Amino Acid Groups
Amino acids are classified into different groups based on the properties of their side chains. The main groups include nonpolar, polar uncharged, acidic, and basic amino acids. Nonpolar amino acids have hydrophobic side chains, while polar uncharged amino acids have hydrophilic side chains. Acidic amino acids have a negative charge at physiological pH, and basic amino acids have a positive charge.
8 Key excerpts on "Amino Acid Groups"
eBook - ePub- David Hames, Nigel Hooper(Authors)
- 2011(Publication Date)
- Taylor & Francis(Publisher)
...SECTION B – AMINO ACIDS AND PROTEINS B1 Amino acid structure Key Notes Amino acids All proteins are made up from the same set of 20 standard amino acids. A typical amino acid has a primary amino group, a carboxyl group, a hydrogen atom and a side-chain (R group) attached to a central α-carbon atom (C α). Enantiomers Amino acids with four different groups arranged tetrahedrally around the C α atom can exist in either the D or L configuration. These two enantiomers are nonsuperimposable mirror images that can be distinguished on the basis of their different rotation of plane-polarized light. Only the L isomer is found in proteins. The 20 standard amino acids The different side-chains or R groups display different physicochemical properties. They may be polar, acidic, basic, aromatic, bulky, conformationally inflexible, able to form hydrogen bonds, able to cross-link and be chemically reactive. Glycine (Gly, G) has a hydrogen atom as its R group. Alanine (Ala, A), valine (Val, V), leucine (Leu, L), isoleucine (Ile, I) and methionine (Met, M) have aliphatic side-chains of differing structures that are hydrophobic and chemically inert. The aromatic side-chains of phenylalanine (Phe, F), tyrosine (Tyr, Y) and tryptophan (Trp, W) are also hydrophobic in nature. The conformationally rigid proline (Pro, P) has its aliphatic side-chain bonded back on to the amino group and thus is really an imino acid. The hydrophobic, sulfur-containing side-chain of cysteine (Cys, C) is highly reactive and can form a disulfide bond with another cysteine residue. The basic amino acids arginine (Arg, R) and lysine (Lys, K) have positively charged side-chains, whilst the side-chain of histidine (His, H) can be either positively charged or uncharged at neutral pH. The side-chains of the acidic amino acids aspartic acid (Asp, D) and glutamic acid (Glu, E) are negatively charged at neutral pH...
eBook - ePub- Raymond S. Ochs(Author)
- 2021(Publication Date)
- CRC Press(Publisher)
...=PLGO-SEPARATOR=--]9.11 10.07 Valine val V 2.29 9.74 5.3.1 Polarities The overall polarity of amino acids depends on their R groups. Figure 5.4 shows the structures of the polar amino acids. We can further subdivide them into three categories: neutral, acidic, and basic. Figure 5.5 shows the nonpolar amino acids, which are further divided into alkyl chains, branched-chains, aromatics, and a pair of unique nonpolar structures. FIGURE 5.4 Polar amino acids. Three subdivisions shown are: acidic, basic, and neutral. FIGURE 5.5 Nonpolar amino acids. Three major subdivisions are: alkyl, branched-chain, and aromatic. Methionine and proline are the single examples of a thioether and secondary amine, respectively. 5.3.2 Functional Groups Figure 5.6 presents a chemical categorization of some of the amino acids. Here, acids include not only aspartate and glutamate, but also cysteine, histidine, and tyrosine, as these can act as acids under some biological conditions. All of the pK values of the side chains of these acids are shown in Table 5.2. The bases shown in Figure 5.6 are lysine, arginine, and histidine. The duplicate categorization of histidine means that it can act as both an acid and a base. To understand this phenomenon, consider first the side chain alone, which is an imidazole ring: FIGURE 5.6 Functional groups in amino acids. A cross-categorization of amino acids that groups together all acids, bases, and hydroxyl groups. Cysteine and methionine are single examples of the functional groups of sulfhydryl groups and thioether, respectively. (5.1) Protonation of the neutral histidine ring at the left side produces a resonance-stabilized intermediate with electrons spread over both nitrogens of the ring and the carbon atom between them. Dissociation of this intermediate can proceed either by reversal of the first equilibrium or by loss of a proton from the other nitrogen to produce the molecule on the right side of Equation (5.1)...
eBook - ePub- Lars Backman(Author)
- 2019(Publication Date)
- De Gruyter(Publisher)
...If going from the group with highest priority to the next in rank is clockwise, the chiral center has an R-configuration (R for rectus, Latin for right). If the order is counter-clockwise, the chiral center has an S-configuration (S for sinister, Latin for left). Thus, the α-carbon in the l -α-amino acid in Figure 3.5 has an S-configuration. In fact, all but one (cysteine) of the α-amino acid has an α-carbon in the S-configuration. 3.1 Twenty different α-amino acids Since three of the substituents bound the α-carbon are the same, it is obvious that different chemical and physical properties of each of the 20 α-amino acids depend on the side chain. The size of the side chain differs; the smallest side chain is only a proton (–H). Some side chains contain a carboxyl or an amino group, and can be ionized depending on the pH of the solvent. Some side chains are very nonpolar, whereas others are polar, which will influence their solubility in water. Some contain a conjugated ring system, giving them useful optical properties. Some side chains are branched. The 20 amino acids are usually classified as nonpolar, polar-uncharged, polar-charged or aromatic. It should be noted that some amino acids fit in more than one group; a nonpolar-uncharged amino acid may have some polar properties (Figure 3.6). 3.1.1 Nonpolar amino acids The nonpolar amino acids are glycine (Gly; G), alanine (Ala; A), valine (Val; V), leucine (Leu; L), isoleucine (Ile; I), methionine (Met; M) and proline (Pro; P). These amino acids are characterized by an aliphatic side chain of varying length whose hydrophobicity increases with increased chain length. The side chains of these amino acids cannot participate in hydrogen bonding and have a propensity to avoid contact with water. Therefore, the amino acids of this group are usually found in the interior of proteins, shielded from water contact...
eBook - ePubBiochemistry
An Organic Chemistry Approach
- Michael B. Smith(Author)
- 2020(Publication Date)
- CRC Press(Publisher)
...11 Amino Acids There is an important class of difunctional molecule that is critical to an understanding of biological processes. Amino acids comprise the backbone of peptides, and thereby of enzymes. This chapter will discuss the structure, nomenclature, and characteristics of amino acids. 11.1 Characteristics of Amino Acids An amino acid, as the name implies, has one amine unit (–NR 2) and one carboxylic acid unit (a carboxyl group, COOH). The nomenclature for a generic amino acid is dominated by the carboxyl, so the parent name is “acid” and the NR 2 unit is treated as a substituent. When an amine unit is a substituent the name “amino” is used, so these compounds are amino carboxylic acids, or just amino acids. Amino acids are easily named using IUPAC nomenclature and the carboxylic acid is the parent for each new compound. Two examples are 2-aminopropanoic acid (known as alanine) and 5-amino-3,5-dimethylheptanoic acid. There are a variety of structural variations for amino acids. If the amine unit is attached to C2, the α-carbon of the carboxylic acid chain, the compound is an α-amino acid. If the amine group is on C3, the β-carbon it is a β-amino acid. Similarly, there are γ-amino acids, δ-amino acids, and so on. Due to their biological importance, α-amino acids will be discussed most of the time. The common names of α-amino acids are presented in Table 11.1 in Section 11.2. To distinguish α-amino acids from other amino acids, the term non-α-amino acids is used. 5-Amino-3,5-dimethylheptanoic acid is a non-α-amino acid, for example. Table 11.1 Structures, Names, Three-Letter Code and One-Letter Code of the 20 Essential Amino Acids, Based on the Structure in Figure 11.5 R Name Three-Letter Code One-Letter...
eBook - ePubBiochemistry Explained
A Practical Guide to Learning Biochemistry
- Thomas Millar(Author)
- 2018(Publication Date)
- CRC Press(Publisher)
...4 Amino Acids and their Functions In this chapter you will learn: the functional groups: an amine and carboxyl groups to understand the general structure of amino acid the structures, names and single letter symbols for the 20 amino acids found in proteins how 2 cysteines may be oxidised to form the bridging amino acid cystine how the carbons of amino acids are named or numbered the terms ampholyte and zwitterion and how these relate to amino acids the structure of an amide bond and the special case a peptide bond special functions of amino acids (e.g. neurotransmitters) and structural relationships between amino acids how ketones are formed from amino acids by removing ammonia from the αC the synthesis of the bioactive amines dopamine, noradrenaline, adrenaline and serotonin. to understand the basis for Parkinson’s disease and phenylketonuria that tyrosine, serine and threonine are phosphorylation sites in proteins the importance of decarboxylation in the formation of some active amines such as histamine how sugars may attach to the amino acids serine, threonine and asparagine Basic structure and nomencalture of amino acids The name amino acid suggests that these structures have an amine and an acid group. Indeed this is true; amino acids have an amino group and a carboxylic acid. The structure of a typical L-amino acid is illustrated below. This type of amino acid is the basis of proteins. Q&A 1 : Draw the chemical structures of a carboxylic acid, and an amine group. There is a central carbon that has bonds to an amine group, a carboxylic acid, an hydrogen and a variable R group. Since this central carbon has 4 different groups attached to it, it is a chiral carbon and hence there are 2 possible isomers, L and D. Nearly all amino acids in biochemistry are of the L-form (L for life). Note that this is the opposite of sugars, which nearly always occur as the D isomer. You need to learn their structure in this orientation...
eBook - ePub- J Fisher, J.R.P. Arnold, Julie Fisher, John Arnold(Authors)
- 2020(Publication Date)
- Taylor & Francis(Publisher)
...The configuration of the naturally occurring α-amino acids is L (Section E2). The amino acids differ in the nature of their side chain ‘R’: The side chain may be polar, nonpolar, positively charged or negatively charged (Section L1). The properties of ‘R’ dictate the structure of the protein and hence its function (see below). The polymerization process involves the ‘condensation’ (loss of water) of a free amino group of one amino acid and a free carboxyl group of another to form a peptide bond (Section L1), which generally has a trans, planar geometry (Section E2): The polymerization process occurs such that the first amino acid in the final protein will have a free amino group (or N-terminal) and the last, a free carboxyl (or C-terminal) group. Protein structure Proteins are long chain molecules that in some instances contain several hundred amino acids; it is not surprising therefore that they do not generally exist in an extended chain form. Rather these polymers fold. Polypeptide chains fold in a variety of ways and in doing so enable favorable interactions between backbone (amide) or side chain atoms and remove unfavorable interactions, such as those between like charges or hydrophobic side chains (Sections H1 and H2) and water, the solvent. Thus, in describing a protein it is not sufficient to simply know the amino acid composition; the sequence, which dictates the folding, must also be known. The sequence of the amino acids, with residue ‘1’ the N-terminal residue (see above), is referred to as the primary structure (Figure 1a). From this, together with knowledge of the ‘state’ of cysteine residues (Section L1) it is possible to predict, with varying degrees of success, where folds in the molecule may occur, i.e. the location of secondary structure elements (Section H1 and Figure 1b)...
eBook - ePub- 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 B 6, vitamin B 12, 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...
eBook - ePub- S. P. Bhutani(Author)
- 2019(Publication Date)
- CRC Press(Publisher)
...That means they have the same relative configuration as L -glyceraldehyde. As the two functional groups present in amino acids are acidic and basic, all amino acids are amphoteric and actually exist as zwitterions. Thus, the simplest amino acid glycine exists in the form shown below rather than aminoacetic acid. H 2 N—CH 2 — COOH ⇄ H 3 N + — CH 2 — CO O ¯ Aminoacetic acid Zwitterion 2.3 CLASSIFICATION OF AMINO ACIDS The 22 α-amino acids that are obtained from proteins can be classified into four different groups on the basis of the structures of their side chains: 1. Neutral Amino Acids 2. Acidic Amino Acids 3. Neutral Amino Acids with Polar Side Chains 4. Basic Amino Acids These are listed with their symbols, abbreviations and structures in Table 2.1. Only 20 of the 22 amino acids listed in Table 2.1 are actually used by cells when they synthesise proteins. Hydroxyproline is synthesised from proline and cystine is synthesised from cysteine. Asparagine and glutamine are derived from aspartic acid and glutamic acid. TABLE 2.1 Amino Acids Commonly Found in Proteins 2.4 THE ESSENTIAL AMINO ACIDS Amino acids are synthesised by all living organisms, animals and plants for their protein requirements. The biosynthesis of proteins requires the presence of all the constitutent amino acids. If one of the 20 amino acids is missing or in short supply, protein biosynthesis is inhibited. Some organisms, such as E.Coli can synthesise all the amino acids that they need. However, the human body is unable to synthesise some of these amino acids required for making proteins. These are called essential amino acids. For adult humans there are ten amino acids, which have been designated with the superscript e in Table 2.1. They must be included in our diet. We eat proteins, break them down in our body to their constituent amino acids and then use some of these amino acids to build up other proteins which we require to maintain good health...
