Organic Molecules and pH

Organic Molecules

• Contain carbon covalently bound to hydrogen.
• Carbon has 4 electrons in the outer shell and bonds covalently to fill the outer shell with 8 electrons.
• In the body, carbons are linked to form chains or rings.
• Serve as a "backbone" to which more reactive functional groups are added.
• Functional groups include carbonyl, hydroxyl, and carboxyl.

Four Basic Macromolecules in the Body

1. Carbohydrates

• Organic molecules contain carbon, hydrogen, and oxygen.
• General formula for monosaccharides: $C<em>nH</em>{2n}O_n$
• Include simple sugars (monosaccharides) and longer molecules (polysaccharides).
  • Examples: glucose, galactose, and fructose.
• Two monosaccharides can join to form a disaccharide (double sugar).
  • Examples: sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose x2).
• Major polysaccharides are chains of repeating glucose subunits.
  • Examples: starch and glycogen.

2. Lipids

• Insoluble in polar solvents (nonpolar) such as water (hydrophobic).
• Consist primarily of hydrocarbon chains and rings.

Triglycerides

• Formed by dehydration synthesis (condensation) of 1 glycerol and 3 fatty acids (monomer of lipids).
  • Saturated: Hydrocarbon chains of fatty acids are joined by single covalent bonds.
    • Example: butter.
  • Unsaturated: Double bonds within hydrocarbon chains.
    • More liquid form, like oil.

Phospholipids

• Lipids containing a phosphate group.
  • Phosphate part is polar and hydrophilic.
  • Lipid part is nonpolar and hydrophobic.
• Aggregate into micelles in water.
  • Polar part interacts with water; nonpolar part is hidden in the middle.
• Act as surfactants by reducing (breaking) surface tension.

3. Steroids

• Nonpolar and insoluble in water
  • All have three 6-carbon rings joined to a 5-carbon ring
  • Cholesterol is a precursor for steroid hormones
• Is a component of cell membranes

4. Prostaglandins

• Are fatty acids with cyclic hydrocarbon group
• Produced by and active in most tissues
• Serve many regulatory functions

5. Proteins

• Made of long chains of amino acids (20 different types).
• Contain an amino group at one end and a carboxyl group at the other end.
• Differences between amino acids are due to differences in functional groups (R).
• Amino acids are linked by peptide bonds, creating peptides formed by dehydration reactions.
  • <100 amino acids: polypeptide.
  • >100 amino acids: protein.
• Four levels of structure:
  • Primary: Sequence of amino acids.
  • Secondary: Weak hydrogen bonding of amino acids results in alpha helix or beta-pleated sheet shapes.
  • Tertiary: Bending and folding of polypeptide chains to produce 3-dimensional shape.
    • Formed and stabilized by weak bonds between functional groups.
    • Can be denatured by heat or pH.
  • Quaternary: Forms when a number of polypeptide chains are covalently joined.
• Many proteins are conjugated with other groups.
  • Examples: glycoproteins or lipoproteins.

6. Nucleic Acids

• Include DNA and RNA, made of long chains of nucleotides, which consist of:
  • A 5-carbon sugar.
  • A phosphate group.
  • A nitrogenous base.
    • Purines: guanine (G) or adenine (A).
    • Pyrimidines: cytosine (C) or thymine (T).
• Deoxyribose sugar (5C) is covalently bonded to 1 of 4 bases.
• Each base can form hydrogen bonds with other bases, holding two strands of DNA together, forming a double helix.
• Law of complementary base pairing:
  • Adenine with thymine.
  • Cytosine with guanine.
• RNA:
  • Sugar ribose is bonded to 1 of 4 bases:
    • Guanine or adenine
    • Cytosine or uracil (replaces thymine)
  • Single-stranded
  • Three types are synthesized from DNA and allow it to direct activities of a cell:
    • Messenger RNA (mRNA).
    • Transfer RNA (tRNA).
    • Ribosomal RNA (rRNA).

Dehydration Synthesis

• Bonding together of subunits to form a longer molecule, resulting in the production of a water molecule.

Hydrolysis

• Splitting of a larger molecule into its subunits, using a water molecule.

Acids and Bases & The pH Scale

• Acids: Release protons ($H^+$) in a solution (proton donor).
  • pH less than 7.
    • Examples: hydrochloric acid, phosphoric acid, nitric acid, sulfuric acid, carbonic acid.
• Bases (alkaline): Lower $H^+$ levels of a solution (proton acceptor).
  • pH between 7-14.
    • Examples: sodium hydroxide, potassium hydroxide, calcium hydroxide, ammonium hydroxide.
• Buffer: A system of molecules and ions that prevents changes in $H^+$ concentration, stabilizing pH.
  • Slows pH changes by combining with or releasing $H^+$.
• Blood pH normal range: 7.35-7.45.
  • Maintained by buffering action.
    • Acidosis occurs if pH < 7.35.
    • Alkalosis occurs if pH > 7.45.

Equation for pH

• Measures concentration of $H^+$.
• $pH = \log \frac{1}{[H^+]}$

Acidic & Basic Numbers

• Acids: pH < 7 (0-7).
• Bases: pH > 7 (7-14).
• Neutral water: pH = 7.

Peptide Bonds

• Covalent bond linking two amino acids in a protein or peptide chain.
  • Forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH₂) of another.
• Formation process:
  • Dehydration synthesis.
    • Carboxyl group reacts with the amino group.
    • A water molecule ($H_2O$) is removed.
    • A covalent bond forms between the carbon of the carboxyl group and the nitrogen of the amino group.

Structure of Nucleotides

• Basic building block of nucleic acids (DNA and RNA).
• Three components:
  1. Phosphate group ($PO_4^{3-}$).
  2. Pentose sugar (5-carbon sugar):
     • Deoxyribose in DNA.
     • Ribose in RNA.
  3. Nitrogenous base (one of five possible bases):
     • Purines: Adenine (A), Guanine (G).
     • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA).

Law of Complementary Base Pairing

• In double-stranded DNA, each nitrogenous base on one strand pairs with a specific, complementary base on the opposite strand.
• Governed by hydrogen bonding and the shapes of the bases.