This assessment evaluates your understanding of the learning objectives and activities covered in Weeks 1 to 5 of the unit. It includes pre-tutorial materials such as weekly lecture notes, videos, and other relevant resources, as well as topics discussed during scheduled classes. The assessment comprises various question formats, including short-answer questions, extended-response questions, terminology-based questions, and process/arrangement questions.

The assessment will be conducted online and will have a total duration of 2 hours for writing, plus an additional 15 minutes allocated for reading, downloading, and uploading materials. It is worth 20% of your final grade and is designed to evaluate your progress at the mid-point of the term. This will help you identify strengths and areas for improvement and familiarize you with the structure and types of questions expected in the final exam.

Please note that this assessment will be open from Friday 18th April, at 2:00 PM until Monday 21st April 9:00 am. Once started, you will have 2 hours and 15 minutes to complete the assessment.

Mode: Online submission

Format: The assessment may include (but not be limited to) some short answer questions & some with a more extended type of response, terminology questions, process and arrangement questions & case study/ies. Marks will range from 1-2 marks for short answer questions and 4-5 marks where more detailed information will be required.

A detailed marking criteria and marks allocated for each question will be provided with this assessment. You will be provided with support and examples of the types of questions you are likely to encountered in this assessment during your scheduled classes; this will assist you in learning and understanding the expectations of this assessment. You are therefore strongly encouraged to regularly attend and actively participate in the weekly scheduled classes, engage and ask
questions where you are uncertain and make sure you come prepared for each class by having reviewed any pre-class learning material. If you still have questions or areas you do not understand following each weekly tutorial class you will be encouraged to address these promptly by posting your questions on the Discussion forum and engaging in discussion on this/these topics with fellow students and academics, and the Unit coordinators. Doing this will ensure you 'arrive' to this.

Task Overview

As a senior scientist in a pharmaceutical company, you have been assigned to a project involving the virtual mass production of a protein implicated in several diseases. You have been provided with the name and molecular weight of the protein (in kilodaltons, kDa). Your objective is to clone the gene encoding the protein of interest (using functional cloning approach) into an expression plasmid DNA vector and mass-produce it in a host system. You must utilize the protein and nucleotide sequences obtained from NCBI to complete this task. A detailed report outlining your recommended strategies and methodologies is required. Before proceeding, visit the subject Moodle site and watch the instructional video provided for Assessment 2. Additionally, an example report is available on the Moodle site to guide you in formatting your assignment.

Important: You should start this assessment early, as it requires approximately eight weeks of preparation and involves significant work. It is essential to attend the scheduled tutorial session, carefully review the provided guidelines, and watch the instructional recording(s). These resources will help clarify expectations, offer valuable insights, and effectively guide you through the process. Please post any questions in the subject forum. 

Project Overview and Guidelines

Topic Selection:

• Choose a protein from the list provided under Assessment 2 on Moodle. The list includes 17 topics, and each topic can accommodate up to two students. 
• Selection operates on a first-come, first-served basis.
• If a topic is already selected by two students, choose another from the remaining options.
• Deadline for topic selection: Monday, March 24th, 11:59 PM
• Assessment 2 is due on week 9 - Friday, May 16th, by 11:59 PM.

Report Format:
Prepare the report in PowerPoint format and record your presentation using Zoom. Please use the following guidelines:

• Maximum of 26 slides (including the cover page, references and the acknowledgement slides)
• Record your presentation using Zoom. Maximum recording time must not exceed 20 minutes +/- 2 minutes)!.
• Upload your recorded presentation to the Moodle site under Assessment 2 Submissions using Echo360. For detailed instructions, refer to the subject Moodle site under Assessment 2.
• Ensure your face is clearly visible while talking and recording the presentation. Your live video feed must appear in the top-right corner of the presentation. Failure to display your live image during the presentation will result in a failing grade for Assessment 2. 
• Assessment 2 is due on week 9 - Monday, May 12th, by 11:59 PM.

 
Presentation Content

Slide 1: Cover page: Include your full name and the name of the selected protein, University logo etc.
Slide 2-Task 1: Introduction (Literature Review): Conduct a short and concise literature review using PubMed and discuss the protein’s structure, molecular weight (kDa), function, and disease associations.
Slide 3-Task 2: Introduction (NCBI Overview): Conduct a brief literature survey via PubMed and provide additional details on the protein.
Slide 4-Task 2: Introduction Continued: Present a general overview of your protein.
Slide 5-Task 3: Gene Information: Retrieve the protein accession number, protein and nucleotide sequences, and basic gene information from NCBI.
Slide 6-Task 4: Post-Translational Modifications: Use the "Features" option in NCBI to determine post-translational modifications associated with your protein.
Slide 7-Task 5: Chromosomal Location: In NCBI, under Genomic Context, Identify the chromosome where the gene is located and the number of exons.
Slide 8-Task 5: Tissue Expression: In NCBI under Expression, determine the tissues where the protein is most highly expressed.
Slide 9: Task 6: Protein Interactions: in NCBI under Interactions, discover proteins interacting with your target gene to assess its function and drug effects.
Slide 10-Task 7: Gene Variants: Gene Variant Analysis: in NCBI under Variation Viewer, explore and highlight different versions of the gene resulting from mutations.
Slide 11-Task 7: Gene Variant Analysis: in NCBI under Variation Data, discover variation types, Perform SNP analysis and discuss relevant gene variants associated with diseases 
Slide 12-Task 8: Amino Acid Sequence: in NCBI under the Amino acid sequence of the protein copy the protein’s amino acid sequence in FASTA format.
Slide 13: Task 9: Nucleotide Sequence: IN NCBI find the nucleotide sequence of the gene encoding the protein in FASTA format.
Slide 14-Task 10: Open Reading Frame (ORF): using the nucleotide sequence of the gene coding for your protein highlight the ORF, start codon, and stop codon(s) within the gene sequence.
Slide 15-Task 11: BLAST Analysis: Use NCBI to run a BLAST analysis to align the sequence with others in the database.
Slide 16-Task 12: Restriction Enzyme Analysis: Use NEBcutter™ v3.0 to construct a restriction enzyme map for cloning.
Slide 17-Task 13: Primer Design (PCR): Use NCBI to design forward and reverse primers for PCR amplification.
Slide 18-Task 14: Primer Design (LAMP): use New England Biolab web site to design primers for Loop-Mediated Isothermal Amplification (LAMP).
Slide 19-Task 15: Expression System Selection: Choose an appropriate expression plasmid DNA vector for cloning.

Slide 20-Task 16: Cloning Strategy: Outline a detailed cloning strategy for inserting the gene into the vector. Optimize the vector for high-yield protein expression.

Slide 21-Task 17:  Select a suitable host for protein expression, either in bacteria or in mammalian cells.                                                                                                                                                               

Slide 22-Task 18:  Determine the purity of the expressed protein. What method(s) would you propose to assess the purity of the expressed protein?

Slide 23 Task 19: Describe the approach you have taken to confirm that the produced protein is biologically active.

Slide 24-TASK 20: Describe the approach you have taken to determine the protein's serum half-life and toxicity.                                 

Slide 25: Provide a list of references.

Slide 26: Acknowledgements- thank people who helped you with this project.

Please refer to assessment 2 'table of Rubics' in the subject Moodle site.