During translation, new tRNAs carrying amino acids enter of the ribosome. A.The A site B.The P site C.The E site D.The X site 1

Which of the following is NOT true about translation? A.Peptide bonds form between the amino acids held by the tRNAs in the P and A positions B.tRNAs leave the ribosome from the E position C.tRNAs carrying their amino acids enter the ribosome initially at the P site D.Amino acids are initially bound to tRNAs at their carboxyl ends 2

tRNA in E site exits, and cycle repeats (new tRNA binds to A site, etc.) Translation movie Cycle repeats…

Termination: Stop codons do not specify any amino acid Release factor protein binds to A site when stop codon is reached

Hydrolysis occurs to break bond between final amino acid and its tRNA in the P position Termination:

You are working at the Center for Disease Control (CDC), when the rest of your team gets sick with an influenza virus they have been studying. Your boss, Dr. Phillips, has given you the responsibility of figuring out which virus they have, because you are the only person on the team who is not sick. 7 In your conversation with Dr. Phillips, she says, “Here is the situation. The team appears to have contracted an atypical flu virus. The symptoms are worse than usual and 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.” “I want you to compare the HA gene for the viruses the team was examining with a typical flu virus. I will get you the nucleotide sequence for a typical HA gene. You can start by finding the coding region for the gene.”

Flu virus contains hemagglutinin (H) and neuraminidase (N) 8

Hemagglutinin (HA) A glycoprotein An antigen that binds with host cell receptors to infect them 9

Antibodies bind to antigens on viral membranes to prevent their activity 10 Binding is highly specific Changes in antigen = antibodies no longer bind = no host cell protection Host cell receptor

Influenza A virus: H and N can vary among species 11 Flu vaccines typically contain H3N2, H1N1, and a B virus

The types of antigens displayed on the surface of a flu virus are a component of the virus’ A.Genotype B.Phenotype 12

Vaccines train your body to produce antibodies that “remember” the viral antigen… 13

…as long as the antigen does not change! Antigenic drift, caused by mutation, is common in influenza viruses

Changing the sequence of amino acids in a protein could change its function by A.Altering the way the protein folds B.Altering the way the protein interacts with other molecules C.Changing the 3-D shape of the protein D.All of the above 15

A.3′-ATCGGCAGGACCTTAAAT-5′ B. 5′-TAGCCGTCCTGGAATTTA-3′ C. 3′-AUCGGCAGGACCUUAAAU-5′ D. 5′-UAGCCGUCCUGGAAUUUA-3′ E. Both A and B F. Both C and D 16 If the DNA molecule above is a gene whose promoter lies to the right of this sequence on the screen, which RNA can be produced from this gene? 3’-ATCGGCAGGACCTTAAAT-5’ 5’-TAGCCGTCCTGGAATTTA-3’ **

5’CACGGUCGAUGAGGUUACAUAAC… 3’ Part of an mRNA molecule is shown above. If this fragment came from the beginning of the mRNA, for which of the amino acid sequences below would it most likely code? A.His-Gly-Arg B.Thr-Val-Asp-Glu- Val-Thr C.Met-Arg-Leu-His- Asn D.Gln-Tyr-Ile-Gly- Val-Ala-Gly 17 **

Dr. Phillips returned with a sheet of paper. “All I have been able to find so far is a partial sequence I believe is at the beginning of the HA gene.* I also found that the promoter for this gene is to the right of the sequence given here, and I have the start of the HA protein sequence. See if you can find the coding region while I look for more info.” 3’CTTACATCGAGTTTCGTTACTATCAGAAGTACCAAT 5’ 5’GAATGTAGCTCAAAGCAATGATAGTCTTCATGGTTA 3’ 18 DNA Sequence Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile… HA amino acid sequence **

3’CTTACATCGAGTTTCGTTACTATCAGAAGTACCAAT 5’ 5’GAATGTAGCTCAAAGCAATGATAGTCTTCATGGTTA 3’ 3’CUUACAUCGAGUUUCGUUACUAUCAGAAGUACCAAU 5’ DNA RNA 19 In this case, the bottom strand is transcribed

3’CTTACATCGAGTTTCGTTACTATCAGAAGTACCAAT 5’ 5’GAATGTAGCTCAAAGCAATGATAGTCTTCATGGTTA 3’ 3’CUUACAUCGAGUUUCGUUACUAUCAGAAGUACCAAU 5’ DNA RNA 20 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ RNA

5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ RNA Reading frame-1 Reading frame-2 Reading frame-3 UAA CCA UGA AGA CUA UCA UUG CUU UGA GCU ACA UUC

5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ RNA Reading frame-1 Reading frame-2 Reading frame-3 UAA CCA UGA AGA CUA UCA UUG CUU UGA GCU ACA UUC Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile

“Great! You found the start for the HA gene coding region. Here are HA genes the team had collected for the flu strains that they were studying. We only have information on the start of the gene, but it might be enough.” The virus that the team has contracted probably had a mutation that results in a different, but still functional version of the HA gene. See if one of the 4 strains of viruses the team was examining would fit this description. 23

How is the HA protein produced by the new flu virus different from a typical flu virus? A.There is no difference. B.One amino acid has been changed. C.Several amino acids have been changed. D.The protein is too short. E.The protein is too long. 24 Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ Strain #1 RNA 5’UAACCAUGAGGACUAUCAUUGCUUUGAGCUACAUUC 3’ **

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #1 RNA 5’UAACCAUGAGGACUAUCAUUGCUUUGAGCUACAUUC 3’ Lys Arg Mis-Sense (substitution) Mutation 25

How is the HA protein produced by the new flu virus different from a typical flu virus? A.There is no difference. B.One amino acid has been changed. C.Several amino acids have been changed. D.The protein is too short. E.The protein is too long. 26 Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #2 RNA 5’UAACCAUGAAGACUAUCAUUGCUUAGAGCUACAUUC 3’ **

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #2 RNA 5’UAACCAUGAAGACUAUCAUUGCUUAGAGCUACAUUC 3’ Leu Stop Non-Sense Mutation (truncation) 27

How is the HA protein produced by the new flu virus different from a typical flu virus? A.There is no difference. B.One amino acid has been changed. C.Several amino acids have been changed. D.The protein is too short. E.The protein is too long. 28 Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #3 RNA 5’UAACCAUGAAGACCAUCAUUGCUUUGAGCUACAUUC 3’ **

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #3 RNA 5’UAACCAUGAAGACCAUCAUUGCUUUGAGCUACAUUC 3’ Thr Silent Mutation 29

How is the HA protein produced by the new flu virus different from a typical flu virus? A.There is no difference. B.One amino acid has been changed. C.Several amino acids have been changed. D.The protein is too short. E.The protein is too long. 30 Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #4 RNA 5’UAACCAUGAAGACAUCAUUGCUUUGAGCUACAUUC 3’ **

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #4 RNA 5’UAACCAUGAAGACAUCAUUGCUUUGAGCUACAUUC 3’ Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile Frame Shift Mutation: alteration of reading frame Met Lys Thr Ser Leu Leu STOP 31 Deletion of this U

Based on the information you have, which of the four strains is most likely to be the one causing the illness? A.Strain 1 (mis-sense) B.Strain 2 (non-sense) C.Strain 3 (silent) D.Strain 4 (frameshift) 32 Be prepared to defend your answer!!!

On your note card: Name Date Explain, in terms of the central dogma, why you need to get a new flu shot every year. Explain your answer in terms of DNA, RNA, protein, antigen, etc. 33