BIO 101 : The genetic code and the central dogma

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1 BIO 101 : The genetic code and the central dogma NAME Objectives The purpose of this exploration is to design experiments to decipher the genetic code; 2. visualize the process of protein synthesis; 3. describe the roles of DNA, messenger RNA, ribosomal RNA, and transfer RNA in protein synthesis; 4. correctly identify the parts of the cell involved in protein synthesis; and 5. review the terms transcription, translation, codon, anticodon, and mutation. Introduction Almost immediately after Watson and Crick presented their model of DNA structure, they and other biologists began to develop and test hypotheses about how DNA could store the information for the enormous number and variety of proteins needed for cell structure and function. Biologists presumed this information must be encoded in the sequence bases in DNA, a hunch that was soon proved correct. It also became apparent that the other nucleic acid, RNA, played important intermediary roles between DNA and proteins. The DNA! RNA! protein flow of information in the cell has become known as the central dogma of molecular biology. Each lab table will have masking tape, chalk, wax pencils or markers, and copies of the genetic code for you and a partner to use in the simulation. The nucleotide bases (M&Ms) and amino acid pool (candy) will be on the instructor s lab bench. 1. Imagine that your table top is a cell. With the chalk, draw a line across the center of the table in front of you to represent part of the nuclear membrane. One side of the line represents the nucleus of the cell and the other side represents the cytoplasm. 2. Tear off two strips of masking tape approximately 50 cm in length. Fold just the end of one strip under, so that the strip sticks to the table, but the sticky side remains up. Place the second strip of tape immediately below the first one. Label the strips by writing DNA at the left end of the top strip and mrna at the left end of the bottom strip. Then label the DNA strip 5 at the left side and 3 on the right side. It is important that you place the strips of tape in the proper area of your cell the nucleus or the cytoplasm! Answer questions 1 and 2 on Lab Worksheet #3.

2 3. The M&Ms represent a pool of nucleotide bases. Each M&M color will represent a specific nucleotide base. Use the following key: Red = Adenine (A) Yellow = Cytosine (C) Green = Guanine (G) Brown = Thymine (T) Orange = Uracil (U) Grab a handful of M&Ms from the nucleotide base pool. Place a brown then a yellow than a red M&M on the DNA tape starting at the 5 end. Then randomly place 24 of the M&Ms in a line on the strip of DNA tape. Remember not to use Uracil (Orange) for DNA and figure out some way to dispose of the blue M&Ms. End your run with the addition of a yellow, a red, and a brown. This strand represents the template strand of the DNA used for your RNA synthesis. (You should have 30 M&M s on the DNA) Answer questions 3 to 7 on the worksheet. 4. Next, select nucleotides that are complementary to your DNA bases and create your mrna strand by placing the appropriate color of M&Ms on the mrna strip. Label the strip correctly with the 5 and 3 ends Answer questions 8 to 11 on the worksheet. 5. With your pencil, mark off the mrna into groups of three. This will help you visualize the triplet code responsible for determining a particular amino acid. Cut lengths of masking tape equal to the length of each triplet code on the mrna, label them trna, and place them below each of the triplet codes. Then, select M&M nucleotides that are complementary to your mrna. (Hint: DNA is always read from 5 to 3 ) Answer questions 12 to 14 on the worksheet. 6. Convert the language of nucleotide bases into the language of specific amino acids: Using one of the genetic codes on your table, determine which amino acid matches with the triplet code in the mrna. Answer questions 15 and 16 on the worksheet. 7. Drawing from the amino acid pool on the instructor s lab bench, place the amino acids in their proper sequence below the trnas. Once two amino acids are in place, they will become chemically bonded, forming your polypeptide. Look around the room to see the polypeptides that your peers have created. Answer questions 17 to 22 on the worksheet. 8. Imagine that the polypeptide you synthesized in step #7 is part of an enzyme and suppose that the active site of the enzyme includes the third amino acid in your polypeptide. Create a substitution mutation at the seventh nucleotide in the original DNA (step 3): Remove the seventh M&M from your DNA base sequence, and replace it with another of your choice. Answer questions 23 and 24 on the worksheet. 9. Be prepared to explain the process of protein synthesis, using your model and correct terminology, to your lab instructors.

3 BIO 101 Genetics Lab NAME DATE 1. Where in the cell are the DNA base sequences found? 2. Where in the cell is the mrna synthesized? 3. What is the direction (in terms of 3 and 5 ) of the DNA template strand you constructed? Why must it be this direction? 4. The process of synthesizing mrna using the information coded in the DNA is called The enzyme that catalyzes (in textbook) the above process is called 6. This enzyme binds to a specific DNA sequence that signals where RNA synthesis should start, called the 7. Using the base letters given in the key in step 3, write down the 24 base sequence of the DNA that you created: 8. Uracil will be a substitute for which base? 9. Write down the 24 complementary base sequence of the mrna that you created: 10. The 3-nucleotide word on the mrna is called a 11. After synthesis, the mrna carries its message to the 12. Write down the 24 complementary base sequence of the mrna that you created, marking it off in triplet codes: 13. The 3 bases in the trna that are complementary to the words in the mrna are called Compare the 3-base sequences described above with the sequence in the original DNA you made in step #3. How are they the same? How are they different?

4 15. The process of converting the language of nucleotide bases into the language of specific amino acids is called 16. Write down the sequence of your amino acids: 17. The bond that links the amino acids together is called a The start codon is, which codes for amino acid. The stop conons are,, and, which codes for amino acid. 18. After the trna molecules release their amino acids they 19. How many amino acids are in your polypeptide? Why? 20. Where does the amino acid pool originate? 21. Looking around the room, are any two polypeptides the same? How many different polypeptides, each composed of 8 amino acids, could possibly be made? 22. For demonstration purposes, the sequence of events was slightly off. When does the amino acid actually attach to the trna? 23. As a result of this substitution mutation, what happened to the amino acid sequence of your polypeptide chain? 24. How might this mutation affect the enzyme s function? What are the four main consequences of a single base substitution that are possible? Explain.

5 Analysis Question A portion of a gene has the following DNA sequence: 5 T T C C T G T G G C A A 3 3 A A G G A C A C C G T T 5 The peptide product of this portion of the gene has the following amino acid sequence: Phe -- Leu -- Trp -- Gln In a particular mutant, this segment of the protein has a Proline (Pro) amino acid substituted for Leucine (Leu). Analyze the mutation below. Which of the following is the best interpretation regarding the mutation? Accept or reject each statement, with explanation A. The fourth base pair in the DNA is changed from C:G to T:A. B. The fifth base pair in the DNA is changed from T:A to C:G. C. The sixth base pair in the DNA is changed from G:C to A:T. D. Either A or C could be the mutation. E. This mutation cannot be explained by a simple substitution mutation.