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MEDED 534 , Autumn 2001
Biology for Informaticists

Exams & Tests

Exam 1 - Due before class Oct 31

Last year in this class the students performed an exercise to develop a Knowledge Organization Template (KOT) for the lung, which is an organ. Here is a slightly modified version of the partially filled out answer sheet for this assignment (Lung KOT). Drawing on the various resources that have been presented so far this quarter (or anything else for that matter), develop your own KOT for a structure that is part of the neuroaxis and that interests you. Since by the FM definition this structure would not itself be an organ, you will need to modify some of the questions to fit the structure (i.e. organ part, organ subdivision, etc.). Feel free to work together in groups and to discuss the exam with other students and faculty, but you must come up with your own answers on a unique structure. Please submit your exam electronically to bio4info@u.washington.edu. -Stu Yarfitz

Exam 2 - Cellular Anatomy & Physiology (Date Due Dec 12)

Choose a biological process that is of interest to you and discuss this process at the cellular level in a specific cell type in the human nervous system. The format is up to you, but include graphical images or links to images to illustrate the important points. Source materials can include textbooks, primary literature, reviews, Internet resources, etc., but you must provide references and credits. Feel free to work in groups, but each person must submit their own paper or project. Stu and Richard are available to discuss topics, resources, and ideas.

1) Discuss the process from the perspective of overall cellular physiology. What are the important changes in cellular activity ( i.e. metabolism, movement, gene expression, secretion) associated with this process? What are the time courses of these events? How are these changes measured and analyzed? Describe the process using the Gene Ontology.

2) What are the cellular structures, organelles, and other components involved in this process? How are changes in these elements measured and analyzed? Describe these structural elements using the Gene Ontology.

3) Discuss three of the important gene products that are involved in this process and their relevant molecular functions. What are the official gene names? Describe these molecular functions using the Gene Ontology. Include EC classifications for the enzymes.

4) Discuss the signaling and regulatory mechanisms associated with the process. How is the process initiated and controlled? What is the critical extracellular signal, how is it detected by the cell, and what are the components and steps of the intracellular signal transduction process ( i.e. receptors, binding proteins, enzymes, second messengers, ion channels, ion fluxes, etc). Include estimates of signal amplification, concentrations, and kinetics if available. Include the inactivation or sensitization steps in this pathway. How have the signaling mechanisms been studied? Describe these mechanisms using the Gene Ontology.

5) Significance of this process for human health and disease. What diseases or pathological conditions are associated with this process? What are the specific defects in the process associated with these pathologies? How are these conditions diagnosed?

Examples from last year's class:
Cliff
Olivia

Exam 3  Molecular Bioinformatics  (Date Due Dec 17)

Choose three human proteins that function in the biological processes that you discussed in Exam 2, and find additional information about these proteins and the genes that encode them.  For each of your proteins one entry (if available) per category is sufficient.  The format is up to you, and for most items you need only to list item names and database-specific accession numbers with live hyperlinks. Include graphical images for items marked with *.

You should be able to find  appropriate resources using the HealthLinks Molecular Biologist Toolkit (suggestions are in parenthesis). Feel free to work in groups, and Richard Phillips and I are available to provide assistance.

  • Protein sequence (SwissProt)

  • Protein structure * (PDB, Entrez, SWISS-3DIMAGE) (any likely ortholog, not necessarily human)

  • Protein structural classification (SCOP) 

  • Protein family (InterPro)

  • Protein functional motifs * (BLOCKS, Interpro, CDD, PFAM)

  • mRNA sequence (Entrez or RefSeq entry if available)

  • Chromosomal map position * (MapView)

  • Genetic disorders (OMIM)

  • Genomic DNA sequence (full length if available) (Entrez)

  • Genomic contig (Refseq)

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 Last Updated:
12/03/2001

Contact the instructor at: stuy@u.washington.edu