Chem 110L
Introductory Biochemistry Laboratory
Fall 2004
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Chem 110L
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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
Section 1: Gary Braun gbraun@chem.ucsb.edu Office hours: Mon 4 PM, Chem 1142 Phone: x8283 Section 2: Ke Kong kgong@chem.ucsb.edu Office hours: Tue 10 AM, PSB-N 4650 Phone: x4930 Section 3: Abril Estrada aestrada@chem.ucsb.edu Office hours: Thu 10 AM, PSB-N 4650 Phone: x4930
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.
Lecture: Mon 10:00-10:50 Place: Phelps 3515 Lab section 1: Tue 2:00-6:00; Thu 2:00-5:50; Lab section 2: Wed 2:00-6:00; Fri 2:00-5:50; Lab section 3: Tue 6:00-9:50; Thu 6:00-9:50; Lab sections are in PSB-N 2619 unless otherwise noted
| Syllabus | General information about the course. | |
| Schedule | Schedule for September 04 | |
| Schedule | Schedule for October 04 | |
| Schedule | Schedule for November 04 |
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: | Experiment design, scientific data analysis and presentation | |
| Exp 1: | Macromolecular visualization | Tutorial |
| Exp 2: | Thermal denaturation of double-stranded DNA | |
| Exp 3: | Agarose gel electrophoresis of DNA isoforms | |
| Exp 4: | Optical microscopy demonstration | |
| Exp 5-1: | Identification of cold-induced proteins. 1. Sample preparation | |
| Exp 5-2: | Identification of cold-induced proteins. 2. Isoelectric focusing | |
| Exp 5-3: | Identification of cold-induced proteins. 3. SDS gel electrophoresis | |
| Exp 5-4: | Identification of cold-induced proteins. 4. SDS gel development | |
| Exp 6-1: | Quantitative enzymatic determination of glucose | |
| Exp 6-2: | Quantitative analysis (glucose): Introduction to Statistics | |
| Exp 7: | Identification of saccharides present in foodstuff by TLC | |
| Exp 8: | Light-induced proton gradient in chloroplast | |
| Exp 9: | Determination of the iodine value of a lipid by 13C NMR |
| Literature | Required or optional reading in PDF | Acrobat |
| Exp 4: | Microscopy: Dr. Matsumoto's Presentation Slides (2003) | |
| Exp 4: | Microscopy: News Story "Resolution Beyond The Wavelength Barrier" | Link |
| Exp 4: | Microscopy: Klar et. al.: " ... Diffraction Resolution Barrier Broken ..." | |
| Exp 5-1: | Proteomics: Plant Proteome Analysis by MS (New & Good!) | |
| Exp 5-1: | Proteomics: Proteome Analysis by MS | |
| Exp 5-1: | Proteomics: Thomashow 2001 | |
| Exp 5-1: | Proteomics: Thomashow 2002 | |
| Exp 5-2: | Electrophoresis: DryStrip Kit Manual | |
| Exp 5-2: | Electrophoresis: Power Supply Manual | |
| Exp 8: | Photosynthesis: Colloquium Paper: Hu et al, PNAS 1998 | |
| Exp 9: | 13C NMR (Lipids): Mercury 200 NMR Manual | |
| Review: | How to prepare for the final (exam topics) | |
| Review: | Sample exam (Chem 110L, 2002) |
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These images of bovine pulmonary arterial epithelial cells were recorded using a fluorescence microscope during a recent 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. |
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| Nuclei | Microtubules | Actin |
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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 |
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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 |
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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 |
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Example Gels (shown right) All 2D Gels TR 2PM Section TR 6PM Section WF 2PM Section |
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Nice Gels '04 |
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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
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