Structure & Function of Bimolecular – Project Work Along the Structure & Function of Bimolecular course, you will get the opportunity to study a specific topic related to the course more in-depth in the form of a project work. The work will be conducted in groups of four students, and include the search for related information in scientific Journals, books and on the internet, summarize your most important findings in a written report and finally present your work orally to the other students and teachers.
Once you have formed a group, you select a topic based on the list below. Since several groups may select the same topic, please also select two backup choices. Two groups will be allowed to have the same topic. Once the topics have been divided between the groups, you will be informed of your topic and each group will be given a mentor to assist them throughout the project work. Below you can find a table describing the different checkpoints in the project work and the dates for when each part of the work should be finished.
Further down you can also find a description of what is expected from you when carrying out the different tasks. First you need to form groups and select your projects. Please send an e-mail to Anna Janssen at the latest Tuesday November 9, 17:00, containing the following information: ; Complete names of all members in your group ; e-mail address that you check frequently to each group member ; Three project topics in the order that you prefer them If you have not found a group by this time, send an e-mail and tell us, so that we can arrange a group for you.
The topics will then be distributed between the groups, and before 10:00 on Wednesday November 10, you will receive an e-mail informing you on which topic oh have received, which group you will be collaborating with in exchanging feedback as well as which mentor you have been appointed. 2 Task what should be done? By when? Project plan Write project plan, version one. Friday 12/11 17:00 Feedback from mentor on project plan. Monday 15/11 17:00 Final project plan should be approved.
Thursday 9/12 18:00 Second round of feedback from your mentor. Monday 13/12 17:00 Hand in final version of report to your mentor. Your mentor will make sure that the opposing group receives a copy of the final report. 15/12 lo:o Presentation Go though oral presentation with your mentor. Wednesday 1 5/12 16:00 Send final version of your presentation to your mentor. Wednesday 1 5/12 17:00 Present your work to your fellow students, the mentors and teachers.
Give oral feedback on the written report and the oral presentation of your opposing group. 16/12 Project plan The project plan should about one AY-page (absolute maximum two pages) and must include: Title of the project Names of group members Aim of the project or question(s) it tries to answer (1 or 2 sentences) Brief background of the subject of your project Plan of attack (how are you going to achieve the aim? ) 3 Report The written report should be 4-5 AY-pages, but not longer than 5 pages.
It should contain similar information as the project plan, but also more in-depth information and an overview of the results obtained, a discussion of these results and their interpretation, a set of conclusions or recommendations, and a list of literature references. A few key figures or tables can be included. The report should be written in Times New Roman apt, single line space. Presentation The presentation on the final day should preferably be done Powering saved in PPTP-format. Make sure you captivate your audience (with blinding science, that is – tot with special effects)!
The presentation should not be longer than 15 minutes (to leave 5 minutes for discussion and feedback from opponents). This means that your The seminar day with the presentations is mandatory! Yes, the whole day! You are not allowed to bring personal laptops to the seminar day. You are expected to give your full attention to the presenting group at all times during the day, be active in discussions and ask questions to the group presenting. Feedback on other group’s work You are expected to give constructive feedback on the written report and oral presentation of another group.
When you evaluate the work, try to answer the following questions. ; Is the works clearly described? ; Are the aim, results and conclusions presented in a clear and convincing way? ; Is the language correct grammatically? ; What could be done different to improve the work? During the project you will get a chance to give written feedback to another group. You will get a second chance to read the same report Just before the oral presentations. On the day of the presentations you will be expected to give short but well thought through feedback on both the written report and the oral presentation f your opponent group.
Assessment of you work The quality of the written report and your oral presentation are very important, but you will also be assessed on other things. These are: How well you perform as a group, your ability to give feedback on another group’s work, and how well you incorporated feedback that you received both from your mentor and from the other group into your report, and how well you kept all your deadlines, and how you planed the work. Grading and bonus points You must obtain a pass on the project work to be able to complete the course. You have passed when your mentor tells you so.
You might need to do additional work on your report that is not included in the time plan. However, there is also a possibility for you to earn two bonus points for the exam if you complete the project with distinction. The focus for earning the bonus points will be the oral presentation, but all parts of the project will be considered. 4 Important! You are most welcome to use any material to find information for your project. However, two things are crucial 1 . You must reference any source you have used for your report. 2. The written text should be your own words.
To copy text or use identical wording is plagiarism, which s strictly forbidden, and will lead to that you fail this part of the course. Suggested project – Case studies Objective: to study a subject in detail, with special emphasis on its structural biology aspects. Description: There are many topics in the area of structural biology that are fascinating in themselves but for which there is no time in the course to study them in great detail. In addition, there are many issues in science, medicine and biotechnology where structural studies of boundlessness’s play or have played an important role.
In these case studies, you select a topic from the list below and study hat in more detail. Find out: what the medical or scientific or technological what role they play for which of them structures are known (or could be predicted) how the molecules of known structure work at the atomic level what studies have been done to alter their behavior (mutations, inhibitors, … ) etc. The precise scope of your project and the questions you would like to answer depend strongly on the topic that you choose to study, of course.
In some cases, it may be opportune to do some homology modeling to get a structural hypothesis for a protein whose structure is not yet known. In others, you may need to do sequence analysis (database searches or multiple alignments). In all cases, you will need to look at structures you get from the PDP, determine their fold, active site residues, interaction surfaces, etc. Snake toxins. Snake venom’s are complicated mixtures of toxins. What do they contain? How do they work (physiologically and at the molecular level)? What structures are known and what can they tell you?
Which molecules do they interact with? Are any toxin-target complex structures known? App and cancer. What is the normal role of this protein and how is it connected with the development f cancer? What have all the structural studies of this protein taught us about its properties and the possibilities for a cure? Antibiotics What bimolecular are targeted by antibiotics? Which structures are known? How do antibiotics work at the molecular level? Increasing resistance to current antibiotics is a major health threat. Why is this? Are new antibiotics being developed? How do they differ from the current ones? Evolution of tarn syntheses The two classes of tarn syntheses are specific for amino acids in a way that appears symmetric. A hypothesis for their evolution has been presented in TIPS 26 2001) 591-596. Use available structures to present and discuss this hypothesis! Ion and lagans channels There are many different types of channel and structures are known for quite a few of these. Select 2-4 different types of channel (e. G. , sodium, potassium, neoconservative, … ) and study their architecture and how the structure explains how the appropriate ion or lagans can be transported.
Compare the structures as well. Explain why some channels are highly specific (e. G. , potassium channel) while others are promiscuous (e. G. , neoconservative channel). Claritin This is a prime example of form following function. What does Claritin do? What is known about its structure, symmetry and assembly? What role do the various adaptor proteins play? What is known about their structures? Allergies The PDP contains many structures with different allergens but very few with leg intolerableness complex. What is known about the cause of allergies and what information is lacking?
There was also one structure published in November 2007 structure? Influenza One of the first applications of structure-based drug design involved influenza. Which proteins are involved? What drugs are on the market? How were they developed? How do they work? Could they play a role in the control of flu pandemics? AIDS How does the disease work at the molecular level? Which proteins are involved? What do they look like? What is their mechanism? Which drugs have been developed? How do they work? Why is resistance a problem?
Cellulose degradation Which industrial applications do cellulose degradation have? Which enzymes are involved? How are they classified? How do they work? How can they be improved? Seascapes – the executioners of apotheosis Study the phenomenon of programmed cell death (apotheosis). What role do seascapes play? How are they regulated? Each student selects a different seascapes structure and studies the architecture, mechanism, specificity, role in apotheosis, etc. Chemical warfare Which agents have been developed? Which molecules do they interact with?
How do they work (physiologically and at the molecular level)? Are any relevant structures known? What do they tell us? 6 Stockroom IPPP enzymes – detoxification and synthesis How do these enzymes help us stay healthy? How do they affect the effect of medication we take? Can they harm us? What chemical reaction do they carry out? What useful compounds do they help synthesize? Pick a few important members of this family (such as COPLAY and PCMCIA; not necessarily human enzymes). What does the structure look like? What does the active site look like?
What do the structures teach us about the mechanism? Rican and the umbrella murder “On 7 September 1978 the Bulgarian dissident George Markova was stabbed in the leg in public on Waterloo Bridge in the middle of London by a man using a weapon built into an umbrella. The weapon embedded a small pellet in Marko’s leg that contained Rican. Markova died four days later. ” (Source: Wisped) Study the structure, function and toxicology of Rican. How does it work? Find similarities and differences with various bacterial toxins (cholera toxin, diphtheria toxin, intervention, … . Could Rican have medicinal applications? Telemetries The Nobel Prize in Physiology and Medicine in 2009 was awarded three scientists for their studies of telemeters. What is the role of telemetries in the cell, and what is known about the structure and function of the enzyme? Studies the architecture, mechanism, specificity, role in apotheosis, etc. Project Green Light Green Fluorescent Protein (GAP) is in the news due to the 2008 Nobel Prize in chemistry. Describe the use of this protein in genetic engineering and in obsessing.
Gestates in translation Elongation factor G is a Stage that catalysts two steps in the translation cycle: translation and ribosome disassembly (good translation review is Scheming & Rumanians (2009) Nature 461 :1234-42). In human mitochondria, it has recently been found that these two tasks are catcalled by two different proteins (Tissue et al. (2009), Molecular cell How are these two proteins different? Compare the sequences of human mitochondrial elongation factor G and ribosome-releasing factor 2 and analyze the preferences based on the available structures of bacterial FEE-G and the complex of FEE- G with the bacterial ribosome.
Can the differences suggest why these two proteins perform different tasks? CRISPS – a bacterial immune system It has recently been discovered that some bacteria and all archer have an inheritable Armbands immune system that can protect them against phage infection (reviewed by van deer Cost et al (2009), Trends in Biochemical Sciences 34( 8):401-407). How does this work? What is structurally known about this system, and what do the available structures explain?