BCH210H Biochemistry-Electronically on Quercus

As you are learning about the structure and function of proteins throughout the beginning of the course, complete the following assignment and submit your answers electronically on Quercus.

The goals of this assignment are to understand how a protein’s structure is related to its function and learn how to visualize and interpret images of a protein’s structure. The use of computational tools and technologies have enabled researchers to understand a protein at the molecular level. The most direct route to study a protein’s structure is the use of a combination of techniques including its initial purification, followed by X-ray crystallography, Nuclear Magnetic Resonance (NMR) and/or Electron Microscopy (EM), to determine the atomic coordinates within a protein. This assignment is designed to take you through some of the tools that can be used to analyze a protein’s structure, and potentially better understand its function based on the amino acids present.

Assignment Requirements:

Include the following information in your assignment using the following headings.

Consult the associated references or additional literature in order to provide clear and concise answers using full sentences. For each of the 5 sections, there is a maximum of 1 page of text + images. The complete assignment should be no more than 5 pages + references (unlimited), 12-point font, single spaced, submitted in pdf format.

1.Describe the role (structure/catalysis, etc.) of any other molecules that can be seen in the structure. Explain if they are physiologically relevant or simply included for purification or structural purposes. This section is just a general introduction, if they are needed for purification or maintaining the structure, you will elaborate on this in later sections.

2. Purification of ‘PDB#’ (replace ‘PDB#’ with the name of your protein) Explain how the protein was purified in order to obtain the structure. Provide details on which cells were used and why (ie. are they different from where it is found  physiologically?), and discuss the various purification techniques used, based on what you have learned in week 2 of the course. Provide a summary of the experimental conditions (types of chromatography columns, purification tags and buffers used) and explain the role of each, as well as the chosen pH for the  urification procedure. Notea ‘summary’ does not mean re-writing the experimental procedure stated in the article(s), it means stating what was done and why, rationalizing why the various techniques were used and in what particular order, drawing on what you have learned from the BCH210H lectures. Discuss how the identity and purity of the protein was confirmed and what experimental technique was used to determine the structure. If multiple techniques were used to determine the structure, provide the rationale on why each one was used

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