Organic Molecules
Organic Molecules
Molecules Reminder
A molecule is a compound formed by bonding two or more elements.
There are two major groups of molecules:
Inorganic
Organic
The primary difference between them is the presence of carbon atoms.
Inorganic Molecules
Compounds that don't typically originate from living organisms.
Often do not contain carbon.
Relatively small, simple molecules.
Examples: CO2, H2O, O2, NH3, H_2.
The compound will always return to its native state, which is its state under normal conditions (e.g., water's native state is liquid).
Energy can be added or released, but the substance can always revert to its native form.
Organic Molecules
Must contain at least one carbon-hydrogen (C-H) bond to be considered an organic molecule.
Historically, organic molecules were thought to be synthesized only in living things; however, most can now be synthesized in the lab.
If energy is added or removed beyond a certain threshold, the compound is irreversibly altered (e.g., cooking an egg).
Organic vs. Inorganic Examples
Examples:
CH_4 (methane) - Organic
CO_2 (carbon dioxide) - Inorganic
NaCl (salt) - Inorganic
C6H{12}O_6 (glucose) - Organic
H_2O - Inorganic
O_2 (oxygen gas) - Inorganic
C2H5O_2N (glycine) - Organic
Carbonic Acid Example
Carbonic Acid: H2CO3
It contains both carbon and hydrogen.
However, it is NOT an organic molecule because it lacks a carbon-hydrogen bond.
What Makes Carbon Special?
The atomic number of carbon (C) is 6.
It has 4 electrons in its valence shell, resulting in 4 vacancies.
Carbon tends to share electrons rather than donating or receiving them.
Covalent bonds, which involve sharing electrons, are typical for carbon.
CH_4: Carbon forms covalent bonds.
Carbon is neither reactive nor inert.
Carbon Bonding
Carbon can form covalent bonds with up to 4 other atoms.
Example: formation of CH_4
Stick Diagrams
Molecules are represented by stick diagrams, where each stick signifies a shared pair of electrons.
Carbon always has 4 sticks around it, representing its four covalent bonds.
Double Bonds
Carbon atoms can also form double bonds with other atoms.
Note: Carbon always has 4 bonds (sticks).
Double and Triple Bonds
Two atoms can share two (double bond) or three (triple bond) pairs of electrons.
Carbon often forms double or triple bonds with another element or with another carbon.
A double bond is represented by “=“.
Ethylene: C2H4, Oxygen = 6 electrons
Carbon Dioxide: CO_2
Acetylene: C2H2
Hydrocarbons
The simplest carbon compound is the hydrocarbon, consisting of carbon chains with exclusively hydrogen attached.
Hydrocarbons contain a carbon "backbone" in various arrangements:
Chains
Branched Chains
Rings
Aromatic Rings (Benzene)
Hydrocarbon Energetics
The C-H covalent bond is a high-energy bond.
Most fuels are hydrocarbons.
Examples:
Methane (natural gas): CH_4
Ethane: C2H6
Propane: C3H8
Functional Groups
Carbon can bind with any of the CHNOPS (Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur).
Organic molecules have a carbon backbone.
The characteristics and function of a molecule depend on the atoms/groups connected to the backbone.
These groups are called functional groups.
A functional group is a combination of atoms attached to the carbon backbone, which always acts in the same way.
Functional Groups Impact
Functional groups are molecular fragments that affect the function and characteristics of a molecule.
The same functional group will react similarly in different molecules, regardless of size.
Example: Estrogen vs. Testosterone
Same backbone
Different functional groups: Hydroxide (-OH), Carbonyl (-C=O), Methyl (CH3) as extra.
Common Functional Groups (List)
Hydroxyl (-OH)
Amine (-NH2)
Carboxyl (-COOH)
Carbonyl (aldehyde) (-CHO)
Carbonyl (ketone) (-C=O)
Phosphate (-PO4)
Sulfhydryl (-SH)
Methyl (-CH3) - Only hydrophobic group
Common Functional Groups: Hydroxyl and Carboxyl
Hydroxyl groups (-OH):
Confer alcohol (hydrophilic) properties to hydrocarbon chains.
Polar due to high electronegativity of oxygen.
Attract water easily.
Carboxyl groups (-COOH):
Confer acid properties to hydrocarbons.
Donate H^+ which decreases the pH in solution.
Important in amino acid structures.
Common Functional Groups: Amine and Phosphate
Amine group (-NH2):
Confer amine properties to hydrocarbons, forming amino acids -> proteins.
Acts as a base because nitrogen attracts H^+ out of solution.
Phosphate group (-PO_n):
Forms when phosphoric acid (H3PO4) dissociates.
Important in energy transfer and in DNA.
Functional Groups Overview
By knowing the functional groups, you can identify different organic molecules and their properties.
A carbon backbone can have more than one type of functional group.
When a functional group is added, the molecule becomes a certain type of compound.
Examples: Acetic Acid (Carboxyl Group), Methane
Functional Group Identification
Examples provided to identify functional groups on different compounds.
Hydrophilic vs. Hydrophobic
Hydrophilic:
'Philic' = love (philos).
Example: Philadelphia (City of Brotherly Love).
Hydrophobic:
'Phobic' = fear/dislike.
Example: Phobia (a strong fear of something).
Most biological reactions take place in water.
Therefore, a molecule's ability to interact with water is crucial for its function.
Hydrophobic vs. Hydrophilic Examples
Hexane (Gasoline): Hydrophobic (contains lots of C-H bonds)
Glucose: Hydrophilic (contains lots of electronegative oxygens)
Isomers
Isomers are two molecules with the same chemical formula but different structures.
Glucose and fructose are carbohydrates with the same chemical formula: C6H{12}O_6
However, the atoms are arranged differently.
Isomer Examples with Structures
Illustrations of Glucose and Fructose structures showing different arrangements.
Isomer Properties
Glucose and fructose have the same formula but different structures.
This rearrangement of atoms changes the taste of the sugar.
Galactose (sugar found in milk) is another isomer of glucose and fructose.
Building Blocks of Life
Organic molecules found in living organisms:
Carbohydrates = C H O (1:2:1 ratio)
Lipids (fats) = C H O (fewer O, more H)
Proteins = C H O N S* (*sometimes S)
Nucleic Acids = C H O N P
Macromolecules and Monomers
All four groups (Carbohydrates, Lipids, Proteins, Nucleic Acids) represent macromolecules.
Large macromolecules are assembled from similar small components called monomers.
The assembled chain of monomers is known as a polymer.
Monomer = one subunit
Polymer = many subunits
Monomer to Polymer: Dehydration Synthesis
All polymers are assembled the same way:
A covalent bond is formed by removing a hydroxyl group (OH) from one subunit and a hydrogen (H) from another.
This is essentially the removal of a molecule of water (H_2O) linking the two subunits together.
This process is referred to as dehydration synthesis.
Dehydration Synthesis Details
Monomers are joined together in dehydration synthesis.
This process requires ENERGY!
Terminology
Single subunits are called monomers.
Two subunits joined together are called a dimer.
Many monomers joined together are called a polymer.
Polymer Dynamics in Living Organisms
Living organisms are constantly building and breaking polymers.
Example: A plant makes starch (a polymer of glucose) to form a potato. When we eat the potato, the starch is broken down into individual glucoses in our intestines. We absorb the glucoses and may re-polymerize them into glycogen to store energy.
Starch as a Macromolecule
Starch is a macromolecule made of repeating subunits of glucose.
Breaking Polymers Down: Hydrolysis
Breaking polymers is the reverse of making them.
Instead of removing water, you add it, which is called hydrolysis.
Hydrolysis Explained
Polymers and dimers are broken into monomers by hydrolysis, where a molecule of water is split.
Enzymes Role
Enzymes are required to perform dehydration synthesis or hydrolysis.
The enzyme brings the two monomers (or the water and the dimers) close together.