Biological Molecules - Session 3

We know that milk is an essential part of our diet. Milk contains a protein called casein. Casein provides nutrition. Have you ever wondered why proteins are such an essential part of our diet? Or what are the proteins made of? Let's explore the fascinating world of protein. Proteins are macromolecules. Proteins are made up of long chains of amino acids. These amino acids are linked together by bonds. Consider protein as a polymer. Amino acid acts as the monomer of protein.

We know that amino acids are the made up of proteins. They are organic compounds that contain both an amino group -NH2 and a carboxyl group -COOH attached to a central carbon atom. This central carbon atom is also bonded to a hydrogen atom and an R group. R represents alkyl group. Alkyl group is a carbon chain that varies depending on the specific type of amino acid.

We know that proteins are made up of long chains of amino acids. But how do these amino acids link together to form long chains? Peptide bond is a type of covalent bond that connects amino acids together to form protein molecules. Amino acids are joined together in a linear chain through a series of peptide bonds.

The formation of a peptide bond involves the condensation of two amino acids. The carboxyl group -COOH of one amino acid reacts with the amino group -NH2 of another amino acid. During this process, a water molecule is eliminated. Peptide bond is formed between the carbon atom of the carboxyl group -COOH of one amino acid and the nitrogen atom of the amino group -NH2 of another amino acid. The resulting molecule is called a dipeptide.

Additional amino acids can be added to the chain through the same process. This will form longer chains called polypeptides. The peptide bond can be broken through a process called hydrolysis. In hydrolysis, water is added to the peptide bond, causing it to break apart. As a result the polypeptide chain breaks-up into its constituent amino acids. This process is important for the digestion of proteins.

Protein folding is the process by which a chain of amino acids twists and turns into a specific three-dimensional shape. Protein folding is necessary for the protein to function properly. The shape of the protein is determined by the sequence of amino acids in the chain. There are four levels of protein structure that determine the overall shape of a protein. The first level is called the primary structure. It is simply the linear sequence of amino acids in the protein chain.

The primary structure of a protein is important. It determines the way that the protein will fold into its final three dimensional shape. A small change in the sequence of amino acids can have a big effect on the function of protein. For example, a mutation in the primary structure of a protein can change the way it folds. This leads to a loss of body function or a cause disease.

The second level of protein structure is called the secondary structure. It refers to the way the protein chain folds into specific shapes, such as an alpha-helix or beta-sheet. In the case of an alpha-helix, the hydrogen bonds form between the oxygen of the carbonyl group C=O of one amino acid and the hydrogen of the amino group NH of an amino acid four places ahead of it. This causes the chain to twist and coil into a regular, cylindrical shape.

In a beta sheet, the polypeptide chain folds back-and-forth on itself, forming a flat, pleated sheet. This sheet is made up of multiple strands of the polypeptide chain that run parallel or anti-parallel to one another. The hydrogen bonds that stabilize the beta sheet form between the carbonyl oxygen of one amino acid in one strand and the amino hydrogen of an adjacent amino acid in a neighboring strand. This hydrogen bonding pattern repeats along the length of the beta sheet. This creates a stable, planar structure.

The third level of protein structure is called the tertiary structure. It refers to the overall three dimensional shape that a single protein molecule adopts. This structure is determined by a combination of chemical and physical interactions between the amino acids that make up the protein chain. What's fascinating about the tertiary structure is that it is essential for the protein's function. Small changes in the protein's shape can have significant effects on its activity.

The tertiary structure of a protein can be affected by external factors such as temperature, and pH. Any small changes in these factors disrupts the protein structure. This causes it to undergo loss of its biological activity. For example, enzymes are proteins that carry out specific chemical reactions in the body. If the shape of protein is altered by changes in the surrounding environment, the enzyme can undergo loss of its ability to function properly.

The fourth level of protein structure is called the quaternary structure. It refers to the way in which multiple protein subunits come together to form a larger, functional protein complex. In some cases, individual protein subunits can come together to form a complex with a specific function. For example, hemoglobin is the protein that carries oxygen in our blood. It is composed of four individual subunits. Each of the subunit contains a heme group that binds to oxygen.

The stability of protein structure is maintained by a variety of interactions between amino acids. These interactions are referred to as protein stabilizing interactions. The first interaction that plays an important role in stabilizing a protein structure is the hydrogen bond. Hydrogen bonds are forces of attraction between a hydrogen atom that is covalently bonded to a highly electronegative atom and another electronegative atom. For example hydrogen bonding between molecules of water is illustrated.

In proteins, hydrogen bonds are formed between the electronegative atoms of the peptide backbone. Lets say two peptide bonds come nearbyto each other in the protein structure. Then the partial positive charge on the hydrogen atom of the N-H group is attracted to the partial negative charge on the oxygen atom of the C=O group. This electrostatic attraction causes a hydrogen bond to form between the two groups. This stabilizes the protein structure. Hydrogen bonding stabilizes secondary structure of protein.

The second interaction that stabilizes protein structure is van der Waals interactions. Van der Waals interactions are caused by fluctuations in the electron distribution around atoms. A side-chain is a chemical group that is attached to a core part of the molecule called the "main chain" or backbone. Lets say two non-polar amino acid side-chains come nearby to each other in the protein structure. Then the electrons around the atoms in one side-chain can cause a temporary dipole in the other side-chain. This creates a weak electrostatic attraction between the two side-chains. This weak electrostatic attraction is known as a van der Waals interaction.

These interactions occur between non-polar amino acid side-chains that have no charge, such as the methyl groups in alanine or isoleucine. While each individual van der Waals interaction is weak, many of them can act together to stabilize the protein structure. In fact, these interactions are thought to be the main driving force behind protein folding, especially in the early stages of the process.