HKUST

CENG 364

Biomolecular Engineering

Spring Semester, 2010

Course Instructor : Professor John BARFORD
Room 4552
Tel: ext 7237
email: barford@ust.hk

Teaching Assistant: WU Jinje
Laboratory: 6116
Tel: ext 8445
email : kexjj@ust.hk

Computing: Mr Kelvin WONG
Laboratory: 6114
Tel : 8823
email: kelvwong@ust.hk

Announcement

Mar 8 - Lecture Note: Introduction; Project : Project 1 Instruction
Apr 16 - Homework: #2 - #6

Files marked with * are non-examinable. They are included on the webpage for completeness and to allow students to further explore the subject in more detail than covered in the lectures.

Lecture Note

Introduction to Biomolecular Engineering
Quantitative Metabolism
- Quantitative metabolism 1 (PDF file) (Revised)
- Quantitative metabolism 2
- Quantitative metabolism 3 (PDF file)
- Miscellaneous Pathways
- Other ATP Forming and Utilising Mechanisms (PDF file)
- Delineation Between Catabolic and Anabolic (PDF file)
- Redox Neutral Reaction Rearrangements (PDF file)
- Quantitative Metabolism Calculation (PDF File)
- Worked Examples for Quantitative Metabolism (PDF file)
- Heat Evolution
- Worked Examples for Heat Evolution (PDF file)
- Y_ATP
  - Notes Written on Class Board CENG364 2009 (up to March 9th, 2009)
  - Notes Written on Class Board CENG364 2009 (March 9th ~ March 16th, 2009)
  - Notes from Class Board March 25th 2009
- Useful Information from the Internet:
  - Biochemical Pathways
  - Molecular and Cellular Processes
- Software Packages :
  - Metabolic calculator
  - Polymath 6.1, Education Version Download (from Polymath web site)
  - Polymath Demonstration: Substrate and Product Inhibition Reaction

Thermodynamics
- Introduction
- Thermodynamics Fundamentals
- Biochemical Thermodynamics (1)
- Example Problems and Solutions
- Examples of how to use thermodynamic expressions in biological systems
- Biochemical Thermodynamics (2) (Brief Introduction)
- Note on Biochemical Thermodynamics (2) (Completed Theory)
- Some Data
- Free Energies (1)
- Free Energies (2)
- pKa (1)
- pKa (2)
- pKa (3)
- pKa of Amino Acids (1)
- pKa of Amino Acids (2)
- pKa of Amino Acids (3)
- Standard Reduction Potentials (1)
- Standard Reduction Potentials (2)
- Some Basic Concepts
  - Steady State vs. Equilibrium
  - Example Models
  - Rate Limiting Step (basic concept for bioreaction network analysis)
  - Example Model for Rate Limiting Step

Enzymes and Kinetics

Metabolic Engineering

Metabolic Flux Analysis (MFA)
Metabolic Control Analysis (MCA)
- Introduction
- Metabolic Control Analysis Theory
- MCA Example (Comprehensive Note) * NON-EXAMABLE
- Note on MCA for Branched Pathways * NON-EXAMABLE
- Using Computer Software Packages to Solve Problems in Metabolic Engineering
- Worked Example on Using GEPASI
- GEPASI Download

System Biology * NON-EXAMABLE

Cell Cycle
Integrative Analysis of Cell Cycle Control in Budding Yeast
What is systems biology? - A short guide: http://www.sysbio.de/info/background/
Background information to cell cycle metabolic processes: http://www-rcf.usc.edu/~forsburg/cclecture.html
Mathematical modelling of cell cycle: http://mpf.biol.vt.edu/research/generic_model/main/pp/getwinpp.php

LECTURE SUMMARIES

CLASSWORK

HOMEWORK
- #1
  - HW 1 Solution
- #2 - Enzyme (Examable)
  - HW 2 Solution
- #3 - Thermodynamics (Examable)
  - HW 3 Solution
- #4 - MFA
  - HW 4 Solution
- #5 - Keq
  - HW 5 Solution
- #6 - MCA
  - HW 6 Solution

Computing Tutorial
- Polymath
  - Note - Polymath Functions
  - Classwork
  - Solution to Classwork
    - How to Convert the Problem into Polymath Model
    - Polymath file
- Polymath + MATLAB + Mathematica + GEPASI: Using Computer Software Packages for CENG 364
- For MCA: GEPASI Worked Example
MFA / MCA Tutorial
- Construct the stoichiometric coefficient matrix for MFA
- Several files from tutorial are put in the Metabolic Engineering section.

Project
- Project 1 Instruction
  - Examples from Previous Class
    - Example Reports #1 - Instrument, Polymath Simulation
    - Example Reports #2 - Instrument, Polymath Simulation
      - Presentation #2 - Instrument, Polymath Simulation

FINAL EXAM
- Past Paper
- Solution to Past Paper (#1, #2, #3, #4, #5, #6, #7, #8, #9, #10, #11, #12, #13, #14, #15, #16)

Spring Semester, 2010