Decoding the Flu Adapted from: Norris Armstrong University of Georgia Adapted by Carole Twichell 1 Image Source:

2 Jason was worried. He had landed a summer internship 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. 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.

3 For starters, the flu virus is atypical. The symptoms are worse than usual. None of the team’s vaccinations give them any protection. This may be a new strain of flu. I need you to find out.

4 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. I will get you the nucleotide sequence for a typical HA gene. You can start by finding the coding region for the gene. Because we don’t have power right now, you will have to do this the old- fashioned way with pencil and paper.

What is a Gene? DNA Coding region Regulatory region Information in genes used to make proteins. Two stages: Transcription Translation Short stretch of DNA on chromosome. Two parts: 5

CQ#1: If the DNA molecule above were transcribed, which of the following RNAs might be produced? 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 G. All of the above H. None of the above 3’-ATCGGCAGGACCTTAAAT-5’ 5’-TAGCCGTCCTGGAATTTA-3’ 6

Transcription 3’-ATCGGCAGGACCTTAAAT-5’ 5’-TAGCCGTCCTGGAATTTA-3’ DNA 3’-AUCGGCAGGACCUUAAAU-5’ RNA 5’-UAGCCGUCCUGGAAUUUA-3’ RNA 7

Translation DNA/RNA Adenine Cytosine Guanine Thymine/Uracil Protein Alanine Arginine Asparagine Aspartate Cysteine Glutamine GlutamateGlycine HistidineIsoleucine Leucine Lysine Methionine Phenylalanine ProlineSerine Threonine Tyrosine Tryptophan Valine 8

CQ#2: If a combination of two nucleotides corresponded to an amino acid, how many different amino acids could DNA code for? 9 A.2 B.4 C.8 D.16 E.32

10 One-letter code A G C T/U Two-letter code AACAGAUA AGCGGGUG ACCCGCUC AUCUGUUU 10

Bases in DNA/RNA form triplet code Second Base UCAG First base U UUUPhe (F)UCU Ser (S) UAU Tyr (Y) UGU Cys (C) U Third base UUCUCCUACUGCC UUALeu (L)UCAUAA Stop UGA Stop A UUGUCGUAG Stop UGG Trp (W) G C CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) U CUCCCCCACCGCC CUACCACAA Gln (Q) CGAA CUGCCGCAGCGGG A AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) U AUCACCAACAGCC AUAACAAAA Lys (K) AGA Arg (R) A AUGMet (M)ACGAAGAGGG G GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) U GUCGCCGACGGCC GUAGCAGAA Glu (E) GGAA GUGGCGGAGGGGG Codon Table: 11

Translation 5′ 3′ UGC mRNA codon ACG tRNA Amino Acid anticodon Each tRNA carries an amino acid and an anticodon complementary to a codon in the mRNA. Transfer RNA (tRNA) molecules “interpret” the nucleotide code. 12 Source: Messenger RNA (mRNA) carries the nucleotide code for the protein to be made. 5′

5’CACGGUCGAUGAGGUUACAUCGC… 3’ CQ#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? 13 A.His-Gly-Arg B.Thr-Val-Asp-Glu-Val-Thr C.Met-Arg-Leu-His-Arg D.Gln-Tyr-Ile-Gly-Val-Ala-Gly

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Not all of mRNA molecule codes for protein. Need punctuation to identify where coding region begins and ends: -Start -Stop 15 csadaksjdfllasdailsdflRaiseyourhandifyoucan readthis.aksdjfjasdkjaskklasdjfkkjajdfiodlskj

Bases in DNA/RNA form triplet code Second Base UCAG First base U UUUPhe (F)UCU Ser (S) UAU Tyr (Y) UGU Cys (C) U Third base UUCUCCUACUGCC UUALeu (L)UCAUAA Stop UGA Stop A UUGUCGUAG Stop UGG Trp (W) G C CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) U CUCCCCCACCGCC CUACCACAA Gln (Q) CGAA CUGCCGCAGCGGG A AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) U AUCACCAACAGCC AUAACAAAA Lys (K) AGA Arg (R) A AUGMet (M) Start ACGAAGAGGG G GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) U GUCGCCGACGGCC GUAGCAGAA Glu (E) GGAA GUGGCGGAGGGGG Codon Table: 16

CQ#4: 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? 17 A.His-Gly-Arg B.Thr-Val-Asp-Glu-Val-Thr C.Met-Arg-Leu-His-Arg D.Gln-Tyr-Ile-Gly-Val-Ala-Gly 5’CACGGUCGAUGAGGUUACAUAAC… 3’

18 Reading Frames Reading frame-1 Reading frame-2 Reading frame-3 5’CACGGUCGAUGAGGUUACAUAAC… 3’

19 Reading Frames Reading frame-1 Reading frame-2 Reading frame-3 5’CACGGUCGAUGAGGUUACAUAAC… 3’ Met Arg Leu His Thr… His Gly Arg STOP Thr Leu His Glu Val Thr STOP

5’GAATGTAGCTCAAAGCAATGATAGTCTTCATGGTTA 3’ 3’CTTACATCGAGTTTCGTTACTATCAGAAGTACCAAT 5’ 20 DNA Sequence Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile… HA amino acid sequence Without computers, 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 have the start of the protein sequence. See if you can find the coding region.

3’CTTACATCGAGTTTCGTTACTATCAGAAGTACCAAT 5’ 5’GAATGTAGCTCAAAGCAATGATAGTCTTCATGGTTA 3’ 3’CUUACAUCGAGUUUCGUUACUAUCAGAAGUACCAAU 5’ 5’GAAUGUAGCUCAAAGCAAUGAUAGUCUUCAUGGUUA 3’ DNA RNA#2 RNA#1 21

3’CTTACATCGAGTTTCGTTACTATCAGAAGTACCAAT 5’ 5’GAATGTAGCTCAAAGCAATGATAGTCTTCATGGTTA 3’ 3’CUUACAUCGAGUUUCGUUACUAUCAGAAGUACCAAU 5’ 5’GAAUGUAGCUCAAAGCAAUGAUAGUCUUCAUGGUUA 3’ DNA RNA#2 RNA#1 22 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ RNA#2

5’GAAUGUAGCUCAAAGCAAUGAUAGUCUUCAUGGUUA 3’ 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ 23 RNA#1 RNA#2 Reading frame-1 Reading frame-2 Reading frame-3 Reading frame-1 Reading frame-2 Reading frame-3 UAA CCA UGA AGA CUA UCA UUG CUU UGA GCU ACA UUC GAA UGU AGC UCA AAG CAA UGA UAG UCU UCA UGG UUA UA ACC AUG AAG ACU AUC AUU GCU UUG AGC UAC AUU C

5’GAAUGUAGCUCAAAGCAAUGAUAGUCUUCAUGGUUA 3’ 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ 24 RNA#1 RNA#2 Reading frame-1 Reading frame-2 Reading frame-3 Reading frame-1 Reading frame-2 Reading frame-3 UAA CCA UGA AGA CUA UCA UUG CUU UGA GCU ACA UUC GAA UGU AGC UCA AAG CAA UGA UAG UCU UCA UGG UUA UA ACC AUG AAG ACU AUC AUU GCU UUG AGC UAC AUU C

5’GAAUGUAGCUCAAAGCAAUGAUAGUCUUCAUGGUUA 3’ 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ 25 RNA#1 RNA#2 Reading frame-1 Reading frame-2 Reading frame-3 Reading frame-1 Reading frame-2 Reading frame-3 UAA CCA UGA AGA CUA UCA UUG CUU UGA GCU ACA UUC GAA UGU AGC UCA AAG CAA UGA UAG UCU UCA UGG UUA UA ACC AUG AAG ACU AUC AUU GCU UUG AGC UAC AUU C Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile Met STOP Met Ile Val Phe Met Val

26 Great! You found the start for the HA gene coding region. Here are the HA gene data the team had collected for the flu strains that they were studying. We only have information on the starts of the genes, but it might be enough to figure out what is different about each strain.

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3’ 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. Strain #1 RNA 5’UAACCAUGAGGACUAUCAUUGCUUUGAGCUACAUUC 3’ CQ#5: How is the HA protein produced by the new flu virus different from a typical flu virus? 27

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #1 RNA 5’UAACCAUGAGGACUAUCAUUGCUUUGAGCUACAUUC 3’ Lys Arg Mis-Sense (substitution) Mutation 28

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 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. Strain #2 RNA 5’UAACCAUGAAGACUAUCAUUGCUUAGAGCUACAUUC 3’ CQ#6: How is the HA protein produced by the new flu virus different from a typical flu virus? 29

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #2 RNA 5’UAACCAUGAAGACUAUCAUUGCUUAGAGCUACAUUC 3’ Leu Stop Non-Sense Mutation (truncation) 30

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 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. Strain #3 RNA 5’UAACCAUGAAGACCAUCAUUGCUUUGAGCUACAUUC 3’ CQ#7: How is the HA protein produced by the new flu virus different from a typical flu virus? 31

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Strain #3 RNA 5’UAACCAUGAAGACCAUCAUUGCUUUGAGCUACAUUC 3’ Thr Silent Mutation 32

Typical HA RNA 5’UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 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. Strain #4 RNA 5’UAACCAUGAAGACAUCAUUGCUUUGAGCUACAUUC 3’ CQ#8: How is the HA protein produced by the new flu virus different from a typical flu virus? 33

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 Met Lys Thr Ser Leu Leu STOP 34

A.Strain #1 B.Strain #2 C.Strain #3 D.Strain #4 CQ#9: Based on the information you have, which of the four strains is most likely to be the one causing the illness? 35

Hemagglutinin protein 36 Source:

37 Good job, Jason! I’ll take your data back to the lab back home. I’ll return in a few hours. Take care of the team until I get back from the airport! Remember to wash your hands frequently so you don’t get sick, too. Goodbye! I wonder if this is still an unpaid internship!

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