Chapter 2 Notes: Chemistry of Carbon

Carbon Backbone and Bonding

  • Carbon forms four covalent bonds; valence = 4, enabling diverse, complex molecules.
  • Bonding shapes:
    • Single bonds: tetrahedral geometry; rotation around bonds is allowed.
    • Double bonds: planar geometry; rotation around the bond is restricted.
  • Hydrocarbons (aliphatic) are C–H chains or rings; basis for organic diversity.

Isomerism and Stereochemistry

  • Isomers: same chemical formula, different arrangement or bonds.
    • Structural isomers: different covalent connectivity.
    • Geometric (cis/trans) isomers: different arrangement around a C=C double bond.
    • Enantiomers: non-superimposable mirror images; differ in 3D arrangement around an asymmetric carbon.
  • Asymmetric carbon (chiral center): a carbon with four different substituents.
  • Enantiomer importance: biological interactions are stereospecific; key in pharmaceuticals.
  • Examples:
    • Ibuprofen and albuterol exist as different enantiomers with varying activity (one may be effective, the other not).
    • Thalidomide history highlights enantiomer safety concerns; one enantiomer is therapeutic, the other teratogenic.

Functional Groups Overview

  • Functional groups are the reactive parts of molecules that drive chemical reactions.
  • Six key groups in biology (plus the methyl group): hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl (-CH3).
  • Recognizing these groups aids in predicting reactivity and properties of organic molecules.

Hydroxyl (–OH)

  • Structure: hydrogen bonded to oxygen bonded to carbon skeleton.
  • Properties: polar; enables hydrogen bonding; increases solubility in water.
  • Note: distinct from hydroxide ion
  • OH⁻.
  • Common in alcohols (names often end in -ol).

Carbonyl (C=O)

  • Structure: carbonyl carbon double-bonded to oxygen.
  • Polar and reactive center.
  • Within carbon skeleton: ketones; at end of chain: aldehydes.
  • Examples: acetone (ketone), propanal (aldehyde).
  • Isomeric relationships: a ketone and an aldehyde can be structural isomers with different properties.

Carboxyl (–COOH)

  • Structure: carbon double-bonded to oxygen and also bonded to a hydroxyl group.
  • Acidity: releases H⁺; forms carboxylate (–COO⁻) in ionized form.
  • Common acids: acetic acid (vinegar).
  • In cells, often exists as carboxylate anion.
  • Reaction example: ext{R-COOH}
    ightleftharpoons ext{R-COO⁻} + ext{H⁺}

Amino (–NH₂)

  • Structure: nitrogen bonded to two hydrogens and to the carbon skeleton.
  • Basic: can accept a proton to form –NH3⁺ under cellular conditions.
  • In amino acids, amino and carboxyl groups coexist (glycine example).
  • Ionization state: generally ionized to carry a positive charge at physiological pH.

Sulfhydryl (–SH)

  • Structure: sulfur–hydrogen bond (thiols).
  • Polar, but less so than –OH.
  • Can form disulfide bonds aiding protein stabilization.
  • Example: ethanethiol.

Phosphate (–OPO₃²⁻ or –OPO₃H₂ in acids)

  • Structure: phosphorus bonded to four oxygens; two oxygens are negatively charged; one oxygen bonds to the carbon skeleton.
  • Ionized form is common in biology.
  • Roles: energy transfer (e.g., ATP) and formation of organic phosphates.

Methyl (–CH₃)

  • Structure: carbon with three hydrogens attached to the carbon skeleton.
  • Property: generally unreactive; influences molecule shape and hydrophobicity.

Functional Group Summary (quick recall)

  • Hydroxyl: polar; alcohols; -ol suffix.
  • Carbonyl: C=O; aldehydes vs ketones.
  • Carboxyl: acidic; R-COOH ⇌ R-COO⁻ + H⁺.
  • Amino: base; amino acids; can be protonated.
  • Sulfhydryl: thiols; disulfide bonding.
  • Phosphate: energy transfer; organic phosphates; negative charges.
  • Methyl: unreactive; shape modifier.

Thalidomide: A Case Study in Enantiomers and Regulation

  • Thalidomide was sedative with teratogenic risks.
  • The body can convert one enantiomer into the harmful form; regulatory challenges highlighted.
  • In 1962, FDA inspector Frances Kelsey blocked approval in the U.S. due to safety concerns, delaying adoption.
  • Kefauver-Harris Drug Amendments Act (1962) tightened drug safety and efficacy requirements, extending development and testing to ensure safer drugs.
  • Impact: modernized drug approval processes; long, regulated clinical trials became standard.

Quick Recall Targets

  • Identify asymmetric carbons: a carbon with four different substituents.
  • Distinguish structural, geometric (cis/trans), and enantiomeric isomers.
  • Name and recognize functional groups: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.
  • Explain why carboxyl groups act as acids: ability to donate H⁺ and form carboxylate.
  • Understand the acid-base and biomolecular relevance of functional groups in biological molecules.