Short videos answering your questions

The following are questions that people have had that can't really be answered via email, and in a normal semester I'd use my office whiteboard to answer them. This semester we'll have to make due with digital discussions and these videos. Any use by unauthorized personnel without the express written consent of the instructor is forbidden. Any unauthorized distribution is prohibited. Enjoy!

Wednesday, 20 January

Titrations of amino acids and Figure 2.6 in your textbook. A lot of people have forgotten titrations from high school or General Chemsitry classes, most likely because they didn't like them the first time around. Understanding how weak acids and bases behave is absolutely critical to understanding biochemistry though because strong acids and bases are lethal to most organisms. The quick rule to remember is: If the pH is above the pKa of the functional group, the functional group will be deprotonated and if the pH is below the pKa of the functional group, the functional group will remain protonated.The pKa values for all functional groups in amino acids are found in Table 2.1 in your textbook.

Tuesday, 2 February

Evolutionary Relationship between Myoglobin and Hemoglobin alpha and beta chains. In this short (~8 min) video, I show you how myoglobin is related to the alpha and beta chains of hemoglobin. We can see that the primary structures of the 3 proteins are just 30% identical, but the tertiary structure is conserved in key areas like the porphyrin binding site and the oxygen binding site. Areas away from the binding site have had their amino acids change over evolutionary time, but since they are not near the binding site, all of the proteins still bind oxygen. In fact, the amino acid substitutions that have occurred have given rise to the quaternary structure of hemoglobin from the monomeric ancestral globin protein.

Thursday, 18 February

Answering the peptide sequencing problem on the test. Peptide sequencing is something that none of you will do in real life, BUT, it involves the skill of taking multiple concurrent lines of information and teasing them apart to construct a whole. That is a real-life skill. Unfortunately, you haven't had to do it very many times in your college courses. In this video, I'll walk you through Question 11 on Test 1 so you can see how to answer the question.

Tuesday, 23 February

The three rules of enzymatic mechanisms explained again in a 15 minute video with some examples. Chapter 9 combines organic chemistry and biological chemistry, and the size of biological molecules can be difficult for folks to deal with. In this brief video, I go over the 3 rules of biological mechanisms (yes, it really is that straightforward) and show you how enzymes follow the 3 rules to catalyze reactions that we will see later in the semester. Once you watch this video, go ahead and take a representative peptide bond (just the C, O, N and H atoms of the peptide bond with an R group on the carbonyl carbon of the amide and another R group on the nitrogen of the amide) and then draw the hydrolytic product generated by a serine (or any) protease. Then go stepwise through the serine protease mechanism. SLOWLY. Draw out each step completely and see where the electrons are going. Be thoughful in your drawing and make a cycle like I did in lecture this morning. Then go ahead and tackle the extra credit if you want by mutating the serine of the catalytic triad to a cysteine and draw out the complete mechanism that the new enzyme would catalyze.