Question

(I've already seen the example "My Name is Slim Shady" I was hoping for another type of example. Deciding which codons to edit is confusing to me.)

A) Use the genetic code to encode a secret message. Use the standard amino acid code as capital letters, as in A for alanine, Y for tyrosine, to make a message in English. Convert the message into a hypothetical mRNA sequence. Write down the mRNA sequence and translate the DNA. The message must be at least 12 characters in length.

B) Re-write a mutant version of your secret code that contains a mis-sense mutation somewhere near the beginning of the sequence.

C) Describe how PCR could be used to produce a DNA fragment that includes the mutation described in B. Hint: think about primer design.  

D) Re-write a mutant version of your secret code that contains a non-sense mutation.

E) Re-write a mutant version of your secret code that contains a neutral mutation.

F) Suppose your message includes the codon “GAG”, which codes for glutamine. What are the chances that a single nucleotide change in this codon will be a non-sense mutation? A mis-sense mutation? A neutral mutation?

G) What is a frameshift mutation? Show how a frameshift mutation would cause your message to become scrambled.

Answer 1

A)

Let's say the message is "Merry Christmas"

Peptide --> MERRYCHRISTMAS

mRNA --> 5'-AUG GAA AGA AGG UAU UGU CAU AGA AUU UCU ACU AUG GCU UCU-3'

DNA --> 5'-ATG GAA AGA AGG TAT TGT CAT AGA ATT TCT ACT ATG GCT TCT-3'

B)

DNA Sequence with mis-sense mutation ->  5'-ATG GTA AGA AGG TAT TGT CAT AGA ATT TCT ACT ATG GCT TCT-3'

Here the 2nd codon is mutated from GAA to GTA (Glutamic Acid to Valine)

C)

The sequence with the mis-sense mutation can be created by amplifying the DNA with the following primers:

Primer 1: 5'-ATGGTAAGAAGG-3'
Primer 2: 5'-AGAAGCCATAG-3'

Since Primer 1 has the mutation, amplification with these primers will result in the sequence being mutated at the 2nd base of the 2nd codon.

D)

The sequence with a non-sense mutation is : 5'-ATG GAA AGA AGG TAA TGT CAT AGA ATT TCT ACT ATG GCT TCT-3'

Here the 5th codon is mutated from TAT (Tyrosine) to TAA, resulting in a premature stop codon.

E)

The sequence with a neutral mutation is: 5'-ATG GAA AGA AGG TAT TGT CAT AGA ATT TCA ACT ATG GCT TCT-3'

Here the 10th codon is mutated from TCT to TCA. Both these codons encode for the Amino Acid Serine. Thus the peptide sequence remains unchanged.

F)

The codon GAG (Glutamic Acid) can be mutated to the following codons:

• GAC --> Aspartic Acid
• GAT --> Aspartic Acid
• GAA --> Glutamic Acid
• GTG --> Valine
• GCG --> Alanine
• GGG --> Glycine
• CAG --> Glutamine
• AAG --> Lysine
• TAG --> STOP

The chances for a Nonsense mutation are 1/12. The chances for a Missense mutation are 10/12 or 5/6. The chances for a Neutral Mutation are 1/12.

Please note, the codon given in the question, GAG, actually encodes for Glutamic Acid. I have answered here accordingly. However, the principle would remain the same regardless of the actual Amino Acid-Codon relationship but the chances of each 'type' of mutation occurring might change.

G)

Let's say the following frameshift mutation occurred:

5'-ATG GAA AGA AGG TTT GTC ATA GAA TTT CTA CTA TGG CTT CT-3' (2nd base of 5th codon deleted)

The new amino acid sequence would be: MERRFVIEFLLWL. Since the frameshift mutation occurred in the 5th codon, everything downstream from there was changed.