Acid-Base Chemistry of Amino Acids PDF

Acid-Base Chemistry of Amino AcidsIntroductionEach of the amino acids has at least two that can exchange protons with their environment. In other words, amino acids can participate in. The extent to which a chemical group on an amino acid is protonated or deprotonated can be modulated by its local e...

Acid-Base Chemistry of Amino AcidsIntroductionEach of the amino acids has at least two that can exchange protons with their environment. In other words, amino acids can participate in. The extent to which a chemical group on an amino acid is protonated or deprotonated can be modulated by its local environment. This chapter examines the protonation states of various amino acid chemical groups under various conditions and explores the effect of protonation on the overall charges of amino acids.1.3.01 Amino Acid Backbone IonizationChemical groups that participate in acid-base chemistry are said to be ionizable because they either become positively charged (ie, cations) by accepting protons, or they become negatively charged (ie, anions) by losing protons. All amino acids have at least two ionizable groups---the backbone amino group and the backbone carboxyl group. As discussed in Lesson 1 of this chapter, the backbone of an amino acid is a zwitterion at physiological pH. The amino group is protonated and positively charged, and the carboxyl group is deprotonated and negatively charged, resulting in a molecule with a net charge of 0.However, the protonation states of the backbone groups can be altered by adjusting the pH, as shown in Figure 1.35. Decreasing the pH increases the number of protons available in the environment, making it easier for an amino acid carboxyl group to pick up one of these protons. Increasing the pH has the opposite effect: fewer free protons are available in the solution, so the amino group more easily loses protons.Consequently, when the pH is low, the carboxyl and amino groups in an amino acid are more likely to be protonated, giving the backbone an overall positive charge. Similarly, at high pH, both the carboxyl and amino groups are likely to be deprotonated, giving the backbone an overall negative charge. Chapter 1: Amino Acids24Figure 1.35 Amino acid backbones are cations (positive charge) at low pH, zwitterions (no net charge) at physiological pH, and anions (negative charge) at high pH.1.3.02 Ionizable Amino Acid Side ChainsThe side chains of most amino acids are electrically neutral at physiological pH, but some side chains can become protonated or deprotonated and carry a positive or negative charge. These amino acids---arginine, lysine, histidine, tyrosine, cysteine, glutamate, and aspartate---are collectively called the ionizable amino acids. They are shown in Figure 1.36.Figure 1.36 The seven ionizable amino acids shown in their ionized (ie, charged) forms. Chapter 1: Amino Acids25The acidity or basicity of a chemical group (ie, its tendency to lose or pick up protons) can also be altered by its environment, as shown in Figure 1.37. For instance, carboxyl groups are normally acidic and are therefore deprotonated under physiological conditions. However, if a carboxyl group is placed near another negative charge, the carboxyl group becomes more likely to accept a proton, neutralizing it and reducing charge-charge repulsion. In other words, the carboxyl group becomes more basic in these conditions.Similarly, if an alcohol (normally neutral) is placed near a positive charge, the alcohol becomes more likely to lose a proton (ie, it becomes more acidic). The resulting negative charge increases attractive interactions with the nearby positive charge.Figure 1.37 Acidity of chemical groups may be altered by their local environments to decrease repulsive forces and increase attractive forces.Consequently, in addition to these seven amino acids, and can be deprotonated and negatively charged in certain contexts, such as the active sites of some enzymes (see Chapter 4). However, because serine and threonine are difficult to deprotonate outside of these contexts, they are typically omitted from the ionizable amino acids.Note that some of the ionizable amino acids (Arg, Lys, and His) are positively charged when protonated, whereas the others (Tyr, Cys, Glu, and Asp) are neutral when protonated. Similarly, Arg, Lys, and His are neutral when deprotonated whereas Tyr, Cys, Glu, and Asp are negatively charged when deprotonated. For the exam, it is sufficient to remember that the ionizable side chains that contain nitrogen can either be positive or neutral, and the ionizable side chains that contain oxygen or sulfur can either be neutral or negative. The charge associated with the protonation state of each side chain is summarized in Figure 1.38. Chapter 1: Amino Acids26 Chapter 1: Amino Acids27Figure 1.38 Some ionizable amino acids are neutral when deprotonated and positive when protonated; others are negative when deprotonated and neutral when protonated.1.3.03 Amino Acid Percent IonizationA single site on an ionizable group may either be protonated or deprotonated, but it cannot be partially protonated. However, in a population of ionizable groups, a percentage are protonated and the remainder are deprotonated. The probability that a given individual group is protonated, and the extent to which a population of ionizable groups is protonated, depends on the of that group and the pH to which it is exposed. As the pH increases, the percentage of deprotonated groups also increases (see Figure 1.39).Figure 1.39 Effect of pH on protonation of the carboxyl groups in amino acid backbones. Chapter 1: Amino Acids28, the pKa of an ionizable group is the pH at which 50% of the population is protonated and 50% is deprotonated. When the pH is below the pKa, the relative abundance of protons in solution makes it more likely for ionizable groups to accept a proton; as a result, decreasing the pH of a solution below the pKa of a group of interest causes more than 50% of its population to be protonated. Similarly, raising the pH above the pKa causes more than 50% of its population to be deprotonated (see Figure 1.40).Figure 1.40 Relative amounts of chemical groups that are protonated when pH is less than, equal to, or greater than the pKa of the chemical group.The backbone amino and carboxyl groups of each amino acid have slightly different pKa values depending on the identity of the side chain. For the exam, however, they can be collectively approximated as 9.6 and 2.2, respectively. The pKa values of these groups along with those of the seven ionizable side chains are summarized in Table 1.1.Table 1.1 Approximate pKa values of α-amino, α-carboxy, and ionizable side chain groups of amino acids.Ionizable grouppKaα-Amino group9.6α-Carboxyl group2.2Arginine side chain12.5Lysine side chain10.5Tyrosine side chain10.0Cysteine side chain8.0Histidine side chain6.0Glutamate side chain4.3Aspartate side chain3.7The extent to which an ionizable amino acid group has been protonated or deprotonated can be calculated using the equation (see General Chemistry Lesson 8.4): Chapter 1: Amino Acids29pH=p𝐾a+log\[A―\]\[HA\]where \[A−\] is the molar concentration of the deprotonated, negative form of the ionizable group and \[HA\] is the molar concentration of protonated neutral form. Alternatively, if the deprotonated form is neutral (A) and the protonated form is positively charged (HA+), this may be expressed as:pH=p𝐾a+log\[A\]\[HA+\]Given the pKa and pH, the ratio of \[A−\] to \[HA\] (or \[A\] to \[HA+\]) can be determined by solving:pH―p𝐾a=log\[A―\]\[HA\] or pH―p𝐾a=log\[A\]\[HA+\]10(pH―p𝐾a)=\[A―\]\[HA\] or 10(pH―p𝐾a)=\[A\]\[HA+\]Percent ionization of an amino acid can then be calculated.% ionization=\[A―\]\[A―\]+\[HA\]×100% or % ionization=\[HA+\]\[A\]+\[HA+\]×100%Concept Check 1.2Calculate the percent ionization of the side chains of tyrosine and histidine, each at pH 7.0.1.3.04 Isoelectric Points of Amino AcidsOften, amino acids are said to have a particular net charge at a particular pH (eg, lysine has a net charge of +1 at physiological pH). However, based on the , at any pH, some amino acids in a population have one net charge, and some have a different net charge. For this reason, it must be recognized that in most cases the amino acids in the sample predominantly have a certain net charge, but a smaller subset have a different net charge.For example, histidine is considered neutral at physiological pH because most of the histidine molecules in solution are neutral, but a small subset are positively charged. This means that at physiological pH, the histidine molecules collectively have a slight positive charge on average, although most individual histidine molecules are neutral.Given this, any population of amino acids can be made to have a net positive charge by sufficiently decreasing the pH, and any population can be made to have a net negative charge by sufficiently increasing the pH. Similarly, every amino acid has a specific pH at which the population of amino acids, on average, has a net charge of 0. This pH is called the (pI) of the amino acid of interest.The pI of any amino acid can be calculated by averaging two pKa values: the pKa below which the amino acid is predominantly positive and the pKa above which the amino acid is predominantly negative. For example, below a pH of 6.0, histidine is predominantly positive, and above a pH of 9.6, histidine is predominantly negative (see Figure 1.41). Chapter 1: Amino Acids30Figure 1.41 Predominant protonation states and net charges of histidine at different pH levels.Therefore, these two pKa values are used in the calculation of pI. The pKa of the backbone carboxyl group (2.2) is not relevant in this case because it is not directly involved in the transition from charged to neutral. Averaging the side chain and backbone amino group pKa values gives the pI of histidine as approximatelypI=6.0+9.62=7.8Note that the neutral form of histidine is the predominant ionization state throughout the entire range of pH values from 6.0 to 9.6, but the charged forms are still present as minor species and contribute to average charge. However, at the isoelectric point (ie, 7.8), the levels of the positively charged and negatively charged species are equal and therefore neutralize each other, yielding a population of histidine molecules with an average charge of 0.Figure 1.42 shows the relative amounts of each protonation state of histidine at various pH levels. Chapter 1: Amino Acids31Figure 1.42 At the isoelectric point of histidine, the average charge of all histidine molecules in a sample is 0. Average charge increases as pH decreases and vice versa.Concept Check 1.3Calculate the isoelectric points of glutamate, alanine, and lysine.1.3.05 Amino Acid Titration CurvesBecause amino acids each have at least two ionizable groups (ie, groups that participate in acid-base chemistry), they can be analyzed by titration (see General Chemistry Lesson 8.6). Typically, an amino acid titration is carried out by bringing the solution containing the amino acid to a pH below its lowest pKa (ie, pH \