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Name: _________________________________________________________________________ Pd: _______Decoding the Flu: A Case Study in Viral Gene Expressionadapted by B. Franckowiak from the National Center for Case Study Teaching in ScienceIntroductionJason was worried. He had landed a summer internship at the National Center for Preparedness, Detection, and Control of Infectious Diseases (NCPDCID). His boss also let him tag along on a CDC research trip to rural Mexico. However, what had appeared to be a wonderful opportunity didn’t seem so great when the team contracted one of the flu viruses they had been studying. So far, he was the only one other than the team leader, Dr. Phillips, who was not sick. Earlier that morning, Dr. Phillips told Jason she had a job for him. “Normally, I would give this to a senior staffer, but they’re all sick. We think there may be a problem with the flu virus the team has caught. Here’s some background. I’ll be right back with your assignment.”Dr. Phillips came back a few minutes later. “Here is the situation. The team appears to have contracted an atypical flu virus. For starters, the symptoms are worse than usual and even healthy adults are getting severely ill. Also, none of the team’s vaccinations protected them from this virus. We’re worried that we are dealing with a new strain of influenza we haven’t seen before. We need to figure out how this virus is different.”“The hemagglutinin (HA) protein helps the flu virus infect cells and the structure of this protein can vary in different virus strains. I want you to compare the HA gene for the viruses the team was examining with a typical flu virus. Because we don’t have power right now, you will have to do this the old-fashioned way with pencil and paper. I will get you the nucleotide sequence for a typical HA gene. You can start by finding the coding region for the gene.” Check for Understanding:What is the most convincing evidence that Dr. Phillips has to indicate that her staff has been infected by an “atypical [unusual] flu virus?”What does the HA protein do?What is one way that flu strains can vary from one another?Why will looking at the nucleotide sequence for the HA gene help Jason determine whether the team has been affected by a new flu strain?Finding GenesRecall that a gene is a stretch of DNA sequence that codes for a protein. Genes actually have 2 general regions: a coding region and a regulatory region:Fig. 1: Regulatory and coding regions of double-stranded DNAThe coding region contains nucleotide sequence that actually determines the amino acid sequence of the final protein. The regulatory region contains nucleotide sequence that signals to the cell where the gene is and when the gene should be expressed. RNA polymerase recognizes specific sequences in the regulatory region and binds at those sites to begin transcription.Fig. 2: Binding of RNA polymerase and transcription of coding region Transcription is similar to DNA replication in that one strand of DNA is used as a template strand, and complementary base pairing rules determine the sequence of the newly synthesized nucleic acid. However, transcription results in the production of single-stranded messenger RNA (abbreviated mRNA).Write the two possible mRNAs that could be produced from the DNA below. Indicate which strand was used as the template strand for each of your mRNA sequences.What is the term used for the stretch of DNA sequence RNA polymerase binds to? 38862006350Fig. 3 : Interaction of mRNA codon and tRNA anticodon00Fig. 3 : Interaction of mRNA codon and tRNA anticodonTranslationOnce the mRNA is formed, it exits the nucleus through a nuclear pore. A ribosome then assembles around the mRNA. (Remember from quarter 2 that ribosomes are small, non-membrane-bound organelles used for protein synthesis.) Ribosomes are made of protein and of special structural RNA called ribosomal RNA (rRNA). Once the ribosome is assembled, protein synthesis can begin.The ribosome holds the mRNA in place while molecules called transfer RNAs (tRNA) carry amino acids to the mRNA/ribosome complex. Each tRNA has an anticodon—a sequence of three consecutive bases that recognize and base pair with the mRNA codons. At the other end of the tRNA is an amino acid. Complementary base pairing allows the tRNA molecules to “translate” the mRNA codons into a polypeptide. Translation occurs in the 5’3’ direction.Fig. 4: Translation occurring in the ribosome If the mRNA codon is AUG, what is the corresponding anticodon?In Fig. 4, what is the difference between the “incoming tRNA” and the “outgoing tRNA” (besides anticodon sequence)?What do the pink circles with three letters in them (“Trp,” “Lys,” “Asp,” etc) represent in Fig. 4?The code has “punctuation” too—codons signaling “start” and “stop.” On the back of this page is a chart indicating which mRNA codons correspond with which amino acids. Use the chart on the back to translate the following mRNA. Pay attention to “start” and“stop.”5’CACGGUCGAUGAGGUUACAUAAC… 3’5’CACGGUCGAUGAGGUUACAUAAC… 3’Reading FramesBecause the genetic code is structured around codons that are three nucleotides in length, there are three possible ways to read any particular mRNA sequence. Each possible interpretation is called a reading frame.Fig. 5: Illustration of three possible reading frames for a single mRNA sequenceIn the mRNA sequence below, mark off the three different readings and indicate which reading frame you think is most likely to contain a gene.5’ G A U G A G A C C C U G U A A C C G C 3’Analyzing Flu Virus SequenceDr. Phillips provides Jason with some DNA sequence from the influenza virus and the known amino acid sequence of the protein:Given this information, find the coding region of the DNA. This will involve transcription and translation (and reading frame analysis); keep in mind that the coding region may be in either the top or bottom strand, and that translation proceeds from 5’ 3’ (so mind the direction of your mRNA).Below is an mRNA sequence from typical influenza hemagglutinin (HA), along with mRNA from the suspected new strain (labeled strain #1). What is the difference between these two mRNAs? (You may need to translate them to fully answer this question.)Now compare the typical influenza HA with part of the HA gene from strain #2. How are these two mRNAs different?Same thing using strain #3:Which of these identified strains--#1, #2, or #3—do you think is most likely causing the vaccine-resistant illness on Dr. Phillips’ team? How did you decide? ................
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