Highlights Basics

1. Students are responsible for completely reading the syllabus and understanding what is in it.

2. Covalent bonds are VERY strong bonds that hold atoms/molecules together. Covalent bonds are the 'glue' that holds together biomolecules.

3. Hydrogen bonds are much weaker bonds that are also important in biological molecules. Hydrogen bonds arise from uneven sharing of electrons betweeen, for example a nitrogen and a hydrogen or an oxygen and a hydrogen. In each case, the hydrogen ends up with a partial positive charge and the other atom has a partial negative charge. The partial positive charge of the hydrogen may be attracted to a partial negative charge on another oxygen or hydrogen. These bonds are weaker than covalent bonds, but are VERY important in stabilizing protein and DNA structures.

4. Water has its relatively high boiling point due to its numerous hydrogen bonds. The double helix of DNA is held together by hydrogen bonds between the individual bases.

5. Hydrogen bonds are additive, so they provide great stability in numbers (as in across a chromosome), but less stability locally (one can easily pull them apart when DNA needs to replicatie).

6. Hydrogen bonds are some of the stabilizing forces of proteins. Since protein function depends on protein structure, forces that disrupt hydrogen bonds (such as heat) tend to disrupt protein structure and function. It is because of this that cooking food kills bacteria, because it denatures their proteins. Since proteins are the "workhorses" of cells, loss of protein function means loss of cell function, which means death.

7. pH is a measure of the proton concentration in a solution. The pH is the negative log of the hydrogen ion concentration. The lower the pH, the higher the hydrogen ion concentration and the stronger the acid. pH + pOH = 14. The pOH is the negative log of the hydroxide ion concentration. The pKa is, therefore, the negative log of the Ka. The lower the pKa for an acid system (such as the acetic acid system discussed in class), the stronger the acid is.

8. Acetic acid (HAc above) is a weak acid, meaning that it doesn't completely dissolve in water. HCl, by contrast is called a strong acid because it completely dissociates in water.

HAc <=> H+ + Ac-

We can write the general equation for the dissociation of ANY weak acid as

HA <=> H+ + A-

I will say more about this on Wednesday.