Tuesday, May 9, 2017

Crabapple Blossoms

My favorite time of year is when the crabapple trees are pink and white at the same time. 

Thursday, May 4, 2017

How to Make a DNA Model

Figure 1
One of the students I tutor had to build a DNA model for an assignment for 9th grade biology. We built our model, photographed it and posted it on Facebook. Some friends saw the picture and asked me to post instructions, so they could build similar models with their kids.

Let’s start with the basics.
DNA consists of several units:
  • Phosphates and ribose molecules comprise the backbone. The phosphates and riboses alternate.
  • The two strands of the phosphate-ribose backbone are antiparallel. That means the two strands go in opposite directions.
  • The cross-links are the nucleotide base pairs.
  • The nucleotides are: Adenine (A), Guanine (G), Cytosine (C) and Thymidine (T).
  • Adenine and Guanine are purines. Cytosine and Thymidine are pyrimidines.
  • Correct base pairing is A with T and G with C. (Figure 1)
  • A-T base pairs are connected by two hydrogen bonds.  G-C base pairs are connected with three hydrogen bonds. (Figure 1)
  • DNA forms a right-handed helix. In other words, when you look down from the end, the twist is counterclockwise.
  • One twist occurs about every ten base pairs.
The assignment stated that the model must be made with household items, not a molecular model kit. We chose wire and beads. The assignment also had several criteria to make the finished model as realistic as possible. The criteria were:
  • The phosphate-ribose backbones must be antiparallel. This means that if you start with a ribose on one strand, start with a phosphate on the opposite strand. In our model, the ribose molecules were five-pointed stars, so we were able to emphasize the directionality with the star beads. (Figure 1)
  • The ribose molecules must be larger than the phosphate molecules.
  • The ribose and phosphate molecules must be different shapes or different colors.
  • Base pairing must be correct. (A with T and G with C)
  • Purines (A and G) must be larger than pyrimidines (C and T).
  • Base pairs must be attached to the ribose molecules only.
  • The hydrogen bonds must be smaller than the nucleotides.
  • The model must include at least 15 base pairs.
  • The model must include at least two twists.
  • 18-gauge plastic-coated steel wire for the phosphate-ribose backbone. (This wire is sturdy enough to support the structure, yet malleable enough to bend and twist.)
  • 22-gauge dark annealed steel wire for the cross-links. (This wire was bendable and worked for the project. However, the dark coating rubbed off on our hands. Another type of thin malleable wire might work better.)
  • Pony beads for the phosphate molecules – at least 60.
  • Star-shaped crafting beads for the ribose molecules – at least 60. (The ones I bought were plastic with a metallic-sheen coating.) Make sure the hole in the bead is big enough to allow both the 18 gauge and 22 gauge wires to go through at the same time.
  • Wooden beads of assorted shapes and colors for the nucleotides. You’ll need four types of beads and approximately 15 beads of each. The A and G beads must be larger than the C and T beads. The A beads should be a different color than the T beads. The G beads should be a different color than the C beads. Make sure the 22 gauge wire will go through the hole in the beads.
  • Drinking straws in two colors
  • A sharpie marker
  • Scissors
  • Wire cutters
  • Needle-nosed pliers
  • A platform (We used a piece of Styrofoam. Clay would also work. Alternately, the model can hang from a string.)

Create the phosphate-ribose backbone.
  • Cut two 2.5-foot lengths of the 18-gauge wire.
  • Bend a small loop in one end of each wire so the beads don’t slide off.
  • Start one strand with a phosphate (pony bead). Alternate riboses (stars) and phosphates (pony beads) until you have 30 beads on the wire.
  • The second strand must be antiparallel. That means you need to start with a ribose (star) and follow with a phosphate (pony bead). Make sure the stars point in opposite directions on the two strands. String 30 beads on the wire.
  • Bend a small loop in the far end of the wire so no beads slide off.
Create the nucleotide cross-links.
  • Remember the nucleotides must be connected to the ribose molecules. (The nucleotides are supposed to be connected only to the ribose molecules, but we twisted the 22-gauge wire around the 18-gauge wire for stability. This slight structural convenience is hidden by the beads.)
  • Use the sharpie to label the wooden beads with A, G, C or T. Make sure the As and Gs are larger than the Cs and Ts.
  • Flatten two drinking straws. Make two vertical lines on both sides on one straw with the marker. Make three vertical lines on both sides of the other straw.
  • Cut straws into short pieces (smaller than the nucleotide beads). The pieces of straw are hydrogen bonds.
  • Cut 30 seven-inch pieces of 22-gauge wire.
  • Loop the 22-gauge wire once or twice around the 18-gauge wire between the phosphate and the ribose beads.
  • Twist the 22-gauge wire around the arms of the ribose star. Do not use all of the seven inches.
  • String a nucleotide bead on the 22-gauge wire.
  • String the appropriate hydrogen bond (straw pieces) next. Remember A-T base pairs have 2 hydrogen bonds and C-G base pairs have 3 hydrogen bonds.
  • String the appropriate nucleotide bead to pair with the first on the cross-bridge. (If the first was a C, string a G. If the first was a T, string an A, etc.)
  • Twist the end of the 22-gauge wire around the star on the opposite strand to secure.
  • Repeat until all of the ribose molecules (stars) on the two strands have cross-bridges. 
Create the double helix.
  • You may have extra 18-gauge wire at the top of the phosphate ribose backbones that needs to be trimmed.
  • We made one-inch loops at the top to insert into the Styrofoam platform. Other types of platforms may require different wire accommodations.
  • When you figure out how much wire you’ll need to attach the DNA to the platform, trim the 18-gauge wire and make loops in the ends.
  • Look at the DNA molecule end-on so the loops in the wire are facing you.
  • Twist the structure counterclockwise to create a right-handed helix.
  • Try to get about ten base pairs per turn.
  • Attach the structure to the platform or hang it with string.