Kevin Ahern's Bite-Sized Biochemistry #3: Protein Structure I





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Published on Jun 8, 2011

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Lecture Highlights
Buffers II

1. Molecules can have more than one buffering region.

2. A buffer system will be at maximum capacity when the concentration of the undissociated acid (HA) equals that of the salt (A-)- (Acid = Salt). The Henderson Hasselbalch equation further reveals that when this is true, pH = pKa.

3. Amine systems (also in amino acids) have two forms:
NH3+ and NH2. Note that the NH3+ is the acid and NH2 is the salt in my nomenclature.

4. The Henderson Hasselbalch equation tells us we can predict the ratio of salt to acid as a function of pH if we know the pKa. Consequently, we can predict the charge on amino acids in a protein as the pH changes. Subtle changes in pH in the body can have drastic changes in protein structure and function.

5. It is important for you to be able to use the Henderson-Hasselbalch equation to make predictions relating to pH, pKa, and/or salt/acid.

6. The value of the Henderson Hasselbalch equation is that by knowing the pH and the pKa of a molecule, the approximate charge of it in solution can be determined. For this class, we will assume that if the pH is more than one unit below the pKa of a group, that the proton is ON it. If the pH is more than one unit above the pKa of the group, the proton is OFF it. This is only useful for estimating charge. Determination of the pI (pH at which a molecule has a charge of exactly zero) requires calculation (described in class).

Highlights Protein Structure I

1. Protein structure dictates protein function. The structure of a protein is a function of the sequence of amino acids comprising it.

2. Amino acids are the monomeric (building block) units of proteins. They are covalently joined together in peptide bonds to make proteins (polypeptides).

3. There are 20 amino acids commonly found in proteins and of these 20, 19 have a chiral center and thus can exist in two stereoisomeric forms. The only one that doesn't have a chiral center is glycine. Almost all biologically made amino acids are in the same stereoisomeric form - the 'L' form. The 'D' form occurs only in very rare peptides, such as in the cell wall of bacteria (discussed later in the course).

4. Amino acids are grouped into several structural categories based on the composition of their R groups - simple, aliphatic, aromatic, sulfhydryl bond, cyclic, aliphatic hydroxyl, R-amines (your book calls these basic because they have R groups with relatively high pKa's), carboxyamides, and acidic (have R groups with relatively low pKa's). You will need to know the names of the 20 amino acids of proteins, which of the groups above each one belongs to and will need to be able to predict ionization at given pH values if you are supplied pKa values.

5. I mentioned briefly some of the properties of individual amino acids in the lecture. You should know those general properties (such as glycine, proline, the bulky amino acids, the hydrophobic ones, the hydroxyl containing ones, etc.)

6. Molecules, such as amino acids, that are capable of gaining/losing more than one proton, have pKa's that correspond to each functional group that can lose a proton. For example, a simple amino acid, such as alanine, has an amino group (pKa about 8.5) and a carboxyl group (pKa about 2.5).

7. A titration plot for a simple amino acid (no R groups that can lose protons) has two flattened regions - each one occurring at the respective pKa.

8. A zwitterion is a molecule whose net charge is zero.

9. The pI of a molecule is the point at which its charge is exactly zero. The assumptions above about protons on/off cannot be used to find the pI. It must be calculated. The pI of a molecule is halfway between the pKa values around the point on the titration curve where the charge is zero

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