6. Protein Factory - Logistics

Time
45-55 minutes

Grouping
Whole class.

Materials

• Copies of the Genetic Code handout (see Secret Codes activity)
• 1 assembled paper DNA model, 60 base pairs long (1 codon per student acting as a tRNA)
• Copies of Factory Instructions (follow the teacher instructions on the top of the page for how many copies of each to make)
• Copies of DNA puzzle pieces, each on a different colored paper. For a group of 30 students you will need:
• • 4 copies of S-ribose
  • 3 copies of P-phosphate
  • 2 copies of A, C, G, and U
  • 2 copies of amino acid
  • 10 copies of transfer RNA
  • You also need several DNA model puzzle pieces to create the promotor, translation start, and translation stop sequences. Hopefully, you have some left over from the DNA model activity:
  • 30 S-deoxyribose pieces (1 sheet)
  • 30 P-phosphate pieces (1 sheet)
  • 10 A, C, G, and T pieces (half a sheet)
• Scissors
• 8 rolls of Scotch tape
• Bins or trays on which to keep the puzzle pieces.

Setting
classroom

6. Protein Factory - Background

Teacher Background
The process of turning DNA into protein is called the “central dogma of molecular biology” because it is the foundation of all modern genetics, biotech and pharmacology. There are 6 major players in the process.

1. DNA – the blue print for construction of specific proteins. A section of DNA that codes for a protein is called a gene. More on the structure of DNA can be found in the background section of the DNA Models activity.
2. RNA polymerase – an enzyme responsible for assembling a strand of RNA from a DNA template. It is formed from an assembly of several different individual proteins with various roles.
3. Messenger RNA – temporary courier of information that brings a copy of the information encoded in the DNA to the ribosome where the proteins are actually made. More on the differences between RNA and DNA can be found in the background section of the Secret Codes activity
4. Ribosome – a fairly complex organelle that is like a protein factory. It assembles a chain of amino acids using the messenger RNA as a template. More on the genetic code that governs which amino acids pair with what RNA sequence may be found in the background section of the Secret Codes activity.
5. Transfer RNA – a small length of RNA (less than a hundred base pairs long) that transfers a specific amino acid to the growing protein chain within a ribosome. Each transfer RNA has a site where an amino acid can bind and a special 3 nucleotide sequence celled the “anticodon.” The anticodon matches a 3 nucleotide sequence on the messenger RNA molecule called the “codon”.
6. Protein – the primary building material of cells. Proteins constitute most of the dry mass of a cell and execute nearly all cell functions. Proteins are long single stranded chains constructed of 20 different building blocks called amino acids.

Transcription and translation: Illustration from Radboud University NijmegenThere are 2 major steps in the protein synthesis process. The first is the synthesis of messenger RNA in a process known as transcription. This process is similar to DNA replication, except that only a tiny portion of one strand is copied and it is copied into a single-stranded RNA molecule, not a double stranded DNA molecule.

To start transcription, RNA polymerase binds to a specific DNA sequence known as a promotor. Promotors sequences are very diverse, however, generally are found in the stretch of DNA in front of the gene and contain a place for RNA polymerase to bind as well as a transcriptional start sequence that indicates where transcription should begin. They range in length from less than a hundred base pairs to several thousand base pairs. Many promotor sequences contain the sequence TATAAA, known as a TATA box by biologists. This TATAAA sequence is used in this activity to indicate where the RNA polymerase should bind and begin transcription.

Once, the RNA polymerase binds to the promotor, it follows along the DNA, unzipping the base pairs, reading one of the two DNA strands, matching an RNA nucleotide to each DNA nucleotide, and assembling a messenger RNA molecule. The RNA polymerase continues moving along the DNA until it reaches a specific terminator sequence, at which point it releases the messenger RNA and disassembles. Messenger RNA molecules may extend over 2 million bases in length. At this point, the messenger RNA travels out of the nucleus to the ribosome where proteins are actually made.

This second step of the protein synthesis process is known as translation. First, a ribosome assembles around the messenger RNA molecule. Translation always begins at the messenger RNA sequence AUG. The messenger RNA then feeds its way through the ribosome like a tape. As it proceeds, each codon on the messenger RNA is matched to a transfer RNA. The ribosome forms bonds between the amino acids carried by the transfer RNAs and the empty transfer RNA molecules detach and float away. Gradually, the amino acid chain grows longer and longer until a stop sequence (UAG, UAA, or UGA) is reached. At that point, the protein is released.

From here, the protein may go through many stages of further processing. Depending on the sequence of amino acids, some parts of the protein like water and some curl away from it. Thus, the protein will fold itself up to protect the water-hating parts of the protein from the surrounding cytosol. In addition, proteins may be cut, spliced, joined together, packaged and reshaped into a final functional protein.

Student Prerequisites
Some basic introduction to the protein synthesis process (see Secret Codes lesson).

6. Protein Factory - Getting Ready

Getting Ready

1. If not already assembled, put together a DNA model 60 base pairs long. Check to make sure that none of the stop codons (UAG, UAA and UGA) would be part of the messenger RNA coded by the sequence. Flipping the DNA molecule over or adding 1 or 2 extra bases on one end of the DNA sequence may solve the problem.
2. To one end of the DNA model, add the following sequence (this is your promotor sequence to start transcription and your AUG start sequence to start translation):
   T A T A A A C T T A C x x x ...
   A T A T T T G A A T G x x x
3. To the opposite end of the DNA model, add the following sequence (this is your stop codon).
   ... X X X A T C
       X X X T A G
4. Optional: work out for yourself what the sequence of amino acids would be for the DNA molecule you have. You want to check to make sure that there are no stop codons (UAG, UAA and UGA) within the messenger RNA.
5. Make photocopies of the Factory Instructions handout. Follow the detailed directions at the top of the page.
6. If not already given to students, make photocopies of the Genetic Code handout.
7. Make photocopies of the puzzle pieces, each on a different colored paper.
8. Have students cut out 1 or 2 sheets of puzzle pieces per person, possibly as homework the night before the activity.
9. Place S-ribose, P and half of the A, C, G, and U pieces in one bin for the students playing the role of messenger RNA.
10. Place amino acid, transfer RNA and the remaining half of the A, C, G, and U pieces in several other bins (4-5 bins total for 20 students to share) for the students playing the role of transfer RNA.
11. Designate one area of the classroom as the nucleus with the other areas as the cytosol.

6. Protein Factory - Lesson Plan

Lesson Plan

1. Begin class with a secret DNA message for the students to decode (see assessment section of the Secret Codes lesson).
2. Review the steps of the protein synthesis process: 1) DNA is transcribed into messenger RNA and 2) the RNA is translated into a sequence of amino acids based on 3 nucleotide codons.
3. Give students more detailed background information on how the protein synthesis process works. Discuss the role of RNA polymerase and the ribosome. Describe how RNA polymerase recognizes where to start transcribing the gene (a promotor sequence) and how the ribosome knows where to start (AUG) and stop (UAG, UAA, or UGA) translating the messenger RNA.
4. Give students an overview of the rest of the class period. Show students where the nucleus is and where the cytosol is.
5. Assign students their roles. Each student should get an instruction card and the materials listed on their instruction card.
6. Allow students performing the role of the messenger RNA to create RNA nucleotides. Allow students performing the role of the transfer RNA a few minutes to assemble their transfer RNA molecules.
7. Restore silence to the classroom and begin the process. Have all the students watch as the process unfolds. You may want to describe what is going on at each step for the students that aren’t involved directly. Briefly:

   1. RNA polymerase finds the TATAAA promotor sequence on the DNA molecule.
   2. RNA polymerase unzips the DNA nucleotide after the promotor and finds a matching RNA nucleotide.
   3. RNA polymerase unzips the next DNA nucleotide and finds a matching RNA nucleotide.
   4. RNA polymerase joins the RNA nucleotides together.
   5. RNA polymerase continues unzipping, finding nucleotides, and joining them together until the end of the DNA molecule.
   6. DNA zips itself back up again.
   7. The newly assembled messenger RNA floats out of the nucleus to the ribosome.
   8. The ribosome finds the AUG start sequence on the messenger RNA.
   9. The ribosome finds a matching transfer RNA and lines it up alongside the messenger RNA strand.
   10. The ribosome finds a matching transfer RNA to the next 3 nucleotides.
   11. The ribosome removes the amino acid from the first transfer RNA and attaches it to the amino acid that just arrived.
   12. The ribosome continues finding transfer RNA molecules and joining amino acids until it reaches a stop codon (UAG, UAA, or UGA).
   13. The empty transfer RNA molecules leave the ribosome.

8. If there is extra time, you may be able to have students switch roles and go through the process a second time in a new role.
9. You may want to close the class with a discussion of how the classroom protein factory is different than the actual process taking place in nearly every cell in your body. For instance, the DNA molecule in the model only had 1 gene whereas real DNA molecules have thousands of genes. Also, RNA polymerase and ribosomes are just molecules and act like a machine in a factory, not like a thinking human being.

6. Protein Factory - Assessment

Assessment

1. Ask students to summarize the job of the 5 players – DNA, messenger RNA, RNA polymerase, transfer RNA and the ribosome – in their own words.
2. See the Comic Strip assessment idea for one creative way to gauge kids understanding of the protein synthesis process.

6. Protein Factory - Sources and Standards

Sources
This activity was put together from the bright ideas of several great teachers: Lori Lambertson of the Exploratorium Teacher Institute and Jim Youngblom of CSU Stanislaus.

Standards
Grade 8
Chemistry of Living Systems (Life Sciences)
6. Principles of chemistry underlie the functioning of biological systems. As a basis for understanding this concept:
c.     Students know that living organisms have many different kinds of molecules, including small ones, such as water and salt, and very large ones, such as carbohydrates, fats, proteins, and DNA.

Grade 9-12
Genetics
4.   Genes are a set of instructions encoded in the DNA sequence of each organism that specify the sequence of amino acids in proteins characteristic of that organism. As a basis for understanding this concept:
a.     Students know the general pathway by which ribosomes synthesize proteins, using tRNAs to translate genetic information in mRNA.
b.     Students know how to apply the genetic coding rules to predict the sequence of amino acids from a sequence of codons in RNA.
e.     Students know proteins can differ from one another in the number and sequence of amino acids.