Chem 110L Main Page

Chem 110L

Introductory Biochemistry Laboratory

Lecturer:

Dr. Kalju Kahn
Office: 1511 PSB-N
Office hours: Monday 2:00-3:00 PM and by appointment
Phone: 893-6157
E-mail: kalju@chem.ucsb.edu
Web site: http://www.chem.ucsb.edu/~kalju

Teaching Assistants

Section 1 (TR 2-5:50):		Anh Vu				avu@chem.ucsb.edu
	Office hours: Wed 9:50-10:50, PSB-N 1005C 		Phone: N/A

Section 2 (TR 6-9:50):		Joanna Deek			jdeek@chem.ucsb.edu
	Office hours: Mon 8:30-9:30, PSB-N 1005C 		Phone: N/A

Section 3 (WF 2-5:50):		Richard Chapleau		rchapleau@chem.ucsb.edu
	Office hours: Fri 10-11 AM, PSB-N 4650 		    	Phone: x4930 

Section 4: (MW 6-9:50):		Ke Gong				kgong@chem.ucsb.edu
	Office hours: Wed 10-11 AM, PSB-N 4650 		    	Phone: x4930

Mission statement

The purpose of Chem 110L is to offer hands-on experience with modern methods of separation, identification, and characterization of biomolecules. The course will strengthen your understanding of material taught in Chem 142A (Biochemistry Lecture). In Chem 110L, you will do experiments with biomolecules such as nucleic acids, proteins, sugars, and lipids. The 1 hour lecture series focuses on principles behind each experiment, and explains instrumental techniques and methods that you will use to accomplish your goals.

Schedule for Fall 2005


	Lecture:        Mon 10:00-10:50   Place:  Bren Hall 1414
	
	Lab section 1:  Tue 2:00-5:50;  Thu 2:00-5:50;
	Lab section 2:  Tue 6:00-9:50;  Thu 6:00-9:50;
	Lab section 3:  Wed 2:00-5:50;  Fri 2:00-5:50;
	Lab section 4:  Mon 6:00-9:50;  Wed 6:00-9:50;
	  
	Lab sections are in PSB-N 2619 unless otherwise noted

Syllabus	General information about the course.	PDF
Schedule	Schedule for Section 1 2005	PDF
Schedule	Schedule for Section 2 2005	PDF
Schedule	Schedule for Section 3, 2005	PDF
Schedule	Schedule for Section 4, 2005	PDF
Textbook	Recommended for students who are planning to take also 125L and 112L	Link
Last Year	Course materials from Fall 2004	Link

Experiments

Students in the class do not have to purchase the laboratory manual. Each chapter of the lab manual can be downloaded here in the PDF format. Please note that you can follow hyperlinks that are in the PDF files by clicking on the link. Links to external literature sources are given later below.

Experiments	Download Adobe Acrobat Here	Acrobat
General:	Background on common calculations and operation of micropipets	PDF
General:	Background on experiment design, scientific data analysis and presentation	PDF
General:	Scientific data analysis: Introduction to statistics and linear regresion analysis	PDF
Exp 1:	Macromolecular visualization	Tutorial
Exp 2:	Optical microscopy demonstration	PDF
Exp 3:	Experiment design: molar absorbtivity of urate	PDF
Exp 4:	Agarose gel electrophoresis of DNA isoforms	PDF
Exp 5:	Thermal denaturation of double-stranded DNA	PDF
Exp 6-1:	Identification of cold-induced proteins. 1. Sample preparation	PDF
Exp 6-2:	Identification of cold-induced proteins. 2. Isoelectric focusing	PDF
Exp 6-3:	Identification of cold-induced proteins. 3. SDS gel electrophoresis	PDF
Exp 6-4:	Identification of cold-induced proteins. 4. SDS gel development	PDF
Exp 7:	Quantitative enzymatic determination of glucose	PDF
Exp 8:	Identification of saccharides present in foodstuff by TLC	PDF
Exp 9:	Determination of the iodine value of a lipid by 13C NMR	PDF
Exp 10:	Light-induced proton gradient in chloroplast	PDF

Literature	Required or optional reading in PDF	Acrobat
Exp 2:	Microscopy: Dr. Matsumoto's Presentation Slides	PDF
Exp 2:	Microscopy: Perspective Story "How to Build a Superlens" by David R. Smith	PDF
Exp 2:	Microscopy: Fang et. al.: "Sub-Diffraction-Limited Optical Imaging with a Silver Superlens "	PDF
Exp 6-1:	Proteomics: Plant Proteome Analysis by MS (New & Good!)	PDF
Exp 6-1:	Proteomics: Proteome Analysis by MS	PDF
Exp 6-1:	Proteomics: Thomashow 2001	PDF
Exp 6-1:	Proteomics: Thomashow 2002	PDF
Exp 6-2:	Electrophoresis: DryStrip Kit Manual	PDF
Exp 6-2:	Electrophoresis: Power Supply Manual	PDF
Exp 9:	13C NMR (Lipids): Mercury 200 NMR Manual	PDF
Exp 9:	13C NMR (Lipids): Lecture Slides	PDF
Exp 10:	Photosynthesis: Colloquium Paper: Hu et al, PNAS 1998	PDF
Review:	How to prepare for the final (exam topics)	PDF
Review:	Sample exam (Chem 110L, 2002)	PDF

Student Files

Microscopy Images

These images of bovine pulmonary arterial epithelial cells were recorded using a fluorescence microscope during visit to UCSB's Microscopy Facility. On the right is a color image obtained by combining three individual images, each showing one component of the cell. Below are three images of the same object, taken with a fluorescence microscope at three different wavelengths. An appropriate combination of these three files will give the color image of the cell, similar to the one shown on the right. You can click on each image to download the high-resolution file.

Nuclei	Microtubules	Actin

The images below are of human cheek epithelial cells as seen through the Olympus Provis microscope in three modes: brightfield, Nomarski interference contrast, and darkfield. The spherical structure seen in the center of the cell in brightfield and Nomarski image is the nucleus; the bright dots throughout the cell in the darkfield image are various granules. While the Nomarski image may appear more real a first sight, the dark and bright areas surrounding the edges of the nucleus and granules are artifacts of this imaging technique.

Brightfield	Nomarski	Darkfield

The images below show how fluorescence imaging can be used to visualize specific sub-cellular structures. The first image shows microtubules stained with a fluorescent dye; the image was recorded in black and white. The second image shows nuclei stained with a fluorescent compound DAPI; this image was also recorded in black and white but was obtained using excitation light of different wavelength than the microtubule image. To obtain the last image, separate colors were assigned to the two previous images before combining them into one.

Microtubules	Nuclei	Combination

The images below show how choice of filters allows to improve contrast in brightfield microscopy. The three images show a tissue slice with several cells underging mitosis. The DNA in cells organizes into chromosomes at early stages of mitosis (cell in upper-central part) and the two sets of daugther chromosomes separate in the early anaphase (cells in the lower-central part). The cells are treated with a red dye that binds to DNA. A red dye appears red to our eye in the brightfield microscope because it strongly absorbs blue and green light. The first image shows an unfiltered color view of the tissue. The next two images are recorded in black and white using two different color filters. Notice the improved contrast with an appropriate choice of the filter in the last image.

Unfiltered	Red Filter	Green Filter

Proteomics: Gel Images

One of the projects in Chem 110L involves "discovery" of cold-induced proteins in Arabidopsis thaliana (thale cress). Students will identify proteins that show either up- or down-regulation in expression upon cold-treatment. The identification is based on the comparison of the protein composition of normal and cold-stressed plants using 2D electrophoresis. This technique separates proteins first according to their isoelectric point values, and then, in a perpendicular dimension, according to the molecular weight.

Proteomics	Warm Plant pH 3-10 IEF	Cold Plant pH 3-10 IEF
Example Gels (Last Year) All 2D Gels Sections 1 & 2 Sections 3 & 4
Nice Gels '05

Thin layer chromatography

One of the projects in Chem 110L involves qualitative analysis of sugars present in grapes and milk using thin layer chromatography. The image below is a representative sample. Students in the class may use this image for preparing their "Scientific Communication" about the discovery of milk and grape sugars.

Student Plates