Proteins: terminology and alpha helix

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Definitions

PROTEIN: molecular mass greater than 5000 daltons made up of L-amino acids s linked together end to end by peptide bonds. Smaller molecules are called polypeptides.

SIMPLE PROTEINS yield only amino acids when the peptide bonds are hydrolysed

CONJUGATED PROTEINS yield amino acids and an inorganic component (metal atoms) and/or other organic molecules. These extra species are called prosthetic groups

Organisation of proteins

PRIMARY STRUCTURE: number, configuration and sequence of amino acids linked by peptide bonds in the protein chain.

SECONDARY STRUCTURE: Regular and periodic folding which occurs in the polypeptide backbone of the protein molecule.

TERTIARY STRUCTURE: Irregular folding of the polypeptide backbone which can result in nearly spherical molecules.

QUATERNARY STRUCTURE: Arrangement of individual polypeptide chains in proteins with several subunits.

Categories of proteins

FIBROUS: long rod shaped proteins, often insoluble in water with structural functions.

GLOBULAR: spherical or elipised proteins that are water soluble and have many functions.

TRANSMEMBRANE: span the lipid bilayer

How do polypeptide chains fold up?

The peptide bond has partial double bond character. The distance between the carbon and nitogen is 1.32 which is shorter than C-N but longer than C=N. This is important as double bonds can't be rotated so C=O and N-H are always in the same plane.

Alpha Helix

Helices are described by their:

PITCH: distance for a complete turn

RISE: distance between amino acids

Features of Alpha helix:

Right handed helix: you go left to right as you go up the helix

36 amino acids per 10 turns = 3.6 per turn

PITCH: 0.54nm

RISE: 0.15nm

Why is it stable?

It is stable because: every peptide link is planar; the peptide N-H groups are hydrogen bonded to peptide carbonyl oxygen of the third amino acid further up the helix; axes of hydrogen bonds are parallel to the long axis of the helix which gives a stronger hydrogen bond than if they were at 90o and the side chains stick out from the helix so they don't interfere with each other.

Alpha-keratin

This is a fibrous protien that is found in hair, skin, nails and as intermediate filaments in cells. X-ray diffraction (scattering of x-rays by fibres to give a particular pattern on photographic film) shows a helical structure with a pitch of 0.51nm. This pitch is different to a regular alpha helix due to alpha keratin being coiled which distorts the helix.

Assembly of alpha keratin into fibres involved the chains being cross linked by disulphide bonds between cysteine side chains. The more disulphide bridges the more rigidity.

C-CH2-SH + HS-CH2-C -> C-CH2- S - S-CH2-C

Globular Proteins

These also contain alpha helix e.g myoglobin where ~ 70% of the amino acid side chains are alpha helix's.