Biochemistry Science Course PDF

 Fundamental biochemistry of proteins Lec.7  Based on the properties of the R group Electrochemical Physiological polarity classification Classification of...

 Fundamental biochemistry of proteins Lec.7  Based on the properties of the R group Electrochemical Physiological polarity classification Classification of amino acids structural Metabolic classification classification Metabolic classification Mixed Isoleucein and 3 Aromatic amino acid Figure - Catabolism of amino acids  Function of amino acids A. Building blocks of proteins B. Amino acids may be functional (neurotransmitters) Glutamate and aspartate (excitatory) Glycine (inhibitory) Note : Glycine, proline contribute to 57% of total amino acids (AAs) in collagen. C. are used as Precursors to other molecules 1. Nneurotransmitters ex: serotonin and melatonin (derivatives of tryptophan) , dopamine (Tyrosine). 2. γ‐Aminobutyric acid, or GABA, is produced by the decarboxylation of glutamic acid and is a neurotransmitter 3. Thyroxine (a tyrosine derivative produced in the thyroid gland of animals) and indole acetic acid (a tryptophan derivative found in plants) are two examples of hormones. 4. Epinephrine (also known as adrenaline), derived from tyrosine, is an important hormone. 5. Glycine is a precursor of porphyrins such as heme 6. Histamine (mediator of immune response) (synthesized from histidine) ex: allergies 7. Aspartate, glycine, and glutamine are precursors of nucleotides. 8. Arginine is a precursor of nitric oxide.  How are amino acids joined together???? Amino acids linked by a series of peptide bonds constitute a peptide chain, each amino acid of which is referred to as an amino acid residue. Polymers composed of less than 50 amino acid residues are termed oligopeptides, while larger polymers (more than 50 amino acid residues) are known as polypeptides. Thus, a protein molecule is a polypeptide chain composed of many amino acid residues, with each residue linked to the next residue by a peptide bond.  Peptide Bonds Link Amino Acids The amino acid can be connected by a dehydration synthesis reaction (condensation reaction) in which the nucleophilic addition-elimination reaction between: The amino group of one amino acid and the carboxyl group of another amino acid forms a covalent bond (peptide bond), and releases one molecule of water as a by- product. Form when the acid group (COOH) of one amino acid joins with the amine group (NH2) of a second amino acid Formed through condensation Broken through hydrolysis The formation of the peptide bond consumes energy, which, in organisms, is derived from ATP.  Four levels of structure Primary structure Secondary structure Tertiary structure Quaternary structure Any alteration in the structure or sequencing changes the shape and function of the protein  1. Primary structure A protein’s primary structure is the unique sequence (Linear sequence) of amino acids in each polypeptide chain that makes up the protein. Basic level of protein structure. List of amino acid linked together in a specific order. Amino acid are covalently linked by covalent or peptide bond. Each component amino acid in a polypeptide is called (Residue). Primary structure of protein starts from the amino terminal end (N) and ends in carboxyl terminal (C) end. For example :insulin has two polypeptide chains A,B The first protein sequenced by fredrieck sanger (insulin) Coo- NH3 2. Secondary structure Secondary structure is made by folding of the polypeptide chain. Secondary structures arise as Hydrogen bonds form between backbone atoms. There are two main types of secondary protein structures: the α-helix (the most common ) and the β-pleated sheet.  3. Tertiary Protein Structure A protein isn’t fully functional until it has a 3D shape. The 3D structure of a protein is referred to as its tertiary structure and is made by further folding of secondary proteins. Tertiary structure is formed due to interaction between R groups of the amino acids that make up the protein. R group interactions that contribute to 3D structure include; hydrogen bonding , ionic bonding, noncovalent bonding , hydrophobic bonding, disulphide bonding. Disulphide bond is covalent linkage between the Sulphur containing side chain of cysteine, are much stronger than other types of bonds.  All of these interactions, weak and strong, determine the final three- dimensional shape of the protein. When a protein loses its three-dimensional shape, it is no longer functional.  4. Quaternary Protein Structure Many proteins are made up of more than one polypeptide chain to perform their function. The complete structure of such a protein is designated its quaternary structure, and each polypeptide chain is referred to as a subunit. The quaternary structure is stabilized by the same bonds as for the tertiary structure, including different noncovalent bonds and disulfide bonds. These bonds hold the subunits together and arrange themselves to form a larger protein complex. Proteins made from a single polypeptide will not have a quaternary structure. Ex: Hemoglobin has two subunits (two alpha and two beta). Ex :DNA polymerase , an enzyme that synthesize new strand of DNA and is composed from ten subunits. 4. Quaternary Protein Structure Heteromeric complexes Homomeric complexes - Protein complexes formed from - Protein complexes formed from different subunits. identical subunits or very similar - Each subunit has a distinct amino in term of ; amino acid sequence, acid sequence, 3D structure , 3D structure , function. function. - Ex: Hemoglobin - Ex: Ferritin  Denaturation Denaturation A process in which a protein loses its native shape due to the disruption of weak chemical bonds and interactions, thereby becoming biologically inactive. ⟰ Loss of secondary, tertiary and quaternary structure of proteins. ⟰ Primary structure is unchanged by denaturation. ⟰ Change in physical, chemical and biological properties of protein molecule Ex: Denaturation by heat