Which of the following terms describes the DNA–protein complexes that look like beads on a string?

a) 30-nanometer fiber.

b) Histones.

c) Nucleosome.

d) Chromatin.

Diagram of DNA wrapped around nucleosome histones
Diagram of DNA wrapped around nucleosome histones

The correct answer is c) Nucleosome.

A nucleosome is a structure that is formed when DNA is attached to two pairs of four histone proteins. These histones consist of the types: H2A, H2B, H3 and H4, and they form a structure called an octamer. Histone 1 protein acts to bind these more closely to the DNA.

Several nucleosomes occur at every 200 base pairs along the DNA, and they make the chromatin appear to have beads on a string when the structure is unfolded.

Chromatin material is a series of nucleosomes and DNA which occurs in different forms depending on if the cell is undergoing cell division or genetic transcription.

Processes of methylation and acetylation are important in changing the form of the chromatin to enable gene transcription and mitosis or meiosis to occur.

In both processes, chemical modifications of the histone proteins occur. This changes how tightly they are bound to DNA molecules. Acetylation involves the addition of acetyl groups which loosens the structure of the chromatin. This then enables DNA transcription and ultimately gene expression to be possible.

Deacetylation has the reverse effect and increases the packing of the material. Methylation is the addition of a methyl group to various histones.

The methylation either loosens the chromatin or makes it pack more tightly depending on where the group is added on the protein. Methylation thus can either increase or decrease transcription and genetic expression.

Nucleosome

The DNA of eukaryotic cells is found in a membrane-bound organelle known as the nucleus. This nucleic acid molecule also attaches to proteins known as histones to form chromatin material. Modifications to the structure of the chromatin enable such processes as DNA replication and transcription processes.

A nucleosome is a name used to describe the situation when four pairs of histones attach to DNA such that the entire unfolded structure looks like beads on a string. The nucleic acid though usually is wrapped around the proteins.

Each nucleosome consists of an octamer, which describes the 8 histones. The four histones that make up the octamer are H3, H4, H2A, and H2B. A nucleosome can be found at about every 200 base pairs along a molecule of DNA. A histone known as H1 helps to seal the structure by binding to the DNA where it attaches to the core of the octamer.

The nucleosomes become coiled up to form a structure called a solenoid, which is a spiral structure that is 30 nm in size. The reason for this arrangement is that it enables the chromatin to easily be packed into the nucleus.

Chromatin types

The chromatin has to be able to change form to some extent in order for transcription of DNA to occur. When the chromatin is very condensed it is known as heterochromatin. For transcription to occur the material has to become less condensed to form euchromatin.

It is important to realize that chromatin also becomes modified during the first stage of cell division in mitosis and meiosis. Chromatin becomes visible during this time and a centromere with kinetochore proteins have to be organized and ready for the attachment of spindle fibers.

Researchers have found that there is another type of chromatin that is different from the euchromatin and heterochromatin.

Centromeric chromatin (CEN) is a type of material located at the centromere region of chromosomes. It consists largely of nucleosomes with H3 and H3 variant histone proteins known as CENP-A nucleosome.

The CEN may be involved in helping organize the centromere of the chromosomes and also may play a role in influencing gene expression.

Modifications of chromatin

Histones are globular proteins that have N-terminal tails which form bonds with the DNA. Gene transcription is the necessary first step of protein synthesis. This is the stage when a messenger RNA molecule is made from the coding strand of the DNA molecule.

In order for transcription to occur the chromatin has to be modified and unpacked so that the DNA helix can unwind and bonds between bases can break.

Scientists have found that transcription, and hence, gene expression, are carefully controlled by processes of acetylation and methylation. These processes both involve chemical changes to the histone proteins that are found in the octamer of the chromatin.

Acetylation

Acetylation is the process that assists in the unpacking of the chromatin material. The process of acetylation entails the addition of an acetyl group to some of the histone proteins on the chromatin.

The enzyme known as histone acetyltransferase catalyzes the reaction and often the process involves changes to the lysine residue on the histone.

The acetyl group of the lysine is moved from one place to another, which causes a loss of the positive charge on the residue. It is this charge that causes the strong bonding and packing of the chromatin material.

The acetylation occurs more frequently near the promoter sections of the DNA and near the 5’ end of the molecule. It, therefore, does not happen at every region along the DNA of the chromatin.

The opposite process to acetylation is deacetylation, which involves the activity of the enzyme histone deacetyltransferase. The end result of this process is to actually ensure that the chromatin is tightly packed which is achieved by the bonding of residues of the histone proteins to the DNA.

Methylation

The methylation of histones is an additional way that chromatin can be modified. This process involves a methyl group being added to an N-terminal tail of a histone protein. It either increases or decreases transcription depending on which histone is methylated.

Methylation of H3K4, H3K79, and H3K36 on H3 histone causes an increase in transcription, while it has been found that the same process acting on H3K27, H3K9, H4K20 reduces transcription activity.

References

  1. L Mariño-Ramírez, MG Kann, BA Shoemaker, et al. (2005). Histone structure and nucleosome stability.  Expert review of proteomics.
  2. T Kouzarides (2007).  Chromatin modifications and their function. Cell.
  3. WY Chen, TM Townes (2000). Molecular mechanism for silencing virally transduced genes involves histone deacetylation and chromatin condensation. Proceedings of the National Academy of Sciences.
  4. Editors of Encyclopedia Britannica (2018). Histone. Retrieved from Encyclopedia Britannica.
  5. JY Lee, TL Orr-Weaver (2001). Chromatin. Retrieved from sciencedirect.com.

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