Question 4. (Answer all eight parts a h (Total: 20 marks You have just begun wor

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Question 4. (Answer all eight parts a h (Total: 20 marks You have just begun work as an employee of UQ Genome Analysis Ltd. and your first assignment is to analyse two pieces of DNA (called A and B) that have just been sequenced. Each has been assembled into a single contiguous region about 20 thousand nucleotides in length. One of the pieces is from a bacterial genome and the other is from a human nuclear genome, but the sequencing team lost the identification labels and you don't know which piece of DNA came from which organism. You begin by computationally scanning each piece for long uninterrupted open reading frames (ORFs) that begin with a start codon and end with a stop codon. In Piece A you find 19 such regions packed quite closely together. In Piece B you find only one short stretch of nucleotides that could initiate and code for a protein; otherwise, B has a high frequency of termination codons in all three frames. a. Based on the information above, which piece of DNA (A or B) comes from the bacterium, and which comes from human? Explain briefly. (3 marks) b. Next you compare (BLAST) the 20 potential protein-coding regions against GenBank. Of the 19 regions in Piece A, 17 show nearly perfect (>99.8% identity) full-length matches with genes annotated in the genome of a particular organism (let's call it Organism A), and slightly weaker matches (97-99% identity) with genes in its close relatives. However, the other two regions present in Piece A do not have any significant matches in the genome of Organism A or its relatives Suggest a likely explanation. (3 marks) c. Four of these 17 matching genes are physically adjacent in the genome of Organism A and encode successive steps in the tryptophan biosynthesis pathway. From the primary literature you discover that these four genes are always expressed together, or not at all. What word describes this set of four genes? (1 mark)

Explanation / Answer

a. The genome is the set of genes of a particular organism. The bacterial genomes are only about 0.1% as big as the human genome and only 10% of the genes are present compared to humans. There are few specifications that distinguishes the bacterial genes from the human genes. The bacterial genes have no introns, the average number of codons in bacterial genes is less than in human genes, and the neighboring genes are very close together throughout the genome. According the given information piece A has closely packed region which indicates that the Piece A DNA belongs to bacteria. The piece B resembles the human genome because the distribution of genes on chromosomes is irregular. So they either have codons that initiate proetin coding orelse they terminate the action.

b. BLAST the full form is Basic Local Alignment Search Tool, whuch is specifically designed to search nucleotide and protein databases. The query DNA or protein sequence is entered in the BLAST software and then it searches either DNA or protein databases for levels of identity that range from perfect matches to very low similarity. It helps identify the origin of the unknown DNA or protein sample. The unknown query DNA and the sequence is run in BLAST. If the query shows more than 99.8% then the organisms genome is completely identical. But if the match is slightly weaker than the genome of both the organisms is slightly different. Even a small change can decrease the percentage of match.

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