April Bednarski Lindenwood University

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Biochemistry:Metabolism at Lindenwood University

Course Overview

The title of the course is Biochemistry:Metabolism.  Students in this course have taken either Biochemistry I (Structure and Mechanism) or Cell Biology, and Organic Chemistry I and are juniors and seniors. The text for this course is Biochemistry: A Short Course by Tymoczko, Berg, and Stryer.  The lecture portion of the course covers metabolic pathways and regulation (Ch 15-31) and nucleic acid synthesis and eukaryotic gene regulation (Ch 33-38).  The lab for this course is taught in a computer lab and is split into two modules.  The first module includes use of bioinformatics tools to understand the genetic basis of disease with a focus on metabolic diseases.  The last module of the lab introduces students to eukaryotic gene structure with the GEP genome annotation project.  

Implementation

The course size is 12-15 students a semester and the lab has a TA that has gone through the GEP TA training.  The first lab module introduces students to the Gene and OMIM databases at NCBI and using NCBI Blast.  Other bioinformatics programs and databases used in that curriculum include UniProtKB, KEGG, ClustalW, and Firstglance in Jmol (for protein structure viewing).  Students work through an initial exploration of these websites (Day 1 Bioinformatics Exploration), then work through the KRas Tutorial together before being assigned a project from the Bio 3055 website to explore.  Finally students choose a genetic disease from the OMIM database that has a known associated amino acid change and use the bioinformatics tools to explore the molecular basis of the disease.  By the beginning of the annotation module, students should be familiar with working with gene and protein sequences in FASTA format and using NCBI Blast and a few Bioinformatics databases.  For our annotation module, we begin in lab with the Simple Annotation Problem during the first week.  In lecture that same day, I introduce the GEP and the GEP research project.  Next students are assigned a fosmid or contig in pairs to annotate.  The students have 5 weeks in lab to work on their annotation and are also encouraged to work on their own once they understand the annotation process and use lab time to get one-on-one help and help others.  They are required to turn in screenshots of a correctly annotated gene(s) by the end of the week 4.  If they determined no genes were present, they are required to present their evidence (as stated in the Gene Annotation Report).  In week 5, we work on assembling the files for the Gene Annotation Report.  In week 6, the students present their research in a short Powerpoint presentation.

Lessons Learned and Future Plans

I have taught this course with the GEP curriculum for two years now.  The first year was a more collaborative effort among the students than this year, but the computer lab in the 2011 lab was set up with students closer together then the computer lab for this year (2013).  The student TA this semester was excellent, so that helped make up for the lack of collaboration.  Both years, I assigned two students a fosmid, but had students to work on separate computers, side-by-side, and split the work instead of sharing one computer.  This year I had students send me a screen shot of an annotated gene after three weeks to show me their progress.  I found that the background work in BLAST, sequence alignments, and using databases helped them, but they still struggled to dive into their projects once we started the annotation.  Students worked through the Simple Annotation Project quickly and seemed to understand the basic process, but then spent two weeks being overwhelmed and not making much progress once they started in on their fosmids.  I presented a tutorial on UCSC Browser and Gene Record Finder, but didn't give the students a graded assignment using those tools.  Students gradually caught on and by the end most had taken ownership of the project and would have been willing to do more in depth analysis (including RNAseq data and synteny) if we had time.  As I plan for the next time teaching annotation, I will have students begin the annotation projects earlier in the semester and include graded assignments using just Gene Record Finder and UCSC Browser before they are given their fosmids.  

Syllabus

CHM 42200/BIO 42200 Biochemistry: Metabolism Spring 2013

Instructor:            April Bednarski

Requirements:

The prerequisites for this course

 Cell Biology or Biochemistry I and Organic Chemistry I

Required Textbook: 

Biochemistry: A Short Course Tymoczko, Berg, and Stryer

ISBN: 1-4292-8360-2

 Course Objectives

Biochemistry:Metabolism will focus on understanding pathways in metabolism.  The course will focus on understanding how pathways function and interact, and how pathways are regulated and studied.  The lecture part of the course will focus on understanding the details of some well-understood pathways, medical relevance of these pathways, and current research in metabolism.  The lab section of the course will focus on an introduction to bioinformatics tools, studying pathways and metabolic disease on the web, and an opportunity for students to complete their own research project in gene annotation as part of the Genomics Education Partnership (GEP) (www.wustl.edu/gep).

 Grading:

Lab Assignments and Reports: 400 points

Exams: 3 exams worth 100 points each

Homework: 100 points

Total:800 points

Lecture and Lab Schedule

Schedule.JPG

List of Documents