Proteins and Proteomics

Proteins are the fundamental workhorses of life, complex macromolecules built from chains of amino acids that fold into precise three-dimensional structures to carry out a vast array of cellular tasks, including catalyzing biochemical reactions, providing structural integrity, and transmitting signals. Proteomics is the large-scale, system-wide study of these proteins, investigating the entire protein complement (the proteome) of a cell or organism at a specific point in time. By analyzing protein expression levels, modifications, interactions, and localization, proteomics provides a dynamic and functional snapshot of biological systems, offering critical insights into the molecular mechanisms that govern health and disease.

1. Fundamentals of Proteins
   1. Amino Acids: The Building Blocks
      1. General Structure of an Amino Acid
         1. Alpha-Carbon
         2. Amino Group
         3. Carboxyl Group
         4. R-Group (Side Chain)
         5. Hydrogen Atom
      2. Classification of the 20 Common Amino Acids
         1. Nonpolar, Aliphatic R-Groups
            1. Glycine
            2. Alanine
            3. Valine
            4. Leucine
            5. Isoleucine
            6. Methionine
            7. Proline
         2. Aromatic R-Groups
            1. Phenylalanine
            2. Tyrosine
            3. Tryptophan
         3. Polar, Uncharged R-Groups
            1. Serine
            2. Threonine
            3. Cysteine
            4. Asparagine
            5. Glutamine
         4. Positively Charged (Basic) R-Groups
            1. Lysine
            2. Arginine
            3. Histidine
         5. Negatively Charged (Acidic) R-Groups
            1. Aspartic Acid
            2. Glutamic Acid
      3. Physicochemical Properties
         1. Chirality and Stereoisomerism
            1. L- and D- Isomers
            2. Biological Relevance of L-Amino Acids
         2. Acid-Base Properties
            1. Zwitterion Formation
            2. Titration Curves
            3. Henderson-Hasselbalch Equation
         3. pKa and the Isoelectric Point (pI)
            1. Calculation of pI
            2. Relevance to Protein Purification
         4. Hydrophobicity and Polarity
            1. Hydropathy Indices
            2. Membrane Protein Prediction
      4. Non-standard and Modified Amino Acids
         1. Selenocysteine
         2. Pyrrolysine
         3. Post-translationally Modified Amino Acids
            1. Hydroxyproline
            2. Hydroxylysine
            3. Phosphoserine
   2. The Peptide Bond
      1. Formation via Dehydration Synthesis
         1. Mechanism of Peptide Bond Formation
         2. Directionality of Synthesis
         3. Energetics of Bond Formation
      2. Characteristics
         1. Planar Geometry
         2. Partial Double-Bond Character
         3. Rigidity and Rotation Limits
         4. Cis and Trans Configurations
         5. Resonance Stabilization
      3. Polypeptide Chains
         1. N-terminus and C-terminus
         2. Backbone and Side Chains
         3. Peptide Sequence Notation
         4. Oligopeptides, Polypeptides, and Proteins
         5. Phi and Psi Angles
   3. Protein Classification and Nomenclature
      1. Structural Classification
         1. Fibrous Proteins
         2. Globular Proteins
         3. Membrane Proteins
      2. Functional Classification
         1. Enzymes
         2. Structural Proteins
         3. Transport Proteins
         4. Storage Proteins
         5. Hormonal Proteins
         6. Receptor Proteins
         7. Contractile Proteins
         8. Defensive Proteins
      3. Evolutionary Classification
         1. Protein Families
         2. Protein Superfamilies
         3. Homologous Proteins
         4. Orthologous and Paralogous Proteins