Proteins

What are Proteins? The most complex biological molecules Contain C, H, O and N Sometimes contain S May form complexes with other molecules containing P, Fe, Zn or Cu Macromolecules with relative mol. Masses of 10 4 – 10 6 Consist of one or more unbranched polypeptide chains built up of amino acid monomers linked by peptide bonds

Each protein has a characteristic 3-D shape resulting from folding and coiling. It is usual to describe protein structure by the level of organisation of the molecule: –Primary –Secondary –Tertiary –Quaternary Structure

Primary Structure 1’ Structure –The number, type and sequence of amino acids –Specific to each protein –Coded for by DNA

Amino Acids There is a central carbon atom (called the "alpha carbon"), with four different chemical groups attached to it: –a hydrogen atom –a basic amino group –an acidic carboxyl group –a variable "R" group (or side chain) General formula: NH 2.RCH.COOH H

aa’s are cyrstalline solids and soluble in water 20 common aa’s found in living organisms The amino grp has basic properties The carboxyl grp has acid properties Acid and basic properties called amphoteric In organisms, pH usually neutral so both grps become ionised (+ve one end, -ve the other) –refered to as zwitterion

2 aa’s can join (condensation) to form dipeptide Further reactions can occur making polypeptides

Most important role of aa’s is as monomers for protein synthesis Green plants can synthesis all they need from photosynthesis and nitrate from soil Animals can synthesise some, but need to obtain 8 from their diet. These are the essential amino acids Amino acids are also involved in synthesis of other compounds like nucleic acids and cytochromes.

Secondary Structure most basic level of protein folding –consists of a few basic motifs that are found in all proteins. The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. The two most common secondary structure motifs are the α-helix and the β- pleated sheet

The α-helix. The polypeptide chain is wound round to form a helix. Held together by hydrogen bonds running parallel with the long helical axis. Many hydrogen bonds make it very stable and strong. The β-sheet. The polypeptide chain zig- zags back and forward forming a sheet of antiparallel strands. Once again it is held together by hydrogen bonds.

Tertiary Structure Most proteins have α-helix regions and β-pleating But folding of the polypeptide chain into a compact, globular shape is called the tertiary structure The bending and folding is irregular Caused by formation of differing bonds between aa residues.

Bonding in R-groups * Can only happen to end aa residues Other ionic bonds may occur within R-groups e.g. in insulin

Quaternary Structure Complex proteins may contain more than one polypeptide chain If more than one chain it has a quaternary structure The polypeptide chains may be all of the same type or different types

Further Classification of Proteins Because of proteins abundance and diversity it is difficult to classify them in a simple manner. It is customary to group them according to either their structure or function within living organisms.

Classifying according to structure FibrousGlobular Secondary Structure important; consist mainly of α-helix or β- pleated sheets Tertiary structure important; bent and folded into spherical shapes Insoluble in water Soluble in water Structural Functions e.g. keratin, collagen Enzymes, antibodies, hormones e.g. amylase, globulins, insulin

Haemoglobin “a conjugated protein” Made of 4 chains 2 chains contain 141 aa-residues (α-globins) 2 chains contain 146 aa-residues (β-globins) Total of 574

Other conjugated proteins GlycoproteinsLipoproteins

Under some circumstances, the 3D shape of a globular protein can change –May be temporary or permanent Doesn’t affect the primary structure Alteration of structure will affect the biological role of the protein especially in enzymes Denaturation –Increase in heat, pH change, high salt conc., presence of heavy metals and organic solvents.

Chemical (Biuret) test for protein