other larger molecular species. These ionic interactions Most Prokaryotes (e.g. bacteria) have a single, play an important role producing the folding and circular chromosome although some have more than packaging that is required to keep the large linear one chromosome, and some have linear chromosomes molecule packaged inside the microscopic cell. rather than circular chromosomes. Certainly, the most well studied bacteria, e.g. Escherichia coli, has a single In the case of proteins it is clear that the positively circular chromosome that can exist in either a relaxed or charged proteins can interact both by general ionic supercoiled state. interactions, but they can also ingeract in sequence specific ways; i.e. specific proteins only bind to specific Supercoiling involves breaking one of the 2 circular sequences of bases in the DNA strand. Thus, the types helical strands and then rotating the broken ends either of molecular interactions that ionic substances, in the direction of the helix (+ supercoil) or in the particularly proteins, have with DNA molecules play opposite direction of the helix (- supercoil). As important roles in determining the expression of supercoiling is added to the DNA molecule it becomes information that is carried in the DNA molecule. It will coiled (see Figure 3.8.), and therefore can be “tightly” be obvious as we proceed through our study of genomic compacted more easily. This permits the packaging of biology, that such DNA-protein interactions are as the large DNA molecule into the relatively small cells in critical to describing information” as are the which it must exist and function. “genetic base sequences of the DNA molecules themselves. This was obvious well before we btained the first genomic Additional packaging results from the supercoiled DNA sequences, but has become even more apparent DNA being carefully looped onto a scaffold of proteins and significant now that we have the DNA sequences of leading to an organized intracellular structure that can many genomes. Thus, genomic biology is not merely be easily accessible but also keep DNA from twisting the study of DNA nucleotide sequences, but involves the and being damaged du-ring normal cellular processes. study of the structure of the genetic material such as 3.3.2. Eukaryotic chromosome structure chromosomes and chromatin. In general Eukaryotes have much larger genomes than do Archea and other Prokaryotes. This difference 3.3.1. Prokaryotic chromosome structure
other larger molecular species. These ionic interactions play an important role producing the folding and packaging that is required to keep the large linear molecule packaged inside the microscopic cell. In the case of proteins it is clear that the positively charged proteins can interact both by general ionic interactions, but they can also ingeract in sequence specific ways; i.e. specific proteins only bind to specific sequences of bases in the DNA strand. Thus, the types of molecular interactions that ionic substances, particularly proteins, have with DNA molecules play important roles in determining the expression of information that is carried in the DNA molecule. It will be obvious as we proceed through our study of genomic biology, that such DNA-protein interactions are as critical to describing “genetic information” as are the base sequences of the DNA molecules themselves. This was obvious well before we btained the first genomic DNA sequences, but has become even more apparent and significant now that we have the DNA sequences of many genomes. Thus, genomic biology is not merely the study of DNA nucleotide sequences, but involves the study of the structure of the genetic material such as chromosomes and chromatin. 3.3.1. Prokaryotic chromosome structure Most Prokaryotes (e.g. bacteria) have a single, circular chromosome although some have more than one chromosome, and some have linear chromosomes rather than circular chromosomes. Certainly, the most well studied bacteria, e.g. Escherichia coli, has a single circular chromosome that can exist in either a relaxed or supercoiled state. Supercoiling involves breaking one of the 2 circular helical strands and then rotating the broken ends either in the direction of the helix (+ supercoil) or in the opposite direction of the helix (- supercoil). As supercoiling is added to the DNA molecule it becomes “tightly” coiled (see Figure 3.8.), and therefore can be compacted more easily. This permits the packaging of the large DNA molecule into the relatively small cells in which it must exist and function. Additional packaging results from the supercoiled DNA being carefully looped onto a scaffold of proteins leading to an organized intracellular structure that can be easily accessible but also keep DNA from twisting and being damaged du-ring normal cellular processes. 3.3.2. Eukaryotic chromosome structure In general Eukaryotes have much larger genomes than do Archea and other Prokaryotes. This difference