Biochemistry is the study of molecules and their reactions in living organisms.

• The ultimate goal of biochemistry is to understand the structures of biomolecules and the relationships between their structures and functions.

Proteins provide structure (keratin) and support (actin filaments) to tissues and organs throughout our bodies.

• As hormones (oxytocin) and **enzymes (**catalase), they control all aspects of metabolism. In body fluids, water-soluble proteins pick up other molecules for storage (casein) or transport (transferrin).

• And the proteins of the immune system provide protection (Immunoglobulin G) against invaders such as bacteria and viruses.

Amino acid is a molecule that contains both an amino functional group and a carboxyl functional group and protein is a large biological molecule made of many amino acids linked together through amide bonds.

Alpha- amino acid is an amino acid in which the amino group is bonded to the carbon atom next to the ¬COOH group.

Noncovalent forces are forces of attraction other than covalent bonds that can act between molecules or within molecules.

A hydrophobic substance does not dissolve in water.

A hydrophilic substance dissolves in water.

Zwitterion is a neutral dipolar ion that has one positive charge and one negative charge.

Amino acids are present in the ionized form in both the solid state and in aqueous solution. The charge of an amino acid molecule at any given moment depends on the particular amino acid and the pH of the solution.

• The pH at which the net positive and negative charges are evenly balanced to form an electrically neutral molecule is the isoelectric point (pI) for that particular amino acid. At this point, the net charge of all the molecules of that amino acid in a pure sample is zero.

• The pI for each amino acid is different, due to the influence of the side-chain functional groups.

Two or more amino acids can link together by forming amide bonds, which are known as peptide bonds when they occur in proteins.

• A dipeptide results from the formation of a peptide bond between the ¬NH2 group of one amino acid and the ¬COOH group of a second amino acid. Two or more amino acids can link together by forming amide bonds, which are known as peptide bonds when they occur in proteins.

• A dipeptide results from the formation of a peptide bond between the ¬NH2 group of one amino acid and the ¬COOH group of a second amino acid.

Amino-terminal (N-terminal) amino acid is the amino acid with the free ¬NH3 + group at the end of a protein.

Carboxyl-terminal (C-terminal) amino acid is the amino acid with the free ¬COO- group at the end of a protein.

Residue is an amino acid unit in a polypeptide.

Primary protein structure is the sequence in which amino acids are linked by peptide bonds in a protein.

The primary structure of a protein consists of the amino acids being lined up one by one to form peptide bonds in precisely the correct order for a specific protein. The number of arrangements for a set of amino acids can be calculated.

• If you have n amino acids, where n is an integer, then the number of arrangements are n factorial.

Secondary protein structure is regular and repeating structural patterns created by hydrogen bonding between backbone atoms in neighbouring segments of protein chains.

Hydrogen bonds form when a hydrogen atom bonded to a highly electronegative atom is attracted to another highly electronegative atom that has an unshared electron pair.

• The hydrogen atoms in the ¬NH¬ (amide) groups and the oxygen atoms in the ¬C“O (carbonyl) groups along protein backbones meet these conditions.

• This type of hydrogen bonding creates both pleated sheet and helical secondary structures. Individual hydrogen bonds are weak forces, but the sum of many weak forces, as in the helical and sheet structures, is large enough to stabilize the structure.

Alpha helix is a secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone.

Proteins are classified in several ways, one of which is to identify them as either fibrous proteins or globular proteins.

• Secondary structure is primarily responsible for the function of fibrous proteins—tough, insoluble proteins in which the chains form long fibers.

• Unlike fibrous proteins, globular proteins are water-soluble proteins whose chains are folded into compact, globe-like shapes. Their structures, which vary widely with their functions, are not repeating structures like those of fibrous proteins.

Tertiary protein structure is the way in which an entire protein chain is coiled and folded into its specific three-dimensional shape.

Native protein is a protein with the shape (primary, secondary, tertiary, and quaternary structure) in which it exists naturally in living organisms.

Where there are ionized acidic and basic side chains, the attraction between their positive and negative charges creates salt bridges. A salt bridge is a noncovalent bond; it is an ionic bond.

Disulfide bond is a S¬S bond formed between two cysteine side chains; can join two separate peptide chains together or cause a loop in a single peptide chain.

Quaternary structure are two or more protein chains assembled in a larger three-dimensional structure held together by noncovalent interactions.

Denaturation is the loss of secondary, tertiary, or quaternary protein structure due to disruption of noncovalent interactions and/or disulfide bonds that leaves peptide bonds and primary structure intact.

• Agents that cause denaturation include heat, mechanical agitation, detergents, organic solvents, extremely acidic or basic pH, and inorganic salts:

  • Heat: The weak side-chain attractions in globular proteins are easily disrupted by heating, in many cases only to temperatures above 50 °C (323 K). Cooking meat converts some of the insoluble collagen into soluble gelatin, which can be used in glue and for thickening sauces.

  • Mechanical agitation :The most familiar example of denaturation by agitation is the foam produced by beating egg whites. Denaturation of proteins at the surface of the air bubbles stiffens the protein and causes the bubbles to be held in place.

  • Detergents :Even very low concentrations of detergents can cause denaturation by disrupting the association of hydrophobic side chains.

  • Organic compounds: Polar solvents such as acetone and ethanol interfere with hydrogen bonding by competing for bonding sites. The disinfectant action of ethanol, for example, results from its ability to denature bacterial protein.

  • pH change: Excess H+ or OH- ions react with the basic or acidic side chains in amino acid residues and disrupt salt bridges. One familiar example of denaturation by pH change is the protein coagulation that occurs when milk turns sour because it has become acidic as milk bacteria convert lactose to lactic acid.

  • Inorganic salts: Sufficiently high concentrations of ions can disturb salt bridges.