Chapter 4 Notes: Carbon and the Molecular Diversity of Life

Organic Chemistry

• Organic chemistry is the study of compounds that contain carbon, regardless of their origin.
• Organic compounds can range from simple to very large molecules.
• Organic chemistry is key to understanding the origin of life.
• Any molecule that contains carbon is considered an organic compound.
• Carbon forms the basis of living things.

Origin of Organic Molecules

• A key question is whether organic molecules can be made outside of a living organism.
• The Miller-Urey experiment demonstrated that chemical reactions (with no life or oxygen present) could generate organic molecules.

Carbon Bonding

• Hydrogen has a valence of 1.
• Oxygen has a valence of 2.
• Nitrogen has a valence of 3.
• Carbon has a valence of 4.
• Carbon atoms can form diverse molecules by bonding to four other atoms.

Molecular Diversity

• Carbon's ability to bond with four other atoms leads to molecular diversity, which includes:
  • Length
  • Branching
  • Double bond position
  • Presence of rings

Hydrocarbons

• Hydrocarbons are nonpolar and hydrophobic.
• The arrangement of carbon branching affects the shape and function.
• Linear vs. branched hydrocarbons can have different molecular arrangements.
• Isomers are molecules with the same molecular formula but different structures (like a mirror image).

Enantiomers

• Enantiomers are structures that are different due to their arrangements.
• They can result in different isomers.
• Enantiomers won't have the same interactions with other molecules.

Importance of Chemical Groups

• The behavior of chemical compounds (and the reactions they participate in) is dictated by functional groups.
• Slight chemical differences in functional groups can have significant impacts.
• Examples include hormones like estradiol and testosterone, which have different effects due to different functional groups.
• Functional groups can affect polarity and the formation of bonds.

Functional Groups

• The seven functional groups most important in the chemistry of life:

  1. Hydroxyl group (-OH)

     • Example: Ethanol (alcohol)
     • Polar due to electronegative oxygen.
     • Forms hydrogen bonds with water.
     • Compound name: Alcohol

  2. Carbonyl group (C=O)

     • Examples:
       • Acetone (ketone)
       • Propanal (aldehyde)
     • Sugars with ketone groups are called ketoses, and those with aldehydes are called aldoses.
     • Compound name: Ketone or Aldehyde

  3. Carboxyl group (-COOH)

     • Example: Acetic acid (in vinegar)
     • Can donate protons, acting as an acid.
     • Ionized form is -COO- (carboxylate ion), found in cells.
     • Compound name: Carboxylic acid, or organic acid

  4. Amino group (-NH2)

     • Example: Glycine (amino acid)
     • Acts as a base.
     • Ionized form is -NH3+, found in cells.
     • Compound name: Amine

  5. Sulfhydryl group (-SH)

     • Example: Cysteine (sulfur-containing amino acid)
     • Two -SH groups can react to form a cross-link, stabilizing protein structure.
     • Compound name: Thiol
     • Disulfide bridges covalently stabilize protein structures

  6. Methyl group (-CH3)

     • Example: 5-Methylcytosine (in DNA)
     • Affects gene expression and the shape/function of sex hormones.
     • Compound name: Methylated compound
     • Nonpolar.

  7. Phosphate group (-OPO32-)

     • Example: Glycerol phosphate
     • Contributes a negative charge.
     • Allows a molecule to react with water, releasing energy.
     • Compound name: Organic phosphate
     • Found in DNA, proteins, and carbohydrates.

ATP (Adenosine Triphosphate)

• ATP is an important source of energy for cellular processes.
• It's considered the energy currency of the cell.
• It contains adenosine and three phosphate groups.
• When ATP reacts with water, it releases energy and becomes adenosine diphosphate (ADP) and inorganic phosphate ($P_i$).
• The released inorganic phosphate can be harnessed by the cell to do work.
• $ATP \rightarrow ADP + P_i$ releases energy.