How Did They Figure Out The Genetic Code?
J. Jos Bonner; 1/10/01
Modified 11/23/06
There are two scenarios here; some student groups should get one, other student groups should get the other. Then, challenge the students to learn what they can from these scenarios--as a competition. At the end, compare the results of the two groups, building a table of the Genetic Code. Then, give them the data from Set III, and add the results to the table.
After students have wrestled with the data, and after you have
together built a table with a few of the codons identified, give them the
entire table (shown below). The
data from Sets I, II, and III give students the basic information: there are
three bases per codon, sometimes more than one codon specifies a single amino
acid, and some codons do not correspond to amino acids at all (but are, in
fact, "stop" codons that trigger termination of translation). Typically, these three features of the
Code are confusing. However,
working through the data, and discovering these features themselves, will give
students a sense of "ownership" of their discoveries and lessen their
confusion. [They still will not
know why it works this way--none of us
do--but they will know that it
does, and they will know the data upon which these conclusions are based.] When, in the next session, they begin
to hear about the mechanism of translation, with tRNAs and ribosomes, they'll
know there's a code, that it uses 3-base codons, and that the tRNAs provide a
simple explanation for these observations.
Set I
In science, nearly everything is a race among different
laboratories, each one hoping to make the next breakthrough before anyone else
does. Today, in early 1961, the
race is about the Genetic Code. In
just the last few years, we've learned the structure of DNA, and the fact that
genetic information must be
"stored" in DNA as the sequence of bases. We've learned that the cytoplasmic enzymes that build
protein according to the DNA code do not "read" the DNA itself. There is some kind of
intermediate. The best candidate
for this intermediate, or "messenger" is RNA. Now, the question is: how does it work? What is the code?
Whoever cracks the code first wins.
You are a researcher in Marshall Nierenberg's laboratory. You've figured out a way to determine the genetic code. You have:
„ bacterial cells, which you can grind up into a kind of concentrated soup. We call this a "cell-free" system, because it contains all of the material that is inside cells, but has no complete (unbroken) cells in it.
„ synthetic RNA molecules, which you have made in the lab with specific sequences.
„ some radioactive amino acids (a mix of all 20)
„ methods by which you can:
- separate different proteins on the basis of their chemical properties
- break proteins apart completely into individual amino acids
- remove one amino acid at a time from the ends of proteins
- separate and identify different amino acids
To figure out the
code, you repeat the following experiment with each RNA molecule:
1. add one synthetic RNA to the cell-free
system.
2. add the radioactive amino acid mix.
3. wait for the cell-free system to build
protein, using your synthetic RNA as a "template."
4. separate different proteins from the
reaction mix, and determine which (radioactive) amino acids were used to build
protein.
With the first few RNA molecules that you use, you obtain the following data:
|
Experiment # |
RNA used in
reaction |
Protein produced
by cell-free system |
|
1 |
UUUUUUUUUUUUUUU... |
Phe-Phe-Phe-Phe-Phe... |
|
2 |
CCCCCCCCCCCCCCCC... |
Pro-Pro-Pro-Pro-Pro... |
|
3 |
UCUCUCUCUCUCUCU... |
Leu-Ser-Leu-Ser-Leu... |
|
4 |
UCCUCCUCCUCCUCC... |
Ser-Ser-Ser-Ser-Ser... and Pro-Pro-Pro-Pro-Pro... and Leu-Leu-Leu-Leu-Leu... |
Data Analysis for Set I:
1. What are all
the possible codes for Phe?
2. What are all
the possible codes for Pro?
3. How does
experiment #3 help you decide among these choices?
4. In
experiment #3, how many different RNA codes were used by the cell-free
system?
What are they?
5. How do you explain the results of experiment #4?
6. Make a table of the different RNA codes
you have discovered--i.e., what RNA sequence codes for what amino acid.
Set II
In science, nearly everything is a race among different
laboratories, each one hoping to make the next breakthrough before anyone else
does. Today, in early 1961, the
race is about the Genetic Code. In
just the last few years, we've learned the structure of DNA, and the fact that genetic
information must be "stored"
in DNA as the sequence of bases.
We've learned that the cytoplasmic enzymes that build protein according
to the DNA code do not "read" the DNA itself. There is some kind of
intermediate. The best candidate for
this intermediate, or "messenger" is RNA. Now, the question is: how does it work? What is the code?
Whoever cracks the code first wins.
You are a researcher in Fred Hochstein's laboratory. You've figured out a way to determine the genetic code. You have:
„ bacterial cells, which you can grind up into a kind of concentrated soup. We call this a "cell-free" system, because it contains all of the material that is inside cells, but has no complete (unbroken) cells in it.
„ synthetic RNA molecules, which you have made in the lab with specific sequences.
„ some radioactive amino acids (a mix of all 20)
„ methods by which you can:
- separate different proteins on the basis of their chemical properties
- break proteins apart completely into individual amino acids
- remove one amino acid at a time from the ends of proteins
- separate and identify different amino acids
To figure out the
code, you repeat the following experiment with each RNA molecule:
1. add one synthetic RNA to the cell-free
system.
2. add the radioactive amino acid mix.
3. wait for the cell-free system to build
protein, using your synthetic RNA as a "template."
4. separate different proteins from the
reaction mix, and determine which (radioactive) amino acids were used to build
protein.
With the first few RNA molecules that you use, you obtain the following data:
|
Experiment # |
RNA used in
reaction |
Protein produced
by cell-free system |
|
1 |
GGGGGGGGGGGGGGG... |
Gly-Gly-Gly-Gly-Gly... |
|
2 |
CCCCCCCCCCCCCCCC... |
Pro-Pro-Pro-Pro-Pro... |
|
3 |
GCGCGCGCGCGCGCG... |
Ala-Arg-Ala-Arg-Ala... |
|
4 |
GCCGCCGCCGCCGCC... |
Ala-Ala-Ala-Ala-Ala... and Pro-Pro-Pro-Pro-Pro-Pro... and Arg-Arg-Arg-Arg-Arg... |
Data Analysis for Set II:
1. What are all
the possible codes for Gly?
2. What are all
the possible codes for Pro?
3. How does
experiment #3 help you decide among these choices?
4. In
experiment #3, how many different RNA codes were used by the cell-free
system?
What are they?
5. How do you explain the results of experiment #4?
6. Make a table of the different RNA codes
you have discovered--i.e., what RNA sequence codes for what amino acid.
Data Set III
|
Experiment # |
RNA used in
reaction |
Protein produced
by cell-free system |
|
1 |
UUUUUUUUUUUUUUU... |
Phe-Phe-Phe-Phe-Phe... |
|
2 |
AAAAAAAAAAAAAAA... |
Lys-Lys-Lys-Lys-Lys... |
|
3 |
AUAUAUAUAUAUAUA... |
Ile-Tyr-Ile-Tyr-Ile-Tyr... |
|
4 |
AAUAAUAAUAAUAAU... |
Asn-Asn-Asn-Asn-Asn-... and Ile-Ile-Ile-Ile-Ile-Ile-Ile-... |
Data Analysis for
Set III:
This is as
straightforward as Data Set I and Data Set II until we get to experiment
#4. In sets I and II, experiment
#4 gave three different proteins.
Here it gives only two. What
does this tell us?
Extension:
Now, perhaps, we
are ready to look at the complete table of the Genetic Code. We understand that it was experiments
like these that led Marshall Nierenberg's lab to figure out the Genetic Code. We don't need to go through all of the
experiments, or understand all of the techniques; nonetheless, working through
the logic and the data-analysis gives us a pretty good sense of what was
involved.
Some
interesting notes:
When we present protein synthesis in a lecture that describes
what happens, students are left with many puzzles. One of the big ones is "why 3 bases per codon?"
The teaching approach presented here doesnÕt answer this
question. Rather, it illustrates the fundamental nature of science,
and the generic answer to all such "why" questions. We can ask, by means of
experimentation, what the genetic code is; we can obtain the answer to this
question. We can describe what we
find; we cannot address why we didn't find something else. In general:
Science can address how the world works. It cannot address why it works that way.
Once we know the genetic code, and the fact that ribosomes
"read" the code with the help of tRNA molecules that form base pairs
with the codons of the mRNA, we can
address the next question students often ask. They often wonder why ribosomes "walk" down mRNA
in steps of three bases. Here,
answering how ribosomes function
gives us the answer to this "why" question. Once a ribosome has ejected a "used" tRNA, no
longer carrying an amino acid, the ribosome moves down the mRNA by re-adjusting
its position relative to the tRNA that remains H-bonded to the mRNA. Essentially, the ribosome moves the
width of one tRNA--one codon, which happens to be 3 bases. When we speak of ribosomes moving
"3 bases at a time," we imply that ribosomes can count, and have some
kind of mysterious intelligence.
When we speak of ribosomes moving "one tRNA width" at a time,
"counting" becomes unnecessary; it's just a clockwork mechanism. An unintelligent clockwork mechanism is
easier to understand.