Amino Acids and Proteins Overview

Study Notes

Amino Acids and Proteins

Amino acids are the building blocks of proteins.
The "R" group of an amino acid determines its properties (charge, size, polarity).
Chiral molecules cannot be superimposed on their mirror images. Achiral molecules can.
Amino acids exist in L or D forms. L-amino acids are commonly found in proteins.
Amino acids are classified based on their R-groups into:
- Nonpolar aliphatic (e.g., Glycine, Alanine, Valine, Leucine)
- Aromatic (e.g., Phenylalanine, Tyrosine, Tryptophan)
- Polar uncharged (e.g., Serine, Threonine, Cysteine, Asparagine, Glutamine)
- Positively charged (e.g., Lysine, Arginine, Histidine)
- Negatively charged (e.g., Aspartate, Glutamate)
Uncommon amino acids include 4-hydroxyproline, 5-hydroxylysine, 6-N-methyllysine, γ-Carboxyglutamate, Selenocysteine, and Pyrolysine. Ornithine and Citrulline are intermediates in amino acid biosynthesis.
Amino acids are amphoteric, existing as dipolar ions (zwitterions) in water.
The zwitterion form of an amino acid can act as either an acid or a base.
Titration curves of amino acids help determine pKa values and the isoelectric point (pI).
pKa values for different amino acids are provided on page 14.
Amino acids join through peptide bonds to form peptides and proteins.
Peptides and proteins have N-terminal and C-terminal ends.
Forces that stabilize protein structure include disulfide linkages, hydrogen bonds, ionic interactions (salt bridges), van der Waals interactions, and hydrophobic interactions.
Disulfide bonds are formed between cysteine residues.
Hydrogen bonds are directional and stronger when acceptor atoms are at a 180° angle to H-bonded atoms.
Van der Waals forces are transient, weak interactions between uncharged atoms.
Ionic interactions occur between oppositely charged groups (e.g., carboxyl and amino groups).
Hydrophobic interactions occur between nonpolar amino acid residues, typically in the protein core.
Hydropathy index values are provided on page 25.
Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.
Primary structure refers to the linear sequence of amino acids.
Secondary structure includes alpha helices and beta sheets.
Tertiary structure describes the overall three-dimensional folding of a polypeptide chain.
Quaternary structure describes the arrangement of multiple polypeptide chains to form a functional protein.
Fibrous proteins (e.g., keratin, collagen) have long strands or sheets. These structures are generally insoluble in water and often contain repetitive secondary structures.
Globular proteins (e.g., myoglobin, hemoglobin) have folded structures, are usually soluble in water and often carry out specific functions.
Myoglobin is a single polypeptide chain with a heme group that binds oxygen in muscle cells.
Hemoglobin is a tetrameric protein found in red blood cells, responsible for oxygen transport, with two alpha and two beta polypeptide chains. It exhibits cooperative binding and has T and R states which allows it to bind oxygen efficiently.