Organic Chemistry Notes

Organic Chemistry Basics

Carbon

  • Carbon, along with water (H_2O) , is a primary component of living organisms.

  • It forms 4 covalent bonds, allowing for diverse molecular structures.

Functional Groups

  • Functional groups are recognizable groups of atoms that determine how a molecule reacts chemically.

1. Hydroxyl

  • Polar.

  • Forms alcohols.

  • Representation: R-O-H.

2. Carbonyl

  • Polar.

  • Forms aldehydes and ketones.

  • Aldehyde: R-C(=O)-H.

  • Ketone: R-C(=O)-R.

3. Carboxyl

  • Charged, weak acid.

  • Representation: R-C(=O)-OH.

4. Amino

  • Charged, weak base.

  • Representation: R-N-H
    |
    H

5. Sulfhydryl

  • Polar.

  • Representation: R-S-H.

6. Phosphate

  • Charged, acid.

  • Representation: O=P(R)(-OH)(-OH).

7. Methyl

  • Not polar or charged, hydrophobic.

  • Representation: R-CH{_3}.

Monomers and Polymers

  • Monomers are simple building blocks that link to form complex polymer structures through covalent bonds.

  • Monomers \leftrightarrow Polymers.

  • Monomers are common to most living things, while polymers are unique to each species.

  • Monomers are usable in cellular respiration to make ATP, while polymers are a storage form of energy.

  • Monomers can cross biological membranes (e.g., GI tract, blood vessels, cell membranes), while most polymers cannot cross easily.

Dehydration Synthesis and Hydrolysis

  • Dehydration Synthesis: Monomers link together by removing a water molecule (-H_2O).

  • Hydrolysis: Polymers break down into monomers by adding a water molecule (+H_2O).

Biological Macromolecules

  • Monomers and corresponding Polymers:

    • Monosaccharides \leftrightarrow Carbohydrates.

    • Glycerol, fatty acids, phosphates \leftrightarrow Lipids / Fats.

    • Amino acids \leftrightarrow Proteins.

    • Nucleotides \leftrightarrow Nucleic Acids.

1. Carbohydrates

  • Monomers: Primarily C, H, and O.

  • Ring structures with 3-7 carbons.

  • Very hydrophilic due to hydroxyl groups.

  • Examples: Glucose, Fructose, Galactose, Deoxyribose, Ribose.

Making a Disaccharide

  • Monomers link together forming glycosidic covalent bonds.

  • Example: Glucose + Glucose \rightarrow Maltose + {H_2O}.

  • Glycosidic linkage: 1-4.

Higher Order Structure

  • Linear chains (e.g., Amylose).

  • Branched chains (e.g., Amylopectin).

  • Starch.

  • Glycogen.

Functions of Carbohydrates

  • 1-2% of body mass.

  • Energy Storage: Glycogen in animals, Starch in plants.

  • Usable form in cell respiration: Glucose.

  • Structural: Cellulose (fiber in plants), Chitin (exoskeletons in insects/arthropods, fungus cell walls).

2. Fats / Lipids

  • Monomers: Primarily C, H, and very little O.

  • Very hydrophobic.

  • Three major categories of polymers: Triglycerides (neutral fats), Phospholipids, Sterols.

Triglycerides

  • Monomers: 1 glycerol + 3 fatty acids.

  • Monomers link together forming ester covalent bonds.

2. Phospholipids

  • Monomers: 1 Glycerol with a phosphate functional head group (i.e. choline, serine, ethanolamine, etc.) + 2 fatty acids.

  • Hydrophobic tails.

  • Hydrophilic head.

3. Sterols

  • Cholesterol derivatives.

Functions of Fats/Lipids

  • Triglycerides: Energy storage, packing of organs, protection, insulation.

  • Phospholipids: Biological membranes, insulates brain tissues.

  • Sterols: Bile component (aids in digestion), Vitamin D precursor (bone growth), Sex hormones (estrogen, testosterone), Adrenal cortex hormones (cortisol, aldosterone).

3. Proteins

  • Monomers:

  • Backbone comprised of amino and carboxyl functional groups.

  • Amino acid.

Making a Protein polymer

  • Monomers link together forming peptide covalent bonds.

  • Peptide bond.

Higher Order Structures

  • 4 hierarchies:

    • Primary (1º).

    • Secondary (2º).

    • Tertiary (3º).

    • Quaternary (4º).

PRIMARY STRUCTURE

  • Linear sequence of amino acids.

  • Linked by peptide bonds.

  • Amino (N) end vs. Carboxyl (C) end.

SECONDARY STRUCTURE

  • Local organization of nearby amino acids linked by H bonds in the backbone.

  • \alpha-helix.

  • \beta-pleated sheet.

TERTIARY STRUCTURE

  • 3-D arrangement of protein due to interactions between side chains:

    • H bonds.

    • Ionic bonds.

    • Hydrophobic interactions.

    • Disulfide bridges.

QUATERNARY STRUCTURE

  • Association of 2 or more peptide chains to form a functional protein.

  • Not all proteins need this level of organization.

Functions of Proteins

  • ~10-30% of body mass.

    • Structural (elastin, collagen).

    • Enzymes (collagenase, pepsin).

    • Transporters (hemoglobin, ATPases).

    • Hormones (insulin, growth hormone).

    • Motility (myosin, actin).

    • Immunity (antibodies).

    • Etc.

4. Nucleic Acids

  • Nucleotide monomers are made up of three parts

    • 1. Sugar

      • Ribose in RNA

      • Deoxyribose in DNA (no –OH on 2’C)

    • 2. Phosphate group

    • 3. Nitrogenous Bases

      • Pyrimidines

        • Uracil (U) – in RNA only

        • Thymine (T) – in DNA only

        • Cytosine (C)

      • Purines

        • Adenine (A)

        • Guanine (G)

  • Monomers link together forming phosphodiester covalent bonds

    • 5' vs. 3' end

    • Sugar-phosphate backbone

    • Bases

Higher Order Structures - DNA

  • Double helix.

  • Strands are antiparallel.

  • Strands are complementary due to base pairing:

    • A’s and T’s bond with 2 H bonds.

    • C’s and G’s bond with 3 H bonds.

Higher Order Structures - RNA

  • RNAs vary in structure

Functions of Nucleic Acids

  • DNA

    • Basis of inheritance

    • Codes for RNA through a process called transcription

  • RNA

    • Directs protein synthesis through a process called translation

      • Messenger RNA (mRNA) – attaches to ribosomes and specifies order of amino acids linked to form proteins

      • Transfer RNA (tRNA) – brings specific amino acids into the ribosome

      • Ribosomal RNA (rRNA) – primary component of ribosomes