BCH3004 Principles In Biochemistry - Amino Acids PDF

BCH3004 PRINCIPLES IN BIOCHEMISTY 4(3+1) TS. DR. AZZREENA MOHAMAD AZZEME DEPARTMENT OF BIOCHEMISTRY, FACULTY OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES, UPM AMINO ACIDS ▪ Amino acids in protein ▪ Properties, structure and function ▪ Classification of amino acids ▪ C...

BCH3004 PRINCIPLES IN BIOCHEMISTY 4(3+1) TS. DR. AZZREENA MOHAMAD AZZEME DEPARTMENT OF BIOCHEMISTRY, FACULTY OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES, UPM AMINO ACIDS ▪ Amino acids in protein ▪ Properties, structure and function ▪ Classification of amino acids ▪ Chemical reactions ▪ Optical activity ▪ Chirality ▪ Unique amino acid LEARNING OUTCOMES Students are able to: 1. explain properties, structure, function and classification of amino acids 2. explain chemical reaction, optical and chirality activity of amino acids Structure of the Amino Acids ❑ Proteins - all proteins are polymers - monomers that combine to make them are α- amino acids ❑ WHY named as α- amino Side chain, R acids? - amino group is attached to the α-carbon (the carbon next to the carboxylic acid group) α-Carbon  Side chain Amino Carboxyl group group Amino acids are Ball-and stick tetrahedral modelll structures ❑ Near natural pH, - Carboxylic acid group → deprotonated (COO-) - Amino group → protonated (-NH3+) Zwitterion form  20 amino acids are commonly incorporated in proteins during translation process Selenocycteine & pyrrolysine (incorporated into proteins, but they are found in only a relatively small number of proteins) Structure of 20 Amino Acids Commonly Found in Proteins A. Nonpolar (Hydrophobic) Proline also called as imino acid B. Polar (Uncharged) Electrically neutral at neutral pH S & T → Polar group is hydroxyl (-OH) Y → -OH is bonded to an aromatic hydrocarbon, loses a proton at higher pH C → Polar side chain is thiol group (-SH), can react with other cysteine thiol group to form disulfide (-S- S-) bridges Q & N → amide groups, which are derived from carboxyl group C. Acidic Carry negative charges at pH 7 Often referred as aspartate and glutamate Hydrophilic → tend to on surface of a protein molecule, in contact with the surrounding water or a bound substrate  C. Basic Positively charged at or near neutral pH Found on the exterior surfaces of proteins, where they can be hydrated by the aqueous environment or in substrate binding cleft of enzyme  Aromatic amino acids Absorb light in the near ultraviolet region of the electromagnetic spectrum Used for detection and/or quantification of proteins by measuring their absorption at 280 nm Rare Genetically Encoded Amino Acids 21st amino acid: Selenocysteine (Sec), widely distributed but found in few proteins 22nd amino acid: pyrrolysine (Pyl), found in archaea and eubacteria Titration of Amino Acids The reaction of each functional group with a hydrogen ion  The ionization of histidine (an amino acid with a titratable side chain Isoelectric pH (pI) is a point where the average charge is zero. Amino acid Isoelectric Point (pI) - The pH at which a molecule has no net charge is called isoelectric pH or isoelectric point - At its isoelectric pH, a molecule will not migrate in an electric field → use in separation methods - pI of an amino acid that has two ionizable groups, pI = pKa1 + pKa2 2 - pI of an amino acid that has three ionizable groups, ▪ Proteins → have many acidic and basic groups ▪ Called as polyampholytes – may contain tens to hundreds of individual groups ▪ If molecule has both positively and negatively charged groups, there is an isoelectric pH ▪ e.g. human hemoglobin has 148 ionizable groups on its surface, and its pI is 6.85 ▪ pI is determined experimentally using the methods of electrophoresis and isoelectric focusing Two-dimensional electrophoresis Exercise 1 1. 2. Glutamic acid Lysine Stereochemistry of the α-Amino Acids Chiral carbon → has four different substituents attached to it Also known as stereocenter or asymmetric carbon If a molecule contains one asymmetric carbon, two distinguishable stereoisomers exist Stereoisomer of α-amino acids Nonsuperimposable mirror images of one another or enantiomers L and D forms of amino acids All amino acids except glycine contain as asymmetric α-carbon Isoleucine & threonine → additional stereocenter at the β-carbon α-carbon (Cα) β-carbon (Cβ)  Peptides and the Peptide Bond Individual amino acid can be linked by forming covalent bonds The bond is formed between the α-carboxyl group of one amino acid and the α-amino group of the next amino acid Elimination of water molecule Condensation Dipeptide A bond formed is called peptide bond Direction of the peptide chain (N-terminal to C-terminal) The portion of each amino acid remaining in the chain is called an amino acid residue When specifying an amino acid residue in a peptide, the suffix –yl is used to replace –ine or –ate in the name of the amino acid (e.g. glycyl for glycine and aspartyl for aspartate)  Polypeptides are metastable Hydrolyzing rapidly only under extreme condition or when catalyst present E.g. Boiling in strong mineral acid (usually 6 M HCl) E.g. Proteolytic enzymes or protease  Chain containing only a few amino acid residues, like tetrapeptide are collectively referred as oligopeptide > ~ 15 – 20 residues called polypeptide Polypeptides greater than ~ 50 residues are generally referred to as protein How to write sequence of an oligopeptide or polypeptide? Glu-Gly-Ala-Lys or EGAK Always write the N-terminal residue to the left and C- terminal residue to the right Biological functions of small peptide Peptide hormones ❑ Oxytocin – stimulates milk production and involved in emotional bonding ❑ Vasopressin – control of blood pressure by regulating contraction of smooth muscle