Amino Acids and Proteins Part 2

hey guys me again, this is just a continuation from the post proteins and amino acids

Organizations in Proteins

Primary structure refers to the number and sequence of amino acids in the polypeptide chain. This is very important because the juxtaposition of the R group COOH and the NH determines how the protein folds. They only bond maintaining this structure is the covalent peptide bond between these acids.

Secondary structure refers to the way the polypeptides turn or fold upon itself as a result of hydrogen bonding. This results in a more stable and robust structure than a straight chain. There are two types of structures alpha helix and beta pleated sheet.

The alpha helix is the form found in the protein keratin (found in hair, nails, and feathers). This polypeptide chain is twisted into a helix like an extensible telephone cord; successive turns of the helix are linked together by weak hydrogen bonds situated between the amino groups of one term and the carboxyl group of the next.

H bond bond with the carboxyl group of 1 amino acid and he NH group of and amino acid residue 3.6 units away.

The beta pleated sheet is an arrangement of a number of adjacent polypeptide chains running anti-parallel to each other. The neighbouring chains are joined together by hydrogen bonds between C=O and NH groups of one chain and the C=O and NH groups of the adjacent chain. All NH and C=O groups are involved in hydrogen bonding. This arrangement gives a high tensile strength with no stretch. Example silk fibroin is a protein that is entirely beta pleated. Some proteins have regions of beta pleated sheet. The individual chains can pack closely together as the R groups are usually small.

Tertiary structure is the way a polypeptide folds and foils to form a complex molecular shape as a result of bonds formed between the R groups.

Between R groups:

—NH3+ ——COO- ionic bonds

—H————O=C    hydrogen bonds

—S————S          disulphide bonds

—between large ring structures, hydrophilic interactions (van der waal forces)

 

This interaction causes the protein to fold into a precise compact globular shape with the hydrophobic parts on the inside and the hydrophilic parts on the outside. For some proteins this means that a single molecule can be surrounded by a shell of water molecules and become separated thereby making them soluble. Most enzymes fall into this category that is they are globular proteins which are capable of dissolving and catalyzing reactions within a cell.

NOTE: NOT ALL PROTEINS FOLD INTO A TERTIARY STRUCTURE ESPECIALLY IF THEY HAVE LONG CHAINS WITH LOTS OF HYDROPHOBIC AMINO ACIDS E.G. KERATIN, SILK, COLLAGEN ARE ALL INSOLUBLE AND HAVE A NONE SPECIFIC FIBROUS STRUCTURE.

Quaternary structure is only present when proteins consist of two or more polypeptide chains. It refers to the way in which these polypeptides are arranged to form a biologically active protein. E.g. hemoglobin.

Properties of Proteins

 

Denaturation – this is the loss of the specific 3-D conformation of a protein. The change can be temporary or permanent and he sequence of the amino acid remains unaffected. The molecule can no longer perform its biological function. Several agents causes denaturation

• Heat or radiation:- causes the molecule to vibrate violently disrupting hydrogen and ionic bonds.
• Strong acids, alkalis, high concentration of salts: – disrupts ionic bonds. Peptide bonds may break if left for a long time.
• Heavy metals: – cations form strong bonds with ionized carboxylic groups disrupting ionic bonds.
• Urea:- competition for hydrogen bonds, precipitation of soluble proteins. High concentrations of urea molecules denature proteins by allowing water molecules to solvate non-polar groups in the interior of the protein.
• Agitation: – shearing of hydrogen bonds, beating of egg white albumin into a meringue.
• Organic solvents and detergents i.e.

Chaotropic agents (SCN, thiocynate, CLO4; perchlorate, guanidinum ion, and the non-ionic compound urea) are ions that are poorly solvated compared to ions such as NH4+, SO42- and H2PO4-. It enhances the solubility of non-polar compounds in water by disordering the water molecules.

The water molecules disrupt the hydrophobic interactions that normally stabilize the native conformation.

The hydrophobic tails of detergents such as sodium dodecyle sulphate (SDS) also denatured proteins by penetrating the protein interior and disrupting hydrophobic interactions.

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