Study Notes: Aromatic Hydrocarbons, Isomerism, Enantiomers, Functional Groups, and Hydrogen Bonding

Carbon can form five- and six-membered rings (closed chain).
Single or double bonds may connect the carbons in the ring.
Nitrogen may be substituted for carbon.
Benzene – a particularly important hydrocarbon ring – used in some amino acids, cholesterol and its derivatives.
Figure 2.22 references these concepts.

Isomers are molecules that have the same chemical formula but differ in placement/arrangement of atoms or types of bonds between atoms.
Major categories described in the transcript:
- Structural (constitutional) isomers – have a different covalent arrangement of atoms.
- Geometric isomers – have a different arrangement of atoms around a double bond.
- Enantiomers – molecules that share chemical formula and bonds but differ in 3D placement of atoms; mirror images.
Figure 2.24 illustrates isomers: (a) Structural isomers, (b) Geometric isomers, (c) Enantiomers.

Some long-chain hydrocarbons can have one or more double bonds.
Fatty acids with a double bond are unsaturated; fatty acids with no double bonds are saturated.
Trans configuration: carbons are on opposite sides of the double bond.
Cis configuration: carbons are on the same side of the double bond.
Figure 2.25 shows cis (oleic acid) and trans (elaidic acid) fatty acids and the bend caused by the cis configuration.

D-alanine and L-alanine are examples of enantiomers or mirror images.
You cannot superimpose these two structures on each other.
Only the L- forms of amino acids are used to make proteins.
Figure 2.26 illustrates the enantiomers of alanine.
The L/D naming system originates from Latin words for left and right: laevus and dexter, respectively.

Functional Groups – groups of atoms within a molecule that confer consistent specific properties to these molecules.
Each of the four types of macromolecules has its own set of characteristic functional groups.
Functional groups often interact with other functional groups via hydrogen bonds.
Figure 2.27 shows several important functional groups; these groups appear in many different biological molecules.
R, also known as the R-group, is an abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.

Hydrogen bonds between functional groups help stabilize biological molecules and allow them to perform their biological functions.
Hydrogen bonds are essential to DNA structure: they connect two strands to form the double-helix.
DNA structure is vital for DNA function.

Aromatic rings like benzene are foundational in biochemistry, contributing to the structure of amino acids and cholesterol derivatives.
Isomerism (structural, geometric, enantiomeric) affects chemical reactivity, biological activity, and protein synthesis (e.g., only L-amino acids are used in proteins).
Fatty acid saturation and cis/trans configurations influence membrane fluidity and metabolic processing.
Functional groups determine solubility, reactivity, and intermolecular interactions, underpinning macromolecule formation and stability.
Hydrogen bonding is a unifying principle that stabilizes nucleic acid structures and countless biomolecules, enabling complex biological functions.