Discussion: Protein Folding And Polypeptide Chain

Name: _________________________                                                                                               Protein Folding Lab (25 pts)

Below is a DNA sequence. It codes for one polypeptide chain that you will be creating today.

State which direction DNA is read while being transcribed: ______________________

Remember that in transcription, only one strand of the DNA is read. Which strand, the top or the bottom, will be the template to make the protein? _________ Keep that in mind. That is the only strand you will be transcribing.

State the mRNA “start” sequence for an amino acid: ________

Highlight the DNA triplet that codes for this start sequence. Keep in mind the reading direction. Transcribe the template DNA into mRNA. Label the 3’ and 5’ ends of the mRNA. Underneath each codon, write the abbreviation for the amino acid it codes for. Highlight the start codon. (3 pts)

3’            6                               15                                                   30                                   45                                                    60      5’

TAC  AGG  GCA  TAA  CTT  TGT  CGC  CCT  ATG  ACG  GGA  CTG  AAG  AAT  TTC  GTG  ACA  ACC  GTT  CAG  ACT

ATG  TCC  CGT  ATT  GAA  ACA  GCG  GGA  TAC  TGC  CCT  GAC  TTC  TTA  AAG  CAC  TGT  TGG  CAA  GTC  TGA

5’                                                                                                                                                                                                                            3’

Create your Toober Protein

One amino acid (piece of tape) will be placed in between the marks on the toober. To determine which tape colors to use, find each amino acid on the Amino Acid List provided by your instructor. The color of the box will be the color of tape you use.

1. Does the exact order of the amino acids matter? Yes/No             (0.5 ots)
2. Does the stop codon code for an amino acid? Yes/No (0.5 pts)
3. Which level of protein structure is this? ___________ (0.5 pt)
4. Get a stamp from your instructor in the box to the right when you believe you have the order correct.
5. What do the different colors of tape represent and how will the colors affect the end structure and function of your protein? (1 pt)

To fold your protein follow the directions below.

1. Fold all hydrophobic amino acids into a glob together. This will be the inside of the protein. What does hydrophobic mean? _________________ (0.5) What color are they?______________
2. Try to match up the cationic and anionic amino acids. What does this mean? (0.5) _____________ Colors? __________
3. Bond the cysteine amino acids together. Why do these always bond together? __________________ Color? _________
4. The hydrophilic amino acids will be on the outside of the protein to interact with __________. (0.5) Color? __________
5. Get a stamp from your instructor in the box above when you believe you have your protein folded correctly.
6. State which level of protein structure you have just simulated. Explain why it is this level and not a different level. (1)

Mutations and Proteins

1. List the two main categories of mutations. Circle the more devastating of the two. (2pts)

2. Go back to the original template DNA used in the activity. Alter it so that it would result in a silent mutation. In the space below, state exactly how and where the DNA would mutate (What are you changing, deleting, inserting, etc). Explain the resulting effect on the protein. (3pts)

3. Go back to the original template DNA used in the activity. Alter it so that it would result in a nonsense mutation. In the space below, state exactly how and where the DNA would mutate (What are you changing, deleting, inserting, etc). Explain the resulting effect on the protein. (3pts)

4. Go back to the original template DNA used in the activity. Alter it so that it would result in a missense mutation. In the space below, state exactly how and where the DNA would mutate (What are you changing, deleting, inserting, etc). Explain the resulting effect on the protein. (3pts)

5. Explain two ways in which this simulation accurately portrayed protein synthesis/proteins. (2pts)

6. Explain two ways in which this simulation did NOT accurately portray protein synthesis/proteins. (2pts)

7. State the two levels of protein folding not simulated in the activity. Pick one of those levels and explain how it could be simulated if you were to do this activity again. (2pts)