Assignment Topic and Tasks


Assignment Task 1 is on File Formats:
Different molecular biology databases have different file formats.

    (a) List at least 5 different types of file formats

    (b) Provide examples for each

    (c) Cite at least one molecular biology software application and a database in which such a format is used.


Assignment Task 2 relates to protein crystals and their structures:
As you may not have been exposed to protein crystallography and structure determination, the following historical links makes interesting reading for a novice.

        - The Earliest Solutions for Macromolecular Crystal Structures:  A history history of protein crystallisation
        - History of Visualization of Biological Macromolecules: A historical account of methods used for visualising molecules.

Now, for the exercise.
    (a) You will need to choose a protein. You could choose one that you have in mind from your earlier undergraduate readings that interests you, or alternatively, seek assistance from your supervisor in finding one that may be relevant to your research project.

    (b) Search useful literature using ENTREZ at NCBI. You may find that your search produces far too many references for you to handle. Limit your search by changing the search parameters and find the most useful 20 to 25 references.

HINT: If you are not sure how this can be done then the tutorial at NCBI which shows you the power of using ENTREZ should be perused.

    (c) Go to GenBank and find your sequence. Determine whether a 3D model for the protein exists.
                If it exists then go to PDB and locate it. Use RasMol and / or ProteinExplorer to look at the model. You may need to answer some questions later on during the semester. An example of such a question may include identifying the conserved amino acids present in the protein that is found in all similar proteins of the 3 domains (Bacteria, Archaea and Eucarya).

                If a 3D model does not exist, can you draw one. Use  Homology Modeling page to assist you to draw one. You may need to answer some questions later on during the semester. An example of such a question may include identifying the conserved amino acids present in the protein that is found in all similar proteins of the 3 domains (Bacteria, Archaea and Eucarya)


Assignment Task 3 is on gene analysis using molecular biology databases online computational tools:
Small tracts of DNA (less than 5 kb) can now be sequenced much more easily now than ever before. Even students in their formative years of science (2nd year) are capable of achieving this. This has come about due to the explosion in technology, knowledge and availability of kits resulting in cheaper costs and faster data throughput. The complete sequencing of 15 bacterial genomes in the last two years is testimony to this. To complement the high throughput genome sequencing projects, development of data bases and extensive software for data analysis have been developed. Using such tools in conjunction with molecular biology databases makes the internet an extremely powerful learning environment for a range of molecular studies.

The topic is designed to encourage and familiarize you with a range of online molecular biology tools freely and widely available via the internet for sequence analysis. For this, you have been given a DNA sequence. You will use the online tools and molecular biology databases to answer a number of questions which are set out below. You should include the following points as part of your assignment submission:

  1. Identify the primary sequence of the deduced protein expressed by the gene using 6-frame translation and identify the translation frame.
  2. Does the sequence contain a start codon?
  3. What is the deduced molecular weight and the pI?
  4. If this protein was present in E. coli could you identify its location on an E. coli 2-D protein map?
  5. Which family / sub-family does it belong to? Mark the conserved amino acids found in the sequence that identifies it as belonging to the family / sub-family.
  6. Can you determine whether the deduced protein is secreted or cell associated?
  7. Align the deduced protein with 5 of its nearest neighbors. Determine the percent identity and homology. Differentiate between these two terms.
  8. Proteins are compared on the basis of their domain structures. Can you explain what the term means? Draw a domain structure model for the deduced protein and make a comparison with its relatives.
  9. Draw a 3-D model of the deduced protein.

 


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Send comments to Professor Bharat Patel: b.patel@griffith.edu.au
[Created: 03 March 2003]
[Modified: 20 March 2007]