Question 1 (1 marks)
Which type of BLAST search did you choose, and why?
Step 6. Once your BLAST search has returned a result, you will see will see a Graphic Summary of the gene, Descriptions, and Alignments. Hold your mouse over the lower, thinner red line in the Graphic Summary and notice what it tells you above the box. If there is more than one sequence that produced a significant alignment from the Blast search, choose the sequence that you consider has the greatest amount of similarity with your unknown sequence. Notice that the colour of the line in the Graphic Summary represents the alignment score (with red being the highest match, pink is next best, etc) and the length and position of the line represents where the query sequence (your unknown sequence) matches the retrieved sequence.
In the Descriptions section, click on the accession number (the number under ‘Accession’, on the far right of the screen) of the sequence that you think matches (aligns) best with your unknown sequence. (The accession number is a unique identifier given to a sequence when it is submitted to a sequence database.) This will take you to the GenBank entry for the gene. There are many things listed here and some of them will enable you to answer the following questions:
Question 2 (1 marks)
What is the name of the gene?
Hint. The gene name is an acronym of 8 letters that refers to the organism the gene is from, what sort (family) of gene it is, and its particular type. Gene names are usually acronyms or abbreviations that are just a few letters in length; they may include numbers. The nomenclature for naming genes can be different among different species. The entire descriptive name of the gene is written at the top of the page; this is not what we want you to write down as the answer.
Question 3 (2 marks)
3A. (1 marks) What organism has the unknown sequence come from? Provide the binomial speciesname (e.g., humans are Homo sapiens) in the correct scientific format. Note that GenBank does not display the correct scientific format.
3B. (1 marks) Is this organism a prokaryote or a eukaryote?
Hint. In the GenBank entry, there is a line that refers to the Organism that the gene comes from. This gives the species name and the various taxonomic groups, or taxa (see Campbell Fig. 1.14) that the organism belongs in, from biggest to smallest, starting with either Eukaryote or Prokaryote and ending with the genus.
Question 4 (4 marks)
4A. (4 marks) Write the full reference of the publication (i.e., the paper/manuscript) that first described the gene and protein that the unknown sequence is part of. Use the Harvard style of referencing and be as exact as possible. (see Referencing note at end of assignment). Marks will be deducted for incorrect
4
punctuation/formatting – even for a misplaced initial or comma. Journals are very fussy about this, and so should you …
4B. (2 marks) Download the PDF file of this publication (‘paper’, as we call it) through the library website and submit this paper with your assignment to the Dropbox (see supplementary instructions). You may submit as a separate file to the rest of your assignment. Note that the downloaded PDF will include a covering page from the journal; you may omit this last page if you wish. Do not use Google to find the paper: this is an exercise in learning how to correctly source journal articles using the Deakin library, and in following instructions. See Supplementary Information at the end of this assignment sheet.
Now, let’s consider the sequence of the gene and its translation product, that is, the protein. If you haven’t already done so, read the Supplementary Information B (below) on the Klp1 gene and how cDNA sequences are derived from mRNA. The same is true for the gene you are now looking at.
Step 7. Click the blue-highlighted “CDS” (coding segment/sequence), which will shade, in brown, the sequence of nucleotides that codes for the protein.
Question 5 (1 marks)
How many nucleotides are there in the coding sequence for this protein? Hint: use the numbers in the left-hand column to help you count, or the numbers next to CDS and remember the coding sequence is comprised of codons which are 3 nucleotides each. Therefore the total number of nucleotides in the sequence must be divisible by 3.
Question 6 (1 marks)
What is the STOP codon for the gene? Remember, there are 3 alternative stop codons; give the nucleotide sequence (in cDNA format) for the stop codon used by this gene.
Step 8. To retrieve the GenBank entry for the protein that is encoded by this gene, click the highlighted accession number that is next to ‘/protein_id’ (under Features, and CDS). This entry looks similar to the nucleotide one, but gives us a bit more information. Use this entry, the original paper you downloaded in Q4, and any other sources you can think of, to answer Q 7.
Question 7 (1 marks)
How many amino acids are there in the entire protein?
Given that 3 nucleotides code for one amino acid, you might expect that the answer to Q 7 is exactly 1/3 of the answer to Q 5, but it is not.
Question 8 (1 marks)
State why the number of nucleotides that encode the protein is not exactly 3 times the number of amino acids that are translated.

Question 9 (21 marks)
(15 marks) In less than 100 of your own words, write a description of the protein that the gene in Q 2 encodes, that is, the protein that is partially encoded by the unknown sequence. Include in your description: the organelle the protein is targeted to (that is, where it is found in the cell); what the proposed function of this protein is; what other type of protein/s this protein is similar to; what types of cells (not organelles) use versions of this protein to divide themselves, and any other information you would like to provide.

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Posted on May 24, 2016Author TutorCategories Question, Questions