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Lecture 3: "Amino Acids"

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Biochemistry 2280A
Mel Usselman

Biochemistry Lecture No. 3: Amino Acids th 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. Physical Size: - 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 diabetics. 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 be calculated. 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 proton) a
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