Lecture Notes: Amino Acids and Peptides PDF

LECTURE NOTES IN BIOCHEMISTRY Lecture 2 - Amino Acids and Peptides Learning Outcomes By the end of this lesson, students should be able to: 1. Classify amino acids based on side chain polarity. 2....

LECTURE NOTES IN BIOCHEMISTRY Lecture 2 - Amino Acids and Peptides Learning Outcomes By the end of this lesson, students should be able to: 1. Classify amino acids based on side chain polarity. 2. Draw the structures of standard amino acids. 3. Differentiate essential amino acids from non-essential amino acids. 4. Illustrate acid-base properties of amino acids. 5. Explain peptide bond formation and describe the nature of the bond. 6. Identify interactions between amino acid side chains. Amino Acids Amino acids are the building blocks of proteins. 20 standard amino acids are found in proteins. General structure of an amino acid: ○ Amino group (-NH₂) ○ Carboxyl group (-COOH) ○ Side chain group (R group), which determines the amino acid’s identity and properties. Classification of Amino Acids Amino acids can be classified based on the polarity of their side chains: 1. Nonpolar Amino Acids: ○ Contain hydrophobic side chains, such as aliphatic or aromatic hydrocarbons. 2. Polar-Neutral Amino Acids: ○ Side chains are uncharged, but can form hydrogen bonds. 3. Acidic Amino Acids: ○ Contain carboxyl groups in their side chains that lose a proton, resulting in a negatively charged carboxylate. 4. Basic Amino Acids: ○ Contain nitrogen groups in their side chains that can accept a proton, becoming positively charged. 1 Prepared by: CCepeda 2 Prepared by: CCepeda Essential vs Non-Essential Amino Acids Essential amino acids: Cannot be synthesized by the body and must be obtained through diet. ○ Common sources include soy, chicken, tofu, and pork. Non-essential amino acids: Can be synthesized by the body. Side Chain Interactions Amino acids can interact with one another through their side chains. Common interactions include: 1. Disulfide Bonds: ○ A covalent bond between two cysteine residues, important for stabilizing protein structure. 2. Pi-Stacking: ○ An interaction between aromatic rings in amino acids like phenylalanine or tyrosine. The arrangement can be sandwich, T-shaped, or parallel displaced. 3 Prepared by: CCepeda Acid-Base Properties of Amino Acids Amino acids exhibit acid-base behavior due to their amino and carboxyl groups: ○ At neutral pH, the amino group is positively charged (-NH₃⁺) and the carboxyl group is negatively charged (-COO⁻). ○ Amino acids with nonpolar R groups exist as zwitterions with no net charge at neutral pH. ○ Amino acids with acidic R groups have a net negative charge at neutral pH, while those with basic R groups have a net positive charge. Ionization of Amino Acids Amino acids such as glycine, glutamic acid, and lysine undergo ionization depending on the pH of the environment. Isoelectric Point (pI) The isoelectric point (pI) is the pH at which an amino acid has no net charge. At the pI, amino acids do not migrate in an electric field, a property used in separation techniques like isoelectric focusing. Peptide Bond Formation A peptide bond is a covalent bond formed between the alpha-carboxyl group of one amino acid and the alpha-amino group of another. This bond formation results in the release of a water molecule (condensation reaction). Peptide bonds link amino acids together to form polypeptides or proteins. 4 Prepared by: CCepeda