Protein Synthesis Modeling: A Closer Look at Bug Wings



Protein Synthesis Modeling: A Closer Look at Bug Wings

(adapted from Laying the Foundations: Proteins the Essence of Life)

Proteins are the molecules that carry out the “business of living.” Humans can synthesize over 50,000 different proteins. How does a cell synthesize so many proteins? The blueprint for these proteins is found in molecules of DNA. DNA contains the genetic information needed for protein synthesis. DNA is restricted to the nucleus in eukaryotic cells yet the actual synthesis of proteins occurs on ribosomes found in the Rough ER or in the cytoplasm of the cell. This means that there must be some sort of intermediate molecule that moves the information from the nucleus out to the ribosomes.

There are two parts to protein synthesis, transcription and translation. Transcription is the process of converting the information in the DNA molecule into a messenger that will carry it out of the nucleus. This messenger is called messenger RNA or mRNA. The process of transcription occurs in the nucleus. Translation is the synthesis of a protein using the instructions in the mRNA code. Each set of three nitrogen bases (ex. UCC) in mRNA is called a codon. Each codon codes for an amino acid ( ex. UCC codes for the amino acid serine). When these amino acids are hooked together by chemical bonds a chain is formed. Once completed, this chain will twist into a protein with the correct shape and chemical structure needed to perform it’s job in the body. The specific proteins an organism makes will determine the kind of traits it has.

In this activity, you will be give a strand of DNA belonging to the bug you created in the Build-A-Bug activity. Like in Build-A-Bug, this DNA will give you a code to determine another trait for your bug, specifically wing color. In order to find out the wing color of you bug you will need to model all of the steps of protein synthesis. This process will lead to the formation of a protein that will determine your bug’s wing color.

Materials:

a) Cutouts page b) question sheet c) scissors d) tape e) colored pencils

Procedure:

1. Obtain a set of cutouts. Before you cut, color each of the cutouts according to the color code below:

DNA – blue, mRNA – red, tRNA – green, ribosome – purple

2. Cut out the colored shapes from your cut out page. Place the nucleus on your work surface and place all other pieces aside. Place the DNA molecule into the center of the nucleus. Answer question #1 and #2 on your worksheet.

Have your teacher initial your work before you move on: ____________

3. To begin transcription, enzymes break the bonds between the two DNA strands. Use scissors to cut the double stranded DNA into two different strands. This demonstrates how the DNA molecule unwinds on preparation for transcription.

4. Transcription occurs when mRNA nucleotides base pair with DNA nucleotides. An enzyme is responsible for pairing the RNA and DNA correctly. Only one strand of DNA is transcribed. Use the enzyme to transcribe the TOP side of the DNA molecule. Place the enzyme at the “start codon” (see mRNA codon chart) and align the mRNA strand underneath the DNA. Use your knowledge of base pairing to write in the correct nitrogen bases. Move the enzyme along as you move from one codon to the next. Answer questions #3 and #4 on your worksheet.

5. Remove the mRNA from the DNA and “zip” the DNA gene back together with tape. Move your mRNA molecule from the nucleus to the cytoplasm that will be represented by your tabletop. Place the nucleus and DNA aside. Answer question #5.

Have your teacher initial your work before you move on: ____________

6. The second stage of protein synthesis, translation, occurs at the ribosome. Find the ribosome from your cutouts. Notice that there are three sites on the ribosome. These sites are places for transfer RNA or tRNA to attach. The tRNA molecule “transfers” or brings amino acids floating in the cytoplasm to the ribosome. Answer question #6 and #7.

7. To begin translation, place the “start” codon of your mRNA molecule under the P site. Use codon chart to find correct amino acid and the attached tRNA. Now use the base pairing rules to write in the anticodon (opposite nitrogen bases of the codon) in the box provided on the tRNA. Now place the tRNA on top of the P site.

8. You will notice that a second mRNA codon is under the A site. Use the codon chart to find the correct tRNA, write in the anticodon, and place it on top of the A site. This should bring two amino acids (found attached to the tRNA) next to one another. Answer question #8.

9. Join the two amino acids together using tape. This tape represents a peptide bond. Answer question #9

Have your teacher initial your work before you move on: ____________

10. Cut the tRNA off of the amino acid in the P site. This tRNA will leave the ribosome (you may discard it).

11. Move the mRNA down one site, and begin the process again. The tRNA at the A site moves over to the P site. The A site is now open to receive the next tRNA molecule. Bring in a new tRNA and attach the amino acid to the chain. Repeat steps 10-11 until a stop codon is reached.

12. When the stop codon is reached the ribosome releases the mRNA and the polypeptide (amino acid) chain. Answer question #10 and #11

13. Once released the polypeptide chain will fold in on itself to form a functional protein. Proteins need a specific 3D shape to work. Twist your polypeptide into a spiral and then crumple it. You now have a functional protein. Answer question #12

Questions:

1. Where is DNA located in the cell? What are the four nitrogen bases present in DNA?

2. How does this paper model compare to the actual structure of DNA?

3. Describe the process of transcription.

4. What are codons?

5. Write out the sequence of your transcribed mRNA strand.

6. Where does translation occur?

7. What is the role of transfer RNA?

8. What would be the correct anticodon for the codon GCU? __________

9. What type of bond holds the amino acids together?

10. Write the amino acid sequence that your DNA coded for.

11. Describe the process of translation.

12. What is a polypeptide? How is it different from a functional protein?

|Wing Color |glycine/ glutamine/ serine/ alanine |yellow |

| |alanine/ serine/ glutamine/ aspartic acid |purple |

| |aspartic acid/ glutamine/ serine/ alanine |blue |

| |valine/ leucine/ tryptophan/ glutamine |orange |

| |serine/ aspartic acid/ valine/ alanine |red |

13. Use the chart below to determine the wing color of your bug. Add this color to your Build-A-Bug.

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