Amino Acid Properties PDF

Amino Acid PropertiesIntroductionEach amino acid has distinct chemical properties. Because the backbones of the 20 proteinogenic amino acids are identical, the unique properties of an amino acid arise solely from its side chain. The unique properties of each amino acid allow for tremendous diversity...

Amino Acid PropertiesIntroductionEach amino acid has distinct chemical properties. Because the backbones of the 20 proteinogenic amino acids are identical, the unique properties of an amino acid arise solely from its side chain. The unique properties of each amino acid allow for tremendous diversity in the ways different proteins behave and the functions they perform. For instance, proteins with an abundance of positively charged amino acid side chains are likely to interact with negatively charged molecules (and vice versa), and proteins with long hydrophobic regions are often found embedded in the hydrophobic environment of a cell membrane.An understanding of the chemical properties of amino acids can facilitate predictions about interactions between proteins and their environments. Consequently, amino acids are commonly grouped according to their chemical properties. Broadly, amino acid side chains are classified as nonpolar, polar neutral, and charged. This lesson explains the categorizations of each amino acid.1.2.01 Nonpolar Amino AcidsMost of the nonpolar amino acid side chains (Figure 1.26) contain only carbon and hydrogen atoms, which have similar. These C--C and C--H bonds are nonpolar and typically do not give rise to a large net.The lack of polar bonds in many of these amino acid side chains means that they cannot form or interactions with water. Consequently, the nonpolar amino acid side chains interact poorly with water and are considered hydrophobic.However, two of the nonpolar amino acids contain heteroatoms (ie, atoms other than carbon or hydrogen) in their side chain: methionine and tryptophan. Methionine contains a sulfur atom in the form of a methyl thioether. Ethers are already relatively nonpolar despite the inclusion of an electronegative oxygen. Thioethers have a sulfur atom instead of oxygen, and sulfur has nearly the same electronegativity as carbon. Therefore, the thioether in methionine is even less polar than an ether, and methionine is nonpolar.Tryptophan contains a large side chain with a single nitrogen atom, which is bonded to one hydrogen and two carbons. Nitrogen is significantly more electronegative than carbon or hydrogen, so this portion of the tryptophan side chain is polar and capable of acting as a hydrogen bond donor. However, the nonpolar character of the rest of the side chain overwhelms this effect, and tryptophan is considered nonpolar overall. Chapter 1: Amino Acids16Figure 1.26 The nonpolar amino acids.The nonpolar amino acids can be further subdivided into aliphatic and aromatic side chains.Aliphatic Amino AcidsThe aliphatic amino acids are nonpolar amino acids that are not aromatic (ie, they do not contain a fully conjugated, aromatic ring structure). This group includes glycine, alanine, methionine, valine, leucine, isoleucine, and proline (Figure 1.27). Although proline contains a ring, the ring is not aromatic, so proline is aliphatic. Chapter 1: Amino Acids17Figure 1.27 The aliphatic amino acids.Among the aliphatic amino acids, valine, leucine, and isoleucine are commonly grouped as the branched-chain amino acids (BCAAs), shown in Figure 1.28. These three amino acids are grouped both because of their similar structures and because of their involvement in similar metabolic pathways (see Chapter 13) and pathological mechanisms.Figure 1.28 The branched-chain amino acids.Note that although other amino acids such as and also have branch points, these branches link to nonalkyl groups (ie, groups of atoms other than carbon and hydrogen). The BCAAs include only those amino acids with branched alkyl chains; therefore, threonine and arginine are not included.Aromatic Amino AcidsThe remaining nonpolar amino acids (phenylalanine and tryptophan) contain in their side chains, and, consequently, they are grouped as aromatic amino acids (see Figure 1.29). Tyrosine is also included in this group. Although tyrosine has a hydroxyl group in its side chain and is often considered polar (see Concept 1.2.02 in this lesson), its large aromatic ring confers significant nonpolar character on tyrosine and allows it to be grouped with the other aromatic amino acids. Chapter 1: Amino Acids18Figure 1.29 The aromatic amino acids. also has an aromatic ring in its side chain, but it is often omitted from the aromatic amino acids because its smaller size and two-nitrogen side chain cause it to be much more polar than phenylalanine, tyrosine, or tryptophan; it can even carry a positive charge (see Lesson 1.3).1.2.02 Polar Neutral Amino AcidsThe polar neutral amino acids have side chains that have significant polar character (ie, a large net ) but do not predominantly carry an electric charge under physiological conditions (ie, the side chains are neutral). The side chains of these amino acids contain oxygen or nitrogen atoms or, in the case of cysteine, a sulfur atom. They are shown in Figure 1.30. Chapter 1: Amino Acids19Figure 1.30 The polar neutral amino acids.The oxygen and nitrogen atoms in these side chains are much more than the carbon and hydrogen atoms to which they are bonded. Consequently, these chemical groups have significant dipole moments and are capable of with water, making them generally hydrophilic.The amino acids with and side chains (asparagine, glutamine, serine, and threonine) are, for all intents and purposes, truly neutral amino acids. Although it is possible to deprotonate alcohols to yield negative charges, this generally does not happen in the mild conditions found in living cells, except in specific contexts such as enzyme active sites (see Lesson 4.3). Amides require even harsher conditions than alcohols to ionize and are essentially never found to carry a positive or negative charge in biological contexts.In contrast, tyrosine, cysteine, and histidine can carry charges on their side chains, as shown in Figure 1.31, but they are predominantly neutral under physiological conditions. Chapter 1: Amino Acids20Figure 1.31 Relative equilibria of tyrosine, cysteine, and histidine neutral and ionized (ie, charged) forms at physiological pH.The hydroxyl group of tyrosine is linked to a phenyl ring, making it a special type of alcohol called a. The presence of the hydroxyl group outside of the ring allows this functional group to be much more accessible to other molecules and causes tyrosine to be more polar and slightly more hydrophilic than other aromatic amino acids, such as tryptophan. Because of , phenols are much easier to deprotonate than other alcohols and, consequently, a small percentage of tyrosine side chains are deprotonated and negatively charged under physiological conditions.Cysteine, unlike the other polar neutral amino acids, does not contain oxygen or nitrogen atoms in its side chain. Instead, it contains sulfur. The dipole moment of its thiol (--SH) group is weak, and cysteine cannot hydrogen bond with water. However, the of the thiol group exposes the lone electron pairs on sulfur, and the small size of the hydrogen atom improves access to those lone pairs. This allows stronger dipole--induced dipole interactions between water and cysteine.Because of cysteine\'s geometry, at physiological pH, cysteine is slightly more soluble in water than tyrosine is, allowing classification of cysteine as polar neutral. Although cysteine is predominantly neutral, a small but significant percentage of cysteine side chains are deprotonated and negatively charged at physiological pH.Histidine is often excluded from the polar neutral amino acids and instead grouped with the basic (positively charged) amino acids. However, this characterization can be misleading. At physiological pH, most histidine side chains in solution are deprotonated and uncharged. Fewer than 10% of histidine side Chapter 1: Amino Acids21chains are protonated and positively charged at pH 7.4. The acid-base properties of several amino acids are discussed further in Lesson 1.3.1.2.03 Charged Amino AcidsThe remaining amino acids carry electric charges (either positive or negative) on their side chains under physiological conditions. These amino acids are arginine and lysine (positive charges) and aspartate and glutamate (negative charges). The charged amino acids are shown in Figure 1.32.Figure 1.32 The charged amino acids.Positively Charged (Basic) Amino AcidsThe positively charged amino acids are also called basic amino acids (see Figure 1.33) because they become positively charged by acting as (ie, they accept a proton from water or other sources in their environment). Note that, as discussed for polar neutral amino acids, histidine is capable of becoming positively charged by accepting a proton and is often counted among the basic amino acids for this reason. However, under physiological conditions, most histidine side chains are deprotonated and neutral, whereas most lysine and arginine side chains are protonated and positively charged. Chapter 1: Amino Acids2 Figure 1.33 Basic amino acids can carry a positive charge at physiological pH. Lysine and arginine are predominantly charged; histidine is predominantly neutral.Negatively Charged (Acidic) Amino AcidsThe negatively charged amino acids are also called acidic amino acids (see Figure 1.34) because they become negatively charged by acting as (ie, they lose a proton to the environment). When these amino acids are encountered in solution, they have typically already acted as acids and lost a proton. Although they no longer have a proton to lose, they are still called acidic because of the chemistry they underwent (ie, loss of a proton) to gain the negative charge.Figure 1.34 Acidic amino acids carry a negative charge under physiological conditions.Although both tyrosine and cysteine are also able to lose a proton to become negatively charged, they are not usually counted among the acidic amino acids. For tyrosine, this is because the percentage of tyrosine molecules that lose a proton at physiological pH is small (\~0.3%). For cysteine, it is because cysteine\'s most notable physiological role is to undergo a to form or break a (see Lesson 2.2), rather than an acid-base reaction.