Bio385 - SG1 Amino acids

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BIO 385 | Amino Acids & Buffers READING ASSIGNMENT LPoB8 – pgs 70-80, LibreTexts Ch 26-1,2,3 PREPARATION & PONDERING 1. *List the 20 common proteinogenic amino acids with their one letter code and list whether they are aliphatic, aromatic, polar, acidic or basic. Then identify the following special amino acids a. Smallest R group i. b. Largest R group i. c. Alcohol R-groups (Why? because these are sites for phosphorylation) i. d. Thiol R-group i. e. α-amino group forms part of a ring, also disrupts α-helix formation i. 2. Describe both the Absolute D,L- and the R,S-configurations used by chemists to communicate stereochemistry variations. All biological amino acids are found with which rotation? a. All biological amino acids are found on a clockwise rotation. b. All amino acids have L configuration c. L-Glyceraldehyde and the natural amino acids all have the S absolute configuration. The two exceptions are glycine and cysteine 3. Describe the ranking of groups used by chemists to determine R or S configuration for a given chiral carbon. Be able to apply these rules to assign R or S to a chiral carbon. 4. What functional groups commonly act as weak acids and weak bases? Use chemical logic to describe why these groups behave that way. Functional groups in organic chemistry can often act as weak acids or weak bases 1 1

BIO 385 | depending on their chemical properties. Two common functional groups that exhibit this behavior are the carboxylic acid group (-COOH) and the amino group (-NH2). 1. Carboxylic Acid Group (-COOH): - Weak Acid Behavior: The carboxylic acid group consists of a carbonyl group (C=O) and a hydroxyl group (-OH) bonded to the same carbon atom. The oxygen atom in the hydroxyl group is electronegative and can pull electron density away from the hydrogen atom in the -OH group. This results in the formation of a polar covalent bond, where the oxygen is partially negatively charged and the hydrogen is partially positively charged. - When dissolved in water, the hydrogen atom in the -OH group can ionize by donating a proton (H+) to water, forming the hydronium ion (H3O+) and the carboxylate ion (-COO-): ``` -COOH ⇌ -COO- + H+ ``` This reversible reaction represents the weak acid behavior of the carboxylic acid group. 2. Amino Group (-NH2): - Weak Base Behavior: The amino group contains a nitrogen atom with a lone pair of electrons. Nitrogen is less electronegative than oxygen, so it is more likely to share its lone pair of electrons. When dissolved in water, the lone pair on the nitrogen atom can accept a proton (H+) from water, forming the ammonium ion (NH4+) and hydroxide ion (OH-): ``` -NH2 + H2O ⇌ NH4+ + OH- ``` This reversible reaction represents the weak base behavior of the amino group. In summary, the weak acid behavior of the carboxylic acid group is due to the ability of the -OH group to donate a proton (H+) to water, while the weak base behavior of the amino group is due to the lone pair of electrons on the nitrogen atom's ability to accept a proton from water. These behaviors are determined by the electron distribution and electronegativity differences between the atoms in these functional groups. 5. Using amino acids as case, what is the common pKa range for amines? Carboxyl groups? Amino acids contain both amino groups (-NH2) and carboxyl groups (-COOH). These functional groups can act as weak acids and weak bases, and their pKa values can vary depending on the specific amino acid and its local environment. However, there is a common pKa range for amines and carboxyl groups in amino acids. 2

BIO 385 | 1. **Amino Groups (-NH2):** - The amino group in amino acids typically has a pKa value in the range of about 8 to 10. - This means that in a solution with a pH below the pKa (acidic conditions), the amino group will tend to be protonated (NH3+). In a solution with a pH above the pKa (basic conditions), it will tend to be deprotonated (NH2). 2. **Carboxyl Groups (-COOH):** - The carboxyl group in amino acids typically has a pKa value in the range of about 1.5 to 2.5. - This means that in a solution with a pH below the pKa, the carboxyl group will tend to be fully protonated (-COOH). In a solution with a pH above the pKa, it will tend to be deprotonated (-COO-). It's important to note that the exact pKa values can vary slightly among different amino acids due to their chemical structures and local environments. The pKa values of amino and carboxyl groups are critical in the context of amino acids because they determine whether these groups are positively or negatively charged at a given pH, which, in turn, affects the overall charge and reactivity of the amino acid in biological systems. 6. Be able to correctly draw, label, and explain a titration curve. Identify the pKa, buffering region, and what effect a changing the buffer pKa has on the curve. 7. Amino acids are zwitterions. What is a zwitterion? What does the titration curve of a zwitterion look like and be able to draw and discuss the structures that exist and/or dominate at different points along the titration curve for a given amino acid. A zwitterion is a molecule that contains both a positively charged group (cationic) and a negatively charged group (anionic) within the same molecule. In the context of amino acids, zwitterions are the predominant form of these molecules in aqueous solutions. Amino acids have both an amino group (-NH3+) with a positive charge and a carboxyl group (-COO-) with a negative charge, making them zwitterionic in nature. **Titration Curve of an Amino Acid:** The titration curve of an amino acid represents how the pH of a solution changes as a strong acid (H+) or strong base (OH-) is added. Let's discuss the structures that exist and dominate at different points along the titration curve for a generic amino acid: 1. **pH < pKa1 (First Acidic Equivalence Point):** - At very low pH, the solution is strongly acidic. - The amino group (-NH3+) is protonated, carrying a positive charge. - The carboxyl group (-COOH) remains protonated as well, carrying a positive charge. - The predominant form is the fully protonated amino acid with a net positive charge: 3

BIO 385 | NH3+-CH(R)-COOH. 2. **pKa1 < pH < pKa2 (Buffering Region 1):** - In this pH range, the amino group (-NH2) starts to deprotonate and become neutral, while the carboxyl group (-COOH) remains protonated. - The amino acid acts as a buffer because it can accept or donate protons. - The predominant form is a zwitterion, with the amino group (-NH3+) carrying a positive charge, and the carboxyl group (-COO-) carrying a negative charge: NH3+- CH(R)-COO-. 3. **pKa2 < pH < pKa3 (Buffering Region 2):** - In this pH range, the carboxyl group (-COO-) continues to deprotonate and become more negatively charged. - The amino group (-NH2) remains deprotonated. - The predominant form is still the zwitterion, NH3+-CH(R)-COO-. 4. **pH > pKa3 (Second Basic Equivalence Point):** - At very high pH, the solution is strongly basic. - Both the amino group (-NH2) and the carboxyl group (-COO-) are fully deprotonated. - The predominant form is the fully deprotonated amino acid with a net negative charge: NH2-CH(R)-COO-. **Drawing the Titration Curve:** To draw the titration curve of an amino acid, plot pH on the vertical axis and volume of added strong acid or base on the horizontal axis. The curve will show two buffering regions, corresponding to the zwitterionic form of the amino acid, and two equivalence points, where the amino acid becomes fully protonated or fully deprotonated. In summary, the titration curve of an amino acid displays changes in pH as protons are added or removed. At specific pH ranges, the amino acid exists primarily as a zwitterion, with both a positive and a negative charge, making it an effective buffer. The pKa values correspond to the pH values at which specific protonation or deprotonation events occur. 8. Explain why is the pH of a system so important to protein folding and binding? The pH of a system is crucial to protein folding and binding because it directly affects the charge distribution and ionization states of amino acid residues in proteins. The three main reasons why pH is important in these processes are electrostatic interactions, protonation state of ionizable groups, and the stability of protein structures: 1. **Electrostatic Interactions:** - Proteins are composed of amino acids, and many of these amino acids contain ionizable groups, such as carboxyl (-COOH) and amino (-NH2) groups. 4

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