For this assignment, we will consider a protein expressed in the liver of an Afr

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.)

Please Help with all parts of the questions.

Explanation / Answer

1. For a slow, fat, white-furred cheetah, the amino acid sequence is "Met-Gln-Val-Glu-Gln-Cys-Stop"

For a sleek, fast, white-coated cheetah, the amino acid sequence is "Met-Gln-Val-Iso leu-Gln-Cys-Stop"

For an original African cheetah, the amino acid sequence is "Met-Gln-Val-Leu-Gln-Ser-Stop"

2. The difference in amino acids has shown in bold. Yes, is a silent mutation; in a slow, fat, white-furred cheetah and original African cheetah, the valine is coded by GUC, whereas in a sleek, fast, white-coated cheetah, Valine is coded by GUU.

In an original African cheetah, UCC codes for serine, whereas, UGC codes for cysteine in other two varieties in that place. So that it needs a single point mutation from C---->G.

In an original African cheetah, CUC codes for leucine, whereas, in a sleek, fast, white-coated cheetah, AUC codes for isoleucine. So that it needs a single point mutation from C---->A.

3. Between a slow, fat, white-furred cheetah and a sleek, fast, white-coated cheetah there is a good difference from Glutamate to Isoleucine that might greatly affect the protein structure and charge because Glutamate is dicarboxylic polar amino acid with negative charge. Whereas, isoleucine is branched chain non-polar amino acid.

Between an original African cheetah and other two varieties Serine is replaced by Cysteine. Here, the serine is 'OH'-group containing polar amino acid, whereas, cysteine is SH-group containing polar amino acid. There would be a difference in the strength of bonding and bond distance or bond angle between the proteins from cheetah varieties. But, may not much affect the protein structure or function.

4. I do not have knowledge of bioinformatics, so, I cannot answer this question.

5. I can predict that they might evolve from original African cheetah only, but due to the "continental drift" there would be a possibility for the change in few changes according to their habitats or environment. Glutamate in place of Leucine might alter the protein function that becomes active in a slow, fat, white-furred cheetah because their physical activity is very low so that, most of the energy will be stored in the form of glycogen or fat. But, such a great effect we cannot see in between original and sleek, fast, white cheetah since, Leucine to Isoleucine does not affect much in protein function, if it is present in the active site. So in fast sleek cheetah and original cheetah the activity of this protein would be same and normal.

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