Protein Sequence Alignment Q4) The diagram below shows a multiple protein sequen

Question

Protein Sequence Alignment

Q4) The diagram below shows a multiple protein sequence alignment.

A) How many proteins are being aligned in this analysis?

B) What is the name of a bioinformatics tool that is commonly used to produce this alignment output?

C) What is the percentage identity between the rat and lettuce proteins in this aligned region? Show your calculation.

D) Describe ONE thing that a researcher could learn about the gorilla protein from an alignment of this type?

E) Residue 10 shown in each of the sequences is a K or an I. Is K to I a conservative or non-conservative change? Why? Draw structures of the amino acid side chains and explain their properties as part of your answer

Q4. The diagram below shows a multiple protein sequence alignment. Rat 1 TGGVKHRY RPGTVALREIRRY 50 MARTKOTARKSTGGKAPRKOLATKAARPAT Horse HRYRPGTVALREIRRY 50 MARTKOTARKSTGGKAPRKOLATKAARPATGGVK Gorilla 1 MARTKOTARKSTGGKAPRKOLATKAARPAT RPGTVALREIRRY 50 TGGVKHRY Worm HRYRPGTVALREIRRY 50 MARTKOSARISTGGKAPKKOLAATKGARPAAGGVK Fluke MARTKOSARISTGGKAPRKOLATKMARPATGAVKHRYRPGTVALREIRRY 50 Lettuce 1 MARTKOSARISTGGKAPK KOLATKGARPATGAVKHRFRPGTVALREIRKY 50 Answer A, B, C, D and E. A) How many proteins are being aligned in this analysis? (0.5 mark) B) What is the name of a bioinformatics tool that is commonly used to produce this alignment output? (0.5 mark) C) What is the percentage identity between the rat and lettuce proteins in this aligned region? Show your calculation. (5 marks) D) Describe ONE thing that a researcher could learn about the gorilla protein from an alignment of this type? (2 marks) E) Residue 10 shown in each of the sequences is a K or an I. s K to l a conservative or non-conservative change? Why? Draw structures of the amino acid side chains and explain their properties as part of your answer. (6 marks) (Question total 14 marks)

Explanation / Answer

Answer:

(A) One protein from six different species have been aligned.

(B) BLAST: Basic Local Alignment Search Tool for proteins (pBLAST).

(C) There are 7 different amino acids between rat and lettuce protein.

50 total number of amino acids = 100%, i.e, each amino acid difference = 2%

So, 7 different amino acids = 14% difference and similarity = 100 - 14 = 86%.

(D) Protein from rat, horse and gorilla are 100% identical.

(E) K to I is a non conservative change since K has a basic side chain while side chain of I is non polar.

NH2 - (CH2)4 - CH (NH2) - COOH = K (Essential - Proteogenic - Glycogenic and ketogenic, basic side chain)

CH3 - CH2 - CH (CH3) - CH (NH2) - COOH = I (Essential - Proteogenic - Glycogenic and ketogenic, non polar, hydrophobic - aliphatic )

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