Assignment 1: WEB SEARCH

  • 5 points
  • Deadline: Wednesday, March 6th, 2022, 23:59
  • Late submission penalty: -0.5 point per day (but no more than 4 points)
  • Submit to BRUTE.

PAH gene at NCBI

Look at the PAH gene at NCBI. The nucleotide sequence encoding this gene is shown at the bottom of the page. Additionally, you can find a description of parts of the gene (exons for example). Item CDS contains coordinates of protein-coding parts of the gene.

1. On which chromosome is the PAH located?
2. Which disease is this gene linked with?
3. How many exons does this gene consist of?
4. What is exon?
5. How many nucleotide bases are contained in the non-coding part of the first exon?
6. Name the first five nucleotides contained in the first exon?
7. Name the first three codons and the first three amino acids contained in the coding part of the first exon?
8. Which stop codon is used for termination?

PAH gene at UniProt

Visit PAH gene at UniProt.

9. How many amino acids does this protein consist of?
10. Name the first three amino acids. Compare this result with the result from question #7.
11. Find coordinates (position in the sequence) of the first two alfa-helixes in the secondary structure of this protein.

PAH gene at the Protein Data Bank

Look at the description of the PAH gene at the Protein Data Bank //Molecule of the Month//.

12. How many PAH molecules are required to form a functional complex?
13. Briefly describe the function of this protein and how it's mutated form causes disease.

Look at the tetrameric structure of the PAH gene at the Protein Data Bank.

14. What does tetrameric mean?

PAH gene homologs

Lastly, look at the NCBI Blast global alignment page. This page will allow you to compare protein sequences that can be found in the UniProt database.

15. What is the degree of similarity (given by the sequence alignment) of the sequence (amino acid sequence) of the human PAH gene protein sequence and the PAH gene protein sequence of a mouse (Mus musculus)? Compare human PAH protein sequences with the fruit fly's PAH gene (D. melanogaster).

courses/bin/assignments/hw1.txt · Last modified: 2024/02/21 16:55 by rysavpe1