High School SMILE Meeting
1999-00 -- 05-06 Academic Years
Cell Biology and Genetics

28 September 1999: Pam Moy (Morgan Park HS)
passed out materials to us, and described fluid mosaic model of the membrane and the structure of a cell. With some guidance from Pam, we then used the materials to create 2-D models of cells on paper, helping us to understand better and remember this cell model. Very nice!

09 November 1999: John Scavo (Richards Voc HS)
shared DNA Matching with us, an example of a chemistry van program from CSU - 30 experiments available). This was a forensic experience in which we tried to match "evidence cards" containing DNA patterns with a set of 9 suspect DNAs (handout). Interesting, John!

01 February 2000: Chuck Buzek (Spry School)
gave us hands-on insight into evolution. He gave 5 jars out, one for each of 5 groups, each jar with 40 white beans and 40 red beans. (The beans represented genes, with red as dominant.) He had us remove two beans at a time from our jar (without looking!), and record the number of times that we got RR, RW, or WW. We got 9-22-10. Chuck then had us take the 10 WW's and put them into an "eliminate" cup - representing elimination of non-dominant gene combinations. Next, we combined the remaining 9-22 (RR-RW) and repeated the process. Enlightening! We could "see" evolution happening!

23 January 2001: 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

Color

 Allowed Pairing

A

Adenine

Orange

A with T

C

Cytosine

Pink

C with G

G

Guanine

Green

G with C

T

Thiamine

Yellow

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

23 January 2001: 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.

13 March 2001: Karlene Joseph (Lane Tech HS) Handout: Genetic Recombination
directed activities that review meiosis and genetics by employing small stackable block cubes [similar to LEGOTM blocks]. We used 6 cubes for each of 6 different colors, and connected 3 cubes of the same color to represent chromosomes. Then we constructed an original parent cell by placing one chromosome of each color in a matrix of 3 pairs of "homologous" chromosomes, and assigned letters [alleles] to each color; [eg a, b, c, A, B, C]. Capital letters represent the dominant genes, and lower case letters represent recessive genes. We then simulated the following rearrangements.

We indicated the dominant genes for each case.

Here is a list of human traits for which there are contrasting forms.  Within each trait one form (eg oval versus round head shape) was arbitrarily chosen as dominant and the other recessive.  The results of each person's "virtual offspring" (above) could then be converted into a "phenotype" by making interesting and usually humorous sketches of the faces.

* Trait Contrast
1 Head shape Oval vs Round
2 Chin shape Pointed vs Square
3 Eye shape Round vs Almond shaped
4 Hair shape Curly vs Straight
5 Nose size Big vs Little
6 Ear size Big vs Little
7 Earlobes Large hanging vs Small attached
8 Eyebrows Bushy vs Thin
9 Lips Thick vs Thin

11 September 2001: Ben Stark (IIT)                  DNA
Ben showed a copy of the human genome. He then explained how they cut up the base sequence of the chromosomes into pieces small enough to sequence. Bases that comprise the DNA sequence are  A, C, T, and G molecules, each gene corresponding to a different sequence. A computer was used to piece together the sequences to produce the overall DNA sequence of the genome.

A primary feature of the genome is that there are places at which there are many genes, and some regions at which there are very few. There are thought to be about 35,000 genes in the human genome.

Some bacteria have up to 7000 genes, so it was expected that humans would have more than 35,000 genes.

The federally funded sequencing effort first ordered DNA pieces and then sequenced them.  The privately funded effort done by Celera Genomics Corporation http://www.celera.com/ sequenced randomly generated pieces, using a computer to order them by finding overlapping components.

The genome will be refined by comparing the federally funded and privately funded maps, and rectifying any differences. Then the problem of filling in missing genes (if any), will be addressed.

He then talked about butterflies, and the cells that make up all living things. All cells in any organism have exactly the same chromosomes with exactly the same genes.  The genes in all the cells are not active at the same time, so this is why certain butterflies develop wings with, say, black and orange colored patterns. This is analogous to a series of hotel rooms that all have the same number of lights, each with a different combination of bulbs turned "on" and "off".

Harmful bacteria can have their genomes sequenced within a few weeks. The smallest known bacterial genome, that of an obligate  intracellular parasite, has about 450 genes. 

Next he looked at a DNA model to see the bases on the inside and the outer parts. An actual DNA molecule is 19 Å = 1.9 nanometers [nm] in diameter, but the diameter of the model is 0.19 meters.  Thus, the model is larger than the actual molecule by a factor of 100,000,000; or 108.

23 October 2001: Robert McBride (Fuller School) First-time mini-teacher
Rob led a discussion of genetic molecules, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). We generated the following list of words that we felt to be related to these molecules:

heredity, genes, proteins, cells, blueprints, double helix

Rob added the words chromosome and nucleus to the list.  

Rob asked us to role-play 13 year olds, and to make a color drawing of what one of these objects might look like. Rob supplied us with glue, paper, markers, colored pencils, scissors, etc.  We then compared our drawings with  the objects themselves.  Some of the answers were accurate (drawings of double helix, cell, nucleus), whereas others were vague (printing in "blue" for "blueprint", for example).

04 December 2001: Karlene Joseph (Lane Tech HS) Handout: Cell Diversity
Karlene started by asking "What types of cells are there?"
Frana
  mentioned animal and plant cells.  Inside the human body we have these types of cells:

brain, blood, muscle, skin, nerve, follicle, ...

Activity: Karlene distributed clumps of clay of the same volume.  Each person took a clump and molded it into shapes corresponding to the shape of a given type of cell.  Here are some examples:

This led to a discussion of sickle cell anemia, thallassemias, etc, including "balanced polymorphism" of the sickle cell allele.  Even though the rr individuals have sickle cell disease, rR individuals are more resistant to Malaria than RR.   In regions where Malaria is prevalent, the rR individuals are the most fit of the three possibilities [rr, rR, and RR], and this "balances" the presence of both r and R alleles in the population.

This also led to a discussion of the sizes of various types of cells, which vary (generally) from  a few to a few dozen microns in diameter (1 micron = 1 mm = 10-6 meters).  We considered intrinsic limitations in sizes of cells in terms of the surface area/volume ratio.  We made "clay cells" of various shapes using our clumps of clay.  Then we measured the dimensions and calculated the surface/volume ratios.  [For example, a cube of side 2.5 cm has a surface area of 37.5 cm2 and volume of 15.625 cm3, so that the surface to volume ratio is 2.40 cm-1.]  Cells need to be small so that the surface/volume ratio is large,  so that cells are able to absorb O2, food, and other nutrients at rates required to support life.  By contrast, large egg cells already have the nutrients inside them, so that they are not limited so much in size.  (For example, consider ostrich eggs.)

Very interesting, Karlene!.

05 March 2002: Karlene Joseph (Lane Tech HS) -- Gas Laws
Karlene
first showed a diagram that allows us to determine how electrons fill atomic orbitals, from lower energy to higher energy:

Shell
Number
Sub-shells (# electrons) Atomic Number
for Full Sub-shell 
1 1s2   2
2 2s2 2p6   4   10
3 3s2 3p6 3d10 12   18   30
4 4s2 4p6 4d10 4f14 20   36   48   68
5 5s2 5p6 5d10 5f14 38   54   78 102
6 6s2 6p6 6d10 12   84 112 
7 3s2 7p6 86 118

The filled P-subshells occur for noble gases:  Z= 2 (Helium), 10 (Neon), 18 (Argon), 36 (Krypton), 54 (Xenon), 84 (Radon), and 118 (¿¿ Valium ??).  It appears as though atoms with atomic number of 118 are at about the limit of discovery.

Karlene next considered the role of oxygen in cellular respiration.  She began by posing these three questions:

How long can humans live without food? .......... Perhaps 2-3 weeks
How long can humans live without water? Perhaps 2-3 days
How long can humans live without oxygen? Perhaps 5 minutes
So why is oxygen so important?  Because of its role in cellular respiration.  Cellular respiration [http://www.ultranet.com/~jkimball/BiologyPages/C/CellularRespiration.html] is summarized in the following equation:
C6H1206 ® 6 H20 + 6 C02 + energy
We then looked at a diagram of a cell [http://www.ultranet.com/~jkimball/BiologyPages/A/AnimalCell.gif], focusing in on mitochondria -- bean-shaped organelles with "squiggles", the squiggles being folds of an inner membrane system.  Cellular respiration begins in the cytosol (the space outside organelles and the cell nucleus) through the reaction known as glycosis, in which glucose is split into two Pyruvic Acid molecules.
C6H1206 ® 2 C3H403 + 4H (eventually ionized)
Pyruvic Acid then diffuses into the mitochondria. Inside the mitochondria, Pyruvic Acid is eventually converted into carbon dioxide and other products through a biochemical pathway known as the Krebs Cycle.  In this process, as well as in glycosis, ATP [Adenosine TriPhosphate] is produced.  ATP is the chemical produced and used to store energy within cells, and the energy is released in small amounts through release of a phosphate ion P04---
ATP (Adenosine TriPhosphate) ® ADP (Adenosine DiPhosphate) + P04--- + energy
Conversely, ATP may be formed from ADP to store energy in cells:
ADP (Adenosine DiPhosphate) + PO4--- + energy ® ATP (Adenosine TriPhosphate)
For each glucose molecule, we have the potential to produce 2 ATP molecules in glycosis and 2 ATP molecules in the Krebs Cycle.  Energy obtained from these processes can also be stored within  NADH [Nicotinamide Adenine Dinucleotide] and FADH2 [Flavin Adenine Dinucleotide] molecules.

Now we come to the topic of electron transport.  The compounds NADH and FADH2 donate high energy electrons to a transport chain in the inner mitochondrial membrane.  As the electrons are passed from one component of the chain to the next, and ultimately to hydrogen ions H and O2 molecules to form water, energy is released and used to pump hydrogen ions H+ from the mitochondrial matrix into the inter-membrane space.  The hydrogen ion then moves back from the region of high concentration [inter-membrane space] to low concentration [matrix] and releases energy.  The energy released in this process is used to form ATP from ADP, thereby storing more energy in the cell.  It is estimated that as many as 34 ATP molecules can be created from the energy in a single glucose molecule by this process of electron transport. Consequently, one can store the energy in a single glucose molecule by creating up to 38 ATP molecules.

Karlene then had us form a (human) electron transport chain, with each person being either part of the electron transport chain (passing electrons on to the next link) or to a second cycle of (human} "oxygens" taking up electrons at the end of the chain and producing water at the same rate as electrons are passing through the chain.  We then reduced the number of "oxygens" by about 60%, so that the electron chain is forced to move more slowly.  If all the "oxygens" sat down, no electron transport could occur, and we would lose the energy stored in 34 ATP's.

Great activity, and great lesson, Karlene!

02 April 2002: Estellvenia Sanders (CVHS, deaf students)    What is a cell?
Estellvenia 
introduced these key words:  cell, cell wall, cell membrane, nucleus, vacuoles. The focus of the lesson was to identify parts of the cell (key words).  As a model for the cell, she introduced a cucumber slice.  The nucleus of the cell corresponded to the "seeds", the cytoplasm to the fruit , the "membrane: with the inner cucumber wall, and the "cell wall" with the outer skin of the cucumber.  She mentioned that one could also use a transversely sliced hard-boiled egg (which is, in effect, a single cell) to visualize cellular structure.

Next we took a soft, round tortilla shell and used magic markers to draw an image of a single cell to make our own cell picture. She  then passed out a "word finding game" to review the concepts.  Beautiful, Estellvenia!

02 April 2002: Karlene Joseph (Lane Tech Biology)  Facial features with a genetic basis
Karlene
passed out a handout concerning facial features for us to determine for our own faces by looking at ourselves with a hand mirror.  We catalogued some of the following facial features:

eye color protrusion of lips nostril shape cleft chin? ear point?
eyebrow texture eyebrow color eye separation eye shape hairy ears?
eyelash length dimples? ear size hair body freckles?
length of mouth nose size earlobes free or attached?  widow's peak? face shape
thickness of lips nose shape chin shape hair color chin shape

We made quantitative measurements -- wherever possible -- by using a ruler with the mirror and we resorted to descriptive answers only where necessary.  In her handout, the "genotype" as well as the "phenotype" for each of these traits is given. [See http://plato.stanford.edu/entries/genotype-phenotype/ and http://www.brooklyn.cuny.edu/bc/ahp/BioInfo/GP/Definition.html.]  For example, the genotype [coded information] for "pointed nose" is "rr" and the "phenotype" is the physical characteristic of pointed features.

The distances between our eyes varied from 2.8 to 3.5 cm, and it was unclear as to how to separate "eyes close" and "eyes far apart" with our small sample.  Also, it was unclear as to whether the distances should be normalized to overall body size, or taken as absolute indicators.

In a larger class, we could have pooled the data to see whether the "allele frequencies" for the class are consistent with the Hardy-Weinberg equilibrium equation, the basic equation for population genetics.  [Hardy-Weinberg Equation:  http://anthro.palomar.edu/synthetic/synth_2.htm] Attached or unattached earlobes would be a good trait for such a test.  Good, Karlene!

08 April 2003: Chris Etapa [Gunsaulus Academy]        Constructing Models of Cells and Organelles
Chris
showed us models of cells with labeled parts, which were made by her 7-8 grade students.  The students could prepare a model, or do a research project  on cells.  We were very impressed by the artistry and creativity of her students.  Here is a brief summary of the project assignment:

You combined cell biology with creative expressiveness and artistry! Very nice, Chris!

06 May 2003: Marva Anyanwu [Green Elementary School]        Genetic Engineering II [handout]
Marva
continued her previous lesson on genetic engineering, using construction paper cutouts with magnets on the back, so that they would stick nicely to our blackboard.  She showed the basics of making a recombinant DNA molecule by using two colors of construction paper.   The idea is first to cut out a piece of a given DNA strand with an enzyme: cutting.  Then, we use another enzyme to cut a DNA piece from another organism, and insert that piece into the empty space of the first DNA, using still another enzyme:  ligation. The complete process of moving a section of DNA from the genes of one organism to the genes of another organism is called Gene Splicing.  In this way one constructs new forms of DNAGenetic Engineering.  For additional details see the website What is Genetic Engineering? http://www.bootstrike.com/Genetics/Home/index.html or http://agbiosafety.unl.edu/basic_genetics.shtml.

Very nice, Marva!

23 March 2004: Carol Giles [Collins HS]         Defining, Identifying, and Interpreting a Pedigree
Carol
began this Genetics lesson by reviewing the ideas behind a pedigree --- a portrait of the genetic (ancestral) history of a trait in a family.  In particular, she focused attention upon particular hereditary traits, such as D:  detached earlobe versus a: attached earlobe. The D: detached earlobe trait is dominant over the a: attached earlobe trait.  We analyzed the pedigrees of four individuals, indicating the genotypes for each ancestor, and the modes of propagation.

Note that 75% of our population have detached earlobes, whereas 25% have attached earlobes.  See the website Comparing Traits:   http://faculty.southwest.tn.edu/jiwilliams/Human_Traits.htm.  For additional information see also:  http://www.fi.edu/guide/knox/Traits/traitsexamples.pdf.  

Very interesting stuff, Carol!

14 September 2004: Ben Stark (IIT)
then discussed the genetics of sex determination in humans. Normal human males have the sex chromosome composition of XY, and females, XX. In human embryonic development, the default is development into a female. The Y chromosome contains a gene (SRY), which encodes the protein "testis determining factor" (TDF). At a certain point in development the SRY gene is turned on, and TDF is made. It causes the as yet undifferentiated gonads to develop as testes. The testes then secrete testosterone, which results in the development of other male specific characteristics. In the absence of TDF, the undifferentiated gonads develop into ovaries, which secrete female hormones, resulting in female development. Unusual XY individuals can be female if the SRY gene is missing or mutated. Unusual XX males have a piece of the Y chromosome containing the SRY gene "translocated" to one of the X chromosomes. XY individuals that lack a functional testosterone receptor cannot respond to the presence of testosterone and develop as females (although they have vestigial testes instead of ovaries and are thus sterile).

07 December 2004: Chris Etapa [Gunsaulus Academy]               Mutations and Variation
Chris distributed a handout obtained from the Museum of Science and Industry -- written by Melanie Wojtulewicz.

We didn’t have time to do all the activities, all of which involve genetics and DNA, but did talk briefly about the Punnett square analysis with Sickle Cells, isolation of DNA from peas, cloning of Dolly the Sheep, and the activity illustrating the various types of mutations.  What we did today was to make a model of DNA using pipe cleaners, longer continuous pieces for the “sides” of the “DNA ladder” (the “sugar-phosphate” backbone), shorter pieces for each “rung” (“base pair”) of the ladder and colored beads, strung two on each rung, for the bases (one color for each base).  We made sure that for each base pair the appropriate colors (bases) were paired with each other:

C with G   ...  and  ...   A with T

Another great learning activity!

22 February 2005: Marva Anyanwu [Wendell Green Elementary School]           Human Traits (handout)
We worked in pairs and investigated the first three traits in Marva's handout (eye color, "tongue rolling", and "finger crossing". Here are the results for the class:

Eye color: 9: brown  2: blue
Tongue rolling? 6: yes  5: no
Finger crossing? 5: yes  6: no
This information would allow us to infer "dominance" and "recessiveness" of the alleles for the genes responsible for each trait, particularly if our class is representative of a freely interbreeding sample of the population as a whole.

We then used a coin toss to simulate/illustrate the "segregation" of the two alleles of a particular single gene of a parent when gametes are formed ( known as Mendel's First Law), since the process is governed by simple rules of probability.

29 March 2005: Marva Anyanwu [Wendell Green Elementary School]             Genetics
As a followup to her miniteach of last time concerning genetics, Marva brought an exercise illustrating the Punnett square, which is a classic device used to work out elementary genetics problems (see http://anthro.palomar.edu/mendel/mendel_2.htm). In the example that Marva provided, we were looking at a hypothetical case involving inheritance of tail color in "critters". The "T" gene determines tail color, the t allele (recessive) determining orange tail and the T allele (dominant) determining blue tail. We first use the Punnett square (and blue and orange crayons as a mnemonic for the alleles) to predict the fraction of blue and orange tail offspring in a mating between two blue tailed critters, each with a "genotype" of Tt. In this typical example of a monohybrid cross, we expect genotypes in the offspring of TT to Tt to tt in a ratio of 1 to 2 to 1; due to the dominant and recessive relationships, the expected "phenotypes" in the offspring will be blue-to-orange in a ratio of 3 -to-1. Two other examples allowed us to extend our familiarity with this technique/set of concepts.

We continued with a lively discussion of other topics in genetics such as XX, XY sex determination, X-chromosome inactivation, etc.

Enlightening, Marva.