Apr 1, 2025
Amino Acids: A Deeper Dive Your notes correctly identify the basic structure of amino acids, but we can enrich this section. Let's explore the 20 standard amino acids in more detail, categorizing them by their properties and highlighting key examples:
Glycine (Gly, G): The simplest amino acid, with only a hydrogen atom as its side chain. This makes it achiral (lacking a chiral center). Alanine (Ala, A): A methyl group as its side chain. Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I): Branched-chain amino acids, increasingly hydrophobic with larger side chains. Methionine (Met, M): Contains a thioether group in its side chain. While containing sulfur, the C-S bond is relatively nonpolar. 2. Aromatic: These amino acids have ring structures in their side chains, contributing to their hydrophobicity.
Phenylalanine (Phe, F): A benzene ring. Tyrosine (Tyr, Y): A benzene ring with a hydroxyl group, making it slightly polar. This hydroxyl group allows for hydrogen bonding. Tryptophan (Trp, W): A fused benzene-pyrrole ring structure. 3. Polar, Uncharged: These amino acids have polar but uncharged side chains, making them hydrophilic (water-loving).
Serine (Ser, S), Threonine (Thr, T): Contain hydroxyl (-OH) groups, capable of hydrogen bonding. Cysteine (Cys, C): Contains a sulfhydryl (-SH) group, capable of forming disulfide bonds. Asparagine (Asn, N), Glutamine (Gln, Q): Contain amide groups, capable of hydrogen bonding. 4. Polar, Charged (Acidic): These amino acids have negatively charged side chains at physiological pH.
Aspartic Acid (Asp, D), Glutamic Acid (Glu, E): Contain carboxyl groups (-COOH), which deprotonate to form carboxylate (-COO⁻) ions at physiological pH. 5. Polar, Charged (Basic): These amino acids have positively charged side chains at physiological pH.
Lysine (Lys, K): Contains an amino group at the end of its alkyl chain. Arginine (Arg, R): Contains a guanidinium group. Histidine (His, H): Contains an imidazole group; its pKa is close to physiological pH, meaning it can exist in both charged and uncharged forms. Important for enzyme catalysis. Peptide Bond Formation and Properties:
The peptide bond is a covalent bond, characterized by its partial double-bond character, resulting from resonance. This partial double bond restricts rotation around the peptide bond, influencing protein structure.
Protein Structure: Expanded
Your notes provide a good overview of the four levels of protein structure, but additional detail can be added:
Primary Structure: The linear sequence of amino acids dictates all higher-order structures. Mutations (changes in amino acid sequence) can significantly alter protein structure and function. Secondary Structure: The alpha-helix and beta-sheet are stabilized by hydrogen bonds between the backbone amide and carbonyl groups. Other secondary structures exist, like loops and turns, which are crucial for connecting alpha-helices and beta-sheets. Tertiary Structure: This three-dimensional arrangement is determined by interactions between amino acid side chains (R groups). The hydrophobic effect (clustering of hydrophobic residues in the protein's interior) is a major driving force. Disulfide bonds, formed between cysteine residues, are important covalent crosslinks. Quaternary Structure: This level of organization applies to proteins composed of multiple polypeptide chains (subunits). Interactions between subunits are similar to those in tertiary structure. Examples include hemoglobin (four subunits) and antibodies (two heavy and two light chains). Enzyme Kinetics:
Your notes briefly touch on enzyme kinetics, but we can elaborate:
Michaelis-Menten Kinetics: This model describes the relationship between enzyme activity and substrate concentration. The Michaelis constant (Km) is a measure of the enzyme's affinity for its substrate. A lower Km indicates higher affinity. Enzyme Inhibition: Different types of inhibitors can affect enzyme activity, including competitive inhibitors (competing with substrate for binding to the active site) and non-competitive inhibitors (binding elsewhere, altering the enzyme's shape). Protein Denaturation:
Denaturation can be caused by various factors, including heat, extreme pH, detergents, and chaotropic agents (disrupting hydrophobic interactions). While some proteins can refold after denaturation (renaturation), others undergo irreversible changes.