Organic Chemistry Substitution Reactions

Substitution Reaction

• A substitution reaction replaces one functional group in a chemical compound with another.
• Classified as electrophilic or nucleophilic based on the reagent and reaction mechanism.
• Can involve intermediates like carbocations, carbanions, or free radicals.
• Understanding this reaction type aids in predicting product outcomes and optimizing conditions such as temperature and solvents.

Rearrangement Reaction

• Involves the rearrangement of a molecule's carbon skeleton to form structural isomers.
• Typically involves the migration of a substituent within the same molecule.

Organic Redox Reaction

• Redox reactions involve changes in the oxidation states of reactants.
• Consists of simultaneous oxidation and reduction processes.
• The oxidizing agent is reduced, while the reducing agent is oxidized.

Carbohydrates

• Composed of carbon, hydrogen, and oxygen, with a general formula of Cm(H2O)n.
• Disaccharides consist of two monosaccharides linked by glycosidic bonds; examples include maltose, lactose, and sucrose.
• Formed via condensation reactions, and broken down by hydrolysis with enzyme disaccharidases.

Oligosaccharides

• Polymers containing three to ten monosaccharides.
• Serve various functions, including cell recognition and binding (e.g., glycolipids).

Glycoproteins

• Membrane proteins that are linked to oligosaccharides, commonly involved in cell signaling.
• Glycosylation is the process of sugar attachment to proteins, primarily occurring in the endoplasmic reticulum.

Polysaccharides

• Long-chain polymers made of monosaccharides connected by glycosidic linkages.
• Include storage (starch, glycogen) and structural polysaccharides (cellulose, chitin).
• Amylase enzymes catalyze their reaction with water to yield sugars.

Starch

• Major carbohydrate source for humans, making up over 50% of carbohydrate intake.
• Comprised of amylose and amylopectin polymers.

Amino Acids

• Characterized by a carboxyl group and an amino group attached to the alpha carbon.
• Variations are based on R groups, affecting properties and functions.
• Zwitterions are molecules with both positive and negative charges, exemplified by amino acids.

Uncommon Amino Acids

• Modified residues or analogues of common amino acids found in proteins.
• Include derivatives such as 4-hydroxyproline and selenocysteine.

Protein Structures

• Tertiary Structure: Formed by interactions between R groups, determines the protein's 3D shape.
• Different interactions stabilize tertiary structures:
  • Hydrophobic interactions: Non-polar amino acids cluster away from water.
  • Hydrophilic interactions: Polar R groups interact with water.
  • Salt bridges: Ionic bonds between charged R groups.
  • Hydrogen bonds: Between polar groups.
  • Disulfide bonds: Covalent links between cysteine residues.

Quaternary Structure

• Involves the arrangement and interaction of multiple polypeptide subunits.
• Examples include enzymes like DNA polymerase with ten subunits.
• Stability provided by hydrogen bonding, salt bridges, and disulfide bonds.

Protein Denaturation

• Native state refers to a protein's stable conformation.
• Sensitive to external factors like temperature, pH, and ionic strength.
• Denaturation leads to loss of secondary, tertiary, or quaternary structure, resulting in misfolding or random shapes.