Exam Format and Questions on Proteomics and Molecular Biology

Exam Format

What is the exam format? The exam consists of three questions of equal weighting. You must answer all questions. 
Section A is a question on the bioinformatics exercise and will require you to have access to the data you produced during the bioinformatics session. Alternatively, you can obtain the information, once you have seen the exam paper. 
Section B consists of two, essay type, questions, one on the molecular biology content and the other on the proteomics content of the module. You must answer both questions. The word limit for each question is 1000 words. 
 

Exam questions
Write two, 1000-word essays on the following two topics. Word count must be stated at the end of each essay. You are encouraged to include figures and diagrams BUT they must either be original and your own, or the source cited, and the figure fully described in the text. You must refer to and cite appropriate literature used to inform your answer. 

Word count: 1000 words. Content 10% over will not contribute to the determination of the awarded mark 
1. The field of proteomics is evolving from cataloguing proteins under static conditions to making detailed comparative analyses. Defining proteins that change in abundance, form, location, or activity may indicate which proteins are involved in developmental changes or responses to alterations in environmental conditions. Such studies are facilitated by an increasing number of complementary technical options for performing quantitative proteomic comparisons. As with any developing field, however, rapid expansion in new techniques introduces concerns about choosing the appropriate approach. 

As a research scientist you wish to understand plant responses to pathogen invasion. You have obtained an ancestral line of wheat with powdery mildew resistance. 

Design a set of proteomics experiments to define pathogen responsive changes in the wheat leaf proteome. State your experimental aim clearly at the start of your essay. Your answer should consider the following points: 
    a. You should consider number of replicates  
    b. Experimental controls 
    c. Time points 
    d. Protein extraction method 
    e. You should decide upon a comparative analysis methodology and explain how the analysis is conducted including benefits of the approach and any technical limitations 
    f. Finally, in what format is the generated data and how would you interpret it? 

    a. Given the structure of protein coding genes in mammalian cells, describe the process you would undertake to obtain the DNA coding sequence of the target protein.  
    b. Give an overview of the process of molecular cloning and the steps required to obtain a recombinant expression vector for the target protein. 
    c. Explain the different ways the pET vectors are optimised for inducible expression of recombinant proteins in E. coli. 
    d. Suggest one way of purifying the recombinant protein from the E. coli cell proteins. 
    

2. You work in a cancer research laboratory and have discovered a protein that is expressed only in cancer cells and thus may be a good target for novel drug design. As a first step towards this goal, you need to express and purify substantial amounts of the protein in Escherichia coli in order to undertake further studies to design a specific small molecule inhibitor. 
Your answer should consider the following points: 

    a. Given the structure of protein coding genes in mammalian cells, describe the process you would undertake to obtain the DNA coding sequence of the target protein. 
    b. Give an overview of the process of molecular cloning and the steps required to obtain a recombinant expression vector for the target protein. 
    c. Explain the different ways the pET vectors are optimised for inducible expression of recombinant proteins in E. coli.  
    d. Suggest one way of purifying the recombinant protein from the E. coli cell proteins.