Chemistry
Alpha Amino Acids
Alpha amino acids are organic compounds that serve as the building blocks of proteins. They contain both an amino group and a carboxylic acid group, with the amino group attached to the carbon atom adjacent to the carboxyl group. This arrangement gives them the "alpha" designation. There are 20 standard alpha amino acids commonly found in proteins, each with a unique side chain.
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11 Key excerpts on "Alpha Amino Acids"
- 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.
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 - PDF- David R. Klein(Author)
- 2016(Publication Date)
- Wiley(Publisher)
Amino acids of this type are called α-amino acids because the amino group is connected to the car- bon atom that is alpha (α) to the carboxylic acid group. Notice that this α carbon is a chiral center, provided that the R group is not simply a hydrogen atom. The configuration of the α position will be discussed in the coming sections. Amino acids are coupled together by amide linkages, also called peptide bonds: Peptide bonds N C N C N O O R R C H H R O H 25.2 Structure and Properties of Amino Acids 1149 Relatively short amino acid chains are called peptides. A dipeptide is formed when two amino acids are coupled together, a tripeptide from three amino acids, a tetrapeptide from four, and so on. Chains comprised of fewer than 40 or 50 amino acids are often called polypeptides, while still larger chains are called proteins. Proteins serve a wide array of important biological functions, as we will discuss in the final section of this chapter. Certain proteins, called enzymes, serve as catalysts for most of the reactions that occur in living cells, and it is estimated that more than 50,000 different enzymes are needed for our bodies to function properly. In order to understand the structure and function of proteins, we must first explore the structure and properties of the most basic building blocks, amino acids. 25.2 Structure and Properties of Amino Acids Naturally Occurring Amino Acids Hundreds of different amino acids are observed in nature, but only 20 amino acids are abundantly found in proteins. These twenty α-amino acids differ from each other only in the identity of the side chain (the R group, highlighted). H N H C C R O OH H The structures of all 20 amino acids are shown in Table 25.1, together with the accepted three-letter abbreviation and one-letter abbreviation for each amino acid. Except for glycine (R = H), all of these amino acids are chiral, and nature typically employs only one enantiomer of each.
eBook - PDF- Allan Blackman, Steven E. Bottle, Siegbert Schmid, Mauro Mocerino, Uta Wille(Authors)
- 2022(Publication Date)
- Wiley(Publisher)
CHAPTER 24 Amino acids, peptides and proteins LEARNING OBJECTIVES After studying this chapter, you should be able to: 24.1 define the structure of amino acids 24.2 control the charge present on amino acids using pH 24.3 describe the linking of amino acids together to make peptides and proteins 24.4 categorise protein structures as 1°, 2°, 3° or 4° 24.5 explain the functional importance of the three-dimensional shape of proteins 24.6 exploit chemical and physical processes to change protein properties. Amino acids are molecules that contain both an amine functional group (described in the chapter on alcohols, amines and related compounds) and a carboxylic acid functional group (described in the chapter on carboxylic acids). Amino acids are important in their own right, but they are also critically important for life as they provide the building blocks of peptides and proteins. In this chapter we will look at the acid– base properties of amino acids, as these control much of the nature of peptides and proteins. Understanding the chemistry of amino acids allows us in turn to understand the more complex structures and properties of peptides and proteins. Proteins are among the most important of all biological compounds as they are integrally important in the vital functions of: • movement: muscle fibres are made of proteins called myosin and actin • catalysis: virtually all 1that take place in living systems are catalysed by a special group of proteins called enzymes • structure: structural proteins such as collagen and keratin are the chief constituents of skin, bones, hair and fingernails • transport: the protein haemoglobin is responsible for the transport of oxygen from the lungs to tissues, while other proteins transport molecules across cell membranes • protection: a group of proteins called antibodies represent one of the body’s major defences against disease. Peptides are a major component of the supplements and health food sector.
eBook - PDF- Ulo Langel, Benjamin F. Cravatt, Astrid Graslund, N.G.H. von Heijne, Matjaz Zorko, Tiit Land, Sherry Niessen(Authors)
- 2009(Publication Date)
- CRC Press(Publisher)
Amino Acids 7 one-letter abbreviations are used to record the amino acid sequences of proteins and larger peptides, while the three-letter codes are more common for most other pur-poses; the same convention will be employed in this book. 1.1.1 G ENERAL P ROPERTIES All standard amino acids are α -amino acids with the general structure: H 2 N COOH R H C * (1.1) They differ only in terms of the radical R, which is also called the amino acid side chain. According to their chemical nature, amino acids are usually divided into those with the hydrophobic aliphatic, the hydrophilic uncharged, the hydrophilic charged, and the aromatic radical. In all standard amino acids except Gly, the α -carbon atom denoted in Equation 1.1 with an asterisk is asymmetric and in the l-form. Chirality is important in the three-dimensional structures of peptides and proteins, and particularly in the inter-actions with other molecules. It also results in optical activity—the ability to rotate linearly and circularly polarized light. The amount of rotation (i.e., the angle of rota-tion) depends on the concentration of the chiral molecule and other factors, including the temperature and the wavelength of the light employed. This makes it possible to determine high concentrations of free amino acids in solutions by polarimetric methods and is the basis of circular dichroism, a method for analyzing the secondary structure of peptides and proteins (see Chapter 13). Free in solution, pure l-amino acids are subjected to a very slow racemization into an equimolar mixture of both l- and d-enantiomers. The process is dependent on the pH, temperature, and struc-ture of the radical. The racemization of l-Asp, for instance, would take around 3500 years in a neutral pH and at 25 ° C, but it is approximately 100 times faster at 100 ° C.
eBook - PDF- BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
- 2013(Publication Date)
- Butterworth-Heinemann(Publisher)
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). A hydrogen atom is also attached to the -carbon atom, as well as a fourth group, known collectively as a sidechain or R-group. It is through the structure of this sidechain that differences in amino acids arise. The simplest sidechain consists of a hydrogen atom (R=H), giving the amino acid glycine. The types of sidechains will be discussed shortly. COOH a 1 H 2 N~C-H I R Figure 2.1 The general structure of a- amino acids. The sidechain, which is different in different amino acids, is shown by the letter R. 18 Chapter 2 So far, we have depicted an -amino acid as 2-dimensional. In reality, it is of course 3-dimensional. Carbon has a valency of 4, meaning that it can form 4 single covalent bonds with other atoms. When a carbon atom does have 4 substituent groups, the bonds will be evenly distributed in space: the bonds will point to the four corners of a tetrahedron tetrahedron, with the -carbon atom at the centre of tetrahedron. A widely used way of describing chemical structures is by ball-and-stick models. If we do this for a-amino acids, and we symbolise each substituent group of the -carbon atom by a different coloured ball (-NH2, -COOH, -H and -R), we find that we can draw two structures.
eBook - PDF- David R. Klein(Author)
- 2020(Publication Date)
- Wiley(Publisher)
The relationship between structure and activity is perhaps most striking for biological molecules called proteins. Proteins are polymers that are assembled from amino acid monomers that have been linked together, much like jigsaw puzzle pieces (Figure 25.1). Each amino acid contains an amino group and a carboxylic acid group. FIGURE 25.1 An illustration showing how amino acids serve as building blocks for proteins. H N H C C R O OH H Amino acid H N H C C R O OH H Amino acid Protein N H C C R O H N H C C R O H N H C C R O H OH C C R O H N H H N H C C R O H It is the presence of these two functional groups that enables amino acids to link together. An amino acid can have any number of carbon atoms separating the two functional groups, but of particular interest are the alpha (α) amino acids in which the two functional groups are separated by exactly one carbon atom. H N H C C R O OH H COOH R H 2 N An α-amino acid Functional groups are separated by only one carbon atom. Amino acids of this type are called α-amino acids because the amino group is connected to the car- bon atom that is alpha (α) to the carboxylic acid group. Notice that this α carbon is a chiral center, provided that the R group is not simply a hydrogen atom. The configuration of the α position will be discussed in the coming sections. Amino acids are coupled together by amide linkages, also called peptide bonds: Peptide bonds N C N C N O O R R C H H R O H 1140 CHAPTER 25 Amino Acids, Peptides, and Proteins Relatively short amino acid chains are called peptides. A dipeptide is formed when two amino acids are coupled together, a tripeptide from three amino acids, a tetrapeptide from four, and so on. Chains comprised of fewer than 40 or 50 amino acids are often called polypeptides, while still larger chains are called proteins. Proteins serve a wide array of important biological functions, as we will discuss in the final section of this chapter.
eBook - PDFHandbook of Food Analysis
Volume 1: Physical Characterization and Nutrient Analysis
- Leo M.L. Nollet(Author)
- 2004(Publication Date)
- CRC Press(Publisher)
The molecular mass and structure of all these amino acids are compiled in Tables 1 , 2 , and 3 . All amino acids, except proline, contain one primary amino group (-NH 2 ) in the position in relation to the carboxy group (-COOH). Each amino acid has a characteristic side chain (R group), which has a strong influence on its physicochemical properties. So, amino acids are usually grouped according to the polarity of this group (nonpolar or hydrophobic side chains, polar or hydro-philic side chains, positively or negatively charged groups). The stereochemical L isomer is the most usual form in nature and, in practice, all amino acids found in hydrolyzates from animal and vegetable proteins are isomers of the L form. The D isomers may be found in some specific cases like in the cell walls of certain microorganisms and polypeptides with antibiotic action. II. WHY ANALYZE FOR AMINO ACID CONTENT? A. Nutritional Purposes Amino acids constitute essential components in the living cell, being necessary either in their free form or forming part of proteins. Amino acids are generally supplied in foods and/or may be synthesized through different metabolic pathways from other amino acids inside the organism. As mentioned above, some of these amino acids, known as essential amino acids, cannot be synthesized in the organism and must be supplied in the diet. In addition, some amino acids are essential at certain ages, like infancy, or in total parenteral nutrition. The importance of amino acid analysis, in order to obtain a good knowledge of the 83 amino acid composition of a particular protein, food, or diet, is thus evident. Furthermore, the knowledge of a limiting amino acid is also very important in basic foods or when designing foods for populations with specific dietary needs such as the elderly or infants. Accurate compositional data for all the amino acids is essential for assessing the nutritional quality of infant formulas.
eBook - PDF- William H. Brown, Thomas Poon(Authors)
- 2017(Publication Date)
- Wiley(Publisher)
Without enzymes, these many reactions would take place so slowly as to be useless. 18.1 596 C H A P T E R 1 8 Amino Acids and Proteins ● Movement —Muscle expansion and contraction are involved in every movement we make. Muscle fibers are made of proteins called myosin and actin. ● Transport —A large number of proteins perform transport duties. The protein hemo- globin is responsible for the transport of oxygen from the lungs to tissues. Other pro- teins transport molecules across cell membranes. ● Hormones —Many hormones are proteins, including insulin and human growth hormone. ● Protection —The production of a group of proteins called antibodies is one of the body’s major defenses against disease. The function of the protein fibrinogen is to promote blood clotting. ● Regulations —Some proteins not only control the expression of genes, thereby regulat- ing the kind of protein synthesized in a particular cell, but also dictate when such syn- thesis takes place. Proteins have other functions as well. Even this brief list, however, should convince you of their vital role in living organisms. A typical cell contains about 9,000 different proteins. 18.2 What Are Amino Acids? A. Structure An amino acid is a compound that contains both a carboxyl group and an amino group. Although many types of amino acids are known, the α‐amino acids are the most significant in the biological world because they are the monomers from which proteins are constructed. A general structural formula of an α‐amino acid is shown in Figure 18.1. Although Figure 18.1(a) is a common way of writing structural formulas for an amino acid, it is not accurate because it shows an acid ( COOH) and a base ( NH 2 ) within the same molecule. These acidic and basic groups react with each other to form an internal salt (a dipolar ion) [Figure 18.1(b)]. This internal salt is given the special name zwitterion. Note that a zwitterion has no net charge; it contains one positive charge and one negative charge.
eBook - PDFAmino Acid
New Insights and Roles in Plant and Animal
- Toshiki Asao, Md. Asaduzzaman, Toshiki Asao, Md. Asaduzzaman(Authors)
- 2017(Publication Date)
- IntechOpen(Publisher)
In bacteria, d-amino acids are involved in the synthesis and cross-linking of peptidoglycan [ 4]. In humans, amino acids participate in various physiological processes, such as skeletal mus -cle function, atrophic conditions, sarcopenia, and cancer. They play key roles in cell signal-ling, homeostasis, gene expression, synthesis of hormones, phosphorylation of proteins and © 2017 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. also possess antioxidant abilities [ 2, 5]. Amino acids are also key precursors in the synthesis of low molecular weight nitrogenous compounds, which have numerous biological importance. The existence of amino acids and their metabolites, such as glutathione, polyamines, taurine, sero-tonin and thyroid hormones, in physiological amounts is important for proper body functions [ 5]. Traditionally, amino acids were classified as essential and nonessential amino acids [ 5]. However, another class known as conditionally essential amino acids now exists. These clas -sifications are based on whether the body is able to synthesise the amount that it needs for metabolic maintenance [ 1]. Essential amino acids are those that cannot be synthesised or those that are synthesised inadequately by the body relative to needs and hence must be obtained from diets to meet physiological requirements. Amino acids which the body can synthesise in sufficient amounts to meet the body’s maximum requirements are known as nonessential amino acids. Conditionally essential amino acids are those which the body can synthesise in adequate amounts, but under situations of higher utilisation rate, the body obtains them from diets in order to meet optimal requirements [ 5].
eBook - PDFSecondary Plant Products
A Comprehensive Treatise
- E. E. Conn(Author)
- 2013(Publication Date)
- Academic Press(Publisher)
Nonprotein Amino Acids L. FOWDEN 8 I. Introduction 215 II. Chemistry and Biogenesis 218 A. Acidic Amino Acids 219 B. Imino Acids 222 C. Basic Amino Acids 225 D. β-Substituted Alanines 226 E. Branched-Chain and Cyclopropyl Amino Acids 228 III. Nonprotein Amino Acids as Indexes for Chemotaxonomy . . . 232 IV. Nonprotein Amino Acids as Analogues and Antimetabolites . . 236 A. Amino Acid Uptake 237 B. Analogues and Amino Acid Biosynthesis 238 C. Analogues and Aminoacyl-tRNA Synthetases 242 V. Concluding Remarks 246 References 246 I. INTRODUCTION The characteristic properties of an amino acid are conferred by carboxyl and amino groups which are features of all compounds of this type (see Larsen, this series, Vol. 5, Chapter 6). The possession of an amino group places these compounds among the nitrogenous constituents of plants. Of the elements essential for plant growth, nitrogen tends to have a special position, for it is the element among those taken up by root systems whose partial deficiency most frequently causes stunted growth. The reasons for this must lie partly in the very ramified pathways by which nitrogen is assimilated to produce a great variety of cell constituents including proteins, nucleic acids, chlorophyll, and certain growth hormones—all indispensible components of The Biochemistry of Plants, Vol. 7 215 Copyright © 1981 by Academic Press, Inc. All rights of reproduction in any form reserved. ISBN 0-12-675407-1 216 L. Fowden living plants. It is then a little surprising that many plants channel nitrogen, sometimes in substantial amounts, into compounds that seem to be of sec-ondary importance, and that they continue to do this when the plant's supply of nitrogen is less than optimal. Such compounds include alkaloids (the most numerous class of plant nitrogenous compounds), cyanogenic glucosides and glucosinolates, and about 200 amino acids which occur only free or as simple peptides in plants and not as constituents of protein.
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