Amino Acids Are Like the Letters of the Alphabet

Written by SuEarl McReynolds, Palo Alto College, San Antonio, TX

When I’m talking about proteins, I tell the students that there are only 20 different amino acids. Yet from just those 20 “building blocks”, an infinite number of proteins can be formed. At first that idea is hard to grasp. Then I ask how many letters there are in the alphabet. They reply “26”. Then I ask how many words can be formed from those 26 letters. The light goes on. Then I comment on the fact that there are 26 letters but only 20 amino acids, but in forming words what makes the difference is the particular letters that are used, the number of those letters and the sequencing of those letters. All of the same variables are true in forming proteins from amino acids—PLUS the three-dimensional arrangement of the amino acids. It’s like playing 3-dimensional Scrabble.

Relating Chemical Bonds to Everyday Ideas

Written by SuEarl McReynolds, Palo Alto College, San Antonio, TX

I use several analogies when talking about chemical bonds. I compare them to different kinds of glue. I ask the students if they have a “junk drawer” at home. They smile, and I ask if it’s got some different kinds of glue in it—maybe paper glue, Elmer’s glue, wood glue, Super Glue.  Just like you need different kinds of glue to stick different materials together, you need different kinds of bonds to hold different kinds of atoms together. Probably a lot of people compare the attraction of the oppositely charged ions in an ionic bond to the attraction of the opposite ends of a magnet. Another common analogy probably is to compare the sharing of electrons in covalent bonds to holding hands (as in carbon is an atom that has four hands sticking out to hold with other atoms). Covalent bonds could also be compared to kids who want to play with the same toy. So they set a timer and switch off who gets to play with the toy.

When I talk about polar covalent bonds, which result from an unequal sharing of electrons, such as in the water molecule, I tell this story: “Suppose I come to class with a big chocolate chip cookie. I tell you that I’m feeling generous and am going to share my cookie with you. You anticipate that I’m going to break the cookie in half and keep half and give you half. But that’s not what I do! I really, really like chocolate chip cookies—so I break off a little piece for you and keep most of it for myself! Well, I did share.  I just didn’t share equally!”

When I get to the much weaker hydrogen bonds, I compare them to Post-It notes. I ask the students to visualize some inventor trying to formulate a new kind of Super Glue. He tries a lot of different variations and comes up with something that will hold things together when you want them held together but will release them without tearing them up or using a lot of energy when you want them separated. That’s the kind of adhesive that’s found in Post-It notes. It’s just a good thing he didn’t throw it in the trash because he had started out looking for a new kind of Super Glue! What would we do without Post-It notes? (I usually have one or two on my folders right there.) That’s what hydrogen bonds are like. An example would be the hydrogen bonds holding the two strands of DNA together. The strands need to be reliably held together most of the time, but sometimes they need to separate (of course I haven’t talked about replication or protein synthesis yet). It must happen without tearing the strands up or using an atom bomb’s worth of energy to make it happen. Then sometimes the strands will need to go back together (protein synthesis). That’s why the weak hydrogen bonds are important.