Biochemistry_slides_S5-6 (1)

Chapter 3: Amino Acids and Peptides

Chapter Outline

• 3-1 Amino acids are three-dimensional

• 3-2 Structures and properties of amino acids

• 3-3 Amino acids can act as both acids and bases

• 3-4 The peptide bond

• 3-5 Small peptides with physiological activity

Amino Acids Are Three-Dimensional

• Definition: Amino acids consist of an amino group and a carboxyl group attached to the α-carbon.

  • Amino Group: -NH2 functional group

  • Carboxyl Group: -COOH, dissociates into carboxylate anion (-COO–) and hydrogen ion (H+)

• α-Carbon: Central carbon atom bonded to an R (side chain) group and a hydrogen atom.

• Stereoisomers: There are two forms of amino acids, L- and D-amino acids, based on their configuration in relation to glyceraldehyde.

Structures and Properties of Amino Acids

• Chirality: All amino acids, except glycine, are chiral due to having at least one chiral center (α-carbon).

• Configuration: Most α-amino acids have the L configuration.

• Naming: Amino acid side chains are named using Greek letters starting from α (α-, β-, γ-, δ-, ε-, ω-).

• Abbreviations: Amino acids can be referred to by three-letter or one-letter codes.

Common Amino Acids

Table 3.1 - Names and Abbreviations

Notes on Abbreviations

• One-letter codes typically match the first letter of the amino acid name; exceptions use phonetic names for clarity.

Nonpolar Amino Acids

• Group Characteristics: Nonpolar side chains help in hydrophobic interactions.

  • Members: Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Methionine.

  • Structure: Aliphatic or aromatic hydrocarbons.

Polar-Neutral Amino Acids

• Group Characteristics: Polar side chains are neutral at pH 7.

  • Members: Serine, Threonine, Tyrosine, Cysteine, Glutamine, Asparagine.

  • Functional Groups: Hydroxyl (-OH) or thiol (-SH) in side chains.

Acidic and Basic Amino Acids

Acidic Amino Acids

• Members: Glutamic Acid and Aspartic Acid

• Characteristics: Have additional carboxyl groups in their side chains, creating negatively charged carboxylate anions at neutral pH.

Basic Amino Acids

• Members: Histidine, Lysine, Arginine

• Characteristics: Have positively charged side chains at or near neutral pH. Histidine features an imidazole group.

Peptide Bonds

• Definition: Amide bond formed between amino acids through condensation (removal of water).

• Structure: The bond is between the α-carboxyl group of one amino acid and the α-amino group of the next.

• Stability: Peptide bonds are strong and exhibit partial double bond character, restricting rotation, which is reflected in the planar arrangement of peptide bonds.

Titration and pKa Values

• Titration: Amino acids can be titrated, with their curves depicting the reaction of functional groups with hydrogen ions.

• pKa Values: These values indicate the pH at which half the molecules are ionized.

Isoelectric Point (pI)

• Definition: pH at which an amino acid has no net charge.

• Calculation: pI can be calculated as the average of the pKa values of the carboxyl and amino groups.

• Classification: pI < 7 indicates an acidic amino acid; pI > 7 suggests a basic amino acid.

Examples and Problem Solving

• Example problems illustrate how to determine amino acid properties, ratios of charged to uncharged states, and how to calculate pI from pKa values.

Physiological Activity of Small Peptides

• Examples: Oxytocin and vasopressin, both crucial hormones with cyclic structures, exhibiting physiological importance.