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BIOENG 304 Engineering Physiology

Herbert M Sauro

Course Schedule for BIOEN 304 (2010) - updated Sept. 10

This course is a mixture of basic physiology and engineering aspects related to physiology.

Schedule

Week

Date

Lecture

304 Lab

Book Chapters

1

Sept.30

Oct. 2

Fundamentals of Physiology

Page 2 to 41 of textbook

No lab this week

2

Oct. 5

Oct. 7

Oct. 9

Intro Biochem – All week

3

Oct. 12

Oct. 14

Oct. 16

Biochem Quiz

Fundamentals of Physiology

Fundamentals of Physiology

4

Oct. 19

Oct. 21

Oct. 23

Enzyme

Enzyme Kinetics

Basic Statistics

5

Oct. 26

Oct. 28

Oct. 30

Digestion and Nutrition

Digestion and Nutrition

Digestion and Nutrition

6

Nov. 2

Nov. 4

Nov. 6

Digestion and Nutrition

Digestion and Nutrition

Digestion and Nutrition

7

Nov. 8

Nov. 10

Nov. 12

MidTerm

Digestion and Nutrition
Wrap up

8

Nov. 15

Nov. 17

Nov. 19

Modeling

Compartmental Analysis

Model Discrimination, fitting

9

Nov. 22

Nov. 24

Nov. 26

Biological Control Systems

Quiz

Thanksgiving

10

Nov. 29

Dec. 1

Dec. 3

Biological Control Systems

Biological Control Systems

Biological Control Systems

11

Dec. 6

Dec. 8

Dec. 10

Eye and Ear

Smell, Taste, Heat, Pain and ESP

12

Dec. 16
(830-1020)

MEB 103

Final Exam in MEB 103

at 8.30 to 10.20

No Lab this week 

 

 

Topics

Topics for Bioeng 309: 2010

Three main areas:

1.       Non-quantitative Physiology

2.       Quantitative Multi-cellular Physiology

3.       Quantitative Cellular Physiology

1.  Non-quantitative Physiology

Topics

½ Food stuffs including Vitamins

1 Carbohydrate and Protein digestion

½ Homeostasis, Body Weight

½ Large Intestine , Vitamin Absorption, Water and Mineral Absorption

¼ Gastrointestinal (GI) Tract; Overview

¼ Basic Circulatory System

½ Neural and Hormonal Integration

1 Organ integration of Carbohydrate and Protein

¼ Teeth, Saliva and Swallowing

½ Starvation

1 Stomach Structure and Motility, Gastric Juice

½ Small Intestine Function, Pancreas

1 Structure and Function of Eye and Ear

½ Excretory Liver Function and Bile

1 Smell, Taste and other Sensors

1 Lipid Digestion, Distribution and Storage

 

Ten classes in total.


2.  Quantitative Cellular Physiology

1 Enzymes and Kinetics
2 Feedback Control in Cellular Systems

Roughly 4 classes

3. Quantitative Multi-Cellular Physiology

1 Negative Feedback Control
1 Hormonal Control: Insulin/Glucagon
2 Compartmental Analysis
2 Model Discrimination, Model Fitting
1 Pupil/Iris Control

Roughly 6 classes

Midterm Test Topics

Digestion:

Pages: 234-239; 242-247; 248-265; 266-267
  • Challenges faced by digestion
  • Function of digestion
  • Basic Anatomy of digestive system, blood flow and immune defense
  • Saliva, not fig B, C, D on page 239
  • Anatomy of stomach and intestinal wall (see handouts)
  • Overview of function of each part of the digestive system
  • Stomach motility
  • Gastric Juice
  • Small intestine function, not fig B,C,D on page 247
  • Pancreas, not fig A, B on page 249
  • Bile, not fig C, E on page 251
  • Liver Function, only fig B on page 254
  • Digestion of different food types
  • Lipid Digestion
  • Lipid distribution and storage
  • Digestion of Carbohydrates and Protein
  • Enzymes involved in digestion
  • Vitamin B12 absorption
  • Basic water and electrolyte absorption, not fig B, C, D on page 265
  • Large Intestine, not fig A, B on page 267
  • Basic knowledge of hormones, endocrine, paracrine etc
  • Basic Hormones involved in digestion
  • Neural and Hormonal control in the stomach and intestine

Miscellaneous

Circulatory system

Additional Material from Pages of the Text Book

  • 2-7
  • 16-19
  • 228-229

Topics for Final Exam in December

Biochemistry

Review the biochemistry notes given to you by Prof. Ratner

Transport:

Pages: 20-29; 30 (not including cell migration); 32 (Nernst Equ); 34-35
  • Diffusion, Fick's law, diffusion coefficients (units)
  • Stokes-Einstein Equation
  • Root mean square distance and time
  • Membrane bilipid layer
  • Diffusion through membranes
  • Transport by passive and facilitated diffusion, active transport
  • Channels (aquaporins etc)
  • Carriers - uniport, symport, antiport
  • Examples: Na/K ATPase etc.
  • Origin of resting potential
  • Nernst Equation
  • Osmosis - how to measure molecular weight using osmosis

Nutrition

  • Vitamins and Minerals, see class handouts
    1. Do NOT learn chemical structures of vitamins just what they are called and what they are responsible for.
  • Lipid Distribution and Storage (Pages 256-259)
  • Carbohydrate Metabolism (Pages 284-285)
  • Starvation (see these notes)
  • Organ Integration (see these notes)

Sensors:

  • Types of senses and their roles
  • Eye including effects on split brain personality
    1. Pages 350-351, Not Fig C
    2. Pages 352-353
    3. Pages 354-355
    4. Pages 358-359, Not Fig A and B
    5. Pages 360-361
    6. Pages 362-363
    7. Pages 364-364, Not Fig C
  • Taste (p344-345, Not Fig C)
  • Smell (p346-347, Not Fig B)

Prof Ratner

  • Refer to Prof Ratner for the nature of this questions.

Topics Not Included in the Exam

  • The Ear
  • Pain and Pain Killers
  • Hot and Cold Sensors
  • Not pages 356-357 (Biochemistry of Photoreception)
  • Error Propagation and Basic Statistics
  • Reaction Order
  • Equilibrium Constant
  • Irreversible Michaelis-Menten Kinetics
  • Linear plots for Estimating Kms and Vms

Assignments Schedule

Assignment Schedule

Week

Quiz

Assignments

Essays

Exams

0

 

A (due week 3) 

 

 

1

 

 

 

2

Biochemistry 

 

 

3

 A

 

 

4

 

 

Essay 1

 

5

 

 A

 

 

6

 

 

 

Mid Term 

7

 

 A

 

8

 

 A (Model)

Essay 2

 

9

Modeling

 

 

10

 

 

 

 

11

 

 

 

Final

 

Essay 1 (2000 to 2500 words): Three of the most important health related advances in the last 200 years include sanitation, vaccination and antibiotics. Discuss the development of each and their societal and economic impact.

**NO LONGER REQUIRED** Essay 2 (1000 to 1500 words): Write a popular technical article on what advances bioengineering might bring to health, environment and other areas in 40 years time (say 2050). Do no focus exclusively on health advances (points will be removed if you do). Write the essay as if it were to be published as an article for BusinessWeek or the Science and Technology section of the Economist

All assignments and essays must be made available in electronic form. Plagiarism will lead to loss of grades.

Assignments

Grading

Grading will be based on Mastery-Based Grading which is based solely on a students' master of the material. In terms for breakdown, the final grade is based on the following partitioning:

  • 20% Homework problems (almost weekly)
  • 35% Labs
  • 20% Midterm quizzes
  • 25% Final exam

Grades will be made available on the new Catalyst online grading system.

Late assignments:

A late assignment will loose 5% of the grade. After that every further 2 days will incur addition looses of 5%.

Eg is you are four days late, you loose 15% of the grade.

Text Book

This course will use the pocket sized text book:

Color Atlas of Physiology (Thieme Flexibook) (Paperback)

Agamemnon Despopoulos and Stefan Silbernagl

Amazon Link

41rgr4mx0bl._sl500_aa240_.jpg

You can also pick up inexpensive copies of Silverthorn, Human Physiology an Integrated Approach (3rd or 4th Edition or above) which can supplement the Color Atlas Text.

Notes

If you have problems reading the pdf files, use Internet Explorer to access the suite.

Origins of Physiology

Biochemistry Notes

Analysis Protocol for Lab

How to Plot Data

Statistics Notes on Error Propagation

Circulatory System

0: Lympth drainage into subclavian vein

Veins:

  • 1. Jugular
  • 2. Subclavian
  • 3. Vena cava
  • 3a Superior vena cava
  • 3b Inferior vena cava
  • 4 Pulmonary vein
  • 5. Hepatic Vein
  • 6. Hepatic portal vein
  • 7. Renal
  • 9. Illiac

Arteries:

  • 10. Carotid Artery
  • 11. Subclavian
  • 12. Aorta
  • 13. Pulmonary Artery
  • 14. Heptic Artery
  • 16. Mesenteric Artery
  • 18. Renal Artery
  • 20. Illiac Artery

Some numbers are missed out intentionally.

Diffusion Simulator, go to catalyst to download

 
sysbio/labmembers/304_engineering_physiology_2010.txt · Last modified: 2010/12/12 14:21 (external edit)
 

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