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MEDICAL BIOCHEMISTRY Structure and classification of amino acids. Essential and nonessential amino acids.  The Genetic Code Specifies 20 L-α-Amino Acids Although huge number of amino acids occur in nature, proteins are synthesized almost exclusively from the set of 20 L-α- amino aci...

MEDICAL BIOCHEMISTRY Structure and classification of amino acids. Essential and nonessential amino acids.  The Genetic Code Specifies 20 L-α-Amino Acids Although huge number of amino acids occur in nature, proteins are synthesized almost exclusively from the set of 20 L-α- amino acids encoded by nucleotide triplets called by multiple codons. Some proteins contain additional amino acids that arise by the post- translational modification of an amino acid already present in a peptide. Examples include the conversion of peptidyl proline and peptidyl lysine to 4- hydroxyproline and 5-hydroxylysine; Proteins undergo methylation, formylation, acetylation, prenylation, and phosphorylation of certain aminoacyl residues. These modifications significantly extend the biologic diversity of proteins by altering their solubility, stability, catalytic activity, and interaction with other proteins.  Selenocysteine is the 21st Protein L-α-Amino Acid Selenocysteine is an L-α-amino acid found in proteins from every domain of life. Selenocysteine is not the product of a posttranslational modification, but is inserted directly into a growing polypeptide during translation. Selenocysteine thus is commonly termed the “21st amino acid.” However, unlike the other 20 protein amino acids, incorporation of selenocysteine is specified by a large and complex genetic element for the unusual tRNA called tRNASec which utilizes the UGA anticodon that normally signals STOP. However, the protein synthesis apparatus can identify a selenocysteine-specific UGA codon by the presence of an accompanying stem-loop structure, the selenocysteine insertion element, in the untranslated region of the mRNA  Nutritionally essential and non-essential amino acids In biochemical terms, Nutritionally Nonessential amino acids are defined as those for which a synthetic pathway is present in the body, which is of sufficient capacity to satisfy the normal requirement. Nutritionally Essential amino acids are defined as those for which a synthetic pathway is not present. Some Amino acids are semiessential since for synthesys of these amino acids nutritionally essential amino acids are needed.  Essential amimo acids Gene with codons for nucleus Val, Leu Ile Phe Met, Thr, Lys, Arg*, Hys*, Trp amino acids Non essential amino acids transcription Gly, Ala, Ser, Pro, Cys, Tyr, Asn, Gln, Asp, Glu, mRNA containing codon sequence for amino acids Derived amino acids translation Cystine, desmosine, isodesmosin of elastin hydroxyproline and hydroxylysine of collagen Protein with specific γ-carboxyglutamate-prothrombin amino acid sequence phosphoserine, phosphotyrosine, phosphothreonine of many proteins Each amino acid (except for proline, which has a secondary amino group) has a carboxyl group, a primary amino group, and a distinctive side chain (“R-group”) bonded to the α-carbon atom. At physiologic pH (approximately pH 7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (–COO–), and the amino group is protonated (–NH3+). In proteins, almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not available for chemical reaction except for hydrogen bond formation. Tetrahedral Arrangement of α-carbon Substituents H Methyl Pyrrolidine Isopropyl γ-Isobutyl β-Isobutyl Methyl thiol esther Benzene Phenol Heterocyclic Indole: Benzene fused with pyrrole The principal components of a spectrophotometer. A light source emits light along a broad spectrum, then the monochromator selects and transmits light of a particular wavelength. The monochromatic light passes through the sample in a cuvette of path length I. The absorbance of the sample, log (Io/I), is proportional to the concentration of the absorbing species. The transmitted light is measured by a detector. Alcohol containing Thiomethyl Amino group containing carboxyl side chain Butyl amine Guanidinium Imidazole In aqueous solutions, a polar environment proteins the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein. This phenomenon, known as the hydrophobic effect, thus fill up the interior of the folded protein and help give it protein’s native three-dimensional conformation. However, for proteins that are located in a hydrophobic environment, such as a membrane, the nonpolar R-groups are found on the outside surface of the protein, interacting with the liquid environment  Derived Amino Acid Produced by Reverseble Formation of Disulfide Bond Between Two Cysteines Disulfide bond: The side chain of cysteine contains a sulf hydryl group (–SH), which is an important component of the active site of many enzymes. In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (–S–S–). Proline differs from other amino acids in that proline’s side chain and α- amino N form a rigid, five-membered ring structure. Proline, then, has a secondary (rather than a primary) amino group. It is frequently referred to as an imino acid. The unique geometry of proline contributes to the formation of the fibrous structure of collagen and often interrupts the α-helices found in globular proteins Sickle cell disease is an inherited blood disorder marked by defective hemoglobin. It inhibits the ability of hemoglobin in red blood cells to carry oxygen. Sickle cells tend to stick together, blocking small blood vessels causing painful and damaging complications. This disease results from the substitution of polar glutamate by nonpolar valine at the sixth position in the β subunit of hemoglobin  Buffers A buffer is a solution that resists changes in pH when small amounts of acid or base are added to it. Buffers are typically composed of a weak acid and its conjugate base (or a weak base and its conjugate acid) in roughly equal amounts. The presence of both the weak acid and its conjugate base allows the buffer to absorb or release hydrogen ions (H⁺) in response to changes in pH, helping to maintain the pH of the solution relatively stable. Buffers are crucial in various biological, chemical, and laboratory applications where maintaining a stable pH is essential for processes such as enzymatic activity, cell culture, and chemical reactions.  Titration Amino acid titration refers to the process of determining the concentration of amino acids in a solution by gradually adding a titrant solution of known concentration until a specific endpoint is reached. During the titration, the pH of the amino acid solution is monitored, and changes in pH occur as the titrant is added. At the endpoint, the pH reaches a certain value, indicating that the stoichiometric equivalence point has been reached. Amino acid titration can be used to determine various parameters, such as the pKa values (acid dissociation constants) of the amino acid functional groups, the total concentration of amino acids in a sample, or the concentration of a specific amino acid in a mixture. This process is fundamental in biochemical and analytical chemistry for characterizing amino acids and understanding their behavior in solution. Leucine is an Amino Acid Lacking Ionizing R Group Titration of Monoamino-Monocarboxylic Amino Acid Leucine with NaOH pH meter For Leucine pKa1(α-COOH) = 2.33 pKa2(α-NH3+) = 9.74 The isoelectric point (pI) of a molecule, such as a protein or amino acid, is the pH at which it carries no net electrical charge. At this pH, the molecule's positive and negative charges balance out, resulting in overall neutrality. In the case of amino acids or proteins, the isoelectric point is determined by the presence of ionizable functional groups, such as amino groups (NH2) and carboxyl groups (COOH), which can lose or gain protons depending on the pH of the solution. At a pH above its pI, the molecule carries a net negative charge because it has more ionized acidic groups than basic groups. Conversely, at a pH below its pI, the molecule carries a net positive charge due to an excess of ionized basic groups. The isoelectric point is an important parameter in biochemistry and protein chemistry, influencing the solubility, stability, and behavior of proteins under different pH conditions.  General Relationship between charge Properties of Amino Acids and Proteins and pH At the pH less than pI, the molecule is positively charged, whereas at pH greater than pI, the molecule is negatively charged As proteins are complex polyelectrolytes that contain many ionizable groups that regulate zwitterion form, calculation of protein pKa value utilizing Henderson-Hasselbalch relationship is difficult. Accordingly, pI values are experimentally measured by determining the pH value at which the protein does not move in an electric field Proteins; Enzymes Act as General Acid and/or Base The enzymes can add (general acid) or remove (general base) protons from a substrate changing its charge The removal of a proton makes a group more nucleophilic (necleophile is a group that will attack a positive center. e.g. OH- is more nucleophilic than a water and ionized cysteine is more nucleophilic than is the ionized sulfur atom The advantage of the enzymes using general acid and general base catalysis is that at physiological neutral pH, thay can catalyse a reaction even though the concentration of OH- and H+ is very low Enzymaticaly Catalized Dehydration Reaction Peptide Bonds in trans AND cis configuration  LITERATURE Ferrier, Denise R. Lippincott Illustrated Reviews: Biochemistry. 7th ed. Philadelphia, PA: Wolters Kluwer, 2017. MLA Citation. Ferrier, Denise R. Robert K. Murray-Harper’s Illustrated Biochemistry (Lange Medical Book)- McGraw-Hill Medical; 31th edition (2018) David L. Nelson, Michael M. Cox - Lehninger Principles of Biochemistry - Worth Publishers Inc.,U.S.; 6th edition (2013)