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.

I’m Not Sure I Liked James Watson: Using a Video to Tell the Most Exciting Discovery in Biology

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

Learning Outcomes:

– To learn the structure of DNA and the names of famous scientists that contributed to its dicsovery

– To appreciate that scientific discovery and competition involves real people with real personalities

Activity Description: Students watch part of the PBS special, The Secret of Life. Students have questions to fill in while watching to keep them actively engaged. Students then write short comments about the characters in the race.

Time Needed: 1 hour and 15 minutes (approximately 55 minutes video time, plus time to write comments and discussion)

Materials Needed: Worksheet and possibly notecards

Activity Instructions: Play the Secret of Life Video Part 1. I was able to show it online via:

http://videosift.com/video/DNA-The-Secret-of-Life-part-1-of-5

After the video, ask students to write their thoughts about two of the characters. Students can write short essays to be graded, or in a large class, students can write some anonymous comments on a small notecard. If using a notecard, students can then swap them with classmates. Classmates then volunteer to read the comments on the card they are holding. Students have fun reflecting on the different personalities and it brings a personal aspect to science.

More to discover at the PBS website: http://www.pbs.org/wnet/dna/episode1/index.html

Worksheet: I’m Not Sure I Liked James Watson Worksheet

Reviewing Macromolecules

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

*Adapted from an activity presented by Dawn Tamarkin, Springfield Technical Community College at the National Association for Biology Teacher (NABT) Conference 2010.

Learning Outcomes:

– To review nomenclature related to macromolecules

– To practice organizing and making connections between concepts

Activity Description: Students are given a sheet of paper covered with words related to macromolecules. They will first cut the words out (like flashcards) and organize them into piles with a partner. Students are encouraged to discuss different ways to group the same set of words.

Time Needed: Approximately 25 minutes

Materials Needed: Worksheets and scissors for each group

Instructions:

  1. Have the students cut out the words.
  2. Let them organize them into piles without telling them how the organization should be done.
  3. Allow them time to see how other groups grouped their words. Allow time for questions and discussion about the different ways to group words.

Worksheet: Reviewing Macromolecules Worksheet

Appreciating the Diversity of Primary Sequences in Protein Structure

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

Learning Outcomes:

– To gain an appreciation for the diversity of proteins in amino acid sequence and length

– To examine an internet tool utilized by research scientists

– To appreciate quantitative biology

Activity Description: A classroom demonstration involving one student and multiple pairs of mittens of different colors is used as an analogy to the 20 amino acids that can be ordered in a multitude of ways in primary protein structure. Students can then use theNationalCenter for Biotechnology Information (NCBI) website to explore real proteins.

Time Needed: The activity should take approximately 15 minutes

Materials Needed: Multiple pairs of mittens or gloves

Activity Instructions:

One student comes to the front of the room in which there are two pairs of mittens (say a red and a blue pair). The student is allowed to choose one for each hand. Ask the audience, “How many possible combinations are there?” (Answer: 4)

Students won’t need a mathematical equation to figure this out:

Right – red, Left – red or Right – red, Left – blue or Right – blue, Left – blue or Right – blue, Left –red

Next put another pair of mittens on the table for your student to choose from (there are three pairs total at this point). Ask the audience, “How many combinations are now possible?” (Some students may start forming combinations of colors. Give them time to see how difficult this can be. Others may see the need for a calculation more quickly.) This is a good time to point out that biology is quantitative (many students will not recognize at the introductory level that as biology advances it intersects with mathematics more and more.)

The equation for the two hands and three pairs of gloves is: 32 = 9

Two hands and four pairs of gloves: 42 = 16

Next ask the audience, “How many amino acids exist?” (Answer: 20). Make the analogy clear by explaining that you could bring 20 pairs of mittens to your student. And ask them, “For a dipeptide sequence, how many different combinations would be possible?” (Answer: 202 = 400).

(Be sure to note that Ala-Leu is indeed different from Leu- Ala because polypeptides have directionality with an amino end and a carboxyl end.)

Lastly, ask students how long a typical polypeptide is. Let them take guesses and then explain the variation that exists. You can let them name a few proteins they know and go to:

http://www.ncbi.nlm.nih.gov/protein

to show them how many amino acids are in their named proteins. (This is a great site to show them as a collaborative tool that scientists use in the research.)

Ask them to calculate the number of combinations in a protein with say 125 amino acids:

Answer:  20125 = 4.25352959 × 10162

Note: You can bring in this same idea again when you discuss the triplet nature of the DNA code. With 4 nucleotides and a triplet sequence there are 43 = 64 combinations or codons.

A Student “Bully” Demonstrates the Polar Covalent Bond

Written by Jennifer Wiatrowski, Pasco-Hernando Community College

Learning Outcomes:

– To help students visualize the relationship that exists between atoms in a polar covalent bond

Activity Description: Three students use paper to demonstrate how electrons are equally shared in non-polar covalent bonds and unevenly shared in polar covalent bonds. This works well in a class of any size.

Time Needed: A few minutes

Materials Needed: Five pieces of paper and 3 students

Activity Instructions: I usually look for a large male student to be “oxygen” and then two smaller students to be “hydrogen.”  I have the students stand in a row with oxygen in the center. Between each hydrogen and the oxygen, I have them hold a piece of paper with two large dots on it. These represent the shared pairs of electrons. I have them start out holding the electron pairs at equal distance from one another (like in a non-polar relationship). But, then I tell oxygen to be the “bully” and pull those electrons closer to his body. I then hold signs over their heads indicating partial positive and partial negative charges. (A more creative person could probably come up with some funny hats representing the charges for the students to wear.)