Materials Protein synthesis kit. This kit consists of 24 amino acids, 24 transfer RNAs, four messenger RNAs and one ribosome (see below).

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1 Protein Synthesis Instructions The purpose of today s lab is to: Understand how a cell manufactures proteins from amino acids, using information stored in the genetic code. Assemble models of four very short proteins based on four mrna sequences. Identify several types of mutations and to evaluate their impact on protein synthesis. Successfully use the genetic code to reverse-engineer a protein with a specific function. The structure and operation of the human body (as well as all other organisms) is based on proteins. Everything from skin and bones to hair, muscle and internal organs are constructed from proteins. The enzymes that digest food and the hormones that regulate metabolism are all proteins. Although some of these compounds are highly specialized and have additional materials associated with them (e.g., calcium found in bone tissue), all have proteins as their foundation. Activity 1. Translating Messenger RNAs Materials Protein synthesis kit. This kit consists of 24 amino acids, 24 transfer RNAs, four messenger RNAs and one ribosome (see below). anticodon trna ribosome amino acid mrna Codon conversion table (attached) Procedure 1. Pair up your trna molecules with the appropriate amino acids (see image on right for help). trna amino acid 103

2 2. Chain initiation. Insert the 5 end of an mrna into the ribosome until the first codon (AUG) is exposed in the peptidyltrna binding site. Select the trna with an anticodon that base-pairs with the exposed codon and join it to the mrna. 3. Chain growth. a. The next codon is exposed in the amino acyl-trna binding site. Again, select an appropriate trna with its attached amino acid and join it to the mrna. b. The amino acid (or peptide) that is presently joined to the trna at the peptidyl-trna binding site is separated from the trna and joined instead to the amino group of the amino acid positioned at the amino acyl-trna binding site. The result is a peptide bond between the two amino acids. The free trna is released from the peptidyl-trna binding site and floats away. c. The ribosome now slides down the mrna three nucleotides exposing the next codon in the amino acyl-trna binding site. d. Repeat steps a-c until the protein is synthesized (you reach the end of the mrna). Note: There are no stop codons on these mrnas! 4. Record the amino acid sequences for this protein in the observation section of the report. 5. Repeat this procedure with the other three mrnas. 6. Answer the questions in the lab report. 7. Return all parts to the envelope and return to the instructor s bench. Answer Questions 1-11 on the Lab Report. Activity 2. Designer Proteins Note: This activity uses a DNA-to-amino acid conversion table (also attached). 1. Follow the instructions on the laptop activity. 2. Try to get up through Challenge #2 on the third page of the activity. This challenge will ask you to design a protein that can catch a positively-charged ion. 3. You will first need to determine which amino acids your protein will have, and then you will have to reverseengineer a DNA sequence that encodes this information. Answer Question 12 on the Lab Report. There is no need to print anything from the laptop, nor do you have to answer any of the questions in the activity. 4. If you would like to continue with the laptop activity beyond Challenger #2, please feel free to do so. (There is only one more page afterwards.) 104

3 mrna sequence Protein sequence 105

4 DNA sequence Protein sequence 1 3 amino acid properties DNA codons A Ala alanine hydrophobic GCA GCC GCG GCT C Cys cysteine hydrophobic TGC TGT D Asp aspartic acid acidic ( ) GAC GAT E Glu glutamic acid acidic ( ) GAA GAG F Phe phenylalanine hydrophobic TTC TTT G Gly glycine hydrophobic GGA GGC GGG GGT H His histidine basic (+) CAC CAT I Ile isoleucine hydrophobic ATA ATC ATT K Lys lysine basic (+) AAA AAG L Leu leucine hydrophobic TTA TTG CTA CTC CTG CTT M Met methionine hydrophobic ATG N Asn asparagine hydrophilic AAC AAT P Pro proline hydrophobic CCA CCC CCG CCT Q Gln glutamine hydrophilic CAA CAG R Arg arginine basic (+) AGA AGG CGA CGC CGG CGT S Ser serine hydrophilic AGC AGT TCA TCC TCG TCT T Thr threonine hydrophilic ACA ACC ACG ACT V Val valine hydrophobic GTA GTC GTG GTT W Trp tryptophan hydrophobic TGG Y Tyr tyrosine hydrophobic TAC TAT 106

5 Protein Synthesis Lab Report Name Activity 1. Translating Messenger RNAs 1. For each of your four mrnas, fill in the nucleotide and corresponding amino acid sequences below. mrna 1 sequence Protein 1 mrna 2 sequence Protein 2 mrna 3 sequence Protein 3 mrna 4 sequence Protein 4 2. Compare protein 2 to protein 1. Does the amino acid sequence of protein 2 differ from the sequence of protein 1? If yes, which amino acid(s) differ? 3. Compare mrna 2 to mrna 1. Does the codon sequence of mrna 2 differ from the codon sequence of mrna 1? If yes, which codons differ? 4. Note that the second amino acid is the same in both proteins, even though their codons are different. Write all of the codons that can code for that specific amino acid. 5. Where does the amino acid sequence of protein 3 differ from the sequence of protein 1? 6. Where do the codons of mrna 3 differ from mrna 1? 107

6 7. Compare protein 4 to protein 1. Where does the amino acid sequence of protein 4 differ from the sequence in protein 1? 8. Where does the codon sequence of mrna 4 differ from mrna 1? 9. A frameshift mutation is caused by either an insertion or deletion of bases that results in the displacement in the coding region of a gene. Assume that mrna 1 is the normal (wild-type) version of this gene. Which of the other mrnas displays a frameshift? 10. Where has the frameshift occurred in this mrna? 11. What has been the effect of this frameshift on the amino acid sequences of these two mrnas? Activity 2. Designer Proteins 12. In the space below, write out the DNA sequence, mrna sequence, and amino acid sequence of the protein you designed to catch the positively-charged ion. 108