydrophobic (water-hating) R-groups of amino acids point into the molecule. They are attracted to each other by hydrophobic interactions.

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Haem group

• each of the 4 polypeptide chains of Hb has a haem group

• the haem group is not made of amino acids – it is

known as a prosthetic group.

• The haem group contains an ion of iron (Fe2+).

(An ion is a charged atom – the “2+” refers to the fact that this atom is lacking 2 electrons).

• Each haem binds with one molecule of oxygen (O₂)

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The 4 different colours are the 4 different

polypeptide chains that make up the Hb protein.

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Haemoglobin – a quaternary level protein

You would say that this protein has:

• Primary structure (it has a specific order of amino acids),

• Secondary (I can see several alpha-helices), • Tertiary (because each polypeptide chain is

folded up into a precise 3D shape) and

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Collagen

• Made out of three polypeptide chains coiled into a helix

• This type of protein is known as a

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• Collagen has a quaternary structure as it is made out of more than one polypeptide

chain.

• Each chain has an α-helix shape.

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Other example of proteins:

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Keratin

• Fibrous or globular protein?

• Primary structure? • Tertiary structure? • Quarternary

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Aquaporin

• Fibrous or globular protein?

• Primary structure? • Tertiary structure? • Quarternary

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Antibody

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