• All the quizzes will be scheduled during your lectures in week 2, 4, 7, 10 and 12 class and will include the lecture material covered. They may incorporate problem-solving exercises or short assays concerning pet protein.
• If you are not able to sit for a quiz, you may consider applying for Special Consideration.

• Although you worked in a team, each report should be written up individually.
• A full report must be made of your experimental data and discussion and analysis of your findings.
• Submit the report via the assignment box located in the FSE student centre (14 Sir Christopher Ondaatje Avenue, Ground, 14 SCOA, Ground Floor) including a completed and signed cover sheet stapled to the front cover.
• Electronic submission to the Turnitin program (see iLearn site) is also required for this task by the due date.
• Bibliography listings must conform to an acceptable style (for guidance, see http://libguides.mq.edu.au/Referencing
• Marking rubric can be found on ilearn. Expected sections are outlined below:

  Introduction (15%)

  • address the goals and aims of the segments of the practical.
  • overview the methods used

  Results        (40%)

  • summarize laboratory experience and data obtained. 
  • Do not reproduce details of the instructions given in the practical notes.

  Discussion   (40%)

  • this is the most detailed and important section
  • interpret data and relate laboratory observations concerning purity, mass measurements and melting temperature range. 
  • Conclude with a summary of properties of your protein sample.

  References    (5%)

  • correctly formatted (author list, full title, journal, page numbers). 
  • Web url addresses are to be avoided.

• Hand in the worksheet.
• In addition to filling in the worksheets issued on the day of the practical, a specific 3-D structure essay will be assigned. A reflective essay, 2000-3000 words (maximum) i.e. approximately 2-3 printed pages of 12 point font single line spaced.
• Work must be submitted via the assignment box located in the FSE student centre (14 Sir Christopher Ondaatje Avenue, Ground, 14 SCOA, Ground Floor) including a completed and signed cover sheet stapled to the front cover.
• Electronic submission of the essay on the Turnitin program (see iLearn site) is also required by the due date.
• The marking rubric will be available on ilearn. The report should be written up individually, and should contain the information as outlined below

  Reflective essay  (60%)

  • The essay should present a molecular description of the protein, its structure fold, and some relationship to its function as a GTPase (and maybe even oncogenicity). 
  • The data (xray coordinates) used should be described, including how the structure was determined and by whom?
  • Should also give a brief description about the structure solving mechanism.

  A good report will note binding characteristics of the protein and discuss conserved features of the sequences.

  Completed worksheet    (30%)                              

  • should present all lab records created and AS OBSERVED ON THE DAY. 

  Bibliography (10%)

  • appropriate bibliography style and use of references

• This is assessment of your research and analytical skills, and continues throughout the semester to enhance each topic area.

•  Your individual protein for your own “Pet Protein” project will be distributed during week1 of the tutorial. 

• There are two parts to this assessment task. Details are given below.

  As well as presenting analysis of your own case study in written form, you will transmit your understanding of the individual protein to fellow students via seminars and presentation of your own constructed three-dimensional protein model:
  • Pet Protein A: Purification, written report: due Mar 29 - 15%
  • Pet Protein B: Structure, Seminar and Model, due Jun 7-20%  ​

This assignment will require extensive literature searching to locate prime sources in books and journals.  You will be given the name of a protein of industrial/medical importance. In addition, each student will be given a journal/research paper related to your pet proteins to be used for writing the purification sections in the report as below. The given paper will describe the initial purification steps of your protein and may also include the description of a medical or industrial purification. The marking rubric will be made available online:

•  

  • 1. The primary structure (amino acid sequence).         

    20%

     

    • Prepare your own figure (not a journal extract) of the protein sequence, clearly showing the numbering relevant to the mature sequence.
    • Outline and label any sub-regions or domain units important in this protein. Indicate on this figure the disulfide connections (if any), as well as any amino acids known to be glycosylated.

     

    2. The physico-chemical properties of the protein such as the

    • pI,
    • MW,
    • GRAVY value of the protein

    that are important for determining a purification protocol.

     

    20%

     

    • Use the tools in ExPASy to analyse your sequence. Check you have the mature sequence of your protein (i.e. remove any signal peptide)
    • If a glycoprotein, detail the full chemical nature of the carbohydrate portion.
    • Present a hydropathy plot of the marure seqeunce of your protein (see ProtScale: web.expasy.org/protscale/).
    • Discuss (i) the features of this plot with relation to the specific amino acid sequence and (ii) how it can be used to determine the GRAVY (grand average hydropathy) value.
    • Comment on the link between the pI, GRAVY value and amino acid composition.

    3. How the protein was initially purified from its natural source when it was first discovered.

     

     

     

     

    50%

     

    • Present a summary for this first purification as a simplified flow chart. It must present a summary overview of the chemical partitioning events, not detailed methods & reagents. Clearly label discarded and retained fractions at each partition.
    • Within your report, give a detailed description of the molecular events and chemistry of each separation step in the specific procedure, at the same detailed level as theory from lectures.
    • Where possible, include and discuss column traces or stained gel images that indicate the purification achieved at specific steps.
    • consistent bibliography style and use of references

    Note:  your flowchart must include branch points to clearly show how the mixture is successively partitioned to remove unwanted components and achieve purification.

    4. References

    10%

    • consistent bibliography style and use of references

This is a continuation of the pet protein case study

Pet Protein B: Structure, model, seminar & questions: due June 7, model - 10% and presentation - 10%

• Overall, project work will be assessed according to:
  • the quality and extent of your research
  • the depth and molecular detail of your analysis
  • appropriate use of internet tools
  • the clarity of your communication (verbal and written) and molecular analysis
  • the extent to which your model successfully shows the shape and form of your protein in three-dimensions
  • correct bibliography layout (i.e. alphabetical or numbered listing), with reference to all primary source material (i.e. journal articles, not web-based information)

    Seminar

     

     

    Transmit understanding of the individual protein structure to your fellow students in a 10 minute powerpoint presentation.  You are required to:

    Research the literature concerning the three-dimensional structure and structure determination method relevant to your protein. The percentages given are for reference only and can be split around based on your presentation.

    • Locate the coordinate file in the Protein data Bank (www.rcsb.org/pdb/) and pertinent paper
    • Outline the method(s) used to derive its structure
    • Outline the fold features and spatial organization of the molecule
    • Describe the structural features that relate to the function of your protein
    • In addition to your presentation, addressing the questions asked by your reviewer will also count towards the total marks

    Model

    • Construct a model  (hint: wire, tape, kitchen utensils...) that shows the three-dimensional shape of this macromolecule.
    • If your protein is particularly large, with two or more distinct domains, only select one of these for your model.

    Advanced work for bonus mark:

    Use the BLAST tool available through ncbi (/blast.ncbi.nlm.nih.gov) to locate some interesting sequence homologues to your selected Pet Protein sequence.  Align these in CLUSTAL (/www.clustal.org/).

    • Present these aligned  sequences and indicate the location of secondary structure (helices, sheets) important in the 3D structure of your Pet Protein.
    • Note any relationship between sequence varation in this protein family and 2^o (and 3^o) structure.