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  • What is the difference between a cell’s genotype and its phenotype?
  • How does DNA fit inside cells?

Noncoding dna

In addition to genes, a genome also contains many regions of noncoding DNA that do not encode proteins or stable RNA products. Noncoding DNA is commonly found in areas prior to the start of coding sequences of genes as well as in intergenic regions (i.e., DNA sequences located between genes) ( [link] ).

A chromosome drawn as an X shape. As the strand unravels we see that it is a long double helix with genes interspersed with noncoding regions.
Chromosomes typically have a significant amount of noncoding DNA, often found in intergenic regions.

Prokaryotes appear to use their genomes very efficiently, with only an average of 12% of the genome being taken up by noncoding sequences. In contrast, noncoding DNA can represent about 98% of the genome in eukaryotes, as seen in humans, but the percentage of noncoding DNA varies between species. R.J. Taft et al. “The Relationship between Non-Protein-Coding DNA and Eukaryotic Complexity.” Bioessays 29 no. 3 (2007):288–299. These noncoding DNA regions were once referred to as “junk DNA”; however, this terminology is no longer widely accepted because scientists have since found roles for some of these regions, many of which contribute to the regulation of transcription or translation through the production of small noncoding RNA molecules, DNA packaging , and chromosomal stability. Although scientists may not fully understand the roles of all noncoding regions of DNA, it is generally believed that they do have purposes within the cell.

  • What is the role of noncoding DNA?

Extrachromosomal dna

Although most DNA is contained within a cell’s chromosomes, many cells have additional molecules of DNA outside the chromosomes, called extrachromosomal DNA , that are also part of its genome. The genomes of eukaryotic cells would also include the chromosomes from any organelles such as mitochondria and/or chloroplasts that these cells maintain ( [link] ). The maintenance of circular chromosomes in these organelles is a vestige of their prokaryotic origins and supports the endosymbiotic theory (see Foundations of Modern Cell Theory ). In some cases, genomes of certain DNA viruses can also be maintained independently in host cells during latent viral infection. In these cases, these viruses are another form of extrachromosomal DNA. For example, the human papillomavirus (HPV) may be maintained in infected cells in this way.

A drawing of a cell. the cell has a large sphere labeled nucleus, smaller ovals labeled mitochondria and small green ovals labeled chloroplasts.
The genome of a eukaryotic cell consists of the chromosome housed in the nucleus, and extrachromosomal DNA found in the mitochondria (all cells) and chloroplasts (plants and algae).

Besides chromosomes, some prokaryotes also have smaller loops of DNA called plasmids that may contain one or a few genes not essential for normal growth ( [link] ). Bacteria can exchange these plasmids with other bacteria in a process known as horizontal gene transfer ( HGT) . The exchange of genetic material on plasmids sometimes provides microbes with new genes beneficial for growth and survival under special conditions. In some cases, genes obtained from plasmids may have clinical implications, encoding virulence factors that give a microbe the ability to cause disease or make a microbe resistant to certain antibiotics. Plasmids are also used heavily in genetic engineering and biotechnology as a way to move genes from one cell to another. The role of plasmids in horizontal gene transfer and biotechnology will be discussed further in Mechanisms of Microbial Genetics and Modern Applications of Microbial Genetics .

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Source:  OpenStax, Microbiology. OpenStax CNX. Nov 01, 2016 Download for free at http://cnx.org/content/col12087/1.4
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