Biochemistry : Amino Acids and Proteins
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Example Question #61 : Macromolecule Fundamentals
If a certain functional group on a peptide has a pKa of 
In this question, we're given the pKa of a peptide's functional group and we're told that the peptide is in a solution at a certain pH. We're asked to estimate the proportion of the functional group that we would expect to be protonated.
The first thing we can realize about this problem is that the peptide is in a solution that is far more acidic than the pKa of the functional group. Therefore, we would certainly expect a lot of it to be protonated. The question is, by how much?
We can make use of the Henderson-Hasselbalch equation to quantify the degree to which the functional group will become protonated.
In the equation above, we can take base to mean the deprotonated functional group, while acid we can take as the protonated functional group.
We can also rearrange the above expression in order to isolate the base to acid ratio.
Next, we can plug in the values given to us in the question stem.
We can rewrite this expression alternatively to make it more intuitive.
In other words, for every one equivalent of base, there are 
Thus, 
Example Question #61 : Amino Acids And Proteins
Which amino acid is the primary source of ammonia?
Glutamine
Glycine
Tyrosine
Glutamate
Serine
Glutamate
Glutamate is the primary source of ammonia. Glutamine is similar however it is the amide free form of ammonia. Glutamate plays an important role in the urea cycle. The urea cycle serves to rid the body of ammonia, which can be toxic in high amounts.
Example Question #62 : Amino Acids And Proteins
What is true concerning charged hydrophilic amino acids?
They can traverse the plasma membrane via simple diffusion
The side chains are insoluble in water
The side chains carry at net charge at or near neutral pH
They are nonpolar
The side chains form hydrogen bonds
The side chains carry at net charge at or near neutral pH
Charged hydrophilic amino acids are polar and their side chains carry a net charge at or near a neutral pH. For instance, lysine has a positive charge at a pH of 7. Examples of essential amino acids that are in this group include arginine, histidine, and lysine.
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