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.
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?
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.
Numerous elements add to making up the character of an individual, their mental self portrait and how they depict themselves. Some of these components include: convictions, culture, sexual orientation, race, among others. For the most part, individuals in a general public tend to base their underlying information of other individuals on cliché speculations that begin from these different parts of personality. Much of the time, these speculations that hurriedly turn into the known myths don't really come clean about a specific gathering of individuals with significant likenesses like social foundation or race. This winds up making a standard that society by implication gives on these individuals who consequently, might possibly fit in with these models. By and by, I fall under the classification of individuals that don't live as per what may appear like societal measures while breaking down the normal Canadian young person. My social and racial personality total up the significant angles that impact my mental self portrait in light of the fact that my physical qualities makes society not see past my social foundation, sexual orientation and qualities. As an outline, my social and racial foundation is physically obvious in light of the fact that I have unmistakable highlights like my skin shading, that show I am Black. Additionally, when I talk my intonation plainly portrays that I am a West-African, all the more particularly a glad Nigerian young lady. This effects my mental self view enormously on the grounds that it fills in as a steady indication of my place of inception. Being a genuine Nigerian kid accompanies the preparation I get the chance to empower me turn into a mindful woman in the closest future. This is on account of I have certain duties and norms to live by because of my childhood as a youngster. For instance, in my youth the significance of buckling down was continually lectured by my folks, older folks at chapel, school and even my environment. House tasks were viewed as the essential obligations of the kids in the home and being the most youthful of five did not by any stretch of the imagination help this reality. My place in the family as the last conceived place me in the situation of the errand individual. My more established ones were more similar to my bosses and to them, having me help at whatever point there was a need to wash garments, cook, clear the house and some more, made me more mindful as I became more established. Up until this point, this influences me to consider myself to be a dynamic part player in my life and development process. Then again, this is not the same as how the general population around me would judge me. A current illustration is the point at which I moved into home at York University. Being clearly African, a kindred understudy living on a similar floor conceded she figured I would be truly "tighten". By this, she implied her desires of me were low. She thought I was the noisy party young lady that each person knew and had sexual history with. She was astonished to discover I am really a held and straightforward young lady who is scholastic arranged. Her purpose behind reasoning along these lines originated from her experiences with couple of other Black young ladies in the past who did not act mindfully due to their issues with medications, smoking and young men. This made her judge me before she even became acquainted with me for who I genuinely am. Besides, being a young lady impacts my mental self view since it is one physical part of my character that represents me before I do. As a female youngster naturally introduced to a male centric culture like that of the Nigerian culture, your optimal stages in life have for all intents and purposes been laid out for you to take after. It begins from growing up being capable and dedicated, at that point endeavoring to ensure you are scholastically effective on the grounds that training is vital. After this, you get your profession and at the "perfect time", get hitched when your foreordained spouse discovers you. For example, when I was a more youthful youngster growing up, my mum dependably disclosed to me stories of how being a decent mother or spouse isn't simple, however justified, despite all the trouble. She would dependably urge me to watch her at whatever point she was cooking, serving my father his sustenance or orchestrating the house. She always stressed on the significance of being innovative as a woman and potential spouse. This implies as a female in the normal Nigerian home, your motivation in life appears to be deficient on the off chance that you don't anticipate getting hitched and having youngsters. As such, after you achieve a specific age as a young lady, you better begin expecting the entire discuss marriage, having grandchildren for your folks and being a decent spouse, cook and mother when you wed. I don't have an issue with this in any capacity since I trust that piece of the satisfaction of a lady originates from her wedding her genuine romance, having a family and bringing up her kids eventually in her life. Besides, my qualities which are a noteworthy segment of my personality decide the sort of individual I be and in the long run move toward becoming. My principle esteems incorporate, my confidence in Jesus Christ as my hero, forbearance from sex, liquor and any kind of medications. This influences me to consider myself to be a rebel since I can barely fit into my condition or society without changing or bargain my convictions a bit. Most circumstances, individuals consider me to be abnormal and think that its difficult to trust that I have never gone clubbing, smoked or possibly accomplished something "cool". An event that I don't figure I will ever overlook was in the late spring of review eleven which is around two years back. I met a person who happened to be a companion of my dear companion. The three of us hung out at the shopping center while the person was attempting to become more acquainted with me better by getting some information about my school, foundation among others. I thought he was a pleasant individual. Inevitably, he inquired as to whether we could "chill" and I didn't know of what he implied. Notwithstanding, I said no in light of the fact that and gave a reason of going lift my nephew up from school. In all trustworthiness, I didn't have a craving for going out with a person, particularly somebody I just met out of the blue. To stop the long story, he wound up strolling mostly home with me since he guaranteed he lived in an indistinguishable neighborhood from me. Later on, I assumed that by "chill" he implied he was sexually pulled in to me and he simply needed to get something from me since he thought I was that sort of young lady. I could see disillusionment composed everywhere all over when I completely declined his headways towards me. He said he had never been rejected by any young lady with a comparable racial or social foundation as me. Without a doubt, I was disturbed at the way that somebody of the contrary sex would really ignore my faith in sexual immaculateness and forbearance at that point, judge me in such an ill bred way due to my skin shading and social foundation. All things considered, I trust that my body goes past my physical magnificence and what I resemble. It envelops every little thing about me, going from the littlest to the greatest. The way I see myself is additionally because of a blends of every one of these variables like how other individuals see me and judge me. I can't point the finger at society for their judgements of me, however I can expect better in light of the fact that a man goes past his or her cover which is the body. You need to evacuate the cover in this sense and see each and every thing is contains underneath it. Because of this mental self portrait consistently creates as a man develops and this is my story. I realize that regardless of what my social and racial character involves, I will constantly flabbergast myself with self-awareness and development. I will reach past the set limits and desires. Need assistance with your paper? 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