Proteins and Enzymes
Data-Handling Coursework
Answer all Questions.
ANSWER THE QUESTIONS IN THE SPACE PROVIDED AND SUBMIT AS A SINGLE PDF DOCUMENT VIA THE TURNITIN LINK ON THE MODULE BLACKBOARD SITE.
This assessment is marked out of 40.
Question 1
Using an appropriate online tool, give the amino acid sequence encoded by the following DNA sequence:
atgtccaaaaaaatcagtggcggttctgtggtagagatgcaaggagatgaaatgacacgaatcatttgggaattgattaaagagaaactcatttttccctacgtggaattggatctacatagctatgatttaggcatagagaatcgtgatgccaccaacgaccaagtcaccaaggatgctgcagaagctataaagaagcataatgttggcgtcaaatgtgccactatcactcctgatgagaagagggttgaggagttcaagttgaaacaaatgtggaaatcaccaaatggcaccatacgaaatattctgggtggcacggtcttcagagaagccattatctgcaaaaatatcccccggcttgtgagtggatgggtaaaacctatcatcataggtcgtcatgcttatggggatcaatacagagcaactgattttgttgttcctgggcctggaaaagtagagataacctacacaccaagtgacggaacccaaaaggtgacatacctggtacataactttgaagaaggtggtggtgttgccatggggatgtataatcaagataagtcaattgaagattttgcacacagttccttccaaatggctctgtctaagggttggcctttgtatctgagcaccaaaaacactattctgaagaaatatgatgggcgtttta aagacatctttcaggagatatatgacaagcagtacaagtcccagtttgaagctcaaaagatctggtatgagcataggctcatcgacgacatggtggcccaagctatgaaatcagagggaggcttcatctgggcctgtaaaaactatgatggtgacgtgcagtcggactctgtggcccaagggtatggctctctcggcatgatgaccagcgtgctggtttgtccagatggcaagacagtagaagcagaggctgcccacgggactgtaacccgtcactaccgcatgtaccagaaaggacaggagacgtccaccaatcccattgcttccatttttgcctggaccagagggttagcccacagagcaaagcttgataacaataaagagcttgccttctttgcaaatgctttggaagaagtctctattgagacaattgaggctggcttcatgaccaaggacttggctgcttgcattaaaggtttacccaatgtgcaacgttctgactacttgaatacatttgagttcatggataaacttggagaaaacttgaagatcaaactagctcaggccaaactt
2 marks
ii) Give the full names and the single AND three codes for the N and
C terminal amino acids for the translated sequence.
4 marks
Give the PDB identifiers of the four best matches to your protein sequence in the PDB.
Answer:
PDB ID:
PDB ID:
PDB ID:
PDB ID:
4 marks 10 marks
Question 2
The multiple sequence alignment below shows the alignment between three members of an enzyme family:
| What is the name of the enzyme family shown is this alignment? Give a balanced equation for the reaction catalysed by this enzyme family. |
| Answer:
Name of enzyme family: Balanced equation for reaction catalysed by enzyme family:
|
4 marks
| i) Using Enz_1 as a guide (Hint: check the Uniprot entry for this protein), clearly highlight in the alignment below the four conserved key amino acid residues in this enzyme family that are involved in metal binding.
ii) What is the function of the bound metal ion in the functioning of this enzyme family? |
| Answer:
i) Clearly highlight the metal binding residues in the above alignment.
ii) What is the function of bound metal ion in this enzyme family?
|
6 marks 10 marks
Question 3
Download the following protein sequences (P26492, Q01095, P18086, P00323, P71165, P80312, Q01096) from UniProt and carry out a multiple sequence alignment using ClustalW and paste your correctly formatted and labelled alignment into the space over the page:
Insert your multiple sequence alignment here:
2 marks
Re-copy your alignment into the space below and highlight the three conserved motifs in the protein alignment involved in binding the FMN prosthetic group. Also highlight the TWO conserved amino acids that flank the isoalloxazine ring of the FMN prosthetic group.
Insert your multiple sequence alignment her8 marks
10 marks
Question 4
| i) Summarise the multiple sequence alignment shown below in the
form of a Prosite signature sequence (e.g., [FY]-[LIV]-[GV]-[DE]-E-[ARV]-[QLAH]-x).
Your motif should be no longer than 12 amino acids long.
1 5 10 Seq_1 LSEKIEYYFPLS Seq_3 MADKVESAFSIS Seq_4 VHQKLEYMFALS Seq_6 IVNKLETLYGVS Seq_7 AFEKIETIFWLT Seq_8 ILEKVESWFHVS
ii) For position 7 and position 10 in your motif clearly explain the basis for your choice of amino acid(s) at those positions. |
| Answer:
i) Give your Prosite signature sequence below:
ii)
Rationale for your choice of amino acid(s) at Position 7?
(50 words) Rationale for your choice of amino acid(s) at Position 10?
(50 words) |
10 marks
