I showed a YouTube video in class last Wednesday, but didn't have time to show it to the Thursday class. The video presents the mechanism of the chemical reaction catalyzed by lysozyme enzyme, a chemical reaction that is also discussed in Sorrell 5.5.
You can watch the video (under 2 min) here. You can also get a copy of the lecture slides for this and other lectures by going to the Syllabus page and scrolling to Day 11.
Some interesting things about the video:
- energy, binding, and ring strain – while the video doesn't offer a reaction coordinate diagram, it gives you information about energy if you know where to look. When the substrate and enzyme bind to each other, their (combined) free energy decreases because bonding is always favorable. But even though binding occurs, the substrate is forced into an awkward conformation. This destablizes the bonds in this ring, making them easier to break. Still, the increase in substrate strain energy is more than offset by the overall drop in energy caused by substrate-enzyme binding.
- acid-base chemistry & amino acid sidechains – the mechanism depicts proton transfers between the enzyme and the substrate. The reactive groups in the enzyme are amino acid sidechains. This is virtually always the case. Even though we may think of a single amino acid as containing a reactive amino group and a reactive carboxylic acid group, these groups have been converted into unreactive peptides (amides). An enzyme's catalytic properties are due to its amino acid sidechains.
- curvy arrows – the video draws curvy arrows for the proton transfer that are incorrect. One arrow correctly shows electrons in the A-H bond moving towards A. The other arrow incorrectly shows H moving towards B. Come to think of it, the video's voice doesn't say these are curvy arrows, but if they were ….
- electrophiles & nucleophiles – are these polar reactions? Do they form new bonds? Yes and yes. You should be able to identify electrophiles and nucleophiles for each step.