Chemical Properties of Amino Acids

11 Key excerpts on "Chemical Properties of Amino Acids"

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  eBook - ePub

  Biochemistry

  • Donald Voet, Judith G. Voet(Authors)
  • 2021(Publication Date)
  • Wiley

    (Publisher)

  Chapter 3 Amino Acids

  1 The Amino Acids of Proteins

  A. General Properties

  B. Peptide Bonds

  C. Nomenclature of Amino Acids

  D. Classification and Characteristics

  2 Stereochemistry of Amino Acids

  A. An Operational Classification

  B. The Fischer Convention

  C. The Cahn–Ingold–Prelog System

  D. Chirality and Biochemistry

  3 Chemical Properties of Amino Acids

  A. Acid–Base Properties

  B. Reactions of Amino Acids

  4 “Nonstandard” Amino Acids

  A. Amino Acid Derivatives in Proteins

  B. Specialized Roles of Amino Acids

  It is hardly surprising that much of the early biochemical research was concerned with the study of proteins. Proteins form the class of biological macromolecules that have the most well-defined physicochemical properties, and consequently they were generally easier to isolate and characterize than nucleic acids, polysaccharides, or lipids. Furthermore, proteins, particularly in the form of enzymes, have obvious biochemical functions. The central role that proteins play in biological processes has therefore been recognized since the earliest days of biochemistry. In contrast, the task of nucleic acids in the transmission and expression of genetic information was not realized until the late 1940s and their catalytic function only began to come to light in the 1980s, the role of lipids in biological membranes was not appreciated until the 1960s, and the biological functions of polysaccharides are still somewhat mysterious.

  In this chapter we study the structures and properties of the monomeric units of proteins, the amino acids. It is from these substances that proteins are synthesized through processes that we discuss in Chapter 27 . Amino acids are also energy metabolites and, in animals, many of them are essential nutrients (Chapter 23

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  Genetic Databases

  • (Author)
  • 1999(Publication Date)
  • Academic Press

    (Publisher)

  Properties of Amino Acids in Sequences 83 Table 5.1 Physical properties of the amino acids. The 20 amino acids are tabulated (with their abbreviations) showing their number of non-hydrogen atoms (beyond the a-carbon), the number of which are polar (non-carbon) and the number of bonds (including the a-p carbon bond) which can be rotated to move the position of non-hydrogen atoms. The latter property corresponds to flexibility. Amino acid Aspartic acid Serine Threonine Glycine Proline Cysteine Alanine Valine Isoleucine Leucine Methionine Phenylalanine Tyrosine Tryptophan Histidine Arginine Lysine Asparagine Glutamine Glutamic acid Single-letter code D S T G P C A V 1 L M F Y W H R K N Q E Three-letter code Asp Ser Thr Gly Pro Cys Ala Val lie Leu Met Phe Tyr Trp His Arg Lys Asn Gin Glu All atoms 4 2 3 0 3 2 1 3 4 4 4 7 8 10 6 6 5 4 5 5 Polar N,0,S 0,2,0 0,1,0 0,1,0 0,0,0 0,0,0 0,0,1 0,0,0 0,0,0 0,0,0 0,0,0 0,0,1 0,0,0 0,1,0 1,0,0 2,0,0 3,0,0 1,0,0 1,1,0 1,1,0 0,2,0 Rotate bonds 2 1 2 0 0 1 0 2 2 3 3 2 2 2 2 4 4 2 3 3 5.2.7.2 Chemical properties The most hydrophobic residues (those composed entirely of carbon) have, on the energy scales of proteins, effectively no chemistry. Binding specificity and enzymic activity reside in the variety of chemical function associated with the polar atoms in the more hydrophilic residues. What was classed above simply into nitrogen, oxygen and sulphur containing groups, in chemical terms, become acids (Asp, Glu), bases (Arg, Lys), hydroxyl (Ser, Thr, Tyr) amide (Asn, Gin), imidazol (His) and sulphydryl (Cys). From a structural viewpoint, the differences in these functions are manifest mainly in their differing propen-sity to form hydrogen bonds or salt-bridges (between the acids and bases). Most polar atoms can both accept a hydrogen bond (onto their electronegative 84 1/i/. R. Taylor Figure 5.1 Physical properties of the amino acids (defined in Table 5.1) are plotted in space (as a stereo pair).

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  Chemistry, 5th Edition

  • Allan Blackman, Steven E. Bottle, Siegbert Schmid, Mauro Mocerino, Uta Wille(Authors)
  • 2022(Publication Date)
  • Wiley

    (Publisher)

  In the meantime, as we await these results, chemists on Earth continue to undertake research into the factors in the primordial solar system that may have favoured the formation of specific enantiomers of amino acids and other organic molecules. Discoveries from this research, from space missions and from meteorites on Earth are likely to continue to offer us tantalising glimpses of the roles organic molecules played in the formation of life on Earth as we know it today. 24.2 Acid–base properties of amino acids LEARNING OBJECTIVE 24.2 Control the charge present on amino acids using pH. Amino acids are unusual molecules in that they possess both an acidic functional group and a basic functional group in the same molecule. This means that in the biological environment they can play the role of proton (H + ) donors or proton (H + ) acceptors. Acidic and basic groups of amino acids Among the most important Chemical Properties of Amino Acids are their acid–base properties; all can be weak polyprotic acids because of their COOH and NH 3 + groups. The exact ability of these groups to accept or donate H + is indicated by their pK a values. (Recall from the chapter on acids and bases that the smaller the pK a the more acidic is the group. At lower pH, carboxylic acids are found in the RCOOH form and amines are found in the RNH 3 + form. At higher pH, the opposite is true; carboxylic acids are present as the salt RCOO - and amines are present as uncharged RNH 2 . Figure 24.9 shows how this looks at different pH.) Table 24.4 gives pK a values for each ionisable group of the 20 protein-derived amino acids. Acidity of -carboxyl groups The average value of pK a for an -carboxyl group of a protonated amino acid is 2.19. Thus, the -carboxyl group is a considerably stronger acid than acetic acid (pK a = 4.74) and other low-molar-mass aliphatic carboxylic acids. This greater acidity is accounted for by the electron-withdrawing inductive effect of the adjacent NH 3 + group.

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  Food Protein Chemistry

  An Introduction for Food Scientists

  • Joe Regenstein(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  Chapter 4

  Chemistry of the Amino Acids

  Publisher Summary

  Every amino acid has a primary amino group and a primary carboxyl group. Either of these groups could also appear on a side chain. One of the common ways to mark a specific amino acid to facilitate studying its changes is to make a radioactive iodine derivative. Other chemical changes that are of potential importance to food scientists include those that modify the protein and change its food functionality. The degree of reaction is often different in the free amino acids because of the zwitter ion nature of the compound. The isoelectric point of an amino acid is the point at which the amino acid has no net electrical charge. It is an important characteristic for any amino acid, because every amino acid has at least two acid-base groups. Another important property of an amino acid is the association constant of the individual reactive groups. It is expressed as pK , the negative log of κ (the dissociation constant). These numbers change as the solution conditions change. The pK values of the α-carboxyl and the α-amino groups are not influenced by the side chains, and the pK values of the side chains are not much influenced by the α-carboxyl or α-amino groups.

  Every amino acid has a primary amino group and a primary carboxyl group. Either of these groups could also appear on a side chain. Lysine is the amino acid with a side chain amino group; arginine and histidine have reactive nitrogen groups that are somewhat similar chemically. Glutamic and aspartic acids are the amino acids with side chain carboxyls.

  Certain reagents react with amino groups; others react with carboxyl groups. Some chemical groups react preferentially with the primary amino group (α

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  Principles of Animal Nutrition

  • Guoyao Wu(Author)
  • 2017(Publication Date)
  • CRC Press

    (Publisher)

  4 Chemistry of Protein and Amino Acids

  The word “protein” originated from the Greek word “proteios ,” meaning prime or primary (Meister 1965). A protein is a large polymer of amino acids (AAs) linked via the peptide bond (–CO–NH–). Different proteins have different chemical properties (e.g., AA sequences, molecular weights, ionic charges, three-dimensional (3D) structures, hydrophobicity, and function). The general structure of an AA is shown in Figure 4.1 . There may be one or more polypeptide chains in a protein, which contains its constituents (nitrogen, carbon, oxygen, hydrogen, and sulfur atoms). A protein may be covalently bonded to other atoms and molecules (e.g., phosphates) and non-covalently attached with minerals (e.g., calcium, iron, copper, zinc, magnesium, and manganese), certain vitamins (e.g., vitamin B6 , vitamin B12 , and lipid-soluble vitamins), and/or lipids. Protein is the major nitrogenous macronutrient in foods and the fundamental component of animal tissues (Wu 2016). It has structural, signaling, and physiological functions in animals (Table 4.1 ).

  Figure 4.1 Fisher projections for configurations of AAs relative to l - and d -glyceraldehydes. The general structure of an AA in the non-ionized form is shown. For AAs, l - or d -isomers refer only to the chemical configuration of their α

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  Polysaccharides Peptides and Proteins

  Pharmaceutical Monographs

  • R. T. Coutts, G. A. Smail, J. B. Stenlake(Authors)
  • 2014(Publication Date)
  • Butterworth-Heinemann

    (Publisher)

  To the organic chemist an amino acid refers to any molecule possessing both an amino and an acid group. The bio-chemist, on the other hand, tends to reserve the term for those compounds in which an amino group occurs on the same carbon atom as a carboxyl group—α-amino acids (I)—and which have largely been isolated from protein hydrolysates. H H I I R—C—COOH R—C—COO~ I I NH 2 NH 3 (I) + da) 80 AMINO ACIDS The side group (R in I) in most cases is neutral and thus the amino acid is neutral since under most conditions it is the salt-like dipolarionic form (la) which is favoured. A few amino acids con-tain a second acidic or basic function in the side-chain and the molecule as a whole then departs from neutrality. Table 2 illus-trates the common amino acids of which proteins are largely com-posed, whereas Table 3 shows amino acids which are of less com-mon occurrence and are not all derived from proteins. In general the salt-like nature of the amino acids confers on them characteris-tic non-volatility, classical insolubility in organic solvents and high indefinite melting points which are almost invariably accom-panied by decomposition. The condensation of the amino group of one amino acid with the carboxyl group of another and the elimination of water results in the formation of a peptide linkage (—CONH—). Two or more amino acids joined by this linkage represents a peptide, and the prefixes di-, tri-, tetra-, etc. indicate the number of constituent amino acids. The term oligo-peptide is sometimes used to refer generally to these smaller peptides. The term polypeptide can be used to designate all but the simplest peptides. The proteins con-stitute the largest group of anhydrocopolymers of amino acids. An arbitrary distinction is usually drawn between polypeptides and proteins on a basis of molecular weight. The term polypeptide is usually reserved for those molecules whose molecular weight is less than 10,000.

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  Guide to Biochemistry

  • James C. Blackstock(Author)
  • 2014(Publication Date)
  • Butterworth-Heinemann

    (Publisher)

  Today the immense variety of protein molecules is recognized. Proteins are the most abundant macromolecules found within cells and perform a wide variety of functions (Section 1.6). A protein can be considered as a unique polymer of amino acids (Section 1.4) which determine its chemical and structural properties. It is therefore imperative to consider the amino acids before embarkation upon a discussion of protein structure. Of the 308 catalogued natural amino acids, only 20 (plus a few derivatives) occur in proteins in which all are α-amino acids of the L -series (Section 1.3). They conform (except proline) to a general formula (Figure 4.1) in which an amino group and a carboxylic acid group are attached to the α-carbon (C α) atom. Proline, an imino acid, is normally included because of its occurrence in proteins. The properties of individual amino acids vary according to the nature of the R group called the side chain (Table 4.1). Asparagine and glutamine are considered as amide derivatives of aspartic acid and glutamic acid respectively. Tyrosine may be classified either by its hydroxy or aromatic group. To refer to amino acids in polypeptide sequences, three- or one-letter codes are frequently employed. L -α-Amino acids, with the exception of glycine, contain a chiral α-carbon atom (Section 1.3). These amino acids exhibit optical activity; in some cases, dextrorotatory, e.g. alanine, in other cases laevorotatory, e.g. phenylalanine. Because of the conjugated double-bond system of their aromatic rings, tyrosine, tryptophan and phenylalanine absorb light in the ultraviolet region

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  Plant Nonprotein Amino and Imino Acids

  Biological, Biochemical, and Toxicological Properties

  • Gerald Rosenthal(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  Chapter 1 These materials (amino acids) are at the same time substituted bases and substituted acids. Their capacity to function as amphoteric electrolytes has therefore conferred on them many remarkable electro-chemical properties not shared by any other product of natural origin. (Greenstein and Winitz, 1961). A. INTRODUCTION Nitrogen is the most abundant component of Earth's atmosphere but only a handful of higher plants can contribute to the utilization of this indispensable but relatively inert element. These higher plants, by virtue of symbiotic microbial associations, possess the unique ability to fix vast quantities of diatomic nitrogen into ammonia which is toxic and has limited biological utility until it is assimilated into organic linkage. The biosynthesis of amino acids represents the principal means for the assimilation of fixed nitrogen into biologically functional molecules. What exactly then is an amino acid? It is a substance having both an amino group and an organic acid. The labile proton can be de-rived not only from the customary carboxyl group but also by ioni-zation of sulfonic acid. For practical purposes, however, the term amino acid is applied to compounds sharing the general structure R—CH(NH 2 )COOH. While an amino group is usually linked directly to a carbon atom alpha to that of the carboxyl group, the amino group may ι Nomenclature and Certain Physicochemical Properties 2 1. Nomenclature and Certain Physicochemical Properties be associated with any carbon, such as in ß-alanine, H 2 N—CH 2 —CH 2 — COOH, or γ-aminobutyric acid, H 2 N — C H 2 — C H 2 — C H 2 — C O O H . As a group, the nonprotein amino acids are extremely diversified and it is not surprising that several systems can be employed for classifying and ordering these natural products.

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  The Biology and Practice of Current Nutritional Support

  • Rifat Latifi, Stanley J. Dudrick(Authors)
  • 2003(Publication Date)
  • CRC Press

    (Publisher)

  C hapter З Biochemistry of Amino Acids: Clinical Implications Rifat Latifi , Khawaja Aizimuddin Introduction Ajnino acids, as organic compounds, containing both an amino group and a carboxylic acid group, are the monomeric and basic constituents of all proteins. Amino acids occurring in protein are known as alpha-amino acids and have one or two empirical formulae RCH (NH+)COOH' or R-CH-(NH3)COO Beta-amino acids and gamma-amino acids also occur in nature but are not components of pro­ teins, and their significance is not known. This chapter reviews the basic biochemis­ try and physiology of amino acids and their functions as fundamental units of proteins. Their increasingly recognized and valued role in the metabolic and nutritional man­ agement of critically ill patients will be discussed through out this volume. Structure of Amino Acid and Proteins A protein molecule consists of amino acids held together by peptide bonds, which form a long polypeptide chain. The exact sequence of amino acids in the chain, referred to as the primary structure of the protein, is determined genetically and defines how the chain is folded into more complex conformations or shapes. A polypeptide, which is folded into a helical or pleated sheet configuration, is referred to as a secondary structure. If the sequence of amino acids is then folded into a three-dimensional configuration, a tertiary structure is created. Some pro­ teins have a higher level of molecular architecture known as the quaternary struc­ ture, in which several chains aggregate and function as a unit. The amino acid sequence and protein structure determine the nature and function of protein molecules upon which virtually every process of life depends. The folding of polypeptide chains into alpha helix and beta pleated sheets has clinical implications. The alpha helix is a rod-like structure and contains a tightly coiled polypeptide main chain.

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  Biochemistry

  An Integrative Approach

  • John T. Tansey(Author)
  • 2019(Publication Date)
  • Wiley

    (Publisher)

  Specific modifications are sometimes made to particular amino acids within a protein. • The synthesis of the covalent chemical bonds in a protein costs energy. In addition, the assembly of hundreds of amino acids into a single protein has a highly negative entropy. Therefore, the free energy (ΔG) of protein formation from isolated amino acids in a test tube is quite positive. In the cell, the overall reaction becomes favorable (ΔG < 0) by coupling these reactions to the hydrolysis of ATP and GTP. • Unlike the synthesis of the peptide bonds in a protein, the folding of a protein into its final conformation is largely governed by numerous weak forces. Here, increases in entropy provided by liberation of water molecules drive ΔG < 0 and lead to formation of the final structure. DYNAMIC FIGURE 3.1 Amino acids are metabolites with multiple functions in the cell. They can be polymerized into peptides and proteins, complex macromolecules with diverse functions ranging from structure to catalysis. 3.1 Amino Acid Chemistry 69 3.1 Amino Acid Chemistry Amino acids are the building blocks of proteins, and they play critical roles in many meta- bolic pathways. Because of these diverse roles, amino acids are a good place to start a discus- sion of protein chemistry. 3.1.1 The structure of amino acids dictates their chemical properties As their name suggests, amino acids have a single unifying property— they have both an amine and a carboxylic acid moiety (Figure 3.2). Amino acids found in proteins are all α-amino acids; that is, they contain an amino group, a central α-carbon, and a carboxyl group. In 19 of the 20 common amino acids found in proteins, the amine is a primary amine bound only to the α-carbon. The remaining amino acid, proline, is tech- nically an imino acid, containing a secondary amine with the side chain joining the backbone amine, forming a ring.

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  The Molecular Fabric of Cells

  • BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
  • 2013(Publication Date)
  • Butterworth-Heinemann

    (Publisher)

  In this chapter we will examine the structure and properties of these building blocks before examining proteins in the next chapter. We will particularly focus on their ionisation behaviour as this is vitally important if we are to understand the properties of both amino acids and proteins. Amino acids 17 Enzymes Immune/protective proteins Transport proteins Storage proteins Structural proteins Contractile/motile proteins Hormones and their receptors Regulating proteins The catalysts of biochemical reactions Antibodies: recognise and bind to foreign substances Complement: complexes with some antibody -antigen complexes and causes destruction of pathogens Fibrinogen and thrombin: involved in blood clotting Serum albumin - transport of fatty acids Haemoglobin - transport of oxygen Ceruloplasmin or transferrin - transport of iron Ovalbumin - in egg white Casein - in milk Ferritin - storage of iron Storage proteins in seeds eg beans Collagen - in skin Elastin - in elastic tissues Keratin - in hair and nails Viral coat proteins Membrane structural proteins Myosin, actin - involved in movement Insulin, growth hormone. Receptors for signal reception and for transport of material into cells Selective stimulation or inhibition of expression of DNA Table 2.1 The roles of proteins. 2.2 Amino acids ammo groups carboxyl groups a carbon atom All proteins are composed of compounds called amino acids, which are frequently thought of as the building blocks of proteins. Amino acids consist of at least one amino group (-NH 2 ), and at least one carboxyl group (-COOH). Whilst an enormous number of amino acids probably exist, those which are incorporated into proteins are all of a type called -amino acids. Routinely, only 20 different -amino acids are found in proteins. An -amino acid is one in which both an amino group and a carboxyl group are joined to the same carbon atom, which is known as the -carbon atom (Figure 2.1).

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