Genomics II - Genomics II Functional Genomics Proteomics and Bioinformatics Introduction Functional genomics strives to understand gene function in

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1 Genomics II – Functional Genomics, Proteomics, and Bioinformatics Introduction Functional genomics strives to understand gene function in a species. The study of the proteins is called proteomics. The entire collection of proteins in a given species is called the proteome. Functional genomics and proteomics can broadly be categorized as being experimental and computational. Bioinformatics attempts to extract information within genetic sequences using a mathematical approach. Functional Genomics Expressed genes can be identified in a cDNA library. cDNA libraries are made using RNA as the starting material. This is also called an expressed sequence tag (EST) library because the sequences can be used as markers in physical mapping. cDNA libraries can be used to study gene regulation at the genomic level. mRNAs are isolated under different conditions. mRNAs that are found only under a set of conditions indicates genes that are activated under those conditions. A subtractive cDNA library (also called subtractive hybridization) is shown in Figure 21.1. This procedure can be used to isolate genes that are active under a certain set of conditions. A microarray can identify genes that are transcribed. DNA microarrays, or gene chips, make it possible to monitor the expression of thousands of genes simultaneously. A microarray is a microscope slide that is dotted with many different sequences of DNA. The location of each gene is recorded. The microarray can be used as a hybridization tool (Figure 21.2) to identify genes that are related to the probe being used. Microarrays have found a wide variety of applications in the study of functional genomics (Table 21.1).
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2 Experiment 21A. The coordinate regulation of many genes is revealed by a DNA microarray analysis. Cells respond to their environment via the coordinated regulation of genes. One of the earliest uses of microarrays was the study of the yeast Saccharomyces cerevisiae . S. cerevisiae has approximately 6,300 genes. This organism has the ability to metabolize carbon sources using different metabolic pathways. When yeast cells have glucose available, they metabolize the glucose to smaller products during glycolysis. If oxygen is present, these products can be broken down via the tricarboxylic acid cycle (TCA). The process of switching from glycolysis to the TCA cycle, called a diauxic shift, involves major changes in the expression of genes involved with carbohydrate metabolism. The goal. The goal of the experiment was to identify genes that are induced and repressed as yeast cells shift from glycolysis to the TCA cycle. Achieving the goal (Figure 21.3). Inoculate yeast cells into media containing 2% glucose and grow for up to 21 hours. Beginning at 9 hours after inoculation, take out samples of cells every 2 hours and
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This note was uploaded on 02/27/2011 for the course BIO 325 taught by Professor Saxena during the Fall '08 term at University of Texas at Austin.

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Genomics II - Genomics II Functional Genomics Proteomics and Bioinformatics Introduction Functional genomics strives to understand gene function in

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