Study Notes on Biomolecule Structures and Geometries

Biomolecules display a close relationship between their three-dimensional shape and function.
The principle of "structure equals function" indicates that the specific shape of a molecule is fundamental to its activity.

Molecule discussed: Ammonia (NH3)
Three-dimensional shape: Tetrahedron
The tetrahedral shape results from:
- 3 bonds (groups of electrons) with hydrogen atoms.
- 1 lone pair of electrons which counts as a fourth group, occupying space and influencing the shape.
Molecular geometry:
- The lone pair is not included in the geometric name; hence, ammonia has a molecular geometry described as trigonal pyramidal.
- The analogy used: Think of a pyramidal structure like the pyramids of Egypt with a triangle base instead of a square base.

Lone pairs take up space but are ignored when naming molecular shape.
Shape classification: Generally distinguished from the molecule's electron group geometry.

Students are encouraged to choose between two strategies:
- Memorization of necessary shapes and bond angles (though it’s acknowledged this may not be pleasant).
- Failure to understand these concepts if no effort is made.
Emphasis that students do not need to memorize everything in the shape table, focusing instead on the ability to draw shapes and name them.

Bond angles to memorize include:
- Linear: 180 degrees
- Trigonal planar: 120 degrees
- Tetrahedral: 109.5 degrees
- Less than 109.5 degrees or around 120 degrees for other geometries.

Total number of electron groups is important, which includes bonding and lone pairs affecting geometry comprehension.
Key point: Single bonds, double bonds, triple bonds, and lone pairs count as one group each.