Summer Research Program for Science Teachers

Dr. Margaret H. Savitzky

Thomas A. Edison Vocational/Technical HS

 

 

How is the genetic code ultimately translated into a protein?

 

SWBAT: Demonstrate an understanding of the functions of ribosomes, mRNA, rRNA and tRNA

Students will understand/explain the steps in the protein synthesis process.

Materials:

3 chairs

18 5"x8" index cards

3 thick point markers: black, blue and red (so writing can be seen from a distance)

 

Vocabulary:

transcription

ribozyme

translation

wobble

ribosome

Aminoacyl-tRNA synthetase

mRNA, rRNA, tRNA

codon, anticodon

 

Do Now: Transcribe the following DNA fragment into RNA

AATGCATCCTGGA                 [Ans. - UUACGUAGGACCU]

1. DNA is transcribed into pre-mRNA inside the nucleus. Enzymes cleave segments called introns from the transcribed molecule, leaving segments called exons that becomes the messenger RNA (mRNA) that leaves the nucleus.

2. Inside the nucleus, the nucleolus is the site of ribosomal RNA (rRNA) formation. The rRNA will bind with protein in the nucleus and exit to the cytosol as a large or small subunit of the ribosome. Prokaryotes and eukaryotes ribosomes have similar structure and function but do differ. This difference is targeted in the medical field. Antibiotics kill bacterial ribosomes without damaging eukaryotic ribosomes (tetracycline, streptomycin)

3. transfer RNA (tRNA) is also formed in the nucleus and leaves to float in the cytosol. Each tRNA structure has a codon on one end that bonds to an amino acid and a complementary anticodon on the other end that bonds to an mRNA. There is a tRNA formed to match its codon with a single type of amino acid. Although there are 61 different codons that code for the 20 amino acids, there are only 45 different tRNAs because the third base in the tRNA anticodon can recognize two or more different codons on a mRNA. This ability to recognize different codons is called wobble. A modified base called inosine (I) can bond with A, C, or U. So tRNA that has CCI as its anticodon can bond to GGU, GGC or GGA.

4. tRNA binds to the correct amino acid using an specific enzyme called aminoacyl-tRNA synthetase (one enzyme for each type of amino acid). This process requires the use of ATP. The tRNA with the amino acid attached to its codon is called aminoacyl tRNA or activated amino acid.

5. The ribosome is the site where the mRNA and tRNA (carrying an amino acid) meet. The ribosome has 4 important sites:

a. mRNA binding site - the mRNA binds at its 5' end and will move through in a 5' to 3' direction.

b. A site (aminoacyl-tRNA site) - the site where a tRNA can bond to deliver the next amino acid to be added to a polypeptide chain that is being constructed.

c. P site (peptidyl-tRNA site) - the site where the tRNA holding the growing polypeptide chain is located. The chain will be transferred to the tRNA in the A site to add on the amino acid being held there. The first tRNA starts in the P site.

d. E site (exit site) - the site where the tRNA that was in the P site moves to before leaving the ribosome.

 

Class activity

1. Set up 3 chairs in the front of the room. Mark the chairs E site, P site and A site (from left to right). This set-up represents the ribosome.

2. Select 6 students to act as mRNA molecules. Have them line up next to the chair marked A. Give each student a 5"x8" index card that has been inscribed in black ink with one of the following codons:

AUG, GGU, UUU, UGG, AAC, UAG.

3. Select 6 students to act as tRNA molecules. Give each student two 5"x8" index card inscribed as follows:

 

CARD  

(Codon)

 Black ink on left edge of 1st index card

 

 (Anticodon)

Red ink on the right edge of 1st card

 

(Amino acid)

Blue ink on the 2nd index card

1a,b    UAC   AUG   Met/Start
2a,b   CCA   GGU   Glycine
3a,b   AAA   UUU   Phenylalanine
4a,b   ACC   UGG   Tryptophan
5a,b   UUG   AAC   Asparagine
6a,b   AUC   UAG   Stop

  

4. Have the student holding the mRNA card with AUG, written on it, sit in the seat marked P site. The tRNA student that is holding the cards 1a and 1b (Methionine) stand behind this chair.

5. Have the second student in line, holding the mRNA card with GGU sit down in the chair marked A site. The tRNA student that is holding the cards 2a and 2b (Glycine) stand behind this chair.

6. The tRNA student standing behind the P site chair hands his amino acid index card (Methionine) to the tRNA student holding cards 2a & b.

7. The next step requires each student to move over one chair. The student sitting in the P site chair moves into the E site chair, the student sitting in the a site chair moves into the P site chair and the two tRNA students move with them. (The first tRNA student should only be holding card 1a, and the second tRNA student now holds 2a, 1b and 2b cards, representing his tRNA and the two amino acids that have bonded: 1b-2b)

8. The third mRNA student now sits in the empty A site chair holding the index card with UUU. The tRNA student with cards 3a and 3b (Phenylalanine) stands behind the chair.

9. The tRNA student standing behind the P site chair, holding cards 2a, 1b, 2b hands cards 1b and 2b to the third tRNA student behind the A site chair. (The amino acid chain is now 1b, 2b, 3b Met-Gly-Phe).

10. The three tRNA students all move over one position. The student behind the E site chair walks away (empty tRNA returns to the cytosol)and the mRNA student stands up next to the E site chair, the student behind the P site chair moves to the E site, and the student behind the A site chair moves to the P site chair.

11. The fourth mRNA student sits in the A site chair holding the index card marked UGG. The tRNA student holding index cards 4a and 4b (Tryptophan) stands behind this chair. The tRNA student behind the P site chair hands cards 1b, 2b, 3b, to this 4th student.

12. All the students move over one chair again. (The second mRNA student leaves the "ribosome" to stand next to the chair and the first student who stood up, the third student moves into the E site, the fourth student moves into the P site and each tRNA student follows the student they stood behind). The A site chair should be empty again.

13. The fifth mRNA student sits in the A site chair holding the index card marked AAC. The tRNA student with index cards 5a and 5b (Asparagine) stands behind the chair. The tRNA student behind the P site chair hands the amino acid cards 1b, 2b, 3b, 4b to the 5th tRNA student.

14. All the students shift chairs again. The third mRNA student in the E site chair stands up, the fourth mRNA student moves into the E site chair, the fifth mRNA student moves into the P site chair and the sixth mRNA holding the index card marked UAG now sits down in the A site chair.

15. The tRNA student holding index cards 6a and 6b stands behind the A site chair. The tRNA codon AUC pairs up with the mRNA UAG which is the stop codon. When this card appears the peptide chain is done forming and will separate from the ribosome. mRNA codons UAG, UAA and UGA all signal the stopping point of translation; they donít code for any amino acids. *** 3 GTP molecules are used to perform this process

At this time the ribosome subunits will come apart and the mRNA line of students are released to either enter the next ribosome or eventually degrade in the cytosol.

Ribosomes have the ability to line up and have a single mRNA pass through this chain of ribosomes, producing several proteins at the same time. The chain of ribosomes are called polyribosomes.

 

Science Standards

S5f Works individually and in teams to collect and share information and ideas.

S7a Represents data and results in multiple ways, such as numbers, tables, and graphs; drawings, diagrams, and artwork; technical and creative writing; and selects the most effective way to convey the scientific information.