Bio1 9/28 Lecture: Chemical Structure Overview + Pre-Class Videos

Lecture notes incomplete, will continue in 9/30 lecture

What is the maximum number of electrons that can be stored in the first, second, and third energy shells?

First energy level: 2

Second energy level: 8

Third energy level: 18

Most biological molecules are composed of which 6 elements? Which of these 6 don’t always follow the octet rule?

carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur (CHONPS)

P and S don’t always follow the octet rule.

What are three kinds of charge-charge interactions? Why do you need to know these?

1. Full charge-full charge (+1/-1)

2. Full charge-partial charge (+1/δ-)

3. Partial charge-partial charge (δ-/δ-)

These charge-charge interactions are the main determinant for how biological molecules interact. Gravity is insignificant due to the small size of atoms and molecules.

What are lone pairs?

The valence electrons that are not involved in chemical bonding.

What are Formal Charges?

net electrical charges that occur when there is an imbalance of electrons and protons in an atom or molecule

How do you calculate the formal charge of an atom in a molecule?

Formal Charge = # of protons - (# of lone pair electrons + # of bonds + # of inner shell electrons)

How do you determine if a molecular has a valid molecular structure?

Make sure each atom follows the octet rule. For problems, make sure to write the formal charge for every atom.

Why do molecules have 3D structures?

covalent bonds and lone pair electrons are oriented relative to each other in order to maximize the distance between them and minimize electrostatic repulsion

Polar covalent bonds

Covalent bonds between atoms with different electronegativities have partial charges indicated as +δ or -δ.

What makes a covalent bond significantly polar in biology?

The electronegativity difference must be equal to or more than 0.5.

Though technically, any bond with atoms with different electronegativities is polar.

List 3 Types of Non-Covalent Molecular Interactions

Ionic bonding/interaction

Hydrogen bonding

Van der Waals interactions

What is a hydrogen bond?

Attraction between a partially positive +δ hydrogen atom covalently bonded to nitrogen or oxygen (can also occur with fluorine but F is much less common in biological processes) and a lone pair on a different N, O, or F atom.

The +δ hydrogen is the Hydrogen-bond donor while the element with the lone pair is the H-bond acceptor.

Can occur between molecules and also between different parts of the same large molecule

What affects the strength of a hydrogen bond?

The strength of the bond is influenced by the distance between the donor and the acceptor, as well as the orientation of [the donor] and [the lone pair on the acceptor].

How are the H-bond donor and H-bond acceptor oriented relative to each other?

The H-bond donor is oriented with the H-bond acceptor so that they form a 180 degree angle with the donor, the element bonded to the donor, and the acceptor.

What are ionic bonds/interactions?

can occur between formally charged atoms (often found in larger molecules)

What influences the strength of an ionic bond?

Similar to H-bonds, the strength of the interaction is influenced by distance between the formally charged atoms.

Why are ionic bonds not as strong as hydrogen bonds?

Even though ionic crystals take more energy to break than hydrogen bonds, ionic bonds are not usually that strong due to the presence of water.

Hydrated ions (surrounded by water) are less attracted to other ions because water partially shields the charges.