Question

For this assignment, we will consider a protein expressed in the liver of an African cheetah (Acinonyx jubatus). Biochemists determined that this protein is involved in the production of glycogen.

In a stunning announcement, a snowboarder in Antarctica claims to have found a new species of cheetah that is able to survive freezing temperatures and a long, dark winter. The snowboarder described a slow, fat, white-furred cheetah that may be related to the African cheetah. Scientists isolated a fragment of DNA from the obese feline creature which codes for the liver protein:

(3' end) ...CTACGTTCAGCTTGTCACGACTGGTTA... (5' end)

(5' end) ...GATGCAAGTCGAACAGTGCTGACCAAT... (3' end)

At almost the same time, a sleek, fast, white-coated cheetah was found in the Andes in South America where cheetahs were not known to exist. With some difficulty, a geneticist convinced the cheetah to allow her to swab the inside of the big cat's cheek to get a sample of DNA. Soon after, the geneticist was able to isolate the following DNA fragment believed to be involved with glycogen production in the liver:

(3' end) ...TCACCTACGTTCAATAGGTCACGACTGG... (5' end)

(5' end) ...AGTGGATGCAAGTTATCCAGTGCTGACC... (3' end)

The original African cheetah DNA fragment describing the liver protein in question is this:

(3' end) ...CACCTACGTTCAGGAGGTCAGGACTGGTTA... (5' end)

(5' end) ...GTGGATGCAAGTCCTCCAGTCCTGACCAAT... (3' end)

You are part of a team of geneticists, evolutionary biologists, and bioinformatics experts. You will attempt to describe the differences between the three species of cheetah in both genetic and evolutionary terms.

1)For each DNA sequence, transcribe to mRNA and then find the chain of amino acids that it produces. Remember that a gene must begin with the "Start" codon.

2)Describe the differences in the basic genetic code between the three species. How many DNA point mutations would be required to change from one species to the others? How do the amino acid sequences of the proteins differ? Are there any silent mutations that may not effect the function of the protein?

3)Looking at the amino acid substitutions that exist between the species, would you expect there to be large functional differences between the two slightly different proteins based on the properties of the substituted amino acids? Explain why you think this might be the case.

4)Quantitatively assess the evolutionary distance between each pair of the three species using the substitution matrix and PAM scores. (This involves three pairs: African/Andes, African/Antarctic, and Antarctic/Andes.)

5)Propose a scenario describing how the two new cheetah species might have evolved from the African cheetah. Were the two new cheetahs once a single species which then branched to form two separate species? Or did they evolve independently from the African cheetah? Be sure to include in your scenario how the new cheetahs managed to move from Africa to their present locations. Estimate a relative time line for each separate speciation event. (A speciation event is the genetic or environmental event that results in the creation of a new species.) How might the three proteins explain the survivability of the three species in their native habitat? (A little speculation is OK here. You are presenting a hypothesis based on the available evidence. Further research would be required to prove your hypothesis.)

HELP IS APPRECIATED

Answer 1

1. DNA from the obese feline creature-

DNA (3' end) ...CTA CGT TCA GCT TGT CAC GAC TGG TTA... (5' end)

mRNA 5' G AUG CAA GUC GAA CAG UGC UGA CCA AU 3'

amino acid Met Gln Val Glu Gln Cys STOP

DNA fragment for glycogen production in the liver-

DNA (3' end) ...TCACCTACGTTCAATAGGTCACGACTGG... (5' end)

mRNA 5' AGUGG AUG CAA GUU AUC CAG UGC UGA CC 3'

Amino acid Met Gln Val Ile Gln Cys STOP

Original African cheetah DNA fragment:

DNA (3' end) ...CACCTACGTTCAGGAGGTCAGGACTGGTTA... (5' end)

mRNA 5' GUGG AUG CAA GUC CUC CAG UCC UGA CCAAU 3'

Amino acid Met Gln Val Leu Gln Ser STOP