How to use specific bioinformatics tools to research and understand the properties of proteins

Written Assessment

Length: 500 words

Submission Details:

  • Word document

 

Rationale

This assessment provides you with the opportunity to learn how to use specific bioinformatics tools to research and understand the properties of proteins. You will be assigned a protein code from the Protein Data Bank (PDB) called a PDB ID. All proteins deposited in the PDB have had their three dimensional (3D) crystal structure solved. You will answer 5 questions about your protein that will describe what this protein is, how it functions, features of its three-dimensional structure and how it compares to a common protein, adult haemoglobin, that we have covered in lectures.

 

Task

Each student will be assigned a 4 digit/letter PDB ID by Prac 1. Your assigned PDB ID will be the 3D structure of an enzyme that is part of a metabolic pathway that you will study in this course or will represent other abundant protein families such as DNA binding proteins (e.g., transcription factors).

You will be required to research your protein and then synthesize a very concise answer to 5 questions that will show your understanding of protein structure and function.

Your ability to answer the questions with sufficient detail will reflect whether you actually consulted the original research paper that the PDB structure was published in.

These 5 questions are graded from “easy to hard”.

Remember you must stay within the 500 total word limit.

 

5 Questions to answer:

(Q1) What is the name of the protein? (1 mark)

(Q2) What does the protein do? E.g., if it an enzyme of the Citric Acid Cycle – you must state which metabolic process it is involved in and the reaction step it catalyses. (2 marks)

(Q3) What are the structural features of the protein? (4 marks total)

In answering this question you must address the following:

  • You MUST show a 3-dimensional structure of your protein (1 mark)
  • You must describe the structural features of your protein – primary & secondary structure features, the three-dimensional fold. (2 marks)
  • Does your protein have quaternary structure? (1 mark)

(Q4) What are 2 features of your protein’s structure that makes it different or similar to adult haemoglobin? (2 marks)

(Q5) Based on the structural properties of your protein, how  resistant (or sensitive) would your protein be to heat denaturation and why? (1 mark)

 

 

 

 

 

 

Criteria

The breakdown of marks for the 5 questions has been allocated as shown in “Task” section. Overall, you will be assessed on the following:

  • Your ability to research your protein using the PDB, PubMed and other resources. To gain a full understanding of your protein, you will be expected to download and read research papers.
  • Your skill to interpret, analyse and apply what you have researched about your protein to succinctly answer the 5 questions posed.

 

Resources

  • Protein data bank website        http://www.rcsb.org/pdb
  • Literature search database       http://www.ncbi.nlm.nih.gov/pubmed/
  • You can download many research papers for free through the UWS library e-journal portal ExPASy – Bioinformatics Resources Portal       http://expasy.org/protparam

 

These resources provide access to scientific databases & software tools in different areas of life sciences including: Proteomics; Genomics; Phylogeny; Systems Biology; Population Genetics; and Transcriptomics etc. One software tool, ProtParam, allows you to input the amino acid sequence of your protein and retrieve information such as amino acid number, composition, pI of your protein etc.

 

 

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