ACTIVITY: REPLICATION, TRANSCRIPTION, TRANSLATION & MUTATIONS
1. Which of the following is NOT a feature of eukaryotic gene expression?
A. / polycistronic mRNAs are very rareB. / many genes are interrupted by noncoding DNA sequences
C. / RNA synthesis and protein synthesis are coupled as in prokaryotes
D. / mRNA is often extensively modified before translation
E. / multiple copies of nuclear genes, and pseudogenes can occur
2. What is added to the 3'-end of many eukaryotic mRNAs after transcription?
A. / intronsB. / a poly A tail
C. / a cap structure, consisting of a modified G nucleotide
D. / the trinucleotide 5'-CCA
E. / exons
3. The primary RNA transcript of the chicken ovalbumin gene is 7700 nucleotides long, but the mature mRNA that is translated on the ribosome is 1872 nucleotides long. This size difference occurs primarily as a result of:
A. / cappingB. / cleavage of polycistronic mRNA
C. / removal of poly A tails
D. / reverse transcription
E. / splicing
4. RNAs that catalyze biological reactions, such as snRNAs, are known as:
A. / enzymesB. / spliceosomes
C. / ribozymes
D. / lariats
E. / mature RNAs
5. Which statement is NOT true about nucleic acid hybridization?
A. / it depends on complementary base pairingB. / a polysaccharide can hybridize with a DNA strand
C. / a DNA strand can hybridize with another DNA strand
D. / an RNA strand can hybridize with a DNA strand
E. / double strand DNA denatures at high temperature
6. Promoters for eukaryotic mRNA synthesis:
A. / are more complex than prokaryotic promotersB. / can require binding of multiple transcription factors to form a transcription initiation complex
C. / have specific DNA sequences such as the "TATA" box that are recognized by proteins
D. / are the stretches of DNA to which RNA polymerase II binds to initiate transcription
E. / all of these
7. The regions of DNA in a eukaryotic gene that encode a polypeptide product are called:
A. / hnRNAsB. / exons
C. / enhancers
D. / leader sequences
E. / tRNAs
8. mRNA will form hybrids only with the coding strand of DNA because:
A. / DNA will not reanneal at high temperaturesB. / the salt concentration will affect DNA reannealing
C. / DNA will not reanneal at low temperatures
D. / RNA:DNA hybridization follows the base-pairing rules
E. / denatured DNA will not reanneal after it is diluted
9. Which of the following is not part of RNA processing in eukaryotes?
A. / splicing of exonsB. / reverse transcription
C. / addition of a 5' cap
D. / addition of a poly A tail
E. / intron removal
10. Which of the following molecules functions to transfer information from the nucleus to the cytoplasm?
A. / DNAB. / mRNA
C. / tRNA
D. / proteins
E. / lipids
10. Fill in the below table:
Type of RNA / Function / Basic drawingmRNA / Provides the ‘message’ for translation
rRNA / Forms the ribosome along with ribosomal proteins
tRNA / “delivers” the amino acids to the ribosome in translation
11. What is transcription?
The conversion of a DNA template into an RNA transcript.
12. What strand is the template strand used for transcription?
The anti-sense
14. Below is a drawing of a cell. Show where transcription and translation occur. Identify the locations of the DNA and the RNA (all three types!) plus the fully assembled ribosomes:
15. What is the function of:
a. mRNA – the ‘message’ that is translated into a polypeptide strand during translation
b. RNA polymerase II – transcribes the anti-sense DNA template into an RNA transcript
c. tRNA– ‘delivers’ the amino acids to the ribosomes during translation of a polypeptide strand
d.the codon – a group of three nucleotides that will code for an amino acid
e. the anti-codon site – the end of the tRNA opposite to the amino acid binding site; transiently base-pairs with the RNA codon of the mRNA
16. What three modifications are necessary to convert an RNA transcript into mRNA?
1. addition of a 5’ methylated cap
2. addition of a 3’ poly-A tail
3. splicing of introns (and possibly some exons)
17. Using the following sense strand – what would be the eventual sequence of the RNA strand produced following transcription (don’t worry about finding a start and stop codon)?
5’ - G A T T A C A G A T T C A G A T T A C A G A T A G G A A C C T C T C A C T T A – 3’
3- C T A AT G T C T A A G T C T A A T G T C T A T C C T T G G A G A G T G A AT – 5’
mRNA:
5’ - G A U U A C A G A U U C A G A U U A C A G A U A G G A A C C U C U C A C UU A – 3’
a. Where would you put the cap and the tail on this RNA transcript?
Cap at the 5’ end (next to the G base)
Poly-A tail at the 3’ end
b. Write the mRNA so that the codons are obvious
5’ - G A U U A C A G A U U C A G A U U A C A G A U A G G A A C C U C U C A C U U A – 3’
c. Write the anti-codon sequence
3’ C U A A U G U C U A A G U C U A A U G U C U A U C C U U G G A G A G U G A A U-5’
d. Write the amino acid sequence
Asp Tyr ArgPheArgLeuGln Ile GlyThrSer His Leu
18. What are the three stop codons?
UGA
UAG
UAA
19. What codons code for serine?
TCT, TCC, TCA, TCG, AGT, AGC
Or
UCU, UCC, UCA, UCG, AGU, AGC
20.How many codons are there for valine? for asparagine? for tryptophan?
Valine – 4 (GUU, GUC, GUA, GUG)
Asparagine – 2 (AAU, AAC)
Tryptophan – 1 (UGG)
21. These six possible codons for arginine might appear in a molecule of mRNA. For each one, write the anticodon on the tRNA molecule that will carry arginine to the ribosome when that particular codon is read.
Codon / AnticodonC G U / GCA
C G C / GCG
C G A / GCU
C G G / GCC
A G A / UCU
A G G / UCC
22. For the DNA sequences given below, write the correct mRNA sequence that would result following transcription. Where would you modify the mRNA with a methylated cap and a poly-A tail?What are the polypeptide strands that would result following translation? Underline the untranslated regions (if present). BE CAREFUL! You may have to replicate this DNA strand before you transcribe!
a. 5’ A T C A T G C G A G GG C T T A AAA C C G A C A T T A G C C T G A T TT A G GG C 3’
5’ A U C A U G C G A G GG C U U A AAA C C G A C A U U A G C C U G A U UU A G C C G3’
- 5’ CCC G A G A T G GG A T TT C T C G G A AAA T T C A G G T A AA C A T G C 3’
5’ C CC G A G A U G GG A U UU C T C G A AAA U U C A G G U A AA C A T G C 3’
23. For each of the following sequences, complete the series by filling in the missing DNA, mRNA sequence, codon triplet, tRNA anticodons, & the amino acid sequences (don’t worry about finding a start codon). If several amino acid sequences might work choose any one. Stop translating once you find a stop codon.
A. DNA: A T A C G A AA T C G C G A T C G C G G C G A T T C G G
mRNA: U A U G C U UU A G C G C U A G C G C C G C U A A G C C
Codon: UAUGCUUUAGCGCUAGCG CCG CUAAGC C
Anti-codon: AUACGA AAU CGCGAUCGCGGCGAUUCG G
AminoAcids: Tyr Ala Lue Ala Leu Ala Pro Leu Ser
B. DNA: T TT A C G G C C A T C A G G C A A T A C T G G
mRNA: A AA U G C C G G U A G U C C G U U A U G A C C
Codon: AAA UGCCGGUAGUCCGUU AUG ACC
Anti-codon: UUUACGGCC AUC AGG CAA UAC UGG
AminoAcids: Lys CysArg *
C. DNA: T A C G GG C C T A T A C G C T A C T A C T C A T G G A T C G G
mRNA: A U G C CC G G A U A U G C G A U G A U G A G U A C C U A G C C
Codon: AUG CCC GGAUAUGCG AUG AUGAGU ACC UAG CC
Anti-codon: UAC GGGCCUAUACGC UAC UACUCA UGG AUC GG
Amino Acids: Met Pro Gly Tyr Ala Met MetSerThr *
D. DNA: C G A T A C A A T G G A C CC G G T A T G C G A T A T C C
mRNA: G C U A U G U U A C C U G GG C C A U A C G C U A U A G G
Codon:GCU AUG UUA CCU GGG CCA UAC GCU AUA GG
Anti-codon:
AminoAcids:Ala Met Leu Pro Gly Pro Tyr Ala Ile
E.DNA: T A C T G A T C G A C CCCC A T A T G A AAA T C T T
mRNA: A U G A C U A G C U G GGGG U A U U A C U UUU A G A A
Codon: AUG ACUAGC UGG GGGUAU UAC UUUUAG AA
Anti-codon:
Amino Acids: Met ThrSerTrpGly Tyr TyrPhe *
F. DNA – sensestrand: T A C A T G C G C T C C G C C G T C G A C A A T A C C A C T
DNA – anti-sensestrand: A T G T A C G C G A G G C G G C A G C T G T T A T G G T G A
mRNA:U A C A U G C G C U C C G C C G U C G A C A A U A C C A C U
Codon: UAC AUG CGCUCCGCCGUCGAC AAU ACC ACU
Anti-codon:
Amino Acids: Tyr Met ArgSer Ala Val Asp AsnThrThr
G.DNA: T A C T G A T C G A C CCCC A T A T G A AAA T C
mRNA: A U G A C U A G C U G GGGG U A U U A C U UUU A G
Codon: AUG ACU AGC UGG GGG UAU UAC UUU UAG
Anti-codon:
Amino Acids: Met ThrSerTrpGly Tyr TyrPhe *
H.DNA: A T G G T G GGGG C A T A C C G A C CC T T A A T T
mRNA: U A C C A C CCCC G U A U G G C U G GG A A U U A A
codon: UAC CAC CCC CGU AUG GCU GGG AAU UAA
amino acids: Tyr His Pro Arg Met GlyGlyAsn *
I.DNA: A T G G T G GGGG C A T A C C G A C CC T T A T A G
mRNA: U A C C A C CCCC G U A U G G C U G GG A A U A U C
codon: UAC CAC CCC CGU AUG GCU GGG AAU AUC
amino acids: Tyr His Pro Arg Met GlyGlyAsn Ile
J.DNA: T A C T C T C C A AAAAA G T A C C A A C C G
mRNA: A U G A G A G G U UUUUU C A U G G U U G G C
codon: AUG AGA GGU UUU UUC AUG GUU GGC
AA: MET ARG GLY PHE PHE MET VAL GLY
24. For each of the following sense or anti-sense DNA sequences, complete the series by filling in the missing DNA, mRNA sequence, codon triplet, tRNA anticodons, & the amino acid sequences using the correct reading frame. If several amino acid sequences might work choose any one.
SenseDNA: A T A A T G C G A AA T C G C G A T C G C G G C G A T T C G G A A T A G
mRNA: A U A A U G C G A AA U C G C G A U C G C G G C G A U U C G G A A U A G
Codon: AUAAUGCGA AAU CGCGAUCGCGGCGAUUCGGAAUAG
Anti-codon: --UACGCUAAUGCCCUAGCGCCGCUA AGC CUUACU
AminoAcids: Met ArgAsnArgAspArgGlyAspSer Glu *
Anti-senseDNA: C G A T A C A AA T G T G G A C CC G G T A T G C G A T A T G A T C C T G
mRNA: C G U A U C U UU A C A C C U G GG C C A U A C G C U A U A C U A G G A C
Codon: CGU AUG UUU ACA CCU GGG CCA UAC GCU AUA CUA GGA C
Anti-codon:
Amino Acids: Met PheThr Pro Gly Pro Tyr Ala Ile LeuGly
Anti-senseDNA: T A C C G A T G GGG C T C C G C C G T C G A T A C C A A T A C C A C T
mRNA:A U G G C U A C CCC G A G G C G G C A G C U A U G G U U A U G G U G A
Codon: AUGGCU ACC CCGAGGCGGCAGCUAUGGUUAUGGUGA
Anti-codon:
AminoAcids: Met AlaThr Pro Lys ArgGln Leu Trp Leu Trp
DNA MUTATION PROBLEMS
- Transcribe and translate the following DNA strand correctly. Use a codon table for reference.
3’ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 5’
G T T A C T T T G C G G A A A T T G A C T
mRNA:C A A U G A AA C G C C U UU A A C U G A
polypeptide: Met Lys ArgLeu *
A. In the DNA strand given to you in the previous problem, what would be the effect on the resulting polypeptide if T is mutated to A at base 6? Write out the codon mutation changes for the mRNA and all changes to the polypeptide.
C A A U GU A A C G C C U UU A A C U G A
AAA UAA produces a stop codonNonsense mutation
Polypeptide sequence is Met *
- What would be the effect on the polypeptide if the T is mutated to G at base 17 on the DNA of question 1? Write out the codon mutation changes for the mRNA and all changes to the polypeptide.
C A A U G A AA C G C C U UU A CC U G A
UAA UAC changes Stop to TyrMissense mutation
Polypeptide: Met Lys ArgLeu Tyr Leu
- What would be the effect on the polypeptide of deleting base 7 in the DNA of question 1? Write out the codon mutation changes for the mRNA and all changes in the polypeptide.
C A A U G A A C G C C U UU A A C U G A
Polypeptide: Met Asn Ala PheAsn *Frameshift
2. What are the names of these types of base mutations?
Mutation in A: Nonsense
Mutation in B: Missense
Mutation in C: Frameshift
3. Based on the original sequence given below, complete the questions below. Classify each mutation as either: Deletion, Insertion, or Substitution AND as either a: frameshift, missense, silent or nonsense (hint: deletion or insertion will always be frameshift). Assume the DNA sequence given is the anti-sense strand.
Original DNASequence:T A C A C C T T G G C G A C G A C T
mRNA Sequence:UAC ACC UUG GCG ACG ACU
Amino Acid Sequence: Tyr Thr Leu Ala Thr Thr
1. Mutated DNA Sequence #1: T A C A T C T T G G C G A C G A C T (Circle the change)
What’s the mRNA sequence? UAC AUC UUGGCGACGACU
What will be the amino acid sequence? Tyr Ile Leu Ala ThrThr
What kind of mutation is this? Substitution C T or Missense mutation
Will there likely be effects resulting from this mutation? Why? Maybe not. The amino acid Thr becomes Ile but the rest of the polypeptide is fine
2. Mutated DNA Sequence #2: T A C G A C C T T G G C G A C G A C T (Circle the change)
What’s the mRNA sequence?UAC GACCUUGGCGACGAC U
What will be the amino acid sequence? Tyr Asp LeuGly Asp Asp
What kind of mutation is this? Insertion of a G and a frame shift
Will there likely be effects resulting from this mutation? Why? Yes. The insertion causes a frameshift and a new reading frame that will affect the polypeptide made
3. Mutated DNA Sequence #3: T A C A C C T T A G C G A C G A C T (Circle the change)
What’s the mRNA sequence? UAC ACC UUAGCGACGACU
What will be the amino acid sequence? Tyr ThrLeu Ala ThrThr
What kind of mutation is this? Substitution AG or Silent mutation
Will there likely be effects resulting from this mutation? Why? No. This mutation does not change the amino acid sequence and is a silent mutation
4. Mutated DNA Sequence #4: T A C A C C T T G G C G A C T A C T (Circle the change)
What’s the mRNA sequence? UAC ACC UUGGCGACUACU
What will be the amino acid sequence? Tyr ThrLeu Ala ThrThr
What kind of mutation is this? Substitution T G or Silent mutation
Will there likely be effects resulting from this mutation? Why? No. This mutation does not change the amino acid sequence and is a silent mutation
5. Mutated DNA Sequence #5: T A C A C C T T G G G A C G A C T (Circle the change)
What will be the corresponding mRNA sequence? UAC ACC UUGGGACGA CU
What will be the amino acid sequence? Tyr ThrLeuGlyArg
What kind of mutation is this? Deletion of a C nucleotide
Will there likely be effects resulting from this mutation? Why? Yes. The deletion causes a frameshift and a new reading frame that will affect the polypeptide made
6. Five versions of an original sequence of nucleotides in one half of a DNA helix are given as choices a tod. The original DNA sequence is:
T A C C G C A A T G C T T G A G G C
Choices:
a. A T G G C G T T A C G A A C T C C G
b. A U G G C G U U A C G A A C U C C G
c. T A C C G C A AA G C T T G A G G C
d. T A C G C A A T G C T T G A G G C
a. Which of the above choices would result by replicating the DNA sequence?
Choice A is the complementary sequence to the original
T A C C G C A A T G C T T G A G G C
A T G G C G T T A C G A A C T C C G
b. Which of the above choices would be the result of a mutation known as a base substitution?
Choice C originalT A C C G C A AT G C T T G A G G C T A
T A C C G C A AA G C T T G A G G C
c. If you transcribed and translated the sequence you picked in question #4 - what amino acids are coded for by these codons? What amino acids would result from the mutation?
original T A C C G C A AT G C T T G A G G C
Choice C T A C C G C A AA G C T T G A G G C
mRNA A U G G C G U UU C G U A C U C C G (choice C transcribed)
AAs Met AlaPheArgThr Pro
Comparing this to the original sequence and doing the same thing
Original sequence: T A C C G C A A T G C T T G A G G C
Replicated original sequence: A T G G C G T T A C G A A C T C C G
Transcribed original sequence: A U G C G U U A C G A A C U C C G
Polypeptide sequence:Met AlaLeuArgThr Pro
A Leucine amino acid Phenylalanine amino acid in the mutated sequence
d. Which of the choices would be the result of a mutation known as a nucleotide deletion causing a frame shift?
Choice D
originalT A C C G C A AT G C T T G A G G C
T A C G C A A T G C T T G A G G Chighlighted C isdeleted
e. If you transcribed and translated the sequence you picked in question #6d, what would your new polypeptide sequence be?
originalT A C C G C A AT G C T T G A G G C
Choice D T A C G C A A T G C T T G A G G C
mRNAA U G C G U U A C G A A C U C G C (choice D transcribed)
AAsMet Pro Tyr GluLeu
f. Which of the choices would be the primary mRNA transcript created by transcribing the original DNA? Translate this mRNA transcript.
Choice B
Met Ala LeuArgThr Pro
g. Which of the mutations you identified above will have the greatest phenotypic effect? Explain your answer.
While all mutations can effect phenotype – the greatest phenotypic effect will likely be produced from the deletion frameshift mutation. It is possible that the proteins produced upon base substitutions will still function properly if the chemical properties of the protein remain unchanged.
Fill in the following flowchart