Molecular Genetics: differentiating between various molecular databases

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Biology Assignment        Rashmeen Jaggi        31st May 2010

An Investigation into Molecular Genetics

Differentiating between Various Molecular Databases

This unit we looked at molecular genetics and their importance in human life. The experiment was mostly to find out how closely related two species are and how we can identify the differences. Using various protein sequences, we were able to compare and distinguish among various species. This report mainly focuses on relating four different species from the rodent family: Chinchilla, Guinea Pig, Crested porcupine and Hamster.

Research question

        How are the four species; Chinchillas, Guinea Pigs, Crested porcupines, Hamsters of the rodent family related to each other? What are the similarities and differences among the four amino acid sequences and how can they be measured? To what extent are the four species different from each other?

The independent variables of this experiment were the four species: Chinchilla (Chinchilla Brevicaudata), Guinea Pigs (Cavia Porcellus), crested Porcupine (Hystrix Cristata) and Hamsters (Cricetidae). The dependant variables of this experiment were the amino acid sequences of the four sequences. Using the database search capacities on internet, the entire amino acid sequences were found and later using the Fasta programming on internet, the four species were compared with each other. All the data was then collected in a table. The following are the control variables of the experiment:

  • The protein of the amino acid sequences was a control variable. For this experiment, the amino acid sequences for the protein Insulin were used, mainly because these are short and easier to compare.
  • The type of family to which the four species belong to is also a control variable. For this experiment, the four chosen species belong to the rodent family. This will help us investigate the differences among the species of the same family.
  • The characteristics of the species that were compared during the experiment were a control variable. For the experiment the following characteristics were compared only: Number of AA in the beta chain, Number of similar AA pairs (:), Number of conservative AA pairs (.), Number of different AA ( ).
  • The database from which the amino acid sequences were obtained is also a control variable. All the sequences were obtained from  
  • The program used to compare the four amino acids is also a control variable. The variables were compared on the website:
  • Another control variable of the experiment would be the number of species used for the experiment. Throughout the experiment, amino acid sequences of four different species are used.

Hypothesis

        My prediction for this experiment is that the four species will be closely related to each other as they all belong to the same family; the rodent family. Statistics suggest that all species of the rodent family share the same traits such as having a single pair of incisors in each jaw, short and compressed tongues, the bones of the lower arm, the radius and ulna, are distinct, and the elbow joint permits free motion of the forearm. The number of toes and fingers range 3-5, though the thumb may be absent or vestigial. These similarities suggest that the species will share a few nucleotide basses that code the similar protein. The following pictures of my chosen species also suggest that they are linked together. The three species except for the crested porcupine appear to be similar in appearance and share the similar features.

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Guinea Pig           Porcupine           Hamster                  Chinchilla

Table 1: Comparing Chinchilla and Guinea Pig

Table 2: Comparing Crested Porcupine and Hamster

Table 3: Comparing Crested Porcupine and Chinchilla

Table 4: Comparing Guinea Pig and Hamster

Table 5: Comparing Chinchilla and Hamster

Table 6: Comparing Guinea Pig and Crested Porcupine

Table 7: Concluding Table

The first six tables above compare the four species and as we can see, the last table summarizes the overall data in tables 1-6. Table 7 suggests:

  • The order ...

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