2.Amino Acids (8) a.pdf

Amino Acids 09/21/2021 Sopio Dzneladze 1 What is an amino acid ? Amino acids, often referred to as the building blocks of proteins, are compounds that play many critical roles in your body. Although more than 300 different amino acids have been described in nature, only 20 are commonly found as cons...

Amino Acids 09/21/2021 Sopio Dzneladze 1 What is an amino acid ? Amino acids, often referred to as the building blocks of proteins, are compounds that play many critical roles in your body. Although more than 300 different amino acids have been described in nature, only 20 are commonly found as constituents of mammalian proteins. 09/21/2021 Sopio Dzneladze 2 What is a protein Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells, and organisms, and transporting molecules from one location to another. 09/21/2021 Sopio Dzneladze 3 Macromolecule In biology, a micromolecule refers to a molecule of relatively small size and low molecular weight as opposed to a macromolecule, which is large and with greater molecular weight. 09/21/2021 Sopio Dzneladze 4 Macromolecules: A molecule contain a very large numbers of atoms, such as protein, nucleic acid, or synthetic polymer. These are usually created by polymerization of smaller subunits like amino acid for protein, glucose for glycogen, etc. Micromolecules : A molecule that is relatively smaller (than a macromolecule), or have low molecular weight. E. g: monomers of macro molecules like Amino acids are monomers of protein, glucose is a monomer of glycogen, etc. 09/21/2021 Sopio Dzneladze 5 General Formula Amino acids are organic compounds that contain amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. 09/21/2021 Sopio Dzneladze 6 At Physiologic pH (pH=7,4) the carboxyl group is dissociated, forming a negatively charged carboxylate ion and the amino group is protonated. 09/21/2021 Sopio Dzneladze 7 α–carbon The carbon atom next to the carboxyl group (which is therefore numbered 2 in the carbon chain starting from that functional group) is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids. 09/21/2021 Sopio Dzneladze 8 Peptide linkage In proteins, almost all these carboxyl and amino groups are combined through peptide linkage. 09/21/2021 Sopio Dzneladze 9 09/21/2021 Sopio Dzneladze 10 Side chains Each amino acid is identical except for its side chain, or R group. It is the charge, shape, polarity, and size of a side chain that gives each amino acid its unique biochemical properties. Amino acid side chains are typically grouped into non-polar, polar, acidic, and basic categories. 09/21/2021 Sopio Dzneladze 11 Classification of amino acids Side chains dictates the role an amino acid plays in protein; Therefore it is useful to classify the amino acids according to the properties of their side chains: NONPOLAR - have an even distribution of electrons; POLAR - have an uneven distribution of electrons, such as acids and bases. 09/21/2021 Sopio Dzneladze 12 Nonpolar side chains 09/21/2021 Sopio Dzneladze 13 Amino acids with nonpolar side chains They does not gain or lose protons or participate in hydrogen or ionic bonds; The side chains of these amino acids can be thought of as “oily” or lipid-like, a property that promotes hydrophobic interactions. Nonpolar side chains fill up the interior of the folded protein and help give it its three dimensional shape. 09/21/2021 Sopio Dzneladze 14 09/21/2021 Sopio Dzneladze 15 Hydrophobic interactions describe the relations between water and hydrophobes (low water-soluble molecules). Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules. The mixing of fat and water is a good example of this particular interaction. 09/21/2021 Sopio Dzneladze 16 Glycine Simplest amino acid 09/21/2021 Sopio Dzneladze 17 Proline 09/21/2021 Sopio Dzneladze 18 Polar amino acids Zero net charge at neutral pH 09/21/2021 Sopio Dzneladze 19 Disulfide bond Many extracellular proteins are stabilized by disulfide bond, for example Albumin, a blood protein. 09/21/2021 Sopio Dzneladze 20 Amino acids with acidic side chains 09/21/2021 Sopio Dzneladze 21 Amino acids with basic side chains 09/21/2021 Sopio Dzneladze 22 Abreviations and simbols Each amino acid name has an associated three letter abbreviation and a one letter symbol. 09/21/2021 Sopio Dzneladze 23 Unique first letter If only one amino acid begins with a particular letter, then that letter is used as a symbol. 09/21/2021 Sopio Dzneladze 24 If more than one amino acid begins with the particular letter, the most common of these amino acids receives this letter as a symbol. For example: Glycine is more common than Glutamate, so, G=glycine. 09/21/2021 Sopio Dzneladze 25 Some one letter symbols sound like the amino acid they represent. For example, F=phenylalanine, or W=tryptophan. 09/21/2021 Sopio Dzneladze 26 09/21/2021 Sopio Dzneladze 27 Optical properties of amino acids 09/21/2021 Sopio Dzneladze 28 Amino acids that have an asymmetric center at the α – carbon can exist in two forms, designated D and L. The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers. Isomers - each of two or more compounds with the same formula but a different arrangement of atoms in the molecule and different properties. 09/21/2021 Sopio Dzneladze 29 Polypeptide chain Each polypeptide chain is a series of amino acids joined together in a specific sequence. Because each amino acid has a unique R group, a particular amino acid sequence creates a polypeptide whose function is dependent upon its chemical structure. 09/21/2021 Sopio Dzneladze 30 The linking of two amino acids is accompanied by the loss of a molecule of water. A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a polypeptide is called a residue. 09/21/2021 Sopio Dzneladze 31 A peptide is two or more amino acids joined together by peptide bonds; a polypeptide is a chain of many amino acids; protein contains one or more polypeptides. Therefore, proteins are long chains of amino acids held together by peptide bonds. 09/21/2021 Sopio Dzneladze 32 09/21/2021 Sopio Dzneladze 33 Amino acids are classified into three groups: Essential amino acids Nonessential amino acids Conditional amino acids 09/21/2021 Sopio Dzneladze 34 Essential amino acids Essential amino acids cannot be made by the body. As a result, they must come from food. The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. 09/21/2021 Sopio Dzneladze 35 NONESSENTIAL AMINO ACIDS Nonessential means that our bodies produce an amino acid, even if we do not get it from the food we eat. Nonessential amino acids include: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine. 09/21/2021 Sopio Dzneladze 36 CONDITIONAL AMINO ACIDS Conditional amino acids are usually not essential, except in times of illness and stress. their synthesis can be limited under special pathophysiological conditions, Conditional amino acids include: arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine. 09/21/2021 Sopio Dzneladze 37 References: Lippincott’s Illustrated Reviews “Biochemistry”: pp.1-5. 09/21/2021 Sopio Dzneladze 38