Organic Molecules - BIOL-107

Topic 5: Organic Molecules

Molecular Definition

• Molecule: A compound formed by the bonding of two or more elements.

• Two major groups of molecules:

  • Inorganic Molecules

  • Organic Molecules

Differentiation

• Major differentiation criterion: Presence of carbon atoms

Inorganic Molecules

• Definition: Compounds that do not typically stem from living organisms.

• Characteristics:

  • Often do not contain carbon.

  • Generally small and simple structure.

• Examples:

  • Carbon dioxide (CO2)

  • Water (H2O)

  • Oxygen (O2)

  • Ammonia (NH3)

  • Hydrogen (H2)

• Native State: The form an inorganic compound assumes under normal conditions.

  • Example: The native state of water is liquid.

  • Energy may be added or removed, but compounds will return to their native state.

Organic Molecules

• To qualify as an organic molecule, it must contain at least one carbon-hydrogen (C-H) bond.

• Historical context:

  • Initially defined as molecules synthesizable only by living organisms.

  • Currently, many organic molecules can be synthesized in laboratories.

• Energy Influence:

  • Adding or removing energy beyond a threshold can alter chemical composition irreversibly.

  • Example: Cooking an egg changes it irreversibly; it cannot become raw again.

Identifying Organic Molecules

• Examples:

  • Methane (CH4): Organic ✓

  • Carbon Dioxide (CO2): Not organic ✓

  • Sodium Chloride (NaCl): Not organic ✓

  • Glucose (C6H12O6): Organic ✓

  • Water (H2O): Not organic ✓

  • Glycine (C2H5O2N): Organic ✓

Carbon Specialization

• Atomic Number of Carbon (C): 6

• Valence Electrons: 4

  • Vacancies Available: 4

• Electron Sharing: Carbon prefers to share electrons rather than donate or receive them, resulting in the formation of covalent bonds.

• Example of bond sharing: Methane (CH4) illustrates this.

Bonding and Structures

• Carbon can bond with up to 4 other atoms.

  • Example formation of methane:

  $ext{C} + 4 ext{H} <br>ightarrow ext{CH}_4$

• Stick Diagrams: Each stick represents a shared pair of electrons around carbon.

  • Carbon typically has 4 "sticks" (bonds).

Double and Triple Bonds

• Atoms can share two or three pairs of electrons.

• Representations:

  • Double Bond: Represented by "="

  • Example of double bond: Ethylene (C2H4)

  • Triple Bond Example: Acetylene (C2H2)

Hydrocarbons

• Definition: Simplest form of carbon compounds consisting of carbon chains exclusively bonded with hydrogen.

• Backbone: Hydrocarbons have a carbon backbone with various bond arrangements:

  • Benzene Chains

  • Branched Chains

  • Rings

  • Aromatic Rings

• The C-H bond is a high-energy bond crucial in many fuels (e.g., methane, ethane, propane).

Functional Groups

• Carbon can bind with elements from CHNOPS (Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur).

• Most organic molecules have a carbon backbone.

• Definition of Functional Group: A specific group of atoms that determines the characteristics and reactivity of the molecule. Each functional group reacts consistently across different molecules.

• Examples of Functional Groups:

  • Hydroxyl (-OH): Polar; confers alcohol properties to hydrocarbons.

  • Carboxyl (-COOH): Acidic; donates H+ and decreases pH.

  • Amine (-NH2): Basic; involved in amino acid formation.

  • Phosphate (-PO4): Important in energy transfer and DNA structure.

Characteristics of Functional Groups

• Functional groups dictate chemical behavior. A molecule can have multiple functional groups.

• Examples of Structures:

  • Common groups: Hydroxyl, Carboxyl, Amine, Phosphate, Sulfhydryl, Methyl.

  • Functional groups can yield different compounds from the same carbon backbone (e.g., acetic acid).

Hydrophilic vs. Hydrophobic

• Hydrophilic (Water-Loving):

  • Definition: Molecules with functionalities that interact favorably with water (e.g., polar groups).

• Hydrophobic (Water-Fearing):

  • Definition: Molecules that do not interact well with water are termed hydrophobic.

• Biological Relevance: Most biological reactions occur in aqueous solutions; hence the interaction with water is crucial for molecular function.

• Examples:

  • Hydrophilic: Molecules containing many electronegative oxygens (e.g., glucose).

  • Hydrophobic: Hydrocarbons such as hexane (gasoline).

Isomers

• Definition: Two substances that have the same chemical formula but different structures (e.g., glucose and fructose).

• Examples of Isomers:

  • Glucose (e.g., C6H12O6) vs. Fructose: same formula, different structures leading to different properties and tastes.

Building Blocks of Life

• Organic Molecule Types:

  • Carbohydrates: Composed of C, H, O in a 1:2:1 ratio.

  • Lipids: Composed of C, H, O with fewer O's and more H's.

  • Proteins: Composed of C, H, O, N, S (not always S).

  • Nucleic Acids: Composed of C, H, O, N, P.

Macromolecules

• Definition: These groups represent macromolecules made of numerous similar subunits called monomers.

• The assembled chain of monomers is called a polymer.

From Monomers to Polymers

• Covalent Bond Formation: Achieved through the removal of a hydroxyl group (OH) from one subunit and a hydrogen (H) from another, resulting in water removal (H2O).

  • This process is termed Dehydration Synthesis.

  • Reaction formula:

  $(OH)<em>{monomer1} + (H)</em>{monomer2} <br>ightarrow Polymer + H2O$

• Monomers, Dimers, Polymers:

  • Monomer: A single subunit.

  • Dimer: Two subunits combined.

  • Polymer: A chain of multiple subunits.

Reversing Polymerization

• Living organisms continuously construct and break down polymers.

  • Starch from plants is polymerized glucose.

  • When consumed, starch is hydrolyzed back to glucose in the intestines.

Breaking Down Polymers

• Reverse of Polymer Creation: Involves adding water, termed Hydrolysis:

  • Represents the process of breaking polymers into monomers by incorporating water.

  • Hydrolysis example formula:

  $(Polymer + H2O <br>ightarrow OH + H)<em>{monomer1} + (H)</em>{monomer2}$

Role of Enzymes

• Function: Enzymes enable dehydration synthesis and hydrolysis reactions by facilitating interaction between monomers or between water and dimers.