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Genome structure

The eukaryotic genome is composed of multiple linear chromosomes.

The number of chromosomes carried by an organism varies among species.

The human genome consists of 23 pairs of chromosomes. The adder's-tongue fern (a non-flowering plant) has over 600 pairs of chromosomes.

The cell nucleus is only 5-8 micrometres across. Yet it may contain a genome of 10 billion bases over 3 metres long.

Eukaryotic DNA is compressed and wound around histones so that it can fit in the nucleus.

Human chromosomes during metaphase.
Human chromosomes during metaphase.

In a eukaryotic chromosome, DNA is bound to proteins. This combination of DNA and protein is called chromatin. Chromatin packages and protects the DNA.

The most important proteins in chromatin are histones. They make up about half the mass of a eukaryotic chromosome.

Histones act as "spools" around which DNA winds. Histones are positively charged due to their high proportion of arginine and lysine, while DNA is negatively charged.

Tightly wound DNA prevents the enzymes for transcription from reaching the genetic material. Consequently, histones can regulate gene expression.

Non-coding DNA is any part of the genome that does not code for proteins.

Both eukaryotes and prokaryotes have sections of non-coding DNA.

Eukaryotes have far more non-coding DNA than prokaryotes.

About 98% of the human genome is estimated to be non-coding; in prokaryotes, only around 12% of the genome is non-coding.

In general, the more complex the organism, the more non-coding DNA it will have.

Non-coding DNA is essential for both prokaryotes and eukaryotes. Some non-coding DNA is transcribed into RNA but does not code for proteins. Other sections of non-coding DNA is not transcribed.

It consists of sections of DNA that control gene expression, such as promoters, enhancers, silencers and replication sites.

Introns, telomeres and centromeres are also examples of essential sequences of non-coding DNA that are unique to eukaryotes.

DNA packaging in the eukaryotic chromosome reflects how tightly chromatin is bound to proteins such as histones.

Chromatin is found in three states, dependent on the position in the cell cycle.

During mitosis, the chromosome needs to be compact to prevent damage to the DNA during chromosome separation. As a result, DNA is bound tightly to proteins.

During interphase, the chromatin is less compact (the proteins are less tightly bound).

During transcription, transcription factors and RNA polymerase must be able to bind easily. Chromatin is most relaxed at this point.

A nucleosome consists of a cluster of eight histone proteins with a section of DNA wrapping around the outside of them.

Short stretches of DNA join each nucleosome together. These short stretches are known as linker DNA.

The arrangement of nucleosomes joined by linker DNA gives chromatin the appearance of 'beads on a string'.

Sections of chromatin will take on this structure when undergoing transcription. In this formation, transcription factors and RNA polymerase are able to bind to the DNA.

We can see the beads on a string structure in this chicken DNA.
We can see the beads on a string structure in this chicken DNA.

The 30 nanometre fibre is the form of coiling of DNA usually found in the nucleus. This structure enables vast lengths of DNA to fit into a nucleus.

The nucleosome "beads on a string" structure is condensed into a coil with a 30 nm diameter. The extra coiling is achieved by introducing an extra histone protein called histone H1.

During mitosis, the chromatin becomes highly condensed to allow for nuclear division. This prevents damage as the chromosomes are separating.

More proteins are added, causing the 30 nm fibre to loop around itself and create an even more compact structure.

During this phase, chromosomes are visible under a light microscope.

The prokaryotic genome is far simpler than the eukaryotic genome.

The prokaryotic genome usually consists of a single circular chromosome. It may contain additional independently replicating strands. These strands are called plasmids.

The prokaryotic genome is much smaller than the eukaryotic genome. This is partly explained by the fact that it carries fewer genes, but is mainly because it has far less non-coding DNA.

The majority of prokaryotic chromosomes lack structural features that are universal in eukaryotes, including telomeres, centromeres and introns.

Bacterial chromosomes also lack histones and use a different method to condense their DNA.

Non-coding DNA is often considered 'junk', meaning it has no known function. It is a common misconception that all of the DNA within the cell codes for proteins.

In fact, non-coding DNA is essential for both prokaryotes and eukaryotes. The sections of DNA that code for polypeptides are called genes. Genes account for only a small percentage of eukaryotic DNA.

Introns are regulatory regions in eukaryotes that do not code for proteins. They control transcription and are removed after transcription.

Introns are rare in prokaryotes. Prokaryotic genes tend to be organised into groups known as operons. Operons code for proteins that serve similar functions.

Telomeres have a structural function. They are non-coding regions of DNA that help to prevent the chromosome from being damaged.

Some non-coding DNA sections indicate where a gene starts and ends. Other sections contain sequences that allow enzymes to bind to the DNA.

Introns are removed from RNA and DNA.
Introns are removed from RNA and DNA.

Eukaryotes carry far more non-coding DNA than prokaryotes. Several reasons have been proposed to explain this:

  • The eukaryotic genome is more complex and so needs more non-coding DNA to regulate it.

    As a result, eukaryotes carry larger regulatory sequences, have more replication origins and possess introns, centromeres and telomeres.

  • There is selection pressure for prokaryotes to reduce the sizes of their genomes. Prokaryotes are small organisms with less metabolic power.

    Prokaryotes save energy by simplifying their genomes and removing non-essential sequences.

Large stretches of non-coding DNA between eukaryotic genes are thought to have an evolutionary benefit in limiting the effect of mutations.

The centromere is the point where two identical sister chromatids join.

The centromere is a region of highly condensed DNA near the centre of a chromosome.

This essential chromosomal sequence is found in all eukaryotic chromosomes. Centromeres do not code for RNA or polypeptides. Centromeres are therefore classified as non-coding DNA.

Sister chromatids are the identical chromosomes that are the result of DNA replication.

The chromatids remain attached until the cell prepares for mitosis or meiosis.

These chromosomes are in metaphase. The centromere of one is indicated in red.
These chromosomes are in metaphase. The centromere of one is indicated in red.

During mitosis, spindle fibres attach to the centromere and control its position in the cell. The centromere divides when the fibres contract.

This allows the two sister chromatids to move to opposite sides of the cell, leading to nuclear division.

In meiosis I, the centromeres remain intact to ensure that the two sister chromatids remain together. The homologous chromosomes separate but the chromatids remain together.

Subsequently, during meiosis II the centromeres divide. This separates the sister chromatids.

These chromosomes are in metaphase. The centromere of one is indicated in red.
These chromosomes are in metaphase. The centromere of one is indicated in red.

Telomeres are non-coding chromosomal sequences present in all eukaryotes.

Telomeres are regions of repetitive DNA sequences located at each end of a chromosome. They are essential for DNA replication.

DNA is unable to replicate an entire linear chromosome. As a result, after each replication, about 2000 base pairs are lost from the ends of each eukaryotic chromosome on the lagging strand.

Telomeres are present on the ends of chromosomes to prevent degradation of the coding sequences (i.e. genes).

If genes were destroyed every time the cell replicated through mitosis, the cell would quickly fail to function properly and would most likely die.

Prokaryotes do not have telomeres. They solve the end replication problem by having circular chromosomes.

Generalised eukaryotic chromosome
Generalised eukaryotic chromosome

Telomeres play a role in cellular aging. They dictate how many times the cell can divide though mitosis before essential coding DNA is lost.

Most cells can only divide about 50 to 70 times. Beyond this, the telomere sequence gets so short that the cell stops dividing in order to protect its DNA.

Scientists believe that telomere length influences aging and places an upper limit on the maximum lifespan of an organism.

Diseases that affect telomere length highlight the importance of telomeres in cell death and aging.

People who have the disease dyskeratosis congenita have telomeres that shorten at faster rates than usual. As a result, this disease causes premature aging and death.

In some cells, such as epithelial cells, cell turnover is very high. This seems to contradict the idea that cells can only divide a few times.

These cells originate from a population of self-renewing stem cells. Stem cells are able to divide without losing their telomeres.

The enzyme telomerase is able to extend telomeres by adding nucleotides to the ends of the chromosome. It is present in gametes to ensure that newly formed embryos have long telomeres.

Telomeres are reduced after each replication of DNA because of shortening on the lagging strand. Telomerase adds telomere DNA back on after replication.

In most cells, this enzyme is switched off after differentiation. This means that the cell can only replicate a limited number of times before dying.

Telomerase is sometimes turned back on in late-stage cancers. This explains how a cancer cell can divide many times without dying.

Cells called stem cells also have telomerase activated. These are cells that have not yet differentiated - they have the potential to become any type of cell within the body.

Comparison of the eukaryotic and prokaryotic genome

Feature Eukaryotes Prokaryotes
Location of genome Nucleus Cytoplasm
Size in million bases (Mb) 10 - 10 000 0.6 - 10
Shape Linear Circular
Number of chromosomes Nearly always more than one Nearly always one
Number of genes 6000 - 30000 500 - 4000
Ploidy level Diploid (usually) Haploid
Non-coding regions? Mostly non-coding Mostly coding
Plasmids No Yes
Introns Yes No
Operons No Yes
Telomeres Yes No
Histones Yes No
Origin(s) of replication Many One