Every chemistry professor gets this question every single semester. The pKa of a molecule is mathematically defined as: -logKa
Just as pH = -log [H30+], the little "p" just means negative log of something, in this case, the Ka. But what does the Ka mean? Therein lies the rub. You have to understand the meaning a a Ka value of 1.75x10^-5 for example (the Ka of acetic acid) and how that shows you that acetic acid is a weaker acid than say, formic acid, which has a Ka of 1.77x10^-4. The difference in these numbers tells you that formic acid loses its acidic proton "easier" than the acidic proton of acetic acid. In order to understand that, you have to look at the equilibrium constants and think about the algebra.
I've made a short video explaining the meaning of Ka values and pKa values. Watch it, with you calculator in hand, and everything should fall into place.
Ka and pKa tutorial video for CHEM523
I didn't have access to a whiteboard yesterday, so I made a brief video that shows you a couple of things. First, apply a reductionist approach to a problem so that you can understand the basic theory behind it and then work your way up to a complicated example. In this case we are going to remove the proportionality constant, k, and the dielectric constant, D, and simply focus on the types of molecules that are interacting (ion, polar or nonpolar) and how the different types of molecules have different exponents attributed to their distance terms which affects how much or how little they influence each other as they come together or are moved apart.
Explanation of the interactions energies of molecules via IMFs
This is a question that I think a lot of people want to ask, but feel that it is silly. It isn't. Shifting to thinking three-dimensionally is a skill, just like anything, and you have to really think about a molecule to "see" it. Remember, because of the partial sp2 (double bond) character of the peptide bond, the carbonyl carbon and nitrogen involved in the peptide bond between individual amino acids in a protein can't rotate RELATIVE TO EACH OTHER along the axis of the bond. The bond is planar and non-rotatable. Imagine that the backbone atoms in a polypeptide chain (Nitrogen->C-alpha->Carbonyl Carbon ->Nitrogen->C-alpha->Carbonyl->repeat) are like beads on a wire necklace. The carbonyl carbons of every amino acid in the polypeptide (except the last amino acid) are involved in a peptide bond. That means that every amino nitrogen (except the first amino acid) is also involved in a peptide bond. Because atoms involved in peptide bonds can't rotate RELATIVE TO EACH OTHER, glue those beads together. Do that for every peptide bond and a pattern emerges: Double bead -> Single Bead -> Double bead -> Single bead, etc. Grab a double bead in each hand and you should have a single bead (C-alpha) in between them in the necklace. Rotate the double beads in opposite directions and your left hand is adjusting the Phi angle and your right hand is adjusting the Psi angle. Make sense? Clear as mud.
Explanation of Ramachandran angles using figures from your text/Lecture slides