Organic Molecules and Functional Groups

For a compound to be considered organic in chemistry, it must contain both carbon and hydrogen.
This differs from the term "organic" used in grocery stores, which typically refers to pesticide-free produce.

Valence Electrons: Carbon needs $4$ valence electrons to be "happy" (to achieve a maximum of $8$ electrons in its outer shell).
Bonding Needs: This means carbon needs to form $4$ additional bonds to achieve stability.
Covalent Sharing: The most common way carbon forms these bonds is through covalent sharing with other atoms.
Structural Backbone: Carbon's ability to form $4$ bonds makes it highly versatile, allowing it to create various "backbones" and "scaffolding" for all necessary organic molecules.
Types of Bonds: Carbon can form:
- Single bonds: Shares one pair of electrons (represented by a single line).
- Double bonds: Shares two pairs of electrons (represented by a double line).
- Triple bonds: Shares three pairs of electrons (represented by a triple line).
- No quadruple bonds are typically formed by carbon.
Four Bonds Rule: Every carbon atom in a stable organic molecule must have exactly $4$ bonds. This can be checked visually in structures.
- For example, in a $CH_3$ group, the carbon forms $3$ bonds with hydrogen and $1$ bond with another atom.

Valence Electrons: Hydrogen has $1$ valence electron.
Bonding Needs: It is happiest with $2$ electrons, so it needs to form $1$ more bond.
Hydrogen can either give away its electron or, more commonly with nonmetals, share it covalently.
Often, the single bond for hydrogen is understood and not explicitly drawn with a line connecting it to its parent atom.

Definition: Compounds composed only of carbon and hydrogen.
Examples: These can exist as long chains, branched chains, or rings.
Properties: Hydrocarbons are characteristically nonpolar and hydrophobic (do not like water).
Relevance: This property is a key feature in lipids, explaining why oil and water do not mix.
Length: Hydrocarbon chains can vary significantly in length, from just two carbons to $50$ or more.

The most common elements that attach to carbon and hydrogen in organic molecules form the acronym SPONCH: Sulfur, Phosphorus, Oxygen, Nitrogen, Carbon, and Hydrogen.
These elements typically bond covalently by sharing electrons because they are nonmetals.
Valence Electron Requirements:
- Hydrogen (H): Has $1$ valence electron and needs $1$ more bond to be happy.
- Oxygen (O): Has $6$ valence electrons and needs $2$ more bonds to be happy.
- Nitrogen (N): Has $5$ valence electrons and needs $3$ more bonds to be happy.
- Carbon (C): Has $4$ valence electrons and needs $4$ more bonds to be happy.

Definition: Isomers are compounds that have the same chemical formula but a different arrangement of atoms (different structure).
Example: Glucose, Fructose, and Galactose.
- All three have the chemical formula $C<em>6H</em>{12}O_6$ .
- Despite having the same number of carbons, hydrogens, and oxygens, their structural arrangements differ.
- Fructose forms a pentagonal ring, while glucose and galactose form hexagonal rings.
- Glucose and galactose primarily differ by the orientation (flipped positions) of certain $-OH$ (hydroxyl) groups.
Significance: While they are all sugars and serve similar basic functions, their differing arrangements can lead to distinct biological properties.

Definition: Specific groups of atoms attached to carbon chains that impart particular chemical properties and functions to the molecule.
There are six key functional groups to recognize by name and symbol.
One of these groups is particularly hydrophobic (does not like water).
In organic chemistry, one would delve deeper into their specific tasks; here, we focus on recognition.

Symbol: $-OH$
Structure: An oxygen atom covalently bonded to a hydrogen atom, with the oxygen then bonding to the main carbon chain.
Key Distinction: This is a hydroxyl group, not a hydroxide ion ( $-OH^-$ ). The oxygen is covalently bonded, not negatively charged.
Properties: Oxygen needs $2$ bonds (one to hydrogen, one to the carbon chain). Hydrogen needs $1$ bond (to oxygen).
Common Name: Also known as an alcohol when attached to a hydrocarbon.

Symbol: $-C=O$
Structure: A carbon atom double-bonded to an oxygen atom ( $C=O$ ).
Properties: The oxygen atom is happy (forms $2$ bonds). The carbon atom still needs $2$ more bonds, which it forms with other atoms in the chain.
Distinction: This specifically refers to a carbon double-bonded to an oxygen where the carbon is not also bonded to an $-OH$ group (which would make it a carboxyl group).

Symbol: $-COOH$ or $-C(=O)OH$
Structure: A combination of a carbonyl group ( $C=O$ ) and a hydroxyl group ( $-OH$ ) attached to the same carbon atom.
Properties: This unique combination of four atoms works together and has specific functional roles in organic molecules.

Symbol: $-NH_2$
Structure: A nitrogen atom bonded to two hydrogen atoms and one bond to the main carbon structure.
Properties: Nitrogen needs $3$ bonds to be happy (here, $2$ to hydrogens and $1$ to a carbon chain).
Relevance: This group is crucial in proteins, as it forms a part of amino acids, which are the building blocks of proteins.
- Note: While it can become ionized ( $-NH<em>3^+$ ), for this context, recognition of the $-NH</em>2$ structure is key.

Symbol: $-PO_4$
Structure: A phosphorus atom bonded to four oxygen atoms (often with both single and double bonds to different oxygens).
Relevance:
- Found in many important biological molecules.
- Essential for processes involving dehydration synthesis and hydrolysis.
- Plays a massive role in cellular respiration and the production of ATP (adenosine triphosphate).

Symbol: $-CH_3$
Structure: A carbon atom bonded to three hydrogen atoms, with the carbon then bonding to the main chain.
Properties:
- Often found at the end of hydrocarbon chains.
- Incredibly hydrophobic (hates water) and nonpolar.
- This property is a primary reason why lipids (like oil) and water do not mix.

General Nature: Lipids are a diverse group of organic molecules that primarily do not like water.
Types: The four main types include triglycerides, phospholipids, waxes, and steroids.
Key Discussions: In this chapter, we will focus on triglycerides (which store energy/fat) and phospholipids (which form cell membranes).
Hydrophobic/Hydrophilic Interaction: Lipids generally do not like water, explaining why they orient themselves in specific ways.
- Phospholipids in cell membranes are depicted as "two-legged jellyfish" with heads that like water (hydrophilic) and tails (containing methyl groups, making them hydrophobic) that face each other, away from water.
- This orientation creates a barrier that defines the cell's boundaries.