(b) Organisation of DNA – circular chromosomal DNA and plasmids in prokaryotes. Circular plasmids in yeast. Circular chromosome in mitochondria and chloroplasts of eukaryotes. DNA in the linear chromosomes of the nucleus of eukaryotes is tightly coiled and packaged with associated proteins.
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Prokaryotic (Bacterial) cells
abridged from Genome Packaging in Prokaryotes: the Circular Chromosome of E. coli By: Ann Griswold, Ph.D. © 2008 Nature Education
Prokaryotic cells do not contain nuclei or other membrane-bound organelles. In fact, the word “prokaryote” literally means “before the nucleus.” The nucleoid is simply the area of a prokaryotic cell in which the chromosomal DNA is located. This arrangement is not as simple as it sounds, however, especially considering that the E. coli chromosome is much larger than the cell itself. To enable the DNA to fit int he cell, it is “packaged”.
Eukaryotic cells ( see below) wrap their DNA around proteins called histones to make true chromosomes. However, most prokaryotes do not have histones. Instead, their DNA is supercoiled (see Figure opposite).
Imagine twisting a rubber band so that it forms tiny coils. Now twist it even further, so that the original coils fold over one another and form a condensed ball. This is supercoiling.
Another difference between prokaryotes and eukaryotes is that prokaryotic cells often contain one or more plasmids (i.e., extrachromosomal DNA molecules that are circular). They are typically smaller than the chromsome and encode non-essential genes, such as those that aid growth in specific conditions or encode antibiotic resistance. The plasmids replicate independently of the rest of the genome.
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Extension (outside the scope of the syllabus)
Eukaryotic (Animal, plant, fungal) cells
(abridged from DNA Packaging: Nucleosomes and Chromatin
By: Anthony T. Annunziato, Ph.D. (Biology Department, Boston College) © 2008 Nature Education)
The human genome contains approximately 6 billion base pairs of DNA packaged into 23 pairs of chromosomes. The DNA per cell is around 2 metres long, yet a cell is only around 10-100 micrometres.
The ability to hold this length of DNA in every cell in the body is made possible because of DNA packaging.
Certain proteins, called histones pack the chromosomal DNA into the microscopic space of the eukaryotic nucleus, creating a much smaller volume than DNA can fold by itself. The resulting DNA-protein complex is called chromatin.
This protein/ DNA complex forms a nucleosome, which looks like a tiny bead. Around 166 base pairs are wrapped around each nucleosome, so each chromosome (over 100 million base pairs of DNA on average) contains hundreds of thousands of nucleosomes. They are linked by the DNA that runs between them (an average of about 20 base pairs) – and so appear similar to beads on a string.
Histones are a family of small, positively charged proteins and as DNA is negatively charged, due to the phosphate groups in its phosphate-sugar backbone, histones bind with DNA very tightly.
The packaging of DNA into nucleosomes shortens the fibre length about sevenfold. In other words, a piece of DNA that is 1 meter long will become just 14 centimetres long. To fit into the nucleus, which is typically only 10 to 20 microns in diameter, further coiling is required. The diagram below illustrates this process (Click on the diagram to access an interactive presentation on DNA packaging) .
Processes such as transcription and replication require the two strands of DNA to come apart temporarily, thus allowing polymerases access to the DNA template. However, the presence of nucleosomes and further folding pose barriers to the enzymes that unwind and copy DNA. Cells need to open the chromatin fibres and/or temporarily remove histones to permit transcription and replication to proceed. These processes are reversible, so the chromatin can be returned to its compact state after transcription and/or replication are complete.
Prokaryotic DNA replication occurs at a rate of 1,000 nucleotides per second, and prokaryotic transcription occurs at a rate of about 40 nucleotides per second (Lewin, 2007), so bacteria must have highly efficient methods of accessing their DNA strands. But how?
Researchers have noted that the nucleoid usually appears as an irregularly shaped mass within the prokaryotic cell, but it becomes spherical when the cell is treated with chemicals to inhibit transcription or translation. Moreover, during transcription, small regions of the chromosome can be seen to project from the nucleoid into the cytoplasm (i.e., the interior of the cell), where they unwind and associate with ribosomes, thus allowing easy access by various transcriptional proteins (Dürrenberger et al., 1988). These projections are thought to explain the mysterious shape of nucleoids during active growth. When transcription is inhibited, however, the projections retreat into the nucleoid, forming the aforementioned spherical shape.
Other DNA Differences Between Prokaryotes and Eukaryotes
Most prokaryotes reproduce asexually and are haploid, meaning that only a single copy of each gene is present. This makes it relatively easy to generate mutations in the lab and study the resulting phenotypes. By contrast, eukaryotes that reproduce sexually generally contain multiple chromosomes and are said to be diploid, because two copies of each gene exist—with one copy coming from each of an organism’s parents.
Yet another difference between prokaryotes and eukaryotes is that prokaryotic cells often contain one or more plasmids (i.e., extrachromosomal DNA molecules that are either linear or circular). These pieces of DNA differ from chromosomes in that they are typically smaller and encode nonessential genes, such as those that aid growth in specific conditions or encode antibiotic resistance. Borrelia, for instance, contains more than 20 circular and linear plasmids that encode genes responsible for infecting ticks and humans (Fraser et al., 1997). Plasmids are often much smaller than chromosomes (i.e., less than 1,500 kilobases), and they replicate independently of the rest of the genome. However, some plasmids are capable of integrating into chromosomes or moving from cell to cell.
Perhaps due to the space constraints of packing so many essential genes onto a single chromosome, prokaryotes can be highly efficient in terms of genomic organization. Very little space is left between prokaryotic genes. As a result, noncoding sequences account for an average of 12% of the prokaryotic genome, as opposed to upwards of 98% of the genetic material in eukaryotes (Ahnert et al., 2008). Furthermore, unlike eukaryotic chromosomes, most prokaryotic genomes are organized into polycistronic operons, or clusters of more than one coding region attached to a singlepromoter, separated by only a few base pairs. The proteins encoded by each operon often collaborate on a single task, such as the metabolism of a sugar into by-products that can be used for energy (see Figure below).
Because there is no nuclear membrane to separate prokaryotic DNA from the ribosomes within the cytoplasm, transcription and translation occur simultaneously in these organisms. This is strikingly different from eukaryotic chromosomes, which are confined to the membrane-bound nucleus during most of the cell cycle. In eukaryotes, transcription must be completed in the nucleus before the newly synthesized mRNA molecules can be transported to the cytoplasm to undergo translation into proteins.
Prokaryotic DNA replication occurs at a rate of 1,000 nucleotides per second, and prokaryotic transcription occurs at a rate of about 40 nucleotides per second (Lewin, 2007), so bacteria must have highly efficient methods of accessing their DNA strands. But how?
Researchers have noted that the nucleoid usually appears as an irregularly shaped mass within the prokaryotic cell, but it becomes spherical when the cell is treated with chemicals to inhibit transcription or translation. Moreover, during transcription, small regions of the chromosome can be seen to project from the nucleoid into the cytoplasm (i.e., the interior of the cell), where they unwind and associate with ribosomes, thus allowing easy access by various transcriptional proteins (Dürrenberger et al., 1988). These projections are thought to explain the mysterious shape of nucleoids during active growth. When transcription is inhibited, however, the projections retreat into the nucleoid, forming the aforementioned spherical shape.
Other DNA Differences Between Prokaryotes and Eukaryotes
Most prokaryotes reproduce asexually and are haploid, meaning that only a single copy of each gene is present. This makes it relatively easy to generate mutations in the lab and study the resulting phenotypes. By contrast, eukaryotes that reproduce sexually generally contain multiple chromosomes and are said to be diploid, because two copies of each gene exist—with one copy coming from each of an organism’s parents.
Yet another difference between prokaryotes and eukaryotes is that prokaryotic cells often contain one or more plasmids (i.e., extrachromosomal DNA molecules that are either linear or circular). These pieces of DNA differ from chromosomes in that they are typically smaller and encode nonessential genes, such as those that aid growth in specific conditions or encode antibiotic resistance. Borrelia, for instance, contains more than 20 circular and linear plasmids that encode genes responsible for infecting ticks and humans (Fraser et al., 1997). Plasmids are often much smaller than chromosomes (i.e., less than 1,500 kilobases), and they replicate independently of the rest of the genome. However, some plasmids are capable of integrating into chromosomes or moving from cell to cell.
Perhaps due to the space constraints of packing so many essential genes onto a single chromosome, prokaryotes can be highly efficient in terms of genomic organization. Very little space is left between prokaryotic genes. As a result, noncoding sequences account for an average of 12% of the prokaryotic genome, as opposed to upwards of 98% of the genetic material in eukaryotes (Ahnert et al., 2008). Furthermore, unlike eukaryotic chromosomes, most prokaryotic genomes are organized into polycistronic operons, or clusters of more than one coding region attached to a singlepromoter, separated by only a few base pairs. The proteins encoded by each operon often collaborate on a single task, such as the metabolism of a sugar into by-products that can be used for energy (see Figure below).
Because there is no nuclear membrane to separate prokaryotic DNA from the ribosomes within the cytoplasm, transcription and translation occur simultaneously in these organisms. This is strikingly different from eukaryotic chromosomes, which are confined to the membrane-bound nucleus during most of the cell cycle. In eukaryotes, transcription must be completed in the nucleus before the newly synthesized mRNA molecules can be transported to the cytoplasm to undergo translation into proteins.
