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Pre-Lab Questions Arrange the following molecules from least to most specific with respect to the original nucleotide sequence: RNA, DNA, Amino Acid, Protein. Protein Amino acid RNA DNA Identify two structural differences between DNA and RNA. DNA has a double stranded structure while RNA is single stranded. DNA is longer while RNA is shorter. Suppose you are performing an experiment in which you must use heat to denature a double helix and create two single stranded pieces. Based on what you know about nucleotide bonding, do you think the nucleotides will all denature at the same time? Use scientific reasoning to explain why. No, all the nucleotides don't denature at the same time because there are differences between the number of Hydrogen bonds between bases. A and T carry two hydrogen bonds between them. G and C carry three hydrogen bonds between them. Experiment 1: Coding Post-Lab Questions Using the red, blue, yellow and green beads, devise and lay out a three color code (or codon) for each of the following letters (codon). For example Z = green : red : green. C: red, red , red E: blue, blue, blue H: yellow, yellow, yellow I: green, green, green K: red, blue, yellow L: blue, yellow, green M: green, yellow, blue O: yellow, blue, red S: red, blue, green T: blue, red yellow U: green, blue, red C: red, red, red E: blue, blue, blue H: yellow, yellow, yellow I: green, green, green K: red, blue, yellow L: blue, yellow, green M: green, yellow, blue O: yellow, blue, red S: red, blue, green T: blue, red, yellow U: green, blue, red Start: yellow, red, green Stop: blue, green, yellow Space: red, green, red Using your codons, align the beads corresponding to the appropriate letter to write the following sentence (don’t forget start, space, and stope): The mouse likes most cheese How many beads did you use? 87 There are multiple ways your cells can read a sequence of DNA and build slightly different proteins from the same strand. We will not go through the process here, but as an illustration of this “alternate splicing,” remove codons (beads) 52 – 66 from your sentence above. What does the sentence say now? Rewrite the entire sentence. Does the sentence still make sense? Yes, it still makes sense. The sentence now says “The mouse likes cheese”. Mutations are simply changes in the sequence of nucleotides. There are three ways this occurs: Change a nucleotide(s) Remove a nucleotide(s) Add a nucleotide(s) Using the sentence from Step 2B: Change the 24th bead to a different color. What does the sentence say now? Reread the entire sentence. Does the sentence still make sense? The 24th bead was R, and then changed to a B. The sentence now says: The mo_se likes most cheese. Most of it makes sense except for the word mo_se. Replace the 24th beads and remove the 20th bead (remember what was there). What does the sentence say? Rewrite the entire sentence. Does the sentence still make sense? If it doesn’t make sense as a sentence, are there any words that do? If so, what words still make sense? No, it does not make any sense because the deletion of the 20thbead shifted all of the original codons. Only the beginning of the sentence makes sense before the removal of the 20th bead. The sentence now says “[START] The m[START] __ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ e _ _ e” Replace the 20th bead and add one between bead numbers 50 and 51. What does the sentence say now? Does the sentence still make sense? No, it does not make any sense because the addition of a bead shifted all of the original codons. The mouse likes__ _ _ u[START]c _ _ e _ _ _. In Step 3a, you mutated one letter. What role do you think the redundancy of the genetic code plays in this type of change? The beads represent nucleotides, if you change a color bead it means that you are changing a nucleotide, which is a mutation in the amino acid. Based on your observations, why do you suppose the mutations we made in Steps 3b and 3c are called frame shift mutations? In D a bead was removed whereas in E a bead was added. These are called insertions/ deletions, which cause a shift in the lecture frame of the protein. Which mutations do you suspect have the greatest consequence? Why? Insertions/deletions are mutations that can cause a greater consequence in the final protein because the whole protein can change because of the lecture frameshifting. It is not just a change in a single nucleotide or codon. Experiment 2: Transcription and Translation Post-Lab Questions Use a pen or pencil to write a five-word sentence using no more than eight different letters here: Sentence: (start) It is what it is (stop) Use the red, blue, green, and yellow beads to form “codons” (three beads) for each letter in your sentence. Then, create codons to represent the “start,” “space,” and “stop” regions within your sentence. Write the sentence using the beads in the space below. I: RRR T: GGG S: YYY W: BBB H: RRY A: GGR The sentence using the codons is: RRRGGG RRRYYY BBBRRYGGRGGG RRRGGG RRRYYY. How many beads did you use? 36 Assign one Pop-It® bead to represent each codon. You do not need to assign a Pop-It® bead for the start, space, and stop. These will be your amino acids. Connect the Pop-It® beads to build the chain of amino acids that code for your sentence (leave out the start, space, and stop). How many different amino acids did you use? 10 How many total amino acids did you use? 6 Experiment 3: DNA Extraction Post Lab Questions What is the texture and consistency of the DNA? DNA seems to have a slimy and mucus like texture and consistency. Why was salt used in the extraction solution? Salt makes the DNA less hydrophilic. Salt also helps to remove proteins that are bound to the DNA and keep them dissolved in the aqueous layer so they don't precipitate in the alcohol along with the DNA. Is the DNA soluble in the aqueous solution or alcohol? Yes, DNA is soluble in aqueous solution and less soluble in alcohol because alcohol is nonpolar and water is polar. What else might be in the ethanol/aqueous interface? How could you eliminate this? Traces of RNA and DNA might be in the ethanol/aqueous interface. Which DNA bases pair with each other? How many hydrogen bonds are shared by each pair? Adenine - Thymine = 2 Hydrogen Bonds Guanine - Cytosine = 3 Hydrogen Bonds How is information to make proteins passed on through generations? During cell division, DNA replicates and the information in the DNA is passed on to the next generations.
