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Biology Essay on Proteins
Essay Contents:
- Essay on the Introduction to Proteins
- Essay on the Structure of Proteins
- Essay on the Forces Determining Protein Structure
- Essay on Covalent Bond Distances and Torsion Angles
- Essay on the Ramachandran Plot
1. Essay on the Introduction to Proteins:
Proteins are the molecules of life, which perform wide range of functions inside the body, from structural components to catalysts of much metabolic function as well as chemical reactions and control the immune system. Amino acids are the basic building blocks of proteins (Table 3.1).
Fundamentally, amino acids are joined together by peptide bonds to form the basic protein or peptide structures. However, owing to the many ‘side groups’ that are part of the amino acids other sorts of bonds may additionally form between the amino acid units. These additional bonds twist and turn the protein into convoluted shapes that are unique to the protein and essential to its ability to perform certain functions within the human body.
Amino acids are carbon compounds which contain two functional groups- an amino group (NH2) and a carboxylic acid group (COOH). A side chain (R) attached to the compound gives each amino acid a unique set of characteristics.
Though, the amino acids can be classified in different ways; the main two types of classification are given below:
Peptides and Polypeptides:
Two amino acids can combine together with the elimination of a molecule of water to produce a dipeptide.
The formation of peptide bond occurs by the following mechanism:
Three amino acids when joined together form a tripeptide, same way the large number of amino acids combine to form a polypeptide. A protein chain may consists of 50 to 2000 amino acid residues. The end of the peptide chain with the -NH2 group is known as the N- terminal, while the end with the -COOH group is known as C-terminal.
2. Essay on Structure of Proteins:
Proteins are formed from chains of amino acids. The nature of the amino acid side chains has significant influence on the topography of the protein.
The bonds between amino acid side chains generate a complex protein structure, which is considered in four stages:
i. Primary,
ii. Secondary,
iii. Tertiary, and
iv. Quaternary.
i. The Primary Structure:
The primary structure of a protein refers to the sequence of amino acids that makes up the protein. The bonds considered in the primary structure are the peptide bonds between each amino acid. Amino acids when linked to form proteins, the amino group (-NH2) of one amino acid combines with the carboxyl group (-COOH) of the next to form an amide or peptide linkage (-CONH-) which forms -N-C-C-N-C-C-N-C-C-, the backbone structure.
The primary structure is read from the NH2– terminal to the -COOH terminal. There are 20 different amino acids in living organisms. Most polypeptides consist of 50- 1000s amino acids. The shape of proteins is critical to their function. The shape is largely a result of the bonds, which form between the side chains of amino acids, making the protein. In short the primary purpose of the side chains in amino acids is to give proteins their shape, which dictates their function.
ii. Secondary Structure of Proteins:
The secondary structure refers to the shape; the protein is pulled through hydrogen bonds that form between the side chains of the amino acids. There are three common shapes, the α- helix, the β -pleated sheet, and the triple helix. All three shapes are very regular and exist as a result of hydrogen bonds between side chains that occur at regular intervals along the primary structure.
(a) Alpha Helices:
Alpha helices are the most well-known element of protein structure, proposed by Pauling. Alpha-helices have distinctive patterns of hydrogen bonding and phi-psi angles (Fig. 3.10). They are generally between 5 and 20 residues in length, but some proteins are of coiled-coil structures, can be considerably longer.
Alpha helices generally have a pitch of about 3.5 residues per turn, but there are forms of helices with tighter (3 residues per turn) and longer (4 residues per turn). Alpha helices can be coiled about themselves in two coils, three coils and four coils (four helix bundles) conformations. Alpha helices can exist internal in proteins (generally hydrophobic), on the surface of proteins (amphipathic) or in membranes (hydrophobic). Alpha helices can span membranes either singly or in groups.
(b) Beta Pleated Structure:
Beta-strands represent for an extended form in which the side chains alternate on either side of the extended chain. Beta pleated structures are so called because the pleated or folded appearance, when view from the side (Fig. 3.11). Here the polypeptide chain is much more stretched out in comparison to alpha helix. The back bones of beta-strands form hydrogen bond with the backbone of an adjacent beta strand forming a beta-sheet structure. The strands in a beta sheet can be either parallel or anti-parallel and the hydrogen bonding pattern may be different between the two forms.
(iii) Tertiary Structure:
Tertiary structure is the three dimensional conformation of a poly peptide. In other words, they are the folded proteins. Folding occurs during post translational modification. The tertiary structure of proteins is the result of further bonding between side chains within the protein and with water molecules that may be present around the protein. Polar amino acids move to the outside of the shape, while non-polar amino acids move to the inside, when placed in a polar solution.
Bonds that are considered as part of the tertiary structure include: Bonds formed between non-polar side chains, disulfide bonds formed between sulfur atoms in cysteine side chains, ionic bonds formed between acidic and basic side chains, and hydrogen bonds formed between carbonyl groups and hydroxyl or amino groups (Fig. 3.12).
(iv) Quaternary Structure:
Two or more tertiary polypeptides joined together to form the quaternary structure of proteins. The bonds formed are the same as those found in the tertiary structure of proteins. Hemoglobin, the oxygen carrying component of blood, is an example of a protein in a quaternary structure (Fig.3.13). Hemoglobin is comprised of four polypeptide subunits, two with alpha helix secondary structure and two with beta pleated sheet form. All four components carry a heme group that can bind to oxygen, and all four components must be present to form hemoglobin.
The shape of the hemoglobin affects its ability to carry oxygen and travel freely throughout the circulatory system. In sickle-cell anemia a particular glutamic acid is replaced by valine, and an ionic cross-link is not formed, resulting in a severe change of shape of the tertiary structure of the hemoglobin, which is a crescent or sickle in shape that reduces the oxygen carrying capacity of the red blood cells.
3. Essay on the Forces Determining Protein Structure:
There are several covalent and non-covalent forces involved which determine protein structure:
(a) Van der Waals Interactions:
These non-covalent forces result from the attraction of one atom’s nucleus for the electrons of another atom in a non-covalent form (no sharing of orbitals). These forces are much weaker than covalent interactions. The interaction distances are much longer than covalent bonds and much shorter than the other non-covalent interactions.
Van der Waals interactions occur at distances between 3 and 4 A°. They are very weak beyond 5 A° and electron repulsion prevents atoms from getting much closer than 3 A°. van der Waals interactions are non-directional and very weak. However, significant energy of stabilization can be obtained in the central hydrophobic core of proteins by the additive effect of many such interactions.
(b) Hydrophobic Forces:
The hydrophobic force is really a negative non-covalent force. The presence of hydrophobic side chains in aqueous solution induces the formation of structured water. This reduction in entropy of the water molecules is a very unfavorable resulting in a strong force to keep hydrophobic side chains buried in the interior of the protein. The hydrophobic force is one of the largest determinants of protein structure.
(c) Electrostatic Forces:
The attraction of oppositely charged side chains can form salt- bridges which stabilize secondary and tertiary structures. The electrostatic force is quite strong, falling off as the square of the distance between the charged atoms. It also depends heavily on the dielectric constant of the medium in which the protein is dissolved.
(d) Dipole Moments:
Dipole moments are caused by pairs of charges separated by a larger distance than permitting a salt- or ion bridge formation. The dipole moment can give rise to an electric field along the entire length of a structural element and are often used by proteins to attract and position charged substrates and products in their active site. The peptide chain naturally has a dipole moment because the N-terminus carries a partial positive charge and the C-terminus carries partial negative charge. The alpha-helix is known to carry a partial negative charge at its C-terminus and a positive charge at its N-terminus. In order to neutralize this charge distribution, alpha helices often have acidic residues near their N-terminus and a basic residue near their C-terminus.
(e) Hydrogen Bonds:
Hydrogen bonds occur when a pair of nucleophilic atoms such as oxygen and nitrogen shares hydrogen between them. The hydrogen may be covalently attached to either nucleophilic atom (the H-bond donor) and or shared with the other atom (the H- bond receptor). H-bonds are very directional and their strength deteriorates dramatically as the angle changes. Hydrogen bonding between the carboxyl groups and the amino groups in the peptide backbone gives rise to alpha helix and beta strand conformations.
4. Essay on Covalent Bond Distances and Torsion Angles:
The major properties of the covalent bonds that hold proteins together are their bond distances and bond angles. In particular, the bond angles between two adjacent bonds on either side of a single atom, or the dihedral angles between three contiguous bonds and two atoms control the geometry of the protein folding. One of the stabilizing forces in secondary structure of protein is the disulphide linkages. A covalent bridge can be formed by the oxidation of two cysteine residues to a cystine residue. The-S-S-bond is very strong and its presence confers additional stability (Fig. 3.14).
5. Essay on the Ramachandran Plot:
The peptide backbone is constrained by steric hindrance and hydrogen bonding patterns that limit its torsional angles (phi-psi angles) to certain limits. Plots of phi versus psi dihedral angles for amino acid residues are called Ramachandran plots. One can tell if the backbone is following a helical or an extended beta strand structure based on the values of the phi-psi angles over a length of backbone (usually 3-4 residues is sufficient).
In a polypeptide, the main chain N-Cα and Cα-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi (ϕ) and psi (Ψ) respectively. G. N Ramachandran used computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations.
For each conformation, the structure was examined for close contacts between atoms. Atoms were treated as hard spheres with dimensions corresponding to their Van der Waals radii. Therefore, phi and psi angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone.
In the above diagram (Fig. 3.15), the white areas correspond to conformations where atoms in the polypeptide come closer than the sum of their Van der Waals radii. These regions are sterically disallowed for all amino acids except glycine which is unique in that it lacks a side chain. The dark regions correspond to conformations where there are no steric clashes, i.e., these are the allowed regions namely the alpha-helical and beta-sheet conformations. The light shaded areas show the allowed regions if slightly shorter Vander Waals radii are used in the calculation, i.e., the atoms are allowed to come a little closer together. This brings out an additional region, which corresponds to the left-handed alpha-helix.
Disallowed regions generally involve steric hindrance between the side chain C-P methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot. Hence, it frequently occurs in turn regions of proteins where any other residue would be sterically hindered.