Chemistry
Properties of Amino Acids
Amino acids are the building blocks of proteins and contain an amino group, a carboxyl group, and a side chain. They are characterized by their unique side chains, which determine their chemical properties. Amino acids can be classified as polar, nonpolar, acidic, or basic based on the nature of their side chains, and these properties influence their role in protein structure and function.
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10 Key excerpts on "Properties of Amino Acids"
eBook - PDF- (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).
eBook - ePub- 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
eBook - ePub- Guoyao Wu(Author)
- 2017(Publication Date)
- CRC Press(Publisher)
4 Chemistry of Protein and Amino AcidsThe 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
eBook - PDFPolysaccharides 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.
eBook - PDFPlant Nonprotein Amino and Imino Acids
Biological, Biochemical, and Toxicological Properties
- Gerald Rosenthal(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
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. They may be divided arbitrarily into groups according to their structure (e.g., aliphatic, aromatic, or heterocyclic); the number and nature of their ionizable groups; their basic.^acidic, or neutral character; their polar or apolar nature; and finally their physiological properties and biological effects in selected or-ganisms. In this volume, I have selected aspects of the first two group-ings for the ordering of the nonprotein amino acid and imino acids of plants (see the Appendix). A very large number of plant nonprotein amino acids are saturated aliphatic amino acids with an additional amino or carboxyl group; only 2,6-diaminopimelic acid carries both additional groups while 4-carboxy-4-hydroxy-2-aminoadipic acid has three carboxyl groups. A limited number of nonprotein amino acids are unsaturated aliphatics characterized by ethylenic or acetylenic linkages, and recently pyr-rolidine or cyclopropane-ring structures having an exocyclic methylene function have been described. Nearly all nonprotein amino acids occur in the free form but an occa-sional one is isolated attached to a carbohydrate moiety and a few dozen are found as γ-glutamyl-linked peptides. Many of these compounds exist in homologous series and bear some structural analogy to their pro-tein amino acid counterpart. In addition to the 20 or so universally distributed protein amino acids, at this time over 400 others have been obtained from natural sources.* About 240 nonprotein amino acids are found in various plants. Pro-karyotic organisms are the source for an additional 50, while the fungi* provide 75 others.
eBook - PDF- BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
- 2013(Publication Date)
- Butterworth-Heinemann(Publisher)
15 Amino acids 2.1 Introduction and roles 16 2.2 Amino acids 17 2.3 Ionisation of amino acids 24 2.4 Identification and reactions of amino acids 37 Summary and objectives 38 16 Chapter 2 Amino acids 2.1 Introduction and roles metabolism technology importance of proteins diversity of roles of proteins Although this chapter is primarily about amino acids, we shall begin by considering proteins. The reason is that proteins are polymers constructed from amino acids. Thus by establishing the importance of proteins we can more readily appreciate why amino acids should be studied. Of all the types of compounds found in cells, proteins (from the Greek, proteios = 'first') are arguably the most important. Whilst it is true that deoxyribonucleic acid (DNA) holds the genetic information for the cell, without proteins nothing else in the cell (including DNA) would be made. In this and the next two chapters, we are going to explore proteins and nucleic acids, in order to establish some fundamental properties of these molecules. We will see how the structure of proteins is responsible for their shapes and properties: these in turn determine their uses or functions. Thus understanding the structure of biological molecules is vital for a thorough understanding of what they can do. By studying the functional properties of proteins and the roles they perform in cells, as well as by obtaining insights into how cells carry out and regulate chemical processes ('metabolism'), we may also identify how we could use proteins. This will introduce you to the idea of using cells or parts of cells to accomplish processes and show you how technology is now applicable to biology. Proteins are present in large quantities in cells. They typically constitute about 50% of the dry mass of cells. Their importance is in part a result of the enormous variety of structures (and hence properties) which is possible through the manner of their construction.
eBook - PDF- William H. Brown, Thomas Poon(Authors)
- 2016(Publication Date)
- Wiley(Publisher)
• Each amino acid has an acid (a COOH group) and a base (an NH 2 group) that undergo an acid–base reaction to form an internal salt given the special name zwitterion. A zwitterion has no net charge because it contains one pos- itive charge and one negative charge. • With the exception of glycine, all protein‐derived amino acids are chiral. • Whereas most monosaccharides in the biological world have the D‐configuration, the vast majority of naturally occurring α‐amino acids have the L‐configuration at the α‐carbon. D‐amino acids are rare. • Isoleucine and threonine contain a second stereocenter, and four stereoisomers are possible for each. • The 20 protein‐derived amino acids are commonly divided into four categories: nine with nonpolar side chains, four with polar but un‐ionized side chains, four with acidic side chains, and three with basic side chains. 18.3 What Are the Acid–Base Properties of Amino Acids? • Amino acids are weak polyprotic acids because of their COOH and NH 3 + groups. • The average value of pK a for an α‐carboxyl group of a pro- tonated amino acid is 2.19. Thus the α‐carboxyl group is a considerably stronger acid than the carboxyl group of acetic acid (pK a 4.76), a fact due to the electron‐withdrawing induc- tive effect of the nearby NH 3 + group of the α‐amino acid. • The average value of pK a for an α‐ammonium group is 9.47, compared to an average value of 10.76 for a primary ali- phatic ammonium ion. Thus, the α‐ammonium group of an amino acid is a slightly stronger acid than a primary ali- phatic amine. • The side‐chain guanidine group of arginine is a considera- bly stronger base than an aliphatic amine. This remarkable basicity is attributed to the large resonance stabilization of the protonated form relative to the neutral form. • The isoelectric point, pI, of an amino acid, polypeptide, or protein is the pH at which the majority of its molecules have no net charge.
eBook - PDF- Fatih Yildiz(Author)
- 2009(Publication Date)
- CRC Press(Publisher)
Storage proteins are important for human nutrition (plant proteins) and numerous studies con-cerning their structure and biosynthesis have therefore been published during the last few years. Furthermore, there is considerable interest in the production of mutants with increased protein content or increased amount of essential amino acids [6]. 3.1.1 A MINO A CIDS Proteins consist of polymers of amino acids (AA) that are characterized by the following general chemical structure: 2 R – CH(NH )COOH Two hydrogens and a nitrogen comprise the amino group, –NH 2 , and the acid entity is the carboxyl group, –COOH. Amino acids link to each other when the carboxyl group of one molecule reacts with the amino group of another molecule, creating a peptide bond –C(=O)NH– and releasing a molecule of water (H 2 O). Amino acids (AA) are the basic building blocks of enzymes, hormones, proteins, and body tissues. A peptide is a compound consisting of two or more amino acids. Oligopeptides have 10 or fewer amino acids. Polypeptides and proteins are chains of 10 or more amino acids, but peptides consisting of more than 50 amino acids are classified as proteins. The chemical structure of amino acids is given in Table 3.1 [7]. 3.1.1.1 Stereochemistry In all the 20 amino acids, except glycine, the carbon atom with the amino group is attached to four different substituents. The tetrahedral bond angles of carbon and the asymmetry of the attachments make it possible for the amino acids to have two non-superimposable structures, the l and r forms, which are mirror images of each other. Only l-amino acids are found in natural proteins. l-Amino acids have the amino group to the left when the carboxyl group is at the top, as illustrated here. The wedge bonds are above the display plane and the dotted bonds are below the display plane.
eBook - PDF- David Ucko(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
T h e basic unit consists of a triple helix, formed by the twisting of three polypeptide chains. Hemoglobin, the oxygen carrier of the red b l o o d cells, contains four separate chains, each with a h e m e group. Proteins can b e classified according to their shape, solubility in water, and composition as follows: fibrous, globular, and conjugated proteins. O n the basis of function, they can b e divided into enzymes, structural proteins, con-tractile proteins, transport proteins, hormones, storage proteins, protective proteins, and toxins. O n e of the most important properties of a protein is its size; proteins there-fore form colloids rather than solutions. T h e molecule as a whole can b e charged because of its acidic and basic groups. T h e most important chemical reaction of proteins is hydrolysis, the breaking of the peptide bonds by addi-tion of water molecules. Each protein has a normal shape in solution called its native conformation, which is required for activity. Denaturation is the disorganization of this pro-tein structure. It is caused b y heat, organic solvents, acids and bases, metal ions, and oxidizing or reducing agents. Bones and teeth are a unique combination of the protein collagen and the mineral hydroxyapatite. Dental caries produces decalcification, the removal of calcium salts from the tooth structure. er s es er ise s 1. (15.1) Describe an amino acid. What makes one different from another? 2. (15.1) Give an example of an amino acid with (a) a hydroxyl group; (b) a thiol group; (c) an acidic group; (d) a basic group; (e) a nonpolar group; (f) a heterocyclic ring. 3. (15.2) Explain how a zwitterion forms. 4. (15.2) What are essential amino acids? 5. (15.2) Write an equation for the formation of a dipeptide between valine and serine. Draw the structural formulas. 6. (15.3) What is a protein? What is its primary structure? 7. (15.3) Write five isomers of the following tetrapeptide: Gly-Phe-Arg-Ilu.
- Jay A. Glasel, Murray P. Deutscher(Authors)
- 1995(Publication Date)
- Academic Press(Publisher)
This information would probably include the mass of the protein, whether it is a homo- or heteromultimer, its amino acid composition, and its overall shape. With the exception of methods for deter- mining amino acid composition, modern methods for obtaining experimental values for all of these parameters are discussed in this book. In Chapter 9 there is further discussion of analyzing the intramolecular structure of proteins and Chapter I Basic Physical Properties of Proteins and Nucleic Acids 15 nucleic acids by computer methods. The purpose of this section of the intro- ductory chapter is to introduce some fundamental concepts known to underlie all macromolecular structures. As we will see below, the quantitative descriptions of the three-dimen- sional structures of proteins are based on recognizing various different struc- tural motifs whose particular arrangements define each particular protein. For nucleic acids, the overall three-dimensional structural motifs are fewer in num- ber, but within each polydeoxyribonucleotide or polyribonucleotide structure there are subtle structural variants that may have biological importance. An understanding of macromolecular structure is therefore based on understand- ing the descriptions of the structural motifs. These motifs, we shall see, are groups of residues in individual conformations that confer a distinct overall shape to the group. The individual conformation of a residue is described by a set of torsional angles, that is, the angle of rotation about each covalent bond in the molecule (except bonds between heavier atoms and hydrogen atoms). Proteins and nucleic acids have allowed, but sterically constrained, rota- tions about certain covalent bonds. The definitions of the angles have been fixed by international convention (Nomenclature, 1970, 1983).
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