Protein Structure Basics PDF

Protein structure basics  By convention, peptide and protein structures are depicted with the amino acid whose amino group is free (the N-terminal end) on the left and the amino acid with a free carboxyl group (the C-terminal end) to the right.  Dipeptide: A chain consisting of only...

Protein structure basics  By convention, peptide and protein structures are depicted with the amino acid whose amino group is free (the N-terminal end) on the left and the amino acid with a free carboxyl group (the C-terminal end) to the right.  Dipeptide: A chain consisting of only two amino acid units is called a dipeptide Tripeptide: a chain consisting of three is a tripeptide Oligopeptide: 3-10 amino acids Polypeptide: Greater than 10 amino acids Protein Structure  Folding of portions of the polypeptide held primarily by hydrogen bonding between C=O and N−H groups of the polymer backbone The backbone is fairly rigid, while the sigma to the R groups can freely rotate. So, it is mainly the side chains on each residue have flexible conformation Molecules with dipole or charges will attempt to store energy by making electrostatic interactions and amino acids has such feature. So, if this backbone can fold in such a way so as to let each residue interact with other residues, it will do so, in order to adopt the lowest-energy conformation. In the α-helix portion, the polypeptide chain acquires a coil shape spiraling clockwise from N-terminus to C-terminus, held by hydrogen bonds between the carbonly groups and amine groups in the backbone and side chains protruding outwards, as illustrated in the model shown on the right The β -Pleated sheet is a portion of polypeptide chains in which sections of polypeptide chains are aligned parallel or antiparallel and held together by hydrogen bonds between the carbonyl groups and amine groups of the neighboring polypeptide chains. The β-Pleated sheet is usually represented as a ribbon with an arrowhead pointing toward the N- terminus, as shown on the below. Random coil : Most of the proteins have a mix of α-helix and β-pleated sheets and organized but not repeated structures between the two that are called random coils. The random coins are represented by tubes. The interactions stabilizing the tertiary structure include disulfide linkage, salt bridge, coordinate bonds with metal ions, hydrogen bonding, and hydrophobic interaction Globular Proteins: are soluble in aqueous media. In these proteins, the chains are folded so that the molecule as a whole is roughly spherical. Familiar examples include egg albumin from egg whites and serum albumin in blood. Serum albumin plays a major role in transporting fatty acids and maintaining a proper balance of osmotic pressures in the body. Hemoglobin and myoglobin, which are important for binding oxygen, are also globular proteins Fibrous proteins: are insoluble in water and usually serve structural, connective, and protective functions. Examples of fibrous proteins are keratins, collagens, myosins, and elastins. Hair and the outer layer of skin are composed of keratin. Connective tissues contain collagen. Myosins are muscle proteins and are capable of contraction and extension. Elastins are found in ligaments and the elastic tissue of artery walls. QUATERNARY STRUCTURE GAG GTG