Q1

Iron exists in the body as Fe2+, ferrous iron, or Fe3+, ferric iron. Ferrous iron is reactive and easily oxidised to ferric iron, and so there are a number of proteins that catalyse the oxidation of Fe2+ to Fe3+. These have ferroxidase activity.
You task is to identify the proteins that are known to have ferroxidase activity in the human genome.

a) Use the NCBI, EBI or Ensembl portals to retrieve one file for each of the several different ferroxidases found in humans. Each file should contain the complete mRNA sequence (it is not necessary to include the sequences in your answer).

b) Compile a table, similar to the one from tutorial 1, comparing the sequence elements of the mRNA of each different ferroxidase that you find. Include an extra column indicating the length of the protein. Comment on your findings.

c) Retrieve files for two genes encoding different, but homologous, ferroxidase proteins and compare the structure of the genes (it is not necessary to include the sequences in your answer). Comment on your findings.

For all parts describe how you obtained your data by stating the bioinformatics portal used and the search strategy. Accession numbers of all sequence files must be given. Any references used should be cited in your answer. Expect to retrieve less than 10 files. Pay attention to units in the table.

Q2

The tumour suppressor protein p53 functions by inducing growth arrest or apoptosis. Here we aim to learn about the relationship between the human protein sequence (UniProt code P04637) and a number of other species.

(i) Firstly identify the domains present within the human p53 sequence using one of the domain databases discussed in lecture 2. State the range of amino acids within each domain.

(ii) Using UniProt locate the sequence for the full-length human p53 sequence. Then run a BLAST search for this sequence against the Swiss-Prot protein database and identify 7 other different species of p53 with close similarity to the human sequence (make sure they are full length sequences).

(iii) Give the Accession number for each protein sequence identified, together with the species. Give the percentage identity for each of the 7 sequences with that of the human sequence. State E values and the length of each sequence.

(iv) For all 8 sequences run a multiple sequence alignment using program Clustal Omega. Submit your sequence alignment. How many positions along the multiply aligned sequences are fully conserved between species?

(v) Display both the cladogram and phylogram trees for the aligned sequences and submit with the assessment.

Briefly discuss the evolutionary relationship between the 8 species as indicated by the phylogram and cladograms. Which species is the closest relation to the human species?

35 marks

Q3

Detecting remote homologs with BLAST and PSI-BLAST.
The NCBI website (https://www.ncbi.nlm.nih.gov) gives the option to run both BLAST and PSI-BLAST for a query protein sequence. For this question you need to use the NCBI website to run both BLAST and PSI-BLAST.
The enzyme adenosine deaminase (UniProt accession number P00813) and the enzyme imidazolonepropionase (UniProt accession number P42084) perform a similar function and are remote homologs, both belonging to the SCOP superfamily metallo-dependent hydrolase. The two sequences have a percentage identity of only 18%.
Perform a protein-protein BLAST search using the sequence for the adenosine deaminase sequence (UniProt accession number P00813) searching against the UniProtKB/Swiss-Prot database. Search the results for the imidazolonepropionase enzyme (UniProt accession number P42084). Now repeat your search using PSI-BLAST and compare your results from those obtained from protein-protein BLAST.
Discuss what you observe from the BLAST and PSI-BLAST searches. Discuss which of the two search methods proved most effective and why. Include output as appropriate to illustrate your answer. Include the pairwise alignment for the 18% identical sequences P00813 and P42084 obtained from your output.

 

 

 

Sample Solution

Sample solution

Dante Alighieri played a critical role in the literature world through his poem Divine Comedy that was written in the 14th century. The poem contains Inferno, Purgatorio, and Paradiso. The Inferno is a description of the nine circles of torment that are found on the earth. It depicts the realms of the people that have gone against the spiritual values and who, instead, have chosen bestial appetite, violence, or fraud and malice. The nine circles of hell are limbo, lust, gluttony, greed and wrath. Others are heresy, violence, fraud, and treachery. The purpose of this paper is to examine the Dante’s Inferno in the perspective of its portrayal of God’s image and the justification of hell. 

In this epic poem, God is portrayed as a super being guilty of multiple weaknesses including being egotistic, unjust, and hypocritical. Dante, in this poem, depicts God as being more human than divine by challenging God’s omnipotence. Additionally, the manner in which Dante describes Hell is in full contradiction to the morals of God as written in the Bible. When god arranges Hell to flatter Himself, He commits egotism, a sin that is common among human beings (Cheney, 2016). The weakness is depicted in Limbo and on the Gate of Hell where, for instance, God sends those who do not worship Him to Hell. This implies that failure to worship Him is a sin.

God is also depicted as lacking justice in His actions thus removing the godly image. The injustice is portrayed by the manner in which the sodomites and opportunists are treated. The opportunists are subjected to banner chasing in their lives after death followed by being stung by insects and maggots. They are known to having done neither good nor bad during their lifetimes and, therefore, justice could have demanded that they be granted a neutral punishment having lived a neutral life. The sodomites are also punished unfairly by God when Brunetto Lattini is condemned to hell despite being a good leader (Babor, T. F., McGovern, T., & Robaina, K. (2017). While he commited sodomy, God chooses to ignore all the other good deeds that Brunetto did.

Finally, God is also portrayed as being hypocritical in His actions, a sin that further diminishes His godliness and makes Him more human. A case in point is when God condemns the sin of egotism and goes ahead to commit it repeatedly. Proverbs 29:23 states that “arrogance will bring your downfall, but if you are humble, you will be respected.” When Slattery condemns Dante’s human state as being weak, doubtful, and limited, he is proving God’s hypocrisy because He is also human (Verdicchio, 2015). The actions of God in Hell as portrayed by Dante are inconsistent with the Biblical literature. Both Dante and God are prone to making mistakes, something common among human beings thus making God more human.

To wrap it up, Dante portrays God is more human since He commits the same sins that humans commit: egotism, hypocrisy, and injustice. Hell is justified as being a destination for victims of the mistakes committed by God. The Hell is presented as being a totally different place as compared to what is written about it in the Bible. As a result, reading through the text gives an image of God who is prone to the very mistakes common to humans thus ripping Him off His lofty status of divine and, instead, making Him a mere human. Whether or not Dante did it intentionally is subject to debate but one thing is clear in the poem: the misconstrued notion of God is revealed to future generations.

 

References

Babor, T. F., McGovern, T., & Robaina, K. (2017). Dante’s inferno: Seven deadly sins in scientific publishing and how to avoid them. Addiction Science: A Guide for the Perplexed, 267.

Cheney, L. D. G. (2016). Illustrations for Dante’s Inferno: A Comparative Study of Sandro Botticelli, Giovanni Stradano, and Federico Zuccaro. Cultural and Religious Studies4(8), 487.

Verdicchio, M. (2015). Irony and Desire in Dante’s” Inferno” 27. Italica, 285-297.