Amino Acid Polarity
Amino acid polarity refers to the distribution of electric charge within the molecule. Amino acids can be classified as polar, nonpolar, or charged based on the nature of their side chains. This polarity influences the interactions between amino acids and other molecules, impacting their solubility, structure, and function in biological systems.
8 Key excerpts on "Amino Acid Polarity"
eBook - ePub- David P. Clark(Author)
- 2009(Publication Date)
- Academic Cell(Publisher)
...The major division is between those with hydrophilic (water-loving) and those with hydrophobic (water-hating) R-groups. Glycine has only a single hydrogen atom as its side chain, so it does not really fit into either group. Figure 7.03 The Twenty Amino Acids Found in Proteins Amino acids can be grouped by their physical and chemical properties. The R-group for each amino acid is highlighted. alpha- (α-) carbon Central carbon atom of an amino acid that carries both the amino group and the carboxyl group amino acid Monomer from which polypeptide chains are built amino- or N-terminus The end of a polypeptide chain that is made first and that has a free amino group carboxy- or C-terminus The end of a polypeptide chain that is made last and has a free carboxy-group. dipolar ion Same as zwitterion; a molecule with both a positive and a negative charge glycine The simplest amino acid peptide bond Type of chemical linkage holding amino acids together in a polypeptide chain polypeptide chain A polymer that consists of amino acids R-group Any unspecified chemical group; in particular the side chain of an amino acid zwitterion Same as dipolar ion; a molecule with both a positive and a negative charge The twenty amino acids that comprise proteins vary greatly in their chemical and physical properties. The hydrophilic amino acids may be subdivided into basic, acidic and neutral. Basic amino acids contribute a positive charge to the protein whereas acidic residues provide a negative charge. Strictly, this refers to the situation in solution within the physiological pH range. Neutral polar residues have side chains that are capable of forming hydrogen bonds. The side chains of the hydrophilic amino acids carry chemical groups that can take part in reactions...
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- 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 - ePubBiochemistry Explained
A Practical Guide to Learning Biochemistry
- Thomas Millar(Author)
- 2018(Publication Date)
- CRC Press(Publisher)
...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. Remember that the L designation has nothing to do with the way they rotate polarised light, but is purely structural. This is based on the structure of L-glyceraldehyde. Although it is not important to remember this transposition, it is important to remember the amino acids in the L form. To do this, remember the notation that in the flat projection the horizontal arms are coming out to hug you – out of the page. Drawn the way illustrated, the mnemonic co-r-n forms. This is an L amino acid The next part is confusing so pay attention. To number the carbon atoms, C1 is the carbon of the carboxyl group, C2 is the chiral carbon and C3 (or more) is on the R group. However, the chiral carbon is also called the α-carbon. Hence the amino acids we commonly deal with are α-amino acids (they have a carboxyl group and an amine group attached to the α-carbon). The ß carbon is C3 (the first carbon in the R group). With this system of naming, the carbon of the carboxyl group (C1) is referred to as the carbon of the α carboxyl group (the carboxyl group attached to the αC). At pH 7.4, which is the normal pH of the body, this has lost its proton (hydrogen ion) and has a negative charge with the electrons of the double bond shared across the two O atoms. Also attached to the αC is an amine group that at pH 7.4 has an extra proton and so carries a positive charge. Therefore at normal pH, amino acids carry a positive charge on their amine group and a negative charge on their carboxyl group...
eBook - ePubBiochemistry
An Organic Chemistry Approach
- Michael B. Smith(Author)
- 2020(Publication Date)
- CRC Press(Publisher)
...As the groups on the α-carbon of an amino acid change, each new amino acid residue may have a different p K a 1 value and therefore a different isoelectric point. As a practical matter, this means the isoelectric point for each different amino acid is a function of its structure. 11.2 Structure of α-Amino Acids The chemistry of DNA is presented in Sections 15.6 and 15.7. The chemistry of DNA includes the genetic code that provides a set of instructions for the formation of proteins (Section 12.5), which are made up of amino acids linked together in a way that forms a polymer. The genetic code utilizes primarily ~20 α-amino acids, so this discussion is limited to those compounds. Examination of any α-amino acid shows that the α-carbon is a stereogenic center, so α-substituted amino acids are chiral molecules. It is known that the 20 amino acids most commonly found in proteins have the (S) absolute configuration for the α-carbon. Note that the so-called nonessential amino acids are synthesized by mammals, while the essential amino acids must be obtained from dietary sources. All of the 20 amino acids commonly found in proteins contain a hydrogen atom and one alkyl group at the α-carbon rather than two alkyl groups. There is a compound called glyceraldehyde [HOCH 2 CH(OH)CHO], which is drawn using as the usual line notation in Figure 11.4, and also in Fischer projection. If glyceraldehyde is adjusted so the hydroxyl group and the hydrogen atom re projected in front of the page (on the horizontal line), with the CHO group and the CH 2 OH group projected behind the page (on the vertical line), the result is a Fischer projection is obtained...
eBook - ePub- 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...
eBook - ePubWheat
Chemistry and Utilization
- Hugh Cornell, Albert W. Hoveling(Authors)
- 2020(Publication Date)
- CRC Press(Publisher)
...From thermodynamic data, glutamine can be regarded as having the most hydrophilic (polar) side chain. The large hydrocarbon side chain of isoleucine is, of course, the reason for its hydrophobicity. Leucine, tyrosine, tryptophan, and phenylalanine also have high hydrophobicity. The ionic form in which the amino acids exist in solution is governed by the pH of the solution and the pI of the amino acid. Neutral amino acids, such as glycine, are protonated readily in dilute acid and deprotonated in dilute alkali, as shown below: The pI can be calculated from: pI = 1 2 (p K a 1 + p K a 2) when pKa 1 and pKa 2 are the acidity constants for the carboxyl and amino groups, respectively. These values are 2.35 and 9.78 in the case of glycine, giving a pI of 6.07. With basic amino acids, the pKa values of the basic side chain, the α-amino group, and the carboxyl group all need to be considered, although the influence of the carboxyl group is negligible, hence the pI of arginine is: pI = 1 2 (9.04 + 12.48) = 10.76 The pKa of the carboxyl group (2.02) can be neglected for all practical purposes. Likewise, with an acidic amino acid such as glutamic acid, only the pKa values for the carboxyl group and the side-chain carboxyl group need to be taken into account; thus for this amino acid: pI = 1 2 (2.25 + 4.07) = 3.16 In the case of a neutral amino acid such as glycine, if the pH of the solution is 2 units or more below the pKa of the carboxyl group, this group is almost entirely unionized. However, the amino group is almost fully ionized, hence the molecule carries a net charge of + 1. The charge on the molecule at pH 6 is, of course, zero, while at pH values above 8, the molecule carries a net charge of − 1. For acidic amino acids such as glutamic acid, the net charge at pH 1 would be + 1, at pH 3.2 it would be zero, while at pH 6 it would be − 1. At pH 12 the pH is more than 2 units above the pKa of the amino group, hence the —NH 2 group is unionized and the net charge would be −2...
eBook - ePub- Jacob N. Israelachvili(Author)
- 2010(Publication Date)
- Academic Press(Publisher)
...4 Interactions Involving Polar Molecules 4.1 What Are Polar Molecules? Most molecules carry no net charge, but many possess an electric dipole. For example, in the HCl molecule the chlorine atom tends to draw the hydrogen’s electron toward itself, and this molecule therefore has a permanent dipole. Such molecules are called dipolar or simply polar molecules. The dipoles of some molecules depend on their environment and can change substantially when they are transferred from one medium to another, especially when molecules become ionized in a solvent. For example, the amino acid molecule glycine contains an acidic group on one side and a basic group on the other. In water at neutral pH, the NH 2 group acquires a proton and the OH group loses a proton to the solution to produce a dipolar molecule: Quite often the magnitude of the positive and negative charges are not the same, and these molecules therefore possess a net charge in addition to a dipole. Such molecules are then referred to as dipolar ions. Polarity can also arise from internal charge displacements within a molecule, producing zwitterionic molecules or groups. In larger molecules, or “macromolecules,” such as proteins the net dipole moment is usually made up of a distribution of positive and negative charges at various locations of the molecules. It should already be apparent that the interactions and the solvent effects of polar molecules can be very complex. The dipole moment of a polar molecule is defined as (4.1) where l is the distance between the two charges + q and – q. The direction of the dipole moment is as shown in the above figure. For example, for two electronic charges q = ± e separated by l = 0.1 nm, the dipole moment is u = (1.602 × 10 −19) (10 −10) = 1.6 × 10 −29 C m = 4.8 D. The unit of dipole moment is the Debye, where 1 Debye = 1 D = 3.336 × 10 −30 C m, which corresponds to two unit charges separated by about 0.2 Å (~0.02 nm)...
