Proteins are large macromolecules which consist of hydrogen, carbon and oxygen; proteins are polymeric chains that are built from monomers known as amino acids. Proteins have a major function in a living organism, for example, the replication of DNA, catalysing metabolic reactions (catalyst); stimulus response and also transporting molecules form one place to another. There are 20 different types of amino acids which synthesize proteins, however the function and different properties of each type of protein is due to the precise sequence and structure of the amino acids present.
Each amino acid consists of a central carbon atom (C), which is attached to a hydrogen atom (H), an amino group (also known as NH2 group), a carboxyl group (- COOH, this gives up a proton hence why this is known as an acid) and also a unique side chain or R group.
Amino acids are linked linearly via covalent peptide bonds, short chain amino acids are known as peptides whereas long chain formations of amino acids are called polypeptides, where the peptide bond is formed between the carboxyl group of one amino acid and the amino group on the neighbouring amino acid. This reaction occurs as a condensation reaction where there is a removal of a hydrogen atom from the amino group of one amino acid and the removal of a ââ‚¬"OH group from the carboxyl acid from another amino acid forming a water molecule (Fig 1).
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Fig 1: a condensation reaction between two amino acid molecules, there is a formation of a water molecule as a waste product.
The unique side chain or R group is what disguises one amino acid from another; the overall structure and properties of the proteins are therefore dependent on sequence of the R group of each amino acid. Furthermore these variations of the R group and also the arrangements of the other amino acids would form a number of different polypeptides. Each protein consists of a different number of these polypeptide chains which are folded into complex three dimensional shapes therefore different proteins would have different shapes.
There are four levels of protein organization found in polypeptides; these structures are known as: primary structure, secondary structure, tertiary structure and also quaternary structure.
Primary structures is the basic structure of the levels of organization, the primary structure is the linear arrangements/sequence found of the amino acid in the protein, and also could be thought of as the covalent linkages found in the polypeptide chain or the protein, such as a disulphide bond.
The secondary structure is the areas of folding found within the protein, where there is an ordered arrangement of the amino acids in some localized regions of the polypeptide molecule; hydrogen bonds play a vital role in stabilizing the folding patterns which are found in the protein molecule. Although the conformation of each protein molecule are considered unique, there are two main types of secondary structure, or folding patterns, that are often present; these are the alpha helix and the anti-parallel beta-pleated sheets, these two folding patterns are common due to the hydrogen bonding occurs between the N-H and C=O groups in the backbone of the polypeptide. However there are a number of other secondary structures but the alpha helix and the anti-parallel sheets are the most stable form of secondary structures found. Furthermore there may be a number of these two types of secondary structure found in a single polypeptide chain.
An alpha helix is spiral structure where this could be either a right handed or left handed spiral, in which the peptide bonds are found to be Trans conformational and planar, it would also be found that the amino group of each of the peptide bonds is generally in the upward position where as the carboxyl group points in the downwards position.
An alpha helix structure is generated when a single polypeptide chain has turned around itself to form a rigid cylinder where a hydrogen bond is formed between every fourth amino acid (fig 1.2), which links the C=O group of one peptide bond to the N-H group on another amino acid (fig 1.2).
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Fig 1.2: shows the hydrogen bond formed between every fourth amino acid, also linking the N-H group and O=H group.
There are two types of beta sheets; parallel and anti-parallel beta sheets. The Beta pleated sheets are extended polypeptide chains with another neighbouring polypeptide chain extending either parallel or anti-parallel to each other, this occurs due to the hydrogen bonds being formed between the segments of the polypeptide chain so are essentially place side by side. The parallel beta sheets is when the structure is shown to consist a polypeptide chain and neighbouring polypeptide chain that would run in the same direction (from the N-terminus to the C-terminus), is known as the parallel beta sheet (Fig 2.1), whereas when the polypeptide chain runs in the opposite direction of that of its neighbouring chain, it is known as an anti-parallel beta sheet (Fig 2.2).
Fig 2.1: shows the parallel beta sheets, the dotted line represents hydrogen bonds. The polypeptide chains shown are placed side by side but run in the same direction so are parallel to each other.
Fig 2.2: shows the anti-parallel beta sheets, the dotted line represents hydrogen bonds. The polypeptide chains shown are placed side by side but run in the opposite direction so are anti-parallel to each other.
The beta sheet are stable structures that produces a very rigid, pleated structure; this is due to the beta sheet being stabilized by hydrogen bond being formed between the amino group on one polypeptide chain and the carboxyl group on the adjacent chain.
The tertiary structure of a protein is the full three dimensional structure of the arrangements of atoms found within the polypeptide chain, this structure is the final geometric shape that protein assume and would be the highest level structure that a protein can attain, the structures include the alpha helix, beta sheets, random coils and also other structures such as loops and folds, which are formed between the N-terminus and the C-terminus. The tertiary structure is mainly stabilized by the formation of disulphide bonds, this is also known as a disulphide bridge because these bonds are formed by oxidation reaction of the side chains of cysteine, by oxidizing the two thiol groups (SH) which would form a disulphide bond (S-S) (fig 3).
Fig 3: Shows the equation of an oxidation reaction in the tertiary structure to form a disulphide bridge (S-S), where a molecule of water is formed.
The quaternary structure of a protein is the arrangements of many different types of coiled and folded polypeptides to form a unique functional protein and is stabilized by several non-covalent bonding, where some of these types of bonding are also found in tertiary structures, for example; hydrogen bonding, Van Der Waals interactions, hydrophobic interactions and also ionic interactions. These can occur if there is more than one polypeptide chain present in a complex protein.