High School Biology-Chemistry SMILE Meeting
23 January 2001
Notes Prepared by Porter Johnson

Pam Moy (Morgan Park HS)
constructed models of DNA [Deoxyribonucleic Acid] with brightly colored (psychedelic) pipe cleaners.  Long white pipe cleaners were used for the backbone components, which are composed of sugars and phosphates.  These pipe cleaners were formed into an X, twisted in the middle, and then the legs were twisted together to form a loop, or a Figure 8.  The four different colors of short pipe cleaners were each used to represent the four different  nitrogen bases:

Base Symbol

 Base Name


 Allowed Pairing




A with T




C with G




G with C




T with A

The bases (according to the allowed pairing indicated above) were paired , and the base pairs were attached to the white pipe cleaners so that they looked like the rungs of a ladder; for example, an orange pipe cleaner was attached to a yellow pipe cleaner, and the pair was used to span the distance between the two white pipe cleaners.  Each half of the "figure 8" was to have five base pairs.  When making your model, be certain to pair A with T, and C with G. There is no particular order of bases for base pairs, but the pairing arrangements shown above must hold.  For example:
          G  C  A  A  T  C  T  A  A
          C  G  T  T  A  G  A  T  T
Ben Stark (Professor of Biology, IIT) explained how cells replicate their DNA and check that the coding [ordering and pairing] is correct.  He also explained that many problems with defective DNA are linked to genetic diseases, and that many of the defects in DNA are caused by exposure to ultra-violet [UV] light. The most common mutation is a "transition mutation", in which an A is replaced with a G, a G with an A, a T with a C, or a C with a T.

Pat Riley (Lincoln Park HS)
started out by asking what was inside an atom.  After drawing a model of the atom, she stated that protons and neutrons lie inside the nucleus, a tiny, heavy core.  We then went on to explore the functions of the protons and neutrons.

Protons, being positively charged, attract the negatively charged electrons, which move in orbits around the nucleus. Neutrons serve as a kind of nuclear glue to keep the nucleus together, in spite of the "like charged" repulsion of the protons.  These electron orbits may classified according to various orbital shells, which lie further and further from the nucleus, and which may contain more and more electrons.  In the Bohr model, here are the orbits and the various numbers of electrons that they may contain.


Orbit Number

Maximum Number of Electrons
Allowed in Orbit

n = 1


n = 2


n = 3


n = 4


n = 5


The negatively charged electrons move in one of  these orbits and stay close to the nucleus because of the attraction of the positively charged protons.

Pat then went on to tell us that this simple Bohr model is actually too simple!  She made an analogy of these orbitals with the rooms on various floors of a hotel.  These rooms may be of these types:

circular [S-orbitals]
figure-8 [P-orbitals]
4 petaled (daisy-shaped) [D-orbitals]
            ...   and even   ...
6-petaled [F-orbitals].

The rooms will each hold a pair of electrons---two electrons with their spins paired.  As you go higher in the building there are more rooms, so that the hotel can be visualized as an "upside down pyramid".  


Orbital Number

 Floor Number

Number of
Orbitals / Rooms

Number of Each Type

n = 1

First Floor


1:  circular S-orbitals

n = 2

Second Floor


1:  circular S-orbitals
3:  figure-8 P-orbitals

n = 3

Third Floor


1:  circular S-orbitals
3:  figure-8 P-orbitals
5:  4-petaled D-orbitals 

n = 4

Fourth Floor


1:  circular S-orbitals
3:  figure-8 P-orbitals
5: 4-petaled D-orbitals
7: 6-petaled F-orbitals

We should think of the rooms as three dimensional---spherical rather than circular, dumb-bell shaped rather than figure-8, and so forth.

Pat showed how that this model allows us to understand how electrons are packed into the small amount of space around the nucleus.  Also, she pointed out that it is difficult to visualize electrons, since

[1] the electrons themselves are very small, if not "point particles";
[2] the electronic orbitals take up 99.999999... percent of the space inside the atom.

The tiny nucleus contains 99.9 % of the atomic mass, but is very small.  Electrons are difficult to see directly, but their orbital envelopes are easily detectable with electron microscopes, scanning tunneling microscopes, and the like.  One tends to visualize electrons as "energy" rather than "matter".  For example, an electric current is associated with the motion of electrons.  In your electric bill, you are paying for "electrical energy", and not for the "electrons themselves"; you have plenty of electrons already.

 Notes taken by Pat Riley and Pam Moy.