BB 650, 651, and 652

Prerequisite: BB 452/552 or 492/592 or equivalent.

Course content: These are non-sequence courses, taught at an advanced level, and designed to cover the current status of research in various areas of biochemistry. Since the courses are topical, course content varies from year to year. Consult the instructor for further information.

Fall 2007 Offerings:

• BB650-01: Cell Cycle and Cancer (Gary Merrill, 3 credits)
• BB650-02: Protein Evolution (P. Andrew Karplus, 3 credits)

Winter 2008 Offerings (see instructors for more information):

• BB651-01: Neurochemistry (Michael Schimerlik, 3 credits)
• BB651-02: Cell Adhesion & Motility (Jeff Greenwood, 3 credits)
• BB654: Proteins (Sonia Anderson, 3 credits)

Spring 2008 Offerings (3 credits each, see instructors for more information):

• BB656: DNA Repair & Mutagenesis (John Hays & Chris Mathews, 3 credits)

Course Descriptions of full repertoire of advanced selected topics BB courses:

BB 650-01 — Cell Cycle and Cancer

• BB650-01: 3 credits, Fall, Merrill (737-3119; merrillg@onid.orst.edu)
• Course description:The first seven weeks of lectures will be followed by three weeks of student presentations and panel meetings. In covering oncoproteins, tumor suppressor proteins, checkpoint systems, and apoptosis systems, the course will stress the importance of cell cycle control mechanisms in preserving genome stability. For each topic, I will summarize "What we know?" and then describe "How we know it?". The course objective is to identify significant contemporary questions concerning the molecular biology of cancer and to design rational approaches to study them.

BB 650-02 — Protein Evolution

• BB650-02: 3 credits, Fall, Karplus

BB 651-01 — Enzyme Kinetics

• BB650-01: 3 credits, Winter, Schimerlik

BB 651-02 — Single-Molecule Biochemistry

• BB651-02: 2 credits, Winter, Ho & van Holde, TThr 13:00-14:00 ALS 2018
• Prerequisite: BB 450/550, BB 490/590, or consent of instructor.
• Course content: Some of the most exciting recent technologies to emerge in biology are those that study the structure and function of single molecules. This course covers the principles of how single-molecule studies work, how they are designed, and how the results are interpreted, using recent publications that highlight the application of such methods in understanding fundamental biological processes.

BB 654 — PROTEINS

• BB654 3 credits CRN 13311 Fall Anderson MWF 900-950 ALS 2018
• Prerequisite: BB 452/552, BB 492/592, or consent of instructor.
• Course content: Levels of protein structure, amino acid sequence determination, protein isolation and purification, chemical modification of proteins, spectroscopic approaches to protein structure, post-translational protein modification. In order to accommodate shifting interests, the class is consulted in determination of the emphasis that is placed on the various topics.
• Text: Required: Creighton, Proteins
  Optional: Brandén & Tooze, Introduction to Protein Structure
• Curricular purpose of the course: Presentation of experimental methods and concepts in understanding relationships of protein structure to function.

BB 656 — DNA Repair and Mutagenesis

• BB656 3 credits Spring John Hays
• Instructors John Hays, Coordinator
  Andrew Buermeyer
  Christopher Mathews
• Prerequisites BB 551/BB 492, MCB 554, MCB555, or permission of instructor
• Course Description: This advanced topics course examines the biochemical and molecular mechanisms used by eukaryotic cells to maintain genetic stability and to avoid mutations. Special emphasis is directed toward various DNA repair pathways utilized by human cells to avoid genotoxicity, genetic diseases and susceptibility to cancer. Lecture topics will focus on biochemical aspects of DNA damage, DNA precursor balance, DNA replication fidelity, replication-error correction and bypass replication of damaged DNA. DNA damage correction mechanisms will be discussed in detail including mechanisms of base excision, nucleotide excision, transcription-coupled, and mismatch DNA repair. Additional subject matter will focus on human hereditary diseases with defective processing of DNA damage and the impact of mitochondrial mutations on human pathology. Assigned reading from recent scientific literature will form the basis for in-class discussions on current experimental approaches and models of DNA repair. Students will develop an original research proposal and prepare a written grant-like application on a topic related to the subjects presented in the course.
• Grading Based on a written exam, on student-initiated research proposal, and on participation in class discussions.
• Text DNA Repair and Mutagenesis, by E.C. Friedberg, G.C. Walker, and W. Siede, American Society for Microbiology, Washington DC (1995); plus readings from the research literature.

Other offerings (consult Schedule of Classes to determine when these are offered)

BB 653 – PHOTOSYNTHESIS AND PLANT BIOCHEMISTRY

• BB653 3 credits CRN 36095 Spring Arp MWF 1300-1350 ALS 2018
• Prerequisite BB 451/551, BB 492/592, or equivalent.
• Purpose: To examine biochemistry unique to plants, to provide a framework for understanding biochemistry as it relates to plants and to obtain some familiarity with the literature pertaining to plant biochemistry.
• Topics:
  1. Plants as autotrophs Carbon metabolism in plants
  2. Photosynthesis Organic acid metabolism
  3. Light reactions Glycolysis and sugar synthesis
  4. CO2 assimilation Lipid synthesis
  5. NO3- and NH4+ assimilation Secondary plant metabolites
  6. Plant biochemistry and biological N2 fixation Plant cell walls
  7. N2 fixation
  8. Nodule biochemistry Bioenergetics in plants
  9. Leghemoglobin Photophosphorylation
  10. Oxidative phosphorylation
• Text Biochemistry and Molecular Biology of Plants; Buchanan, Gruissen, Jones; American Society of Plant Physiologists, 2000.
• Grading Based on problem sets, critiques of manuscripts, and class participation.

BB 662 – HORMONE ACTION

• BB662 3 credits CRN 36097 Spring Stormshak MWF 900-950 ALS 2018
• Prerequisite: BB 452/552 or 492/592 or equivalent.
• Course content: Current information about the biochemical and molecular characteristics of the mechanism of action of various peptide and steroid hormones is presented. Special emphasis is given to receptor structure, second messengers and downstream signal transduction events that culminate in the characteristic response of the target cell to the hormone. Guest lecturers will introduce subjects of plant hormones and hormonal aspects of human diseases such as cancer.
• Text: None required. Selected reading from the current literature.
• Curricular purpose of the course: To provide current information about the biochemical and molecular aspects by which various types of hormones evoke target cell responses.

BB655 (3 credits) DNA-Protein Interactions

BB657 (3 credits) Nucleotides

BB659 (3 credits) Protein Synthesis

BB660 (3 credits) Eukaryotic Transcription

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