Chemistry II - Organic Chemistry and The Molecules of Life

Chemistry II (Organic Chemistry and The Molecules of Life)

Organic Chemistry

• Organic chemistry is the chemistry of carbon.

Properties of Organic Compounds

The Molecules of Life

• Carbohydrates, lipids, proteins, and nucleic acids are the molecules of life.

Binding Properties of Carbon

• Carbon can covalently bind up to 4 different atoms.

• Carbon can bind itself.

  • This creates an infinite variety of carbon skeletons with energy-rich covalent bonds.

• Carbon can form single, double, and triple bonds.

• Result: Infinite diversity and complexity of organic molecules.

Hydrocarbons

• Composed entirely of carbon (C) and hydrogen (H) atoms.

• Very strong.

• Form stable portions of most biological molecules.

Functional Groups

• Bind to the carbon backbone and convey specific chemical properties to the compound.

  • Example: Estrogen vs. testosterone.

How Cells Build Organic Compounds

• Overview: Monomers become polymers.

• Cells join monomers into chains called polymers via dehydration reactions.

  • This results in covalent linkage of the monomer to the chain through loss of a $H_2O$ molecule.

• Cells break polymers down into monomers via hydrolysis reactions.

Biological Molecules

Carbohydrates

• Functions:

  • Energy-yielding fuel stores.

  • Extracellular structural elements and signals.

  • Provide bulk in feces.

• Composition:

  • Building blocks of monosaccharides.

    • Examples: glucose, fructose, ribose, deoxyribose.

  • Disaccharides

    • Two monosaccharides covalently linked.

    • Examples:

      • Sucrose (table sugar).

      • Lactose (milk sugar).

      • Maltose (grain sugar).

  • Polysaccharides (aka complex carbohydrates).

    • Many sugar units (same or different) covalently linked.

    • Examples:

      • Starch

        • Energy storage in plants.

        • Polymer of glucose subunits.

        • Amylase is an enzyme that breaks starch into monosaccharides usable by humans.

      • Glycogen

        • Energy storage in animal cells.

        • Polymer of glucose subunits.

      • Cellulose

        • Polymer of glucose.

        • Humans do not have cellulase, so linkages cannot be hydrolyzed.

          • Therefore, it acts as "fiber" or bulk in feces.

Lipids

• Introduction:

  • Characterized by their inability to dissolve in $H_2O$.

    • All hydrophobic.

  • Functions: protection, insulation, regulation, vitamins, structure (like membranes, steroids, etc.), energy.

• Types:

  • Fats (aka triglyceride)

    • Building blocks:

      • An alcohol (glycerol) + 3 fatty acids

        • Unsaturated fatty acids

          • Liquid at room temperature.

          • Contain double bonds.

        • Saturated fatty acids

          • Solid at room temperature.

          • No double bonds.

    • Stored in adipose cells.

  • Phospholipids

    • Phosphate replaces one of the fatty acids.

    • Form lipid bilayer with hydrophobic and hydrophilic molecular ends.

  • Steroids

    • Very different from fats in structure and function, but still a lipid (hydrophobic).

    • Carbon skeleton forms 4 fused rings.

    • Different steroids arise from different functional groups.

    • Cholesterol

      • Serves as “base steroid” or building block.

      • Examples: cholesterol, bile salts, estrogen, progesterone, testosterone.

    • Anabolic steroids

Proteins

• Introduction

  • Protein = polymer of amino acid monomers.

  • Each protein has a unique, 3-D structure that corresponds to a specific function.

  • Functions: regulation, transport, protection, contraction, structure, energy.

• The Monomers: Amino Acids (aa)

  • All proteins are constructed from the same 20 amino acids.

  • Each aa differs only in “R group.”

    • Gives each aa its special chemical behavior.

    • AAs are grouped together according to their side chain properties: hydrophobic, hydrophilic, acidic, basic.

• Proteins as Polymers

  • Amino acids are linked together by dehydration reactions, forming a peptide bond.

• Protein Shape

  • A functional protein is one or more polypeptides precisely folded into a unique 3-D shape.

    • The final 3-D conformation facilitates its specific function.

  • Proteins have at least 3 levels of structure. If the protein has more than 1 polypeptide, it has a 4th level: 4° structure.

    • 1° structure

      • Sequence of amino acids held together by peptide bonds.

      • Sequence is determined by inherited genetic info.

      • Even a slight change in 1° structure may affect the structure and function of the protein.

        • Ex: sickle-cell anemia.

    • 2° Structure

      • Hydrogen bonds between the backbone of the 1° structure.

      • Result is a helical coil (α-helix) or a sheet-like array (β-pleated sheet).

    • 3° Structure

      • Final 3-dimensional conformation of a protein that results from weak interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, etc.) between the R groups.

        • Hydrophobic regions congregate in the interior, away from $H_2O$.

        • Hydrophilic regions congregate toward the exterior, in contact with $H_2O$.

        • Chemical bonding (H-bonds, ionic bonds, etc.) between different parts of the polypeptide reinforces the shape.

    • 4° structure

      • Complexing of 2 or more polypeptide chains through weak interactions.

        • Ex: hemoglobin.

• Protein Classifications

  • Fibrous (structural) proteins

    • Extended and strandlike.

    • Insoluble in water and very stable.

    • Ideal for mechanical support and tensile strength.

    • Ex: collagen, keratin, etc.

  • Globular (functional) proteins

    • Compact and spherical.

    • Water-soluble and chemically active.

    • Play crucial roles in virtually all biological processes.

    • Ex: antibodies, peptide hormones, enzymes, chaperones, etc.

• Protein Denaturation

  • Fibrous proteins are stable (some exhibit only 2° structure), but globular proteins are not (most exhibit 3° or even 4° structure) and are therefore highly dependent on weak bonds to maintain their final, 3-D conformation and ultimate function.

  • Since weak bonds are fragile, they are easily broken by chemical and physical factors (high temps, chemicals, extreme pH, etc.).

  • This causes the protein to unravel and lose its normal 3-D conformation; therefore, normal functioning is lost (which is often irreversible).

• Enzymes

  • Globular proteins that speed up chemical reactions (catalysts).

  • Lock and key or hand-in-glove induced fit models.

  • Usually end in “ase”.

    • Examples: lipase, proteases, etc.

  • Clinical: lactose intolerance.

Nucleic Acids

• Nucleotides

  • Composed of:

    • 5-carbon sugar (pentose)

      • Ribose in RNA.

      • Deoxyribose in DNA.

    • A Base

      • A, T, C, U, and G.

    • A phosphate group

  • Polymerize into nucleic acids.

• Nucleic Acids

  • Provide instructions for building proteins (blueprints for life).

  • DNA

    • Double-stranded; forms double helix.

      • Sugar-phosphate backbone.

      • Bases H-bonded between strands.

    • A, T, C, G.

    • Genetic messages are encoded in base sequence.

    • In a gene, the sequence of nucleotide bases is translated into an amino acid sequence to make a specific protein.

  • RNA

    • Single-stranded.

    • A, U, C, G.

    • The function is the assembly of proteins.

Adenosine Triphosphate (ATP)

• Chemical energy used by all cells.

• ATP/ADP cycle

  • Energy is released by breaking the high-energy phosphate bond.

    • A-P-P-P → A-P-P + P + Energy for anabolism and cellular activities.

  • Restoration of energy bonds for future use.

    • A-P-P + P + Energy (from catabolism) → ATP.

• How ATP drives cellular work:

  • Transport work.

  • Mechanical work.

  • Chemical work.