1. AP Biology- Chapter 20 Concept 4: Genome sequences provide clues for important biological questions. 2/8/2011 Rehman Chaudhry and Amanda Rebeaud
2. Genomics A discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleitropy, and other interactions between loci and alleles within the genome. The study of genomes and their interactions, is yielding new insights into fundamental questions about genome organization, the regulation of gene expression, growth and development, and evolution.
3. Identifying Protein-Coding Genes in DNA Sequences Computer analysis of genome sequences helps researchers identify sequences that are likely to encode proteins. Special software scans the sequences for the telltale signs of protein-coding genes, looking for start and stop signals, RNA-splicing sites, and other features. With approximately 25,000 genes in the human genome, this would be a huge undertaking for researchers with out the use of technology. These sequences are available to researchers everywhere via the Internet.
4. Genome Sizes Although genome size increases from prokaryotes to eukaryotes, it does not always correlate with biological complexity among eukaryotes. One flowering plant has a genome 40 times the size of the human genome. An organism may have fewer genes than expected from the size of its genome. The estimated number of human genes is 25,000 or fewer, which is only about one-and-a-half times the number found in the fruit fly. Given the great diversity of cell types in humans, this is surprising.
6. The most common way would be to disable the gene and then observe the consequences in the cell or organism. Application: Using in vitro mutagenesis, specific mutations are introduced into the sequence of a cloned gene, after which the mutated gene is returned to a cell. If the introduced mutations alter or destroy the function of the gene product, it may be possible to determine the function of the gene by examining the phenotype. Researchers can even put the mutated gene into cells from the early embryo of multicellular organisms to study the role of the gene in the development and functioning of the whole organism.
7. Another Method… A simpler and faster method for silencing expression of selected genes exploits the phenomenon of RNA interference (RNAi). This method uses synthetic double-stranded RNA molecules matching the sequences of a particular gene to trigger breakdown of the gene’s mRNA. The RNAi technique has had limited success in mammalian cells but has been valuable in analyzing the functions of genes in nematodes and fruit flies. In one study, RNAi was used to prevent expression of 86% of the genes in early nematode embryos, one gene at a time. Analysis of the phenotypes of the worms that developed from these embryos allowed the researchers to group most of the genes into functional groups.
8. Studying Expression of Interacting Groups of Genes A major goal of genomics is to learn how genes act together to produce and maintain a functioning organism. The basic strategy in global expression is to isolate mRNAs made in particular cells and use the mRNA as a template to build cDNA by reverse transcription. By hybridization, each cDNA can be compared to other collections of DNA. This will reveal which genes are active at different developmental stages, in different tissues, or in tissues in different states of health.
9. DNA Microarray Assays A DNA microarray consists of tiny amounts of a large number of single-stranded DNA fragments representing different genes fixed to a glass slide in a grid. An array is also called a DNA chip. The fragments, sometimes representing all the genes of an organism, are tested for hybridization with various samples of fluorescently labeled cDNA molecules.
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11. Figure 20.14-Research Method DNA microarray assay of gene expression levels 1 2 3 4 APPLICATION TECHNIQUE RESULT Isolate mRNA. Make cDNA by reverse transcription, using fluorescently labeled nucleotides. Apply the cDNA mixture to a microarray, a microscope slide on which copies of single-stranded DNA fragments from the organism’s genes are fixed, a different gene in each spot. The cDNA hybridizes with any complementary DNA on the microarray. Rinse off excess cDNA; scan microarray for fluorescence. Each fluorescent spot (yellow) represents a gene expressed in the tissue sample. The intensity of fluorescence at each spot is a measure of the expression of the gene represented by that spot in the tissue sample. Commonly, two different samples are tested together by labeling the cDNAs prepared from each sample with a differently colored fluorescence label. The resulting color at a spot reveals the relative levels of expression of a particular gene in the two samples, which may be from different tissues or the same tissue under different conditions. With this method, researchers can test thousands of genes simultaneously to determine which ones are expressed in a particular tissue, under different environmental conditions in various disease states, or at different developmental stages. They can also look for coordinated gene expression. Tissue sample mRNA molecules Labeled cDNA molecules (single strands) DNA microarray Size of an actual DNA microarray with all the genes of yeast (6,400 spots)
12. Comparisons of genome sequences from different species allow us to determine evolutionary relationships between those species. The more similar in a sequence a gene is in two species, the more closely related those species are in their evolutionary history. The theory that the three fundamental domains of life are bacteria, archaea, and eukarya is strongly supported by the comparisons of the complete genome sequences of each domain. Comparative genome studies also confirm the relevance of research on simpler organisms to our understanding of biology in general.
13. Closely Related Species The genomes of two closely related species are likely to be similarly organized. Once the sequence and organization of one genome is known, it can greatly accelerate the mapping of a related genome. For example, with the human genome serving as a guide, the mouse genome can be mapped quickly. The small number of gene differences between closely related species makes it easier to correlate phenotypic differences between species with particular genetic differences. The function of speech is one gene that is clearly different in chimps and humans. Researchers may determine what a human disease gene does by studying its normal counterpart in mice, who share 80% of our genes.
14. The systematic study of full protein sets (proteomes) encoded by genomes is an approach called proteomics. It is the next step after mapping and sequencing genomes. Unlike DNA, proteins are extremely varied in structure and chemical and physical properties. Because proteins are the molecules that actually carry out cell activities, we must study them to learn how cells and organisms function. Proteomics
15. SNPs Single nucleotide polymorphisms (SNPs) are single base-pair variations in the genome. It is usually detected by sequencing. Most of our diversity seems to be in the form of SNPs. The double stranded DNA sequence in this region is identical between these two samples save for the 28th base pair. This variation is a SNP.
