Teaching+Points+for+Labs+Spring+13

Teaching Points For VDS Spring 2013 Labs
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/.
 * Tips & Hints **
 * Timestamp for Microsoft Word documents:** ALT + i together, release and hit T
 * Date Stamp for Excel:** CTRL + ;
 * Time Stamp for Excel:** CTRL + SHFT + :

=Beta-lactamase docking (a.k.a. VS4)= Lab Handout:

=Target Discovery= Lab Handout:

=VS3 lab= Lab Handout:

Teaching Points:

=Protein Characterization Lab= Lab Handout:

Teaching Points:

=Virtual Screening 2= Lab Handout:

Teaching Points:

=Protein Purification Lab= NOTE: each pair will pick just one (1) pellet to purify. The other one should just be kept frozen as backup. - each person should still make their own samples 1,2,3,4,5,6 for the Gel Though

Also, if they use Cyanase - they only need 1 ul of it since the stock concentration is greater than that of benzonase.

Lab Handout:

Teaching Points:

=Virtual Screening 1= Lab Handout: The other files for docking are on the DDFE in **/home/chem204/LabVirtualScreening1files**

Teaching Points: (password protected)

=Protein Expression= Lab Handout: Teaching Points:

PyMol 3
Lab Handout:

Teaching Points:

Buffer Titration
Lab Handout:

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H-H Exercise Answers: (password protected) CLASS HANDOUT SOLUTIONS:

LAB HANDOUT SOLUTION - this is VERSION 2 - so, I know its right.....?

PyMol 2
Lab Handout:

Teaching Points:


 * COMMON COMMENTS - PyMol2**

Beer's Law
Lab Handout:

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Correct images show calculations which spec did you use? enough procedures but not onerous detail that is redundant to lab 1 analysis-error conclusion-recap future directions GRAPHS: 1. max wavelength 2. all readings 3. table with data 4.graph with linear regression hypothesis: does it hold for all concentrations?
 * COMMON COMMENTS - Beer's Law**

Should mention creating __linear best fit line__ in Excel (don't need to talk about other aspects of Excel since they have already used it)

LAST WEEK:

Lit Search & Endnote Web
this last one is password protected with Mentor password

=Buffers & Solutions Lab:= Lab Handout:

NOTE: the LB amount is WRONG on the handout - they should only make 100ml of LB.

Teaching Points:

===When they work in pairs - have them start out on the 'expensive' stuff first. That way if they have to finish the lab another day and end up both doing the materials separately - we won't have made too much stuff.===

'Expensive' stuff:
0.100 L LB broth (autoclaved) 200 ml 0.1M Tris base or Trizma base pH 7.5 using conc. HCl (hydrochloric acid) 1 ml 50 mg/ml Amp (filter sterilized)

50 ml 1 M Imidazole (filter-sterilized)

50 ml 10x PBS (Phosphate Buffered Saline, filter-sterilized)

'Cheap' stuff:
50 ml 5 N NaOH (Sodium Hydroxide) 100 ml 5x Tris-Glycine-SDS buffer 10 ml of 30% EtOH (ethanol) in autoclaved water

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=Enzyme Assay Lab= Lab Handout:

Teaching Points:

They can use multiple cuvettes to do their readings faster (i.e. have 9 or 10 of the same cuvettes instead of washing one multiple times)

Make them save their spectrophotometer file – NameEnzymeAssayDATE Make them save their spectrophotometer file – NameEnzymeAssayDATE Make them save their spectrophotometer file – NameEnzymeAssayDATE

MAKE sure they clean up afterwards before you sign them out.

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=Buffer Titration= Lab Handout:

Teaching Points:

Henderson-Hasselbalch exercise answer sheet (password protected).

they need to have all 3 titrations on the same graph in the end - to do so, they will need to creat 3 calculated volume columns and give them each a different name (e.g. CV1, CV2, and CV3).
 * Tips & Hints**

=PyMol2= Lab Handout:

Teaching Points:

show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. to save their Image (.png) and Session (.pse) files. The first time they use it the have to 'sign up' on the Sign Up page. Also there is an 'Advanced Upload' button that lets them have a drag and drop folder instead of uploading each file individually. (Much faster).
 * Tips & Hints**

=Beer's Law= Lab Handout:

Teaching Points:

**File Not Found**

warm up specs for about 10 minutes before use Henry spec reads very high on the Absorbance values - need to make sure they don't record their data if it is saturating the dector (>1.5 or 2 on the absorbance units)
 * Tips & Hints**

Students should empty their cuvettes between EACH reading (i.e. for n=3 replicates, they shoudl empty the cuvette 3 times). This takes longer but reinforces that just hitting the COLLECT button 3 times on the exact same sample does not constitute a true replicate. To speed things up - they can get 3 cuvettes at a time and fill with a given dilution (Dil1, Dil2, Dil3, etc.) -- then measure 3 in a row quickly.

They don't have to measure Dilution 1 - IF they know it is going to be above 1.5 Absorbance units.

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