Classification of Amino acids

11 Key excerpts on "Classification of Amino acids"

• 

  eBook - PDF

  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.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Chemistry, 5th Edition

  • 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.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  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.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  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

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Organic and Biological Chemistry

  • H. Stephen Stoker(Author)
  • 2015(Publication Date)
  • Cengage Learning EMEA

    (Publisher)

  9-2 Amino Acids: The Building Blocks for Proteins 357 contains phosphorus, an element very important in the diet of infants and children. Hemoglobin, the oxygen-transporting protein of blood, contains iron. A protein is a naturally occurring, unbranched polymer in which the monomer units are amino acids. Thus the starting point for a discussion of proteins is an understand-ing of the structures and chemical properties of amino acids. ◀ ▶ The word protein comes from the Greek proteios, which means “of first importance.” This reflects the key role that proteins play in life processes. 1. Which of the following sets of four elements are always present in a protein? a. C, H, O, S b. C, H, N, S c. C, H, O, N d. no correct response 2. Proteins are naturally occurring unbranched polymers in which the monomers are a. monocarboxylic acids b. dicarboxylic acids c. amino acids d. no correct response Section 9-1 Quick Quiz Answers: 1. c; 2. c 9-2 Amino Acids: The Building Blocks for Proteins L E A R N I N G F O C U S Be able to draw the generalized structure for an a -amino acid and be able to classify a -amino acids into four categories based on structures and polarity of their side chains. An amino acid is an organic compound that contains both an amino ( ! NH 2 ) group and a carboxyl ( ! COOH) group. The amino acids found in proteins are always a -amino acids. An a -amino acid is an amino acid in which the amino group and the carboxyl group are attached to the a -carbon atom . The general structural formula for an a -amino acid is -Carbon atom Carboxyl group Side chain H O H 2 N R A COOH O A C Amino group The R group present in an a -amino acid is called the amino acid side chain. The nature of this side chain distinguishes a -amino acids from each other. Side chains vary in size, shape, charge, acidity, functional groups present, hydrogen-bonding abil-ity, and chemical reactivity.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  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).

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Genetic Databases

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

    (Publisher)

  nature and the derived portrayal of the relationships of the acids in Fig. 5.1 contains little reflection of the chemistry of the groups - for example, whether a residue is acidic, basic, aromatic or aliphatic. Much effort has, in the past, been invested in such analy-sis and categorization: for example, Sneath, 1966) and has provided the basis for measures of amino acid similarity (McLachlan, 1971) (see Taylor, 1986 for a review). However, irrespective of the quality of the physico-chemical analy-sis, unless the properties are discriminated in the same way within the protein structure (by the protein itself), they will have little predictive value. This prob- N. R. Taylor lem can be seen more simply by reference to Table 5.1, where the scale of size (by atom count) ranges from zero to 10, while the scale of polarity (by number of polar atoms) ranges from zero to three. This, of course, does not imply that size is three times more important to protein structure and function than polar-ity, and the same applies to any physico-chemical measure. 5.3.1 Sequence substitution matrices By observing the degree to which the amino acids exchange over the course of evolution it is possible to extract a rough idea of the relative importance of properties - for example, by counting the frequencies of substitution at equiv-alent sites in homologous proteins. This analysis, however, is indirect and the resulting relationships among the acids can only be interpreted afterwards in terms of physico-chemical properties. Such analysis also suffers from the prob-lem that averages must be made over a wide variety of proteins; and, as was seen above, different properties will acquire different significance depending on the environment in which the protein functions (for example; extracellu-lar/intracellular or thermophilic/mesophilic). This problem also extends to the 'micro-environments' within a protein structure (for example; buried/exposed or secondary structure state).

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Chemistry of Biomolecules, Second Edition

  • S. P. Bhutani(Author)
  • 2019(Publication Date)
  • CRC Press

    (Publisher)

    2  

  Amino Acids, Peptides, and Proteins

  Learning Objectives In this chapter we will study •  Amino Acids, Classification and Stereochemistry •  The Essential Amino Acids •  Synthesis and Reactions of Amino Acids •  Resolution of Racemic Mixture of Amino Acids •  Stereoselective Synthesis of Amino Acids •  Biosynthesis of Amino Acids •  Amino Acids as Dipolar Ions, as Acids and Bases •  Isoelectric Point •  Separation of Amino Acids •  Polypeptides: Nomenclature and Synthesis •  Solid Phase Peptide Synthesis •  Determination of Primary Structure of Peptides

  •  End Group Analysis – Determination of N – terminal and C – terminal Amino Acids

  •  Some Interesting Peptides •  Importance and Biological Functions of Proteins and Polypeptides •  Molecular Shape and Structure of Proteins •  Denaturation of Proteins

  2.1    INTRODUCTION

  The three important groups of biopolymers are polysaccharides, proteins and nucleic acids. We already know the importance of polysaccharides. They act as food reserves in animals and human beings and in plants as structural materials. Proteins are the most abundant organic molecules in animals and human beings. We consume proteins primarily for growth and maintenance. Any balanced diet must contain an adequate amount of proteins. They perform a variety of functions in living organisms. They are the principal material of muscles, skin, tendons, nerves and blood. As enzymes and hormones, proteins catalyse and regulate the reactions that occur in the body; as haemoglobins they transfer oxygen to its most remote corners. Even in plants, where carbohydrates are more abundant as structural materials, proteins are present in those parts that are responsible for growth and reproduction.

  The fundamental structure of proteins is simple. Proteins are biopolymers of α-amino acids. They consist of long chains of α-amino acids bonded to each other by amide bonds also known as peptide linkages between the carboyxlic group of one amino acid with the amino group of another. Thus, proteins are high molecular weight polypeptides. Their molecular weight may range from 5000–100,000 units. A single protein molecule contains hundreds or even thousands of amino acid units. About twenty different amino acids are the building blocks of proteins. The number of different combinations, that is the number of different protein molecules that are possible, is almost infinite.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  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

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Biochemistry

  An Integrative Approach

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

    (Publisher)

  nanantachoke/ShutterStock Just as these building materials are used in constructing office buildings, amino acids are the building blocks of proteins. CHAPTER 3 Proteins I An Introduction to Protein Structure and Function Proteins in Context Throughout history advances in materials have changed tools and how we make them. Ancient civilizations may have used clay pots or made weapons of bronze or iron. In modern times refined alloys of aluminum have been used in applications ranging from cans to aircraft. Perhaps people in the future will mark our current era by the use of plastics or silicon microchips. In biochemistry, we consider proteins to be a wonder material used in thousands of applications. Proteins are polymers of amino acids which have evolved to have numerous distinct functions: they can be structural or catalytic, transmit information, help protect an organism by binding to foreign molecules, provide motility, store amino acids, or transport molecules within the cell or the organism. This chapter begins by discussing amino acids, the building blocks of proteins, then moves on to the basics of protein structure and a brief description of how these macromolecules fold into their specific confor- mations. The chapter ends by examining several different examples of different proteins. These aspects of protein chemistry are discussed in Dynamic Figure 3.1. CHAPTER OUTLINE 3.1 Amino Acid Chemistry 3.2 Proteins Are Polymers of Amino Acids 3.3 Proteins Are Molecules of Defined Shape and Structure 3.4 Examples of Protein Structures and Functions 67 68 CHAPTER 3 Proteins I COMMON THEMES Evolution’s outcomes are conserved. • Mutations to DNA sequences may result in alterations to a protein’s amino acid sequence. The new protein may function normally, have a new and slightly altered function, or be completely nonfunctional. • The amino acid sequence of proteins can help establish the evolutionary relationship between organisms.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Chemical and Functional Properties of Food Proteins

  • Zdzislaw E. Sikorski(Author)
  • 2001(Publication Date)
  • CRC Press

    (Publisher)

  The largest known proteins are composed of nearly 10,000 amino acids. The average molecular weight (MW) of proteinogenic amino acids, cor-rected for the proportions in which the various amino acids occur in proteins, is 128 Da, and that of an amino acid residue in protein is 110 Da (water is re-moved when a peptide bond is formed). Therefore, the MW of proteins ranges 35 36 PROTEIN STRUCTURE AND PHYSICOCHEMICAL PROPERTIES from 10 kDa to more than 1000 kDa. The fact that proteins are relatively large amphoteric molecules is of crucial importance to their behavior in aqueous solutions. The aim of this chapter is to introduce the reader to the main aspects of pro-tein structural organization. Special emphasis has been put on the molecular basis of classification, physical properties, and chemical reactivity of proteins. Several systems of protein classification based on their structural, functional, or physicochemical properties have been elaborated. A few of them, probably the most popular, are presented below. 3.2. CLASSIFICATION OF PROTEINS 3.2.1. CLASSIFICATION IN RESPECT TO PROTEIN SOLUBILITY Protein solubility was historically the first criterion taken as a basis of the classification system. It was originally introduced when not too much infor-mation on protein structure was available, and nowadays it is supported by structural data. In this system, proteins are divided into five groups. Albumins are readily soluble in water and diluted salt solutions. The amino acid composition of these proteins is not characteristic, although acidic amino acids usually dominate in their structures. Albumins are widely distributed in the body fluids of all organisms. Most are involved in the regulation of osmotic pres-sure or transport processes. Blood serum albumin, egg albumin, or ricin from castor beans may serve as examples of proteins belonging to this class. Globulins are poorly soluble in water but readily soluble in diluted salt so-lutions (salting-in).

  Sign up to read

  Learn more about book