🧫Organic Chemistry II Unit 9 – Amino Acids, Peptides & Proteins in Organic Chem

What's the Big Deal?

• Amino acids, peptides, and proteins play a crucial role in the structure and function of living organisms
• Proteins are involved in virtually every biological process, from catalyzing reactions (enzymes) to providing structural support (collagen)
• Understanding the chemistry of amino acids and proteins is essential for fields such as biochemistry, molecular biology, and medicine
• Proteins are the most abundant organic molecules in living systems, making up about 50% of the dry weight of cells
• Studying amino acids, peptides, and proteins helps us understand the molecular basis of life and develop new technologies (pharmaceuticals, biomaterials)

Key Players: Amino Acids 101

• Amino acids are the building blocks of proteins, consisting of an amino group ($-NH_2$), a carboxyl group ($-COOH$), and a variable side chain ($R$) attached to a central carbon atom ($\alpha$-carbon)
  • The $R$ group determines the unique properties of each amino acid (polarity, charge, size)
• There are 20 standard amino acids found in proteins, each with a specific three-letter and one-letter abbreviation (Alanine - Ala - A, Glycine - Gly - G)
• Amino acids can be classified based on the properties of their side chains:
  • Nonpolar (hydrophobic) amino acids (Valine, Leucine, Isoleucine)
  • Polar (hydrophilic) amino acids (Serine, Threonine, Cysteine)
  • Charged amino acids (Aspartic Acid, Glutamic Acid, Lysine, Arginine)
  • Aromatic amino acids (Phenylalanine, Tyrosine, Tryptophan)
• Amino acids are chiral molecules (except for Glycine), with two possible stereoisomers (L and D)
  • In proteins, amino acids are almost exclusively in the L-configuration
• Amino acids can act as both acids and bases (amphoteric), forming zwitterions in aqueous solutions at physiological pH

Peptide Bonds: Linking It All Together

• Amino acids are joined together by peptide bonds, which are formed through a condensation reaction between the carboxyl group of one amino acid and the amino group of another
• The resulting molecule is called a peptide, with the naming convention based on the number of amino acid residues (dipeptide, tripeptide, oligopeptide, polypeptide)
• Peptide bonds have a partial double bond character due to resonance, which results in a planar structure and restricted rotation around the $C-N$ bond
• The peptide backbone consists of repeating units of $-N-C_{\alpha}-C-$, with the side chains extending outward
• The sequence of amino acids in a peptide or protein is called its primary structure, which is determined by the genetic code
• The formation of peptide bonds is an endergonic process, requiring energy input from ATP hydrolysis during protein synthesis (translation)

Protein Structure: From Simple to Complex

• Proteins have four levels of structure: primary, secondary, tertiary, and quaternary
• Primary structure is the linear sequence of amino acids, which determines the higher levels of structure and ultimately the function of the protein
• Secondary structure refers to the local folding patterns of the peptide backbone, primarily $\alpha$-helices and $\beta$-sheets
  • $\alpha$-helices are right-handed spiral conformations stabilized by hydrogen bonds between the $C=O$ of one amino acid and the $N-H$ of another four residues ahead
  • $\beta$-sheets are extended conformations with two or more $\beta$-strands lying side-by-side, stabilized by hydrogen bonds between the strands
• Tertiary structure is the three-dimensional arrangement of a single polypeptide chain, resulting from interactions between side chains (hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bridges)
• Quaternary structure is the assembly of multiple polypeptide chains (subunits) into a functional protein complex (hemoglobin, DNA polymerase)
• Protein folding is a spontaneous process driven by the burial of hydrophobic side chains in the protein interior and the exposure of hydrophilic side chains on the surface

Chemical Properties and Reactions

• Amino acids and proteins can undergo various chemical reactions due to the presence of functional groups in their side chains
• Disulfide bridges can form between cysteine residues, stabilizing the tertiary and quaternary structure of proteins (insulin, immunoglobulins)
• Amino acids can participate in acid-base reactions, with the $pK_a$ values of their side chains determining their protonation state at a given pH
• Proteins can be denatured by factors that disrupt their native structure (heat, pH extremes, chaotropic agents), leading to a loss of function
  • Denaturation is often reversible if the denaturing conditions are removed, allowing the protein to refold into its native state
• Proteins can be modified post-translationally, adding functional groups or changing the properties of amino acid side chains (phosphorylation, glycosylation, acetylation)
• Amino acids and peptides can undergo chemical synthesis reactions, such as solid-phase peptide synthesis (SPPS) using protecting groups and activating agents

Biological Roles and Functions

• Proteins serve a wide range of functions in living organisms, including catalysis, transport, signaling, and structural support
• Enzymes are proteins that catalyze biochemical reactions, lowering the activation energy and increasing reaction rates (DNA polymerase, ATP synthase)
• Transport proteins move molecules across cell membranes or within the circulatory system (hemoglobin, ion channels, glucose transporters)
• Signaling proteins are involved in cell communication and regulation (hormones, receptors, transcription factors)
• Structural proteins provide mechanical support and stability to cells and tissues (collagen, keratin, elastin)
• Antibodies are specialized proteins produced by the immune system to recognize and neutralize foreign substances (antigens)
• Proteins can also have roles in muscle contraction (actin, myosin), blood clotting (fibrinogen, thrombin), and nutrient storage (ferritin, casein)

Lab Techniques and Analysis

• Various laboratory techniques are used to study amino acids, peptides, and proteins, depending on the specific research question
• Amino acid composition can be determined by acid hydrolysis followed by chromatographic separation (ion-exchange, reverse-phase HPLC)
• Protein sequencing involves determining the primary structure of a protein, traditionally using Edman degradation or mass spectrometry (tandem MS/MS)
• Protein purification is a multi-step process that exploits differences in protein properties (size, charge, hydrophobicity) to isolate a specific protein from a complex mixture (affinity chromatography, gel filtration)
• Electrophoretic techniques, such as SDS-PAGE and isoelectric focusing, are used to separate proteins based on their size or charge
• Immunoassays (ELISA, Western blot) employ antibodies to detect and quantify specific proteins in a sample
• Spectroscopic methods (UV-Vis, fluorescence, circular dichroism) provide information about protein structure and interactions
• X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are used to determine the three-dimensional structure of proteins at atomic resolution

Real-World Applications

• Understanding the structure and function of proteins has led to numerous applications in medicine, biotechnology, and industry
• Recombinant DNA technology allows the production of proteins in large quantities for therapeutic use (insulin, growth factors, monoclonal antibodies)
• Protein engineering involves modifying existing proteins or designing novel proteins with desired properties (enhanced stability, altered specificity, new functions)
• Enzymes are used in various industrial processes, such as food processing (rennet in cheese making), textile manufacturing (cellulases in denim finishing), and detergent formulations (proteases)
• Protein-based biomaterials are being developed for tissue engineering and regenerative medicine applications (collagen scaffolds, silk fibroin fibers)
• Protein biomarkers are used for disease diagnosis, prognosis, and monitoring treatment response (prostate-specific antigen for prostate cancer, troponin for myocardial infarction)
• Protein-based vaccines are designed to elicit an immune response against specific pathogens or cancer cells (HPV vaccine, personalized cancer vaccines)
• Protein-protein interactions are targets for drug discovery, with small molecules or peptides designed to inhibit or modulate these interactions (kinase inhibitors, peptide therapeutics)