Biochemistry Notes - Amino Acids & Proteins PDF

Biochemistry BIO Chemistry For second year Amino acids & protein ‫ﻧﺪﻱ‬/‫ﺩ‬ Lectures 4 part 2 Prepared By Dr. Ahmed Hesho 01289689034 Dr : Ahm...

Biochemistry BIO Chemistry For second year Amino acids & protein ‫ﻧﺪﻱ‬/‫ﺩ‬ Lectures 4 part 2 Prepared By Dr. Ahmed Hesho 01289689034 Dr : Ahmed Hesho 01289689034 Biochemistry The accumulation of mis-folded proteins, especially, in the brain, leads to disease such as Alzheimer’s & Parkinson’s Molecular Protein Structure is considered as Four Organizational Levels: 1. Primary. 2. Secondary. 3. Tertiary. Primary protein structure: Secondary protein structure: Dr : Ahmed Hesho 01289689034 Biochemistry α-Helix Helix breaker Amino acids which breaks the helix are geometrically and/or chemically incompatible with α-helical structure, like: Proline (imino acid). Charged amino acids (acidic & basic amino acids). Amino acids with bulky side chains (Leu, Ile, Trp). β-pleated sheets Dr : Ahmed Hesho 01289689034 Biochemistry Loops & Bends Tertiary protein structure: 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 the protein structure sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand. Tertiary proteins are tightly packed, with hydrophobic groups in the core (inside) and polar side chains in the surface (outside). Tertiary structure is maintained by interactions between the side chains of amino acids as well as interacting with aqueous solvent. Interactions between side chains (R-Groups): Non polar R groups Hydrophobic interactions Van der Val bonding Polar R groups Hydrogen bonding Between H-bond doner and acceptor Ionic bonding Acidic and basic R group (salt-bridges) Ion-Ion Covalent bonding Cysteines (Disulphides) Dr : Ahmed Hesho 01289689034 Biochemistry Quaternary Protein Structure: In protein containing more than one polypeptide chain, the number and the arrangement of polypeptide chains (subunits) is called quaternary structure. In quaternary structure, subunits are held together by non-covalent bonds. There are Two types of quaternary protein structures: Homogenous quaternary structure. Heterogeneous quaternary structure. Homogenous quaternary structure has identical subunits (Homo- quaternary protein). Glycogen phosphorylase a (2 identical subunits). Lactate Dehydrogenase [LDH (H4, M4)]. Heterogeneous quaternary structure has non–identical subunits (Homo-quaternary protein): Hb A (α2 & β2 subunits) LDH (H3M,H2M2,HM3) Denaturation of protein Denaturation is the unfolding & disorganization of protein structure without affecting the primary structure (peptide bonds). Thus, hydrogen bonds, disulphides, Ionic, Van der Val bonds are disrupted. Denaturation occurs when the organized structures of a globular protein, the α-helix, the βpleated sheet, and tertiary folds become completely disorganized. However, it does not alter the primary structure. Denaturation is divided into: Reversible Denaturation. Irreversible Denaturation. Reversible Denaturation: Protein refolds into its original native structure when the denaturating agent is removed. This process is known as Renaturation. Keratin of hair, Actin & Myosin of muscles are present in both forms: Native (relaxed form, α-Helix) and Dr : Ahmed Hesho 01289689034 Biochemistry Denatured (stretched or contracted form, Parallel β-pleated sheets). Ribonuclease enzyme is composed of 124 amino acids in a single polypeptide chain containing 4 disulfide bonds. It can be denaturated by urea & β-Mercapto– ethanol which reduce disulfide bonds into sulfhydryl groups. Gradual removal of denaturating conditions & addition of O2 renaturate ribonuclease into its specific tertiary structure. Native protein is functionally (biologically) active while, denatured protein is functionally inactive. Irreversible denaturation: The denaturating agents disrupt the: Hydrophobic bonds and/or Ionic bonds and/or Disulfide bonds and/or Hydrogen bonds leading to irreversible destruction of 4◦, 3◦& 2◦structures of protein molecule. Consider the effect of increasing temperature on a solution of proteins—for instance, egg white. At first, increasing the temperature simply increases the rate of molecular movement, the movement of the individual molecules within the solution. Then, as the temperature continues to increase, the bonds within the proteins begin to vibrate more violently. Eventually, the weak interactions, like hydrogen bonds and hydrophobic interactions. The protein molecules are denatured as they lose their characteristic three-dimensional conformation and become completely disorganized. Coagulation occurs as the protein molecules then unfold and become entangled. At this point, they are no longer in solution; they have aggregated to become a solid and will precipitate out of the solution Dr : Ahmed Hesho 01289689034