Download DNA Modeling

Education 512
Model Assignment III
November 12, 2003
Jennifer M. Benson, Melissa Birkett, Sylvain Casimir
David Millette, Carla Pignatare, Sandra R Turcios Payne
Introduction
One of the most important concepts in our field is how DNA sequences are transcribed into
RNA and then translated into proteins. This process is often referred as the “Central Dogma” of
molecular biology. It involves the key molecular ideas fundamental to our model of life. In
short, the central dogma reminds us that information is stored in a molecule of DNA that is
transcribed to a related molecule, RNA, which is then translated into proteins that eventually
carry out the functions of the cell. This area of information is a challenge to most introductory
biology students, as they are forced to conceptualize a complex group of biochemical ideas for
what may be the first time in their lives. Because this concept is such a challenge, an accurate,
interesting model of this process is very key to students understanding of not only molecular
biology, but biology as a whole, especially in relation to fields such as genetics, evolution,
medicine, and biotechnology.
Replication. The first part of the central dogma involves a process called replication. This
process occurs during the “S” stage of interphase in the cell cycle. Replication occurs in the cell
nucleus, and involves the separation, or the “unzipping”, of the DNA molecule into its
constituent strands. Each strand serves as a template to create a new complementary strand.
This results into the formation of two identical double–stranded molecules of DNA. Note that
DNA replication is also dubbed semi-conservative replication, for the reason being that each of
the double-stranded molecules now consists of a single strand of old DNA – the template strand.
Several proteins called enzymes work in the cell nucleus on the process of DNA replication. As
a group they are called DNA polymerases. We teach this process in the lessons leading up to the
one you are now reading.
Transcription
DNA is the instruction manual of the cell. All things that do the work of the cell, including the
DNA polymerases that make it, are encoded in the molecules of DNA. In order for a new cell to
exist, the DNA code must leave the nucleus and be translated out in the cell. However, to
protect the DNA from damage, it can never leave the nucleus. What to do? A related molecule,
called Ribonucleic Acid, (RNA) is formed through the process of transcription that also
happens in the nucleus. In this process, the DNA is again unzipped and molecules of RNA are
copied from it. One of the reasons that this is not called simply replication again is that the RNA
is slightly different chemically from DNA. There are 3 kinds of RNA, and they are as follows:
 Messenger RNA (mRNA) is the template that provides the sequencing of the amino
acids via the genetic code. The codon (part of the genetic code, consisting of 3
nucleotides each) is the genetic alphabet, each codon coding for one specific amino acid.
A copy of this alphabet system can be found below.
 Transfer RNA (tRNA) is used for transporting amino acids to their proper place on the
mRNA template. Transfer RNA has anti-codons for proper matching with related
codons.

Ribosomal RNA (rRNA) molecules are the building blocks of ribosomes. Ribosomes
play a major role in protein synthesis, during the translation phase.
Translation
This is the phase where RNA, which to a large degree is still a storehouse of information, is
translated into proteins, which are the workhorses of the cell and carry out the cells daily
business. It is also called protein synthesis. This is the part of the model that we will be
teaching in the lesson to follow. This process is categorized into three steps:
 Initiation: A piece of mRNA is recognized by parts of ribosomes that attach to it and begin
the process of translating it to proteins.
 Elongation: transfer RNA’s bring anticodons attached to amino acids to the ribosomal
machinery to be added to an amino acid chain.
 Termination: a stop codon is reached, signaling the machinery that the protein has been
completely translated. The ribosome units (drop off the chain and begin to look for another
mRNA to translate
Pedagogy
As we noted earlier, the concepts surrounding the central dogma are often the first experience
that high school students have with molecular biology. Straight memorization of the aspects of
protein structure and synthesis has been the traditional way that this is taught, but retention
results are often poor. More recently, teachers have begun to mix different teaching methods to
approach this material. In doing this they attempt to give students as many different ways to
grasp the ideas. Our lesson attempts to de-intellectualize it somewhat, get the students out of
their chairs and associate physical space with the imagined physical space of the inside of a cell.
After investigating the constituents of the model individually, we integrate the concepts as a
play. This enables us to help the students conceptualize the information they’ve processed
differently from the previous lessons of the unit, and to see the mechanism of cellular process in
action in front of them. We will demonstrate how this works with the final process in the chain
described above, translation.
Today’s Lesson Plan, Translation:
1. Review of yesterday’s lesson: DNA to RNA. Review of all the vocabulary related to the
lesson: nucleotides, codons, anti-codons, etc.
2. Overhead of DNA  RNA  protein
Brief lecture, description: emphasize that DNA  RNA happens in the nucleus, while mRNA 
protein occurs in the cytoplasm
3. Video of DNA  RNA  protein. (Review, the students saw this yesterday as part of the
DNA to RNA lesson) The Stanford Marching Band demonstrates the central dogma at a
halftime show. The video describes the dogma as understood in the 1970’s but is more than
suitable for our purposes. (Courtesy of Dr. Adam Porter, UMass Dept. of Entomology.)
Teacher answers any questions students have. Video should give students the general idea of
how transcription and translation occur, and where each part of the process occurs in the cell, so
that they are ready for the next activity.
4. Student “Play” about RNA  protein.
Overview of Activity:
With the whole class, brainstorm molecules and have someone write them on the board.
Different roles (specific T-RNA, specific amino acids, specific codons, a ribosome, DNA) are
written on slips of paper, and put into a hat or a box; students draw out a slip of paper – that is
their role in the play.
Students are instructed to “act out” translation of the first 10 amino acids of a known protein.
The known protein is named on the board, and the students look up the amino acid sequence of
that protein, and extrapolate back to what the mRNA and DNA sequences that code for that
sequence of amino acids would be. The teacher leads them through the process. In general, the
following will happen:
1. The “Ribosome” student has the first “codon” for the protein they are building
at their “active site”.
2. A “tRNA” student recognizes that they carry the anti-codon for the codon that
is at the ribosome.
3. that tRNA student finds on the table what amino acid student they need to look
for.
Table 1 : Codon table. This table illustrates the 64 possible codon triplets.
2nd base
U
UUU
Phenylalanine
UUC
U
Phenylalanine
UUA Leucine
UUG Leucine
CUU Leucine
CUC Leucine
C
CUA Leucine
CUG Leucine
C
UCU Serine
UCC Serine
UCA Serine
UCG Serine
CCU Proline
CCC Proline
CCA Proline
CCG Proline
ACU
1st
Threonine
base
AUU Isoleucine
ACC
AUC Isoleucine
Threonine
A
AUA Isoleucine
ACA
1AUG Methionine Threonine
ACG
Threonine
GUU Valine
GUC Valine
G
GUA Valine
GUG Valine
http://en2.wikipedia.org/wiki/Codon
GCU Alanine
GCC Alanine
GCA Alanine
GCG Alanine
A
G
UGU Cysteine
UAU Tyrosine
UGC Cysteine
UAC Tyrosine
UGA Opal Stop
UAA Ochre Stop
UGG
UAG Amber Stop
Tryptophan
CAU Histidine
CAC Histidine
CAA Glutamine
CAG Glutamine
CGU Arginine
CGC Arginine
CGA Arginine
CGG Arginine
AAU Asparagine
AAC Asparagine
AAA Lysine
AAG Lysine
AGU Serine
AGC Serine
AGA Arginine
AGG Arginine
GAU Aspartic acid
GAC Aspartic acid
GAA Glutamic
acid
GAG Glutamic
acid
GGU Glycine
GGC Glycine
GGA Glycine
GGG Glycine
4.
5.
6.
7.
8.
The tRNA student takes the hand of the specific amino acid they code
for, and brings that student over to the ribosome. (Students may also
choose to use a length of string or other material held between 2 joined
students to represent their relationship.)
The student codon at the ribosome moves over, and the next codon
student is at the ribosome active site.
The tRNA that had the anti-codon that matches the second student
codon finds their corresponding student amino acid, takes their hand,
and brings them over to the ribosome.
The first amino acid and the second amino acid hold hands, “joined
together”.
This process repeats, over and over, until the primary structure (the
amino acid sequence) of the protein is built.
Wrap-up and Assessment:
5. After the play, the teacher leads the class in a discussion about what they observed happening.
Questions such as what was happening to the DNA (emphasizing that the DNA did not play an
active role in the translation process), what was happening to the ribosome, etc. are analyzed.
6. After the translation play, students count off into groups, in which they discuss what happened
during their translation play, and are instructed to come up with a similar type of play to
demonstrate their knowledge of how DNA  RNA (transcription) occurs. Students would be
formatively assessed on how well their play models the process of transcription.
7. Students are then given homework to write 2 or 3 paragraphs describing in their own words
how transcription and translation occurs. They would be encouraged to draw their own diagram
representations of the process (and not simply copy the way it is shown in their textbook).
Additional Resources for the Lesson:
We recommend the following websites as resources for lessons prior to the one we describe.
Again, it is our opinion that giving the students the largest number of options for the integration
of the subject matter will result in better retention.

Protein Explorer, a free, chime-based molecular imaging software model was developed
here at UMass Amherst. It can be accessed online at:
http://www.umass.edu/microbio/chime/explorer/frntdoor.htm. Its developer, Eric Martz,
has also been instrumental in developing Protein Data Bank (PDB) Lite, a way for teachers to
download smaller molecular files for use in the 3-dimensional imaging of molecules.

PDB Lite can be found at: http://www.umass.edu/microbio/rasmol/pdblite.htm. It is a site
that keeps in mind the fact that many of its users are computer novices, and enables them to
bring these wonderful images to their classes. It is our suggestion that the class be shown
DNA and RNA molecules using this technology at least once during the unit preceding this
lesson.
The following sites have an online interactive model of how transcription and translation works:

http://www.mcps.k12.md.us/departments/isa/ninvest/dogma/balttranreg.htm
Simply click on the "DNA Workshop Activity" box for activation

http://gslc.genetics.utah.edu/units/basics/transcribe/
This website includes interactive features to translate and transcribe proteins.

http://gslc.genetics.utah.edu/units/basics/builddna/
This site includes interactive features to build a strand of DNA.