BIOL3140 Advanced Biochemistry and Molecular Genetics Laboratory
BIOL 3140 Lab experiments schedule for Week 2, 3
Protein Analysis for alpha Amylase (3 labs)
Lab Manual: textbook (Lab 5A & 5B, Page 48,55)
Day 1 :
 SDS PAGE Sample prep
 Run SDS-PAGE gel #1 (prepared by Melissa)
 Transfer to membrane overnight for Western blot.
Day 2:
 Western blot detection
 Make 1 gel per group to use the following week (only prepare the separating gel, the
stacking gel will be made before running the gel in the following week.)
Day 3:
 Run SDS-PAGE gel #2
 Stain this gel with Coomassie blue
 Data analysis
Additional information:
Samples for the Western blot and SDS-PAGE:
Note: protein markers used for Western have to be prestained
Lane 1 - Protein Marker, Broad Range (NEB P7701)
Lane 2 - unknown #2
Lane 3 - unknown #1
Lane 4 - alpha amylase from porcine pancreas (Sigma A3176)
Lane 5 - alpha amylase from Aspergillus oryzae (Sigma A6211)
Lane 6 - alpha amylase from B. licheniformis (Sigma A4551)
Lane 7 - Saliva
Lane 8 - B. amyloliquefaciens crude extract
Lane 9 - B. licheniformis crude extract
Lane 10 - Prestained Protein Ladder (NEB P7711S)
Primary antibodies:
(1) Anti-alpha amylase (Bacillus amyloliquefaciens) (RABBIT), Rockland 200-4145.
(2) Anti-alpha amylase (human) (RABBIT), Sigma A8273
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BIOL3140 Advanced Biochemistry and Molecular Genetics Laboratory
Secondary antibody:
(1) Anti-Rabbit IgG (whole molecule), F(ab')2 fragment - Alkaline phosphatase
(GOAT), Sigma A3937
Used 3ul in 30ml Blocking Buffer (dilution factor: 1:10,000)
SDS PAGE recipe
Running Gel (10%): 4ml dH2O, 3.3ml 30% acrylamide, 2.5ml 1.5M Tris (pH 8.8),
0.1ml 10% SDS, 0.1ml 10% APS, 4ul TEMED
Stacking Gel: 2.7ml dH2O, 0.67ml 30% acrylamide, 0.5ml 1M Tris (pH 6.8), 0.04ml
10%SDS, 0.04ml 10% APS, 4ul TEMED
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BIOL3140 Advanced Biochemistry and Molecular Genetics Laboratory
Western Blot Write-up –BIO3140 lab report 1
This report contains all parts that are typical for a scientific paper. The report must have a
cover page which contains the name of the student, student number and the name of the lab
partner. It should be prepared in double spaced format. The figures and tables have
appropriate titles and legend.
Abstract (15%) half to 1 page
Introduction (20%) 1 page
Provide information to understand your lab-report (background information).
Material and Methods (10%) 1page
Please refer to the lab manual except the changes you have made.
Provide brief description of the methods you have used for the experiments mentioned in the
list in a style as seen in the published scientific papers.
Results (30%) Results and discussion 3 pages
Provide description of results in text referring to figures / tables.
Discussion (20%)
Explain, justify and discuss your results based on scientific facts.
References (5%)
Please use the format provided on the next page.
Page limit 6 pages
Excluding figures/tables and references
Results to be covered:
SDS-PAGE
Gel image, standard curve, table of calculation
Description of your results and how do you estimate the size of the tentative a-amylase bands
in each sample
Western-blot
Membrane image,
Description of the blot results
Based on SDS-PAGE and blot results, which sample contains alpha amylase?
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BIOL3140 Advanced Biochemistry and Molecular Genetics Laboratory
References
These should be cited in the text by sequential number only, in order of appearance,
and listed numerically in the References section. Online references should be cited as in
example 5, below. Please see examples 6 and 7 for papers that have been published online in
more than one version. The initial version of a paper published in this way can be cited by
the Digital Object Identifier (doi) but, if available, the reference should also include the
citation of the final version. Authors should check all references carefully, and in particular
ensure that all references in the Reference section are cited in the text. Note that multiple
references or page spans under one number are not allowed. Personal communications,
unpublished results, manuscripts submitted or in preparation, statistical packages, computer
programs and web sites should be cited in the text only, NOT included in the References
section. Accession numbers may be cited either within the text or in the form of a reference
Citations should conform to the following examples. Journal names should be abbreviated in
the style of Chemical Abstracts. Where the list of authors is extensive it is acceptable to list
the first 10 authors followed by et al. NOTE THAT FULL TITLES OF JOURNAL
ARTICLES MUST BE PROVIDED.
1. Schmitt,E., Panvert,M., Blanquet,S. and Mechulam,Y. (1995) Transition state
stabilisation by the 'high' motif of class I aminoacyl-tRNA synthetases: the case of
Escherichia coli methionyl-tRNA synthetase. Nucleic Acids Res., 23, 4793-4798.
2. Huynh,T.V., Young,R.A. and Davies,R.W. (1988) Constructing and screening cDNA
libraries in lambdagt10 and lambdagt11. In Glover,D.M. (ed.), DNA Cloning - A
Practical Approach. IRL Press, Oxford, Vol. I, pp. 49-78.
3. Maniatis,T., Fritsch,E.F. and Sambrook,J. (1982) Molecular Cloning: A Laboratory
Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
4. Burnett,R.C. (1993) EMBL accession no. X52486.
5. Capaldi,S., Getts,R.C. and Jayasena,S.D. (2000) Signal amplification through
nucleotide extension and excision on a dendritic DNA platform. Nucleic Acids Res.,
28, e21.
6. Qiao,D., Chen,W., Stratagoules,E. and Martinez,J. (March 10, 2000) Bile acidinduced
activation of activator protein-1 requires both extracellular signalregulated
kinase and protein kinase C signaling. J. Biol. Chem.,
10.1074/jbc.M908890199
7. Qiao,D., Chen,W., Stratagoules,E. and Martinez,J. (2000) Bile acid-induced
activation of activator protein-1 requires both extracellular signal-regulated kinase
and protein kinase C signaling. J. Biol. Chem., 275, 15090-15098. First published on
May 19, 2000, 10.1074/jbc.M908890199
8. Bernhagen,J., Elkine,B., Geiger,G., Tovar,G. and Vitzthum,F. (1999) Patent DE198198889.2-44; PCT/WO/EP/99/03047
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