The vast majority of an organism’s genome is organized into the cell’s chromosomes, which are discrete DNA structures within cells that control cellular activity. Recall that while eukaryotic chromosomes are housed in the membrane-bound nucleus, most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid. A chromosome may contain several thousand genes.
Organization of Eukaryotic Chromosome
Chromosome structure differs somewhat between eukaryotic and prokaryotic cells. Eukaryotic chromosomes are typically linear, and eukaryotic cells contain multiple distinct chromosomes. Many eukaryotic cells contain two copies of each chromosome and, therefore, are diploid.
The length of a chromosome greatly exceeds the length of the cell, so a chromosome needs to be packaged into a very small space to fit within the cell. For example, the combined length of all of the 3 billion base pairs of DNA of the human genome would measure approximately 2 meters if completely stretched out, and some eukaryotic genomes are many times larger than the human genome. DNA supercoiling refers to the process by which DNA is twisted to fit inside the cell. Supercoiling may result in DNA that is either under wound (less than one turn of the helix per 10 base pairs) or overwound (more than one turn per 10 base pairs) from its normal relaxed state. Proteins known to be involved in supercoiling include topoisomerases; these enzymes help maintain the structure of supercoiled chromosomes, preventing over winding of DNA during certain cellular processes like DNA replication.
During DNA packaging, DNA-binding proteins called histones perform various levels of DNA wrapping and attachment to scaffolding proteins. The combination of DNA with these attached proteins is referred to as chromatin. In eukaryotes, the packaging of DNA by histones may be influenced by environmental factors that affect the presence of methyl groups on certain cytosine nucleotides of DNA. The influence of environmental factors on DNA packaging is called epigenetics. Epigenetics is another mechanism for regulating gene expression without altering the sequence of nucleotides. Epigenetic changes can be maintained through multiple rounds of cell division and, therefore, can be heritable.
Organization of Prokaryotic Chromosomes
Chromosomes in bacteria and archaea are usually circular, and a prokaryotic cell typically contains only a single chromosome within the nucleoid. Because the chromosome contains only one copy of each gene, prokaryotes are haploid. As in eukaryotic cells, DNA supercoiling is necessary for the genome to fit within the prokaryotic cell. The DNA in the bacterial chromosome is arranged in several supercoiled domains.
As with eukaryotes, topoisomerases are involved in supercoiling DNA. DNA gyrase is a type of topoisomerase, found in bacteria and some archaea, that helps prevent the overwinding of DNA. (Some antibiotics kill bacteria by targeting DNA gyrase.) In addition, histone-like proteins bind DNA and aid in DNA packaging. Other proteins bind to the origin of replication, the location in the chromosome where DNA replication initiates. Because different regions of DNA are packaged differently, some regions of chromosomal DNA are more accessible to enzymes and thus may be used more readily as templates for gene expression. Interestingly, several bacteria, including Helicobacter pylori and Shigella flexneri, have been shown to induce epigenetic changes in their hosts upon infection, leading to chromatin remodeling that may cause long-term effects on host immunity.
