the Decoding Flu
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Learning Objectives
1.
2.
3.
4.
Distinguish among the functions of DNA, mRNA, tRNA, and proteins. Explain how cells use information stored in DNA to make protein. Predict the protein coded for by a given DNA molecule. Predict how a change in a molecule of DNA of will potentially change the function of a protein.
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Jason was excited! He had landed a summer internship at the National Center for Preparedness, Detection, and Control of Infectious Diseases (NCPDCID). It didn't pay, but it helped boost his resume before applying to medical school, and his boss had let him tag along on a CDC research trip to rural Mexico.
Jason's excitement changed to concern, though, when the research team accidentally contracted one of the flu viruses they had been studying.
Other than Dr. Phillips, the research team leader, Jason was the only team member who was not sick!
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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."
Hand out the Background information about Influenza
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Clicker Question 1
Based on the Flu Fact Sheet, which of the following statements is true?
A.
B.
C.
D.
Two important proteins on the surface of the Influenza virus are hemagglutinin and neuraminidase. New subtypes of Influenza usually arise due to major changes in the surface proteins of Influenza. The flu vaccine contains two types of live A virus and one type of live B virus. Worldwide, there are 500,000-1 million deaths due to the flu annually. 5
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 seem to have protected them from the 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."
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"Flu viruses often vary in the structure of their HA gene. I want you to compare the HA protein made by viruses the team was examining with a typical flu virus. Because we don't have power, 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." Dr. Phillips left the tent. "Wait!" Jason called after her. "How do I do that?!" It was too late; Dr. Phillips was already gone. Jason hadn't thought about DNA and proteins since intro biology. He pulled the biology textbook he had brought with him to prepare for MCATs out of his backpack. He'd better relearn how DNA is used to make proteins quickly.
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For Discussion
Jason knows that Dr. Phillips wants him to compare the HA protein sequences of the viruses the team was examining with the HA protein of the typical flu virus. He will only have nucleotide sequences for the HA gene.
A DNA sequence: 3'CGCTACATGGGAGTAGCTGGC 5' 5'GCGATGTACCCTCATCGACCG 3' A protein sequence: A-M-T-P-H-R-P
What does Jason need to know to figure out the protein sequence from the nucleotide sequences Dr. Philips gives him? Come up with a list of ideas.
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Clicker Question 2
What are some of the differences between DNA and protein sequences?
A.
B.
C.
D.
E.
They are composed of different types of subunits or building blocks. DNA has a 5' and a 3' end, but proteins do not. DNA sequences are double-stranded and protein sequences are single-stranded. Protein sequences are shorter than DNA sequences. All of the above.
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Human chromosomes: 50 250 million base pairs Average gene: 3000 base pairs < 5% of DNA codes for protein How to find the genes?
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What is a gene?
Short stretch of DNA on chromosome Two parts
Regulatory region
Coding region
DNA
Information in genes used to make proteins Two stages Transcription Translation
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Transcription
Regulatory region has a binding site for RNA polymerase.
RNA Polymerase
Promoter
Terminator
Gene Coding Region
copy of coding region messenger RNA (mRNA)
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Transcription
Similar to DNA replication, but different Copy only one of the two strands Makes a copy as RNA, not DNA
http://www.dnai.org/a/index.html http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.s wf
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Clicker Question 3
Which of the following is NOT a true difference between replication and transcription?
A. B. C.
D.
E.
In transcription RNA, not DNA, is produced. In transcription, uracil is used in place of guanine. In transcription one strand of nucleic acid is produced, while replication produces two strands. Transcription does not require as many accessory enzymes (e.g., primase, helicase) as replication. Transcription copies only a portion of a chromosome, while replication copies the whole chromosome.
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Transcription
RNA DNA
5'-UAGCCGUCCUGGAAUUUA-3' 3'-ATCGGCAGGACCTTAAAT-5' 5'-TAGCCGTCCTGGAATTTA-3'
RNA3'-AUCGGCAGGACCUUAAAU-5'
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Translation
DNA/RNA Adenine Cytosine Guanine Thymine/Uracil Protein
Alanine Arginine Asparagine Aspartate Cysteine Glutamine Glutamate Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tyrosine Tryptophan Valine
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One letter code A G C U
Two letter code AA CA GA UA AGCG GG UG AC CC GC UC AU CU GU UU
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Bases in DNA/RNA form triplet code
Codon Table:
U U Fir C st ba A se G
UUU UUC UUA UUG CUU CUC CUA CUG AUU AUC AUA AUG GUU GUC GUA GUG Phe (F) Leu (L)
Second Base C A
UCU UCC UCA UAU UAC Ser (S) UAA Tyr (Y) UCG UAG CCU CAU His (H) CCC CAC Pro (P) CCA CAA Gln (Q) CCG CAG ACU AAU Asn (N) ACC AAC ACA Thr (T) AAA ACG AAG Lys (K) GCU GAU Asp (D) GCC Ala GAC (A) GCA GAA Glu (E) GCG GAG UGG CGU CGC CGA CGG AGU AGC AGA AGG GGU GGC GGA GGG
G
UGU Cys (C) UGC UGA Trp (W) Arg (R) Ser (S) Arg (R) Gly (G) U C A G U C A G U C A G U C A G
Leu (L)
Thi rd bas e
Ile (I) Met (M) Val (V)
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Translation
messenger RNA (mRNA) carries the nucleotide code for the protein to be made transfer RNA (tRNA) molecules "interpret" the nucleotide code Each tRNA carries an amino acid and an anticodon complementary to a codon in the mRNA
Amino Acid
tRNA
5'
anticodon codon mRNA
ACG UGC
3'
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Translation
Ribosomes use tRNA to "read" messenger RNA and assemble the amino acids they carry into a new protein
http://www.dnai.org/a/index.html http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf
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Clicker Question 4
What are the four anticodons that should be found on the four tRNAs shown in this figure? A. GGG, AAA, UCG, GUC B. CCC, TTT, AGC, CAG C. CCC, UUU, AGC, CAG D. GAC, CGA,
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Clicker Question 5
This RNA sequence was isolated from the beginning of a gene. How many amino acids does this fragment probably code for?
5'GCGAUGUAACCUCAUCGACCG 3'
A. B. C. D.
5 6 7 10
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Clicker Question 6
This RNA sequence was isolated from the beginning of a gene. How many amino acids does this fragment probably code for?
5'GCGAUGUAACCUCAUCGACCG 3'
A. B. C. D.
5 6 7 10
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Clicker Question 7
Dr. Phillips returned with a sheet of paper. "Without computers all I have found so far is a partial sequence for the beginning of the the HA gene. See if you can find the coding region and I'll get more sequence data." 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3'
Based on this RNA sequence, what are the first 5 amino acids you would find at the beginning of the HA protein? A. I-G-T-S-D B. M-K-T-I-I C. K-T-I-K-A D. Does not encode a protein 24
Dr. Phillips returned. "Good job finding the start for the HA gene coding region. "Here is data on the HA genes the team had collected for the flu strains they were studying.
"I want to send a sample of the virus back to the lab for further testing but can only send one. The most likely candidate has probably suffered a mutation that results in a different but still functional version of the HA gene. "See if you can figure out which virus best fits this description. Remember, the HA protein is over 450 amino acids long and we only have the beginning of the gene." Jason went back to work.
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Jason proceeded to compare the HA gene from the four new flu strains to the HA gene from the typical flu strain.
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Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3' Strain #1 5'UAACCAUGAGGACUAUCAUUGCUUUGAGCUACAUUC 3' Jason noticed that the difference between the typical HA and strain #1 was a single nucleotide change (shown in red). Knowing that this mutation was in the second position of the second codon, Jason looked at the codon table to see if AGG codes for a different amino acid than AAG. Indeed, it does!
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Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Lys Strain #1 5'UAACCAUGAGGACUAUCAUUGCUUUGAGCUACAUUC 3' Arg
Mis-Sense (substitution) Mutation
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Jason also compared the HA gene from the other three new flu strains to the HA gene from the typical flu strain; doing this he figured out the predicted severity of each of these mutations. Here is what he found.
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Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Leu Strain #2 5'UAACCAUGAAGACUAUCAUUGCUUAGAGCUACAUUC 3' Stop
Non-Sense Mutation (truncation)
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Clicker Question 8
Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Leu Strain #2 5'UAACCAUGAAGACUAUCAUUGCUUAGAGCUACAUUC 3' Stop How is the HA protein produced by the Strain #2 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 31
Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3 Thr Strain #3 5'UAACCAUGAAGACCAUCAUUGCUUUGAGCUACAUUC 3' Thr
Silent Mutation
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Clicker Question 9
Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3' Thr Strain #3 5'UAACCAUGAAGACCAUCAUUGCUUUGAGCUACAUUC 3' Thr Why is the type of mutation in strain #3 referred to as a silent mutation? Because . . .
A. B. C. D.
the mutation makes the protein too short. the mutation makes the protein too long. the mutation leads to no change in the amino acid. The mutation leads to many different amino acids. 33
Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3
Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile
Strain #4 5'UAACCAUGAAGACAUCAUUGCUUUGAGCUACAUUC 3'
Met Lys Thr Ser Leu Leu STOP
Frame shift Mutation
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Clicker Question 10
Typical HA 5'UAACCAUGAAGACUAUCAUUGCUUUGAGCUACAUUC 3
Met Lys Thr Ile Ile Ala Leu Ser Tyr Ile
Strain #4 5'UAACCAUGAAGACAUCAUUGCUUUGAGCUACAUUC 3'
Met Lys Thr Ser Leu Leu STOP
How is the HA protein produced by the Strain #4 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 35
"Good job Jason," Dr. Phillips commented as she headed out to the truck that would carry her and the samples to the airport. "This will hopefully give the lab back home a head start investigating this new strain of flu. I'll be back in a couple of hours. "The team's condition seems to be getting better so I don't think you will have much trouble while I am gone. Give them plenty of fluids and remember to wash your hands frequently to help keep you from catching this bug. It doesn't appear to be as bad as we feared, but it is still pretty nasty."
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Clicker Question 11 Rank this case using the following scale:
This case was . . . Engaging Boring 1 2 3 4
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Clicker Question 12 Rank this case using the following scale: This case made me feel . . . Emotional Unemotional 1 2 3 4 5