Calendar for CHE 554, Spring 2015

UNDER CONTINUOUS CONSTRUCTION
Please check regularly for updates

Download the calendar of events available on the main web site, see (Dates for lab assignments. . .). In addition, on each day when a lecture is to be presented, the notes will be posted in pdf form via a link provided below in the calendar date of the lecture. On each day when a lab exercise will begin, there will also be links to a protocol for the lab and additional related materials.

 

15 Jan.

Lecture notes on safety and  lab report preparation

Install Swiss PDB viewer and work through the tutorial

20 Jan.

Lecture on modeling and work through the tutorial

locker allocations

Assignment

MSDS' for glucose, aspirin

22 Jan.

Lecture on spectrophotometry.

Textbook chapter on spectrophotometry.

27 Jan.

Lecture on Chromatography

Text material on chromatography

Please complete and turn in your safety contract

Example file collecting amino acid sequences of the hydrogenase domains.

29 Jan.

Lecture on CD.

3 Feb.

Lecture notes on SDS polyacrylamide gel electrophoresis.

For Group A: Chromatography lab, part 1

Text material on electrophoresis

Molecular weight standards for electrophoresis data analysis.

For Group B: the spectrophotometry lab, part 1

MSDS for bromophenol blue.

MSDS for Bradford reagent and Sigma's instruction bulletin

The paper describing the extinction coefficients of aromatic amino acids.

For Group C: the CD lab, part 1

 

5 Feb.

(No lecture)

For Group A: Chromatography lab, part 2

For Group B: the spectrophotometry lab, part 2

For Group C: the CD lab, part 1

 

 

 

10 Feb.

(no lecture)

For Group A: The CD lab, part 1

For Group B: Chromatography lab, part 1

For Group C: Spectroscopy lab, part 1

12 Feb.

(no lecture)

For Group A: The CD lab, part 1

For Group B: Chromatography lab, part 2

For Group C: Spectroscopy lab, part 2

17 Feb.

Lecture on DNA properties and plasmid purification.

For Group A: Spectroscopy, part 1

For Group B: CD lab, part 1

For Group C: Chromatography lab, part 1

Papers on extinction coefficients of some proteins including ovalbumin, the sequence of ovalbumin. More papers, on refolding ovalbumin from urea with CD characterization, CD and refolding ovalbumin from different denaturants, refolding ovalbumin via viscometry.

19 Feb.

No lecture

For Group A: Spectroscopy, part 2

For Group B: CD lab, part 1

For Group C: Chromatography lab, part 2

24 Feb.

Lecture on ELISA.

Textbook Chapter on ELISA

Lab manual for the ELISA kit

Instructions for microplate reader

Group A: plasmid isolation, part 1

Group B: ELISA, part 1

Group C: CD lab part 2

Protocol is in the notes posted on 20 Feb., handouts follow: textbook chapter on isolating bacterial DNA, and how it works. Textbook chapter on plasmid characterization . Source of instructions for agarose gel electrophoresis. A review of technologies for manipulating DNA and genes.

QuickLyse manual and an older but more informative manual on the older version of the kit that explains how the steps work.

MSDS of ethidium bromide and list of the DNA size standards used to calibrate our agarose gels.

26 Feb.

No Lecture

Group A: plasmid isolation, part 2

Group B: ELISA, part 2

Group C: CD lab part 2

3 March.

No Lecture

Group A: CD lab, part 2

Group B: Plasmid isolation, part 1

Group C: ELISA, part 1

5 March.

No Lecture

Group A: CD lab, part 2

Group B: Plasmid isolation, part 2

Group C: ELISA, part 2

10 March.

No Lecture

Group A: ELISA, part 1

Group B: CD lab, part 2

Group : Plasmid isolation, part 1

12 March.

No Lecture

Group A: ELISA, part 2

Group B: CD lab, part 2

Group : Plasmid isolation, part 2

17 March.

Spring Break - recharge

19 March.

Spring Break - recharge

24 March.

Lecture on PCR and primer design.

Group A, B, C: Make-up lab sessions. Please email Prof. Wei and the relevant T.A. if you need to make up any lab exercise

26 March.

Lecture on Enzyme Kinetics

Chapter on enzyme kinetics including description of the experiment.

Background information on enzyme kinetics from our text.

Notes on Analysis for Enzyme Kinetics

Group A: Enzyme Kinetics, part 1

Group B: No lab.

Group C: Set up PCR

Protocol notes.

QuickChange manual for site-directed mutagenesis

Book chapter on Nucleic acid technology and Book chapter on PCR..

31 March

Lecture on site directed mutagenesis and over-expression

Group A: Enzyme Kinetics, part 2

Group B: No lab.

Group C: Transformation

Transformation Protocol from the company from which we purchased the competent T7-express cells.

2 April

No Lecture

Group A: No lab

Group B: Enzyme Kinetics, part 1

Group C: Molecular biology

7 April.

No lecture

Group A: Set up PCR

Group B: Enzyme kinetics, part 2

Group C: no lab

9 April.

No lecture

Group A: Transformation

Group B: Set up PCR

Group C: Enzyme Kinetics, part 1

14 April.

No lecture

Group A: Molecular Biology

Group B: Transformation

Group C: Enzyme kinetics, part 2

16 April.

No lecture

Group A: no lab

Group B: Molecular Biology

Group C: no lab

21 April.

Spare day in case of trouble

23 April.

Spare day in case of trouble

Some slides comparing optical rotation to circular dichroism, including some exercises for you to do to firm up your understanding (answers provided).

28 April.

Group A, B, C:

30 April.

Last report due.