Organic Molecules of Living Systems

Organic Molecules of Living Systems

Dr. A. Gilleland

Basic Concepts

• Organic Compounds:
  • Compounds that contain carbon.
  • Usually a combination of carbon, hydrogen, and various other elements.
• Organic Chemistry: The study of compounds containing carbon.
• Carbon Properties:
  • Has 4 valence electrons.
  • Usually forms covalent bonds with other molecules.
  • Can form as many as 4 stable covalent bonds with up to 4 atoms.
  • Carbon bonded to 4 hydrogens creates a tetrahedral configuration, termed a hydrocarbon (since it consists only of carbon and hydrogen).

Simple Organic Molecules

Molecular Formulas and Models

• Methane: CH₄
  • Ball-and-Stick Model
  • Space-Filling Model
• Ethane: C₂H₆
  • Ball-and-Stick Model
  • Space-Filling Model
• Ethene (ethylene): C₂H₄
  • Structural Formula

Carbon & Structure

• Carbon can form multiple structures:
  • Chain Structure
  • Branched Structure
  • Ring Structure
• Can have double bonds and even triple bonds.
• Bond Representation:
  • A single line between atoms indicates a single covalent bond.
  • A double line represents a double bond.

Structural Variations

a) Length

• Ethane Example:
  • H H
    H-C-C-H
    H H
• Propane Example:
  • HHH
    H-C-C-C-H

b) Branching

• Butane:
• 2-Methylpropane (commonly called isobutane):
  • Both are isomers with the same chemical formula but different geometric arrangements, leading to significant differences in reactivity.
  • Isomers: Molecules with the same chemical formula but different spatial arrangements.

c) Presence of Rings

• Cyclohexane:
  • Represented in two structures: one showing all atoms, the other simplified.
  • Assumption: If points in a ring are not represented, they are carbon atoms with bonded hydrogens.
• Benzene Ring Structure:
• Structural implications show similarity in molecular structure among biologically active compounds such as Estradiol and Testosterone, but differences in function due to spatial arrangement.

d) Double Bond Position

• 1-Butene and 2-Butene:
  • Presence of double bonds introduces bends in the hydrocarbon chain, affecting physical and chemical properties.

Structural Isomers

• Isomers Overview:
  • Identical chemical formulas but different spatial arrangements.
• Types of Isomers:
  • Structural Isomers
  • Cis-Trans (Geometric) Isomers
  • Enantiomers

a) Structural Isomers

• Represented with varying carbon arrangements:

b) Cis-Trans Isomers

• Cis Isomer: The two substituents (Xs) are on the same side.
• Trans Isomer: The two substituents (Xs) are on opposite sides.

c) Enantiomers

• Chiral Carbon:
  • An asymmetrical carbon atom with four different groups attached.
  • Enantiomers are mirror images of each other but differ functionally in biological systems.
• Examples:
  • Effective and ineffective enantiomers include Ibuprofen and Albuterol, where specific forms have therapeutic efficacy, while others do not.

Biologically Important Functional Groups

• Functional Groups:
  • Determinants of a molecule’s function and reactivity due to their shape and arrangement in space.
  • Include specific atom groups:
  • Hydroxyl
  • Carbonyl
  • Carboxyl
  • Amino
  • Sulfhydryl
  • Phosphate
  • Methyl

Structure and Functional Properties of Functional Groups

Hydroxyl (-OH)

• Examples:
  • Ethanol
  • Properties: Polar, enabling hydrogen bond formation with water, thus aiding in the dissolution of organic compounds.

Carbonyl

• Types:
  • Ketones: Carbonyl group within carbon skeleton.
  • Aldehydes: Carbonyl group at chain end.
• Examples:
  • Acetone (ketone), Propanal (aldehyde).
  • Structural isomers may display different properties.

Carboxyl

• Examples:
  • Acetic Acid
  • Properties: Acts as an acid, capable of donating H⁺ due to the polarized bond between oxygen and hydrogen.
  • Exists typically in ionized form in cells as a carboxylate ion.

Amino

• Examples:
  • Glycine
  • Properties: Acts as a base by picking up H⁺; typically ionized +1 charge form can also exist.

Sulfhydryl

• Examples:
  • Cysteine
  • Properties: Form cross-links between sulfur atoms, which stabilize protein structures (for example, affect the curliness or straightness of hair).

Phosphate

• Examples:
  • Glycerol Phosphate
  • Properties: Provides negative charge; potential to react with water and release energy.

Methyl

• Examples:
  • 5-Methyl Cytidine
  • Properties: Methyl group addition affects gene expression and can alter the shape/function of hormones.

Macromolecules

• Giant Molecules: Composed of thousands of atoms.

Major Types of Macromolecules:

• Carbohydrates
• Proteins
• Nucleic Acids
• Polymers: Long chains of monomers linked by covalent bonds.
  • Polymers can be carbohydrates or proteins; monomers are their building blocks.
• Lipids: Important yet typically not classified as macromolecules due to size.

The Macromolecules of Life: A Summary

Biological Reactions and Molecule Interactions

a) Dehydration Reaction

• Function: Synthesizes polymers by removing a water molecule and forming a bond.

b) Hydrolysis

• Function: Breaks down polymers by adding a water molecule, breaking chemical bonds.

Carbohydrates

• Monosaccharides: Simple sugars consisting of carbon, hydrogen, and oxygen in a ratio of 1:2:1.
  • Example: Glucose C₆H₁₂O₆, Ribose C₅H₁₀O₅, Fructose C₆H₁₂O₆
• Aldoses (Aldehyde Sugars) vs. Ketoses (Ketone Sugars):
  • Glyceraldehyde: Trioses (3-carbon sugars).
  • Pentoses: 5-carbon Sugars (e.g., Ribose).
  • Hexoses: 6-carbon Sugars (e.g., Glucose).

Disaccharides and Polysaccharides

• Disaccharides: Formed by joining two monosaccharides via dehydration synthesis.
• Hydrolysis converts disaccharides back into monosaccharides.
• Glycosidic Linkages: Covalent bonds formed between 2 monosaccharides during dehydration.

Carbohydrate Structures

• Starch: Energy storage in plants composed of unbranched chains of alpha glucose.
• Cellulose: Provides structural support in plant cell walls composed of beta glucose, indigestible by humans (fiber).
• Glycogen: Energy storage polymer in animals, found in adipose tissues.
• Chitin: Structural polysaccharide in exoskeletons of insects and fungal cell walls.

Lipids

• Types:
  • Fats and oils (Triglycerides): Composed of glycerol and 3 fatty acids.
  • Saturated Fats: No double bonds between carbon atoms, solid at room temperature.
  • Unsaturated Fats: Contain double bonds, resulting in bends or kinks, liquid at room temperature.
• Phospholipids: Essential for biological membranes, amphipathic molecules with hydrophilic heads and hydrophobic tails.
• Steroids: Lipids characterized by 4 carbon rings (examples: Cholesterol, Testosterone, Estradiol).

Proteins

• Function: Perform numerous functions in the body including enzyme catalysis, structural roles, transport, defense, and signaling.
• Structure: Four levels of protein structure: Primary (amino acid sequence), Secondary (alpha helix and beta sheet), Tertiary (3D folding), Quaternary (multi-polypeptide assembly).
• Amino Acids: Building blocks of proteins; each consists of an amino group, carboxyl group, and a unique R group.
• Peptide Bonds: Link amino acids together via dehydration synthesis.

Nucleic Acids

• Role: Genetic material composed of nucleotides.
  • DNA: Double-stranded structure, contains thymine (T) as a nitrogenous base.
  • RNA: Single-stranded structure, contains uracil (U) in place of thymine (T).
• Nucleotide Components: Consist of a sugar (deoxyribose or ribose), a phosphate group, and a nitrogenous base (A, T, C, G for DNA; A, U, C, G for RNA).

Genetic Code and Protein Synthesis

• Process:
  1. Synthesis of mRNA in the nucleus from DNA.
  2. Movement of mRNA into the cytoplasm.
  3. Translation occurs where ribosomes synthesize polypeptides based on mRNA instructions, linking amino acids as per the genetic code.

Conclusion

• Studying organic molecules reveals their critical roles in biological systems by elucidating their structures, functions, interactions, and the chemical mechanisms underlying life processes.

Optional Information

Biosynthesis of Unsaturated Fatty Acids

• Fatty Acid Desaturase: Enzyme removing hydrogen atoms, creating double bonds in fatty acids.
• Elongases and Desaturases: Enzymes crucial for building essential fatty acids needed in biological functions.

d orbital and Octet Rule Exceptions

• Nonmetals with 3+ energy levels can exhibit hypervalence, accommodating more than 8 electrons.
• Examples of hypervalent atoms and their significance in biological systems.

This comprehensive summary captures the essence of organic molecules in biological systems, integrating key concepts, definitions, and examples necessary for a thorough understanding of the subject matter.