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Sunday, June 18, 2017

Introduction to Biochemistry - Quiz 2.1.1


(A) is the most tricky option, this is an amino acid with a wrong (i.e. D) configuration - so it won't be a natural amino acid.
(B) is glycine with the side chain being simply a hydrogen atom. It is the only amino acid that is achiral.
(C) looks like an amino acid except it has one more carbon - this is obvious if you compare it to (B).
(D) does not have an amine group at all, so it cannot be an amino acid.
(E) is the general amino acid from.

Therefore the answer is (B) and (E).




All these forces are Coulomb forces - the attraction between positive charge and negative charges. Ionic charge is the strongest because they are formal charges, the hydrogen bond is due to partial charges generated by the difference in electronegativity, and Van Der Waal's force is the weakest because it is just due to induced dipoles.

Therefore the answer is Ionic > Hydrogen Bond > Van Der Waals force.


As we have argued above on the strength of the interaction forces, the correct labeling, from top to bottom, should be Van Der Waal's Forces, Hydrogen Bonds and Ionic Bonds.

The energy values are negative because one can think of it as potential energy stored in a spring, if you compress or stretch, the spring would like to restore to what it was. If two atoms are bonded and we stretch them apart, the attraction force in the bond work against the move. Similarly, if we push two atoms in a bond too close the electron cloud repulsion would work against us. That's why we need to give energy in the system to change things, that's why the energy is negative.


Aspartic acid is an acid in physiological pH, which means it should lose a proton. The only feasible answer that lost a proton is either (B) or (C) - I think it should be (B) because at physiological pH the amine group should be basic and accepted the proton to begin with, it shouldn't lost it again just because it has a different side chain.


Here below is a summary of all the amino acid structures:


I failed this one on the first attempt, initially, I thought the smaller the side chain is, the more flexible it is, therefore the answer should be Alanine.

But that's not true, and it is the tricky part of this problem, it is asking about the flexibility of the side chain, not of the amino acid! Lysine have many bond that could be rotated and it is obvious that side chain is very flexible.


Even if I don't know what this molecule is, it is obviously not charged, so the only two options are Non Polar, Aliphatic, small or Non Polar, Aliphatic - is it small or not? I don't know. So I looked it up, it is not small, therefore the answer is Nonpolar, Aliphatic.

I don't know what is an Aliphatic compound is, so I looked it up in Wikipedia, I think it means organic compound without a benzene ring.

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