BME 510: Biology for Biomedical Engineers
Fall 2008


Class schedule: Mondays, Wednesdays, and Fridays, 9:00-9:50am, AHSC 8403.
Two groups will meet at other times on Mon. Sep. 28, Wed. Nov. 4, and Wed. Dec. 9.
There is no final exam.

Course Director:   Marty Pagel, Ph.D.
Associate Professor of Biomendical Engineering and Chemistry
Email: mpagel@u.arizona.edu
Cell Phone: (520)-404-7049
Office: Room 4949B, Arizona Cancer Center
Office Hours: by appointment only
   
Participating instuctors:    Ron Lynch, rlynch@email.arizona.edu
Rick Levine, rbl@neurobio.arizona.edu


Course Description and Overview: The goal of this course is to introduce students to fundamental concepts in molecular biology and cell biology in a Lecture/Discussion format. The course will cover basic biological principles overning biomolecular and cellular processes and link these to applications in medicine, engineering, and applied sciences. The course will emphasize technical approaches, experimental design, and data interpretation.

Course Material: The text for the course is Molecular Cell Biology, 6th edition, editors Lodish, Berk, Krieger, Scott, Bretscher, Ploegh, and Matsudaira (W.H. Freeman and Co, publishers). The Medical Bookstore has copies for purchase. Marty’s lecture slides and optional course materials (journal articles, parts of book chapters) will be available on his web site, at http://www.u.arizona.edu/~mpagel/courses/bme510. Lecture slides will be available in color PDF format, usually one week before the lecture is presented.

See the Publisher's web site for this textbook. Create your login and password for a student account. You do not have to enter the email address of a course instructor, because your quiz, tutorial, and interactive exercise results do not need to be reported to your instructors.
•  View animations for each chapter.
•  View videos for each chapter.
•  Listen to the Podcasts.
•  View the Errata.
•  Review classic experiments.
•  Take the on-line quizzes. You do not have to enter the email address of an instructor, because your quiz, tutorial, and interactive exercise results do not need to be reported to your instructors. Just click "continue" to take the quiz.

Grading policies: Grades for the course will be determined based on three exams and three critiques of journal articles. One critique will be presented orally and the other two critiques are written assignments. Each exam is worth 25% of the course grade. The sum of the three critiques is worth 25%, so that each critique is worth 8.33%.

COURSE SYLLABUS
LectureDateInstructorTitleBook ChaptersDocuments
1Mon Aug 24 Pagel introduction to the course, cell anatomy, atoms & molecules 9.1, 2.1, 2.2 ARCHIVED
2Wed Aug 26 Pagel chemical equilibrium, bioenergetics 2.3, 2.4 ARCHIVED
3Fri Aug 28 Pagel protein structure and folding, enzyme kinetics 3.1 - 3.3 ARCHIVED
4Mon Aug 31 Pagel protein regulation 3.4, 3.5 ARCHIVED
5Wed Sep 2 Pagel Biotechnology: characterizing proteins 3.6 ARCHIVED
6Fri Sep 4 Pagel gene structure, transcription 4.1, 4.2 ARCHIVED
 Mon Sep 7   Holiday    
6Wed Sep 9 Pagel transcription continued 4.1, 4.2 See Above
7Fri Sep 11 Pagel translation 4.3, 4.4 ARCHIVED
8Mon Sep 14 Pagel DNA replication and repair, viruses 4.5 - 4.7 ARCHIVED
9Wed Sep 16 Pagel biotechnology: PCR, DNA microarrays 5.2, 5.3 ARCHIVED
10Fri Sep 18 Pagel DNA cloning, transfection, reporter genes 5.2 ARCHIVED
11Mon Sep 21 Pagel biomembranes 10.1 - 10.2 ARCHIVED
12Wed Sep 23 Pagel No Class: Prepare for Exam 1 and presentations   ARCHIVED
13Fri Sep 25 Pagel Exam 1 2-5 and 10, except 3.7, 5.1, 5.4, and 10.3 Exam 1 Answer Key
14Mon Sep 28 Pagel Presentations   BME510 Presentation Schedule
15Wed Sep 30 Pagel cytoskeleton: actin and myosin 17.1, 17.2, 17.5, 17.6 PowerPoint file for Lecture 15
Slides for Lecture 15 (1 per page)
Slides for Lecture 15 (2 per page)
Slides for Lecture 15 (4 per page)
Actin-Myosin Movie
Troponin-Tropomyosin Movie
16Fri Oct 2 Pagel cytoskeleton: microtubules 18.1 - 18.4, 18.7 PowerPoint file for Lecture 16
Slides for Lecture 16 (1 per page)
Slides for Lecture 16 (2 per page)
Slides for Lecture 16 (4 per page)
Dynamic Instability of Microtubules Movie
Kinesin Movie
The Inner Life of the Cell
The Coolest Chameleon Ever!
17Mon Oct 5 Kuo Guest Lecture   PET-CT for Radiation Therapy Planning
18Wed Oct 7 Pagel mitosis and meiosis 18.6, 20.8 PowerPoint file for Lecture 18
Slides for Lecture 18 (1 per page)
Slides for Lecture 18 (2 per page)
Slides for Lecture 18 (4 per page)
Mitosis Movie (single cell)
Mitosis Movie (multiple cells)
Meiosis Movie
19Fri Oct 9 Pagel stem cells, programmed cell death 21.1, 21.5 PowerPoint file for Lecture 19
Slides for Lecture 19 (1 per page)
Slides for Lecture 19 (2 per page)
Slides for Lecture 19 (4 per page)
Apoptosis Movie
Embryo Movie
First Cell Divisions Movie
20Mon Oct 12 Pagel cell energetics I 12.1 - 12.2 PowerPoint file for Lecture 20
Slides for Lecture 20 (1 per page)
Slides for Lecture 20 (2 per page)
Slides for Lecture 20 (4 per page)
Glycolysis Movie
Electron Transport Chain Movie
ATP Synthase Movie
21Wed Oct 14 Pagel cell energetics II 12.1 - 12.2 PowerPoint file for Lecture 21
Slides for Lecture 21 (1 per page)
Slides for Lecture 21 (2 per page)
Slides for Lecture 21 (4 per page)
PowerPoint file about WRITING for Lecture 21
Slides about WRITING for Lecture 21 (1 per page)
Slides about WRITING for Lecture 21 (2 per page)
Slides about WRITING for Lecture 21 (4 per page)
22Fri Oct 16 Pagel Cell Technologies and Tissue Engineering 9.4 - 9.5 PowerPoint file for Lecture 22
Slides for Lecture 22 (1 per page)
Slides for Lecture 22 (2 per page)
Slides for Lecture 22 (4 per page)
23Mon Oct 19 Pagel membrane transport 11.1, 11.2, 11.5, 11.6 PowerPoint file for Lecture 23
Slides for Lecture 23 (1 per page)
Slides for Lecture 23 (2 per page)
Slides for Lecture 23 (4 per page)
Osmosis Movie
Passive Transport Movie
24Wed Oct 21 Lynch Biotechnology: fluorescence microscopy 9.2 PowerPoint file for Lecture 24
NOTES for Lecture 24
25Fri Oct 23 Lynch Protein sorting and Secretion 14.2-14.4 PowerPoint file for Lecture 25
NOTES for Lecture 25
26Mon Oct 26 Lynch Endocytosis and Calcium I 11.3 PowerPoint file for Lecture 26
NOTES for Lecture 26
27Wed Oct 28 Lynch Calcium II and Vascular Smooth Muscle 14.5 PowerPoint file for Lecture 27
NOTES for Lecture 27
28Fri Oct 30 Pagel Biomedical Ethics   PowerPoint file for Lecture 28
Slides for Lecture 28 (1 per page)
Slides for Lecture 28 (2 per page)
Slides for Lecture 28 (4 per page)
29Mon Nov 2 Pagel Exam 2 parts of chapters 9, 11, 12, 14, 17, 18, 20, 21 Fall 2008 Exam #2 (no answers)
Fall 2008 Exam #2 answer key
Fall 2009 Practice Exam #2
Fall 2009 Exam #2 Answer Key
30Wed Nov 4 Pagel Presentations   BME510 Presentation Schedule
BME510 Presentation Instructions
BME510 Presentation Rubric

Example journal articles:
3D Cell Cultures
Adult Stem Cells and Muscular Dystrophy
Calcium in Muscular Dystrophy
Coworkers of actin filaments
creating endothelial stem cells
ECM in neovascularization
LDL and metabolic syndrome
Movement of ligand-receptors in cells
Neurodegenerative diseases and the cytoskeleton
PepCK and the supermouse
Regulation of pH in insulin secreting cells
SNAREs
Tissue Engineering
ubiquitin and Parkinson's Disease
vSNAREs in epithelial cells
Wiskott-Aldrich syndrome protein
31Fri Nov 6 Pagel cell-cell interactions, extracellular matrix 19.1 - 19.4 PowerPoint file for Lecture 31
Slides for Lecture 31 (1 per page)
Slides for Lecture 31 (2 per page)
Slides for Lecture 31 (4 per page)
32Mon Nov 9 Pagel Signalling Systems Part I PowerPoint file for Lecture 32 and 33
Slides for Lecture 32 and 33 (1 per page)
Slides for Lecture 32 and 33 (2 per page)
Slides for Lecture 32 and 33 (4 per page)
 Wed Nov 11   Veterans Day Holiday    
33Fri Nov 13 Pagel Signalling Systems Part II 15, 16 PowerPoint file for Lecture 32 and 33
Slides for Lecture 32 and 33 (1 per page)
Slides for Lecture 32 and 33 (2 per page)
Slides for Lecture 32 and 33 (4 per page)
34Mon Nov 16 Pagel signalling systems workshop 15, 16  
35Wed Nov 18 Pagel Cancer 25.1, 25.2 PowerPoint file for Lecture 35
Slides for Lecture 35 (1 per page)
Slides for Lecture 35 (2 per page)
Slides for Lecture 35 (4 per page)
36Fri Nov 20 Levine structure of the nervous system 23.1  
37Mon Nov 23 Levine resting membrane potential 11.4  
 Fri Nov 27   Thanksgiving Day Holiday    
38Mon Nov 30 Levine synaptic transmission 23.3  
39Wed Dec 2 Levine synaptic plasticity    
40Fri Dec 4 Levine muscle contraction and excitation    
41Mon Dec 7 Pagel Exam 3 parts of 11 15, 16, 19, 23, and 25  
42Wed Dec 9 Pagel Presentations   BME510 Presentation Schedule
BME510 Presentation Instructions
BME510 Presentation Grading Rubric

Example Journal Articles:
Some review articles are general and long. You may want to focus on only a subset of a review article, and/or investigate a research article with real data that is listed in the reference section of the review article.
Cancer and Jak-STAT signalling
Cell Cycle and Apoptosis in Cancer
Cell Cycle Arrest and Cancer
Cell Cycle Checkpoints and Cancer
Cell Cycle of Stem Cells
Chemokines and T-cell differentiation
DNA Methylation
EGFR and GCPRs
End Plate Potential
Giant Axon of a Squid
hepatitis C and Jak-STAT signalling
patch clamping
the RAS oncogene protein
Sodium Channel Inacivation
Structure and Function of Voltage-gated Ion Channels
Synaptic Transmission without Nerve Impulses
T-cell Differentiation
Tyrosine Kinase Signalling