1. Mini course to understand the biological pathway Yong Jiang(Frank)

2. Purpose of the course  Provide basic knowledge of biological reaction path to student that may not have rich biological background.  Provide online database that students are able to extract valuable information of reaction path.  Help students to integrate they knowledge in the context of bioinformatics  Promote students ’ interests to use possible tools to explore unknown problems.

3. Students will learn …  How to use bio-pathway database (KEGG, Ecocyc) to search for a specific biological reaction or enzyme.  Observing the structure of enzyme in 3D software  Find similar enzyme in different species.  Do sequence and structure alignment and find phygenetic relationship between different species.  Modeling the kinetics of the reaction

4. Case study “ glucose-6-phosphate isomerase “ alpha-D-Glucose 6-phosphate glucose-6- phosphate isomerase beta-D-Fructose 6-phosphate

5. glucose-6- phosphate isomerase Observing 3D structure Sequence and structure alignment Find similar sequence in different species Find phylogenetic tree of different species Modeling kinetics

6. Before the class … Students are divided into groups. Discussion within group is encouraged. Students are divided into groups. Discussion within group is encouraged. Each group will find literatures that relates to the specific biological reaction they are interested in. Each group will find literatures that relates to the specific biological reaction they are interested in. Each group will prepare a proposal talk before class Each group will prepare a proposal talk before class

7. In the class … One student representing each group will give a proposal talk and answer questions from other groups. One student representing each group will give a proposal talk and answer questions from other groups. Find similar enzymes that exist in other species in bioquest workbench. Find similar enzymes that exist in other species in bioquest workbench. Download pdb files of these proteins from pdb databank. Download pdb files of these proteins from pdb databank. Do sequence and structure alignment and find phygenetic relationship between different species. Propose the candidate active site that is crucial for the enzyme function. Do sequence and structure alignment and find phygenetic relationship between different species. Propose the candidate active site that is crucial for the enzyme function. Modeling the process and find the reaction order. Modeling the process and find the reaction order.

8. After the class … Each group will prepare a poster session reporting their finding Each group will prepare a poster session reporting their finding Encourage inter-group discussion. Encourage inter-group discussion. Award will be given to top 3 posters. Award will be given to top 3 posters.