Biochemistry Lecture No. 3: Amino Acids
Tuesday September 11 , 2012
The Formation Of A Peptide Bond:
-The formation of a peptide bond conveys how two amino acids bind together in a chemical reaction.
This bond is created between the N-terminus (amino group) and the C-terminus (carboxyl group).
Essentially, what is taking place is a condensation reaction or dehydration synthesis, as water is being
lost in the process.
-A residue is an amino acid when it is actually within a peptide. In this state, it has lost a hydrogen atom
and a hydroxyl group (collectively identified as water). It is due to the partial double-bond (by way of
resonance) that there is limitation of rotation about the peptide bond and it is a contributing factor to
protein formation and the protein being able to rotate later on. The 3-Dimensional structure of a protein
determines its function.
Know Your Polypeptides:
-Polypeptides are always written from the “N” (amino) to the “C” (carboxyl) terminus as a convention of
biochemistry. If you notice the side chains of a given polypeptide, some are polar or non-polar, while
others have a positive charge or are neutral. Even when writing the single letter representation of amino
acids within a polypeptide, take care in writing form the amino terminus to the carboxyl terminus.
- Starting from glycine (the simplest amino acid), a general trend among amino acids is that they get
bulkier in their physical size. Bigger amino acids placed in strategic locations along the polypeptide
would definitely be a key factor in how that protein functions and how it folds.
Amino Acid Net Charge:
-To predict the properties of a protein in solution we need to calculate the protein’s net charge. And in
order to determine that we start by calculating the net charge of a single amino acid in solution. The
three parts of an amino acid that may carry a charge (take on a proton) in a solution are: the amino
group, the carboxyl group and the side chain/R group (not all; glycine would not take on a charge).
-Knowing the charge of a protein is important in its purification in order for it to be utilized as
pharmaceutical medicine. Charge helps to isolate it for use clinical usage. E.g. Manufactured insulin for
Protons In Aqueous Solutions:
-Protons move continuously in aqueous solutions. For example, acetic acid exchanges protons with
water all the time. This transfer of protons can even occur between two water molecules. H+ atoms are coming on and off the amino acids. This average amount of time a proton spends on an amino acid can
Calculating Net Charge Of An Amino Acid:
- To calculate net charge, you need to know two things: the pKa (the tendency of the groups to attract a