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Is DNA the Genetic Material? The T2 virus’s protein coat staysviruses on the outside the host cell. Using bacteria-killing as aofmodel Virus protein coat New virus particles Nucleic Acids are the Genetic Material. Only T2 DNA, and not the proteins, enters a cell and directs replication Virus protein coat Virus genes Host cell 1. Start of infection. 2. Virus genes direct 3. End of infection. Virus genes enter ONLY VIRAL GENESthe ENTER A CELL THAT IS BEINGNew INFECTED. production of new generation of host cell. Protein virus particles. virus particles bursts coat does not. from host cell. Thursday January 19st, 2017 Class 11 Learning Goals Translation • After this class, you should be able to: – Label each molecule and strand (and give correct polarity for each nucleic acid and amino acid polymer) in a diagram of protein translation – Predict and give a rationale for the effect of a loss-offunction mutation in any component of the ribosome – Compare or contrast the three phases of translation (initiation, elongation, termination) in terms of enzymes and substrates Peer Instruction An ‘adapter molecule’ is needed to hold amino acids and interact with mRNA codons. Amino acids Adapter molecules mRNA Codon Codon Codon Codon Why didn’t transcription require an adapter molecule? How many total adapter molecules are needed? Because NTPs and dNTPs can directly forms base-pairs Peer Instruction 1) What are the important parts of a Transfer RNA (tRNA)? Binding site for the amino acid 3ʹ 5ʹ 3ʹ 5ʹ 3ʹ mRNA 5ʹ 5ʹ mRNA 3ʹ 2) How is a tRNA “charged”? The machine that does translation: The Ribosome tRNA in A site (red) Ribbon model of ribosome during translation tRNA in E site (blue) tRNA in P site (green) Large subunit Small subunit Ribosomes catalyze peptide bond formation Today’s Translation Exercise • Work through the exercise together. • Be ready for clicker questions as we go. Clicker Question #1 8b) Which is the best definition for the anticodon? 1. The three bases of the tRNA that bind to the codon in the mRNA 2. The three bases of mRNA that bind to the codon in the tRNA 3. Any three bases in the mRNA 4. Any three bases in the tRNA 5. None of these Clicker Question #2 10) In which direction must the ribosome translocate along the mRNA? 1. 5’ to 3’ 2. 3’ to 5’ 3. Either direction, depending on the promoter on the RNA Clicker Question #3 ~11) What is the best characterization of the RBS? 1. A strong binding site that helps to start translation 2. A strong binding site that helps to end translation 3. A weak binding site that helps to start translation 4. A weak binding site that helps to end translation Clicker Question #3 ~11) In the schematic in Model 2, what is the next codon that will be read by the ribosome? 1. 5’AUG3’ 2. 5’AGC3’ 3. 5’GAA3’ 4. 5’CGU3’ Clicker Question #4 13C) What establishes the ‘frame’ of the triplet codons for translation? 1. 2. 3. 4. 5. The primary sequence of the codons The location of the start codon The secondary sequence of the codons The distance from the +1 site The RBS Clicker Question #8 21. In Model 4, a covalent bond is broken.! What did that covalent bond hold together? 1. 2. 3. 4. 5. 6. Two tRNAs Two amino acids An amino acid and a tRNA DNA and RNA Two parts of the ribosome A ribosomal subunit and an amino acid Clicker Question #9 Post-Model 4) Which of these is necessary for all three phases of translation? 1. f-Met tRNA 2. mRNA 3. ribosome 4. release factor 5. anticodon Clicker Question #6 Hypothetically, which of the following molecules could work as a replacement for tRNA? 1) A protein that can bind to the major groove of DNA and a specific amino acid. 2) A carbohydrate that can recognize a short RNA sequence and bind to a particular amino acid. 3) A lipid that can basepair with RNA and will bind to any amino acid. 4) An ATP molecule can has been modified to bind only Leucine and will bind to the ribosome Clicker Question #7 What would happen if all the tRNAs in a cell with anticodons for lysine carried glycine amino acids instead of lysine amino acids? Translation would: 1. Still occur but the protein would contain glycines instead of lysines 2. Stop at the first lysine codon 3. Still occur but there would be no lysines or glycines in the protein 4. Still occur but the protein would contain lysines instead of glycines Clicker Question #10 24) How does the structure of the release factor impact its function? 1. The release factor must be at least as big as the ribosome 2. The structure must be made of animo acids to have a tertiary structure 3. The release factor structure must be made of the same monomer components as the tRNA to fit into the ribosome 4. The release factor structure must be similar to the size and shape of a tRNA Clicker Question #11 X3) Should there be tRNAs in the cell that can base pair with a stop codon? 1) No, because they would not be able to enter the ribosome 2) No, because then the peptide chain would keep growing indefinitely 3) No, because the N-terminus of the growing protein chain would not be able to extend out of the ribosome 4) Yes (for any reason) Peer Instruction How does this enzyme create a charged tRNA? ATP 1) 3) 4) 2) Activated enzyme complex What parts of the enzyme give it specificity? Evaluate a molecular history: Clicker Question 12 A nucleotide within a large mRNA polymer has: 1) Lost two phosphates, 2) Formed 2 or 3 hydrogen bonds, 3) Formed a phosphodiester bond, and then 4) Lost 2-3 hydrogen bonds 1. This is the correct and complete process 2. There is something missing in this process 3. There is something extra in this process Concept questions • To practice labeling of translation diagrams: – Build a sequence with 70+ bases of random RNA – Find a start codon and assess the location of ribosome binding – Indicate the codons and anticodons used, as well as the peptide bonds created – Change the sequence of the RNA such that you program the ribosome to create a 10-amino-acid polymer • What would happen to translation if: – The ribosome binding site were lost? – The start codon were mutated? – The stop codon was mutated – The shape of the release factor was altered • Write a complete reaction diagram for each of these: – Binding of the small ribosomal subunit to the RNA – Addition of the 5th amino acid – Termination of translation – Catalysis of charging a single tRNA Lab Next Week • The Central Dogma Lab – A great place to practice what you know about • Trancription • Translation • Mutation – We’ll also talk about mutations and their impact on human disease for the first time