Module 1. Bio-molecules

Lesson 2

2.1 Introduction

Proteins are linear sequences of amino acids linked together by peptide bonds. The amino acids are linked head to tail.
  • The peptide bond is a covalent bond formed between the α-carboxyl group of one amino acid and the α-amino group of another. Once two amino acids are joined together via a peptide bond to form a dipeptide, there is still a free amino group at one end and a free carboxyl group at the other, each of which can in turn be linked to further amino acids. (Fig. 2.1)
  • A long, unbranched chain of amino acids (upto 25 amino acid residues), linked together by peptide bonds is called oligopeptide.
  • A peptide chain having >25 amino acids residues is called polypeptide.
  • Peptide chains are written down with free α-amino (N-terminal) on the left, the free α-carboxyl group (C-terminal) on the right and a hyphen between the amino acids to indicate peptide bonds. Example of a tetrapeptide +H3N-serine- tyrosine-phenylalanine-leucine-COO- would be written simply Ser-Tyr-Phe-Leu or S-Y-F-L.
2.2 Peptide Bond
  • The peptide bond between carbon and nitrogen exhibits partial double bond character due to closeness of carbonyl carbon –oxygen double bond and electron withdrawing property of oxygen and nitrogen atoms allowing the resonance structures.
  • C-N bond length is also shorter than normal C-N single bond and >C=O bond is larger than normal >C=O bond. The peptide unit which is made up of CO-NH atoms is thus relatively rigid and planner, although free rotation takes place about Cα-N and Cα-C bonds ( the bonds either side of the peptide bond), permitting adjacent peptide units to be at different angles.
  • The H of the amino group is nearly always Trans (opposite) to oxygen of carbonyl group, rather than cis (adjacent). (Fig. 2.2)
2.3 Protein Structure

The peptide chain folds up in the protein to form a specific shape (conformation). The conformation is the three dimensional arrangement of atoms in structure and is determined by the amino acid sequence. There are four levels of structure in proteins : primary, secondary, tertiary and, sometimes not always quaternary.

2.3.1 Primary structure
  • The primary structure in a protein is the linear sequence of amino acids as joined together by peptide bonds.
  • This also include disulfide bonds between cysteine residues that are adjacent in space but not in the linear amino acid sequence. These covalent cross-links are formed by the oxidation of SH groups on cysteine residues that are juxtaposed in space between separate polypeptide chains or between different parts of same chain. The resulting disulfide is called a cystine residues.
  • Disulfide bonds are often present in extracellular proteins, but are rarely found in intracellular proteins.
2.3.2 Secondary structure

The secondary level of structure in a protein is the regular folding of regions of the polypeptide chain. The most common types of protein fold are the α-helix and the β-pleated sheet. Pleated sheet

In α-helix, the amino acids arrange themselves in a regular helical conformation in a rod shape. The carbonyl oxygen of each peptide bond is hydrogen bonded to the hydrogen on the amino group of the fourth amino acid away. In an α-helix there are 3.6 amino acids per turn of the helix covering a distance of 0.54 nm and each amino acid residue represents an advance of 0.15 nm along the axis of the helix. The side chain of the amino acids are all positioned along the outside of the cylindrical helix. Certain amino acids are often found in α-helix than others. In particular, Pro is rarely found in α-helical regions as it cannot form the correct pattern of hydrogen bonds due to lack of a hydrogen atom on its nitrogen atom. For this reason, Pro is often found at the end of an α-helix where it alters the direction of polypeptide chain and terminates the helix.


Fig. 2.3 Secondary structure of protein with α-helix

In the β-pleated sheet hydrogen bonds form between the peptide bonds either in different polypeptide chains or in different sections of the same polypeptide chain. The planarity of the peptide bond forces the polypeptide to be pleated with the side chains of the amino acids protruding above and below the sheet. Adjacent polypeptide chains in β-pleated sheet can be either parallel or antiparallel depending on whether they run in the same direction or in the opposite directions, respectively. The polypeptide chain within a β-pleated sheet is fully extended, such that there is a distance of 0.35nm from Cα atom to next. β-pleated sheets are always slightly curved and, if several polypeptides are involved, the sheet can close up to form a β-barrel. Multiple β-pleated sheets provide

strength and rigidity in many structural proteins, such as silk fibroin, which consists almost entirely of stacks of antiparallel β-pleated sheets.


Fig. 2.4 Secondary structure of protein with β-sheet

2.3.3 Tertiary structure

The tertiary structure means the spatial arrangement of amino acids that are far apart in the linear sequence as well as those residues that are adjacent. The term “tertiary structure” refers to the entire three dimensional conformation of a polypeptide. It indicates, in three-dimensional space, how secondary structural features—helices, sheets, bends, turns, and loops— assemble to form domains and how these domains relate spatially to one another. A domain is a section of protein structure sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand. For example in myoglobin, a globular protein, the polypeptide chain folds spontaneously so that the majority of its hydrophobic side chains are buried in the interior, and the majority of its polar , charged side chains are on the surface. Once folded , the three dimensional , biologically active (native ) conformation of protein is maintained not only by hydrophobic interactions, but also by electrostatic forces (including salt bridges, Vander Waals interactions), hydrogen bonding and if present the covalent disulfide bonds.


Fig. 2.5 Tertiary structure of protein

2.3.4 Quaternary structure

Proteins containing more than one polypeptide chains, such as haemoglobin exhibit a fourth level of protein structure called quaternary structure. This level of structure refers to the spatial arrangement of the polypeptide subunits and the nature of the interactions between them. These interactions may be covalent links or noncovalent interactions (electrostatic forces, hydrophobic interactions and hydrogen bonding.


Fig. 2.6 Quaternary structure of protein
Last modified: Tuesday, 23 October 2012, 11:20 AM