Cell nucleus

From Eukaryote:

**Eukaryotes** are organisms whose cells have a nucleus. The nucleus is surrounded by a double membrane (commonly referred to as a nuclear membrane or nuclear envelope), with pores that allow material to move in and out.

* They also have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments, which play an important role in defining the cell's organization and shape.
* Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.

Eukaryotic cells are typically much larger than those of prokaryotes having a volume of around 10,000 times greater than the prokaryotic cell.

1. Nucleolus
2. Nucleus
3. Ribosome
4. Vesicle
5. Rough endoplasmic reticulum
6. Golgi apparatus
7. Cytoskeleton
8. Smooth endoplasmic reticulum
9. Mitochondrion
10. Vacuole
11. Cytosol
12. Lysosome
13. Centriole

## Eukaryotic cell nucleus

From Cell nucleus:

In cell biology, the **nucleus** is a membrane-bound organelle found in eukaryotic cells. The nucleus is the control center of the cell.

The cell nucleus contains all of the cell's genome organized as multiple long linear DNA molecules in a complex with a large variety of proteins, such as histones, to form chromosomes.

The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cellular cytoplasm, and the nuclear matrix (which includes the nuclear lamina), a network within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole.

Because the nuclear envelope is impermeable to large molecules, nuclear pores are required to regulate nuclear transport of molecules across the envelope. The pores cross both nuclear membranes, providing a channel through which larger molecules must be actively transported by carrier proteins while allowing free movement of small molecules and ions.

## Chromosome

From Chromosome:

A **chromosome** is a deoxyribonucleic acid (DNA) molecule with part or all of the genetic material (genome) of an organism. Most eukaryotic chromosomes include packaging proteins which, aided by chaperone proteins, bind to and condense the DNA molecule to prevent it from becoming an unmanageable tangle.

Chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes (histone octamers with part of a DNA strand attached to and wrapped around it). Chromatin fibers are packaged by proteins into a condensed structure called chromatin.

## Nucleosome

From Nucleosome:

A **nucleosome** is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores.

Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter).

Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones.

The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer. Core particles are connected by stretches of "linker DNA", which can be up to about 80 bp long.

## Gene

From Gene:

A **gene** is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA. The RNA is the template for a protein that performs a function.

The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. Some genetic traits are instantly visible, such as eye color or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas the genomes of complex multicellular organisms, including humans, contain an absolute majority of DNA without an identified function. This DNA has often been referred to as "junk DNA".

## RNA splicing

From RNA splicing:

**RNA splicing**, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns are removed and exons are joined together.

Splicing takes place within the nucleus immediately after transcription. Splicing is usually required in order to create an mRNA molecule that can be translated into protein.

For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleo proteins (snRNPs).

## Intron

From Intron:

An **intron** is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. The term *intron* refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts.

RNA splicing follows transcription and precedes translation.

Introns can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA).

Sequences that are joined together in the final mature RNA after RNA splicing are exons.

## Non-coding DNA

From Non-coding DNA:

Introns are non-coding sections of a gene, transcribed into the precursor mRNA sequence, but ultimately removed by RNA splicing during the processing to mature messenger RNA. Many introns appear to be mobile genetic elements.

Studies of group I introns from *Tetrahymena* protozoans indicate that some introns appear to be selfish genetic elements.

It was originally suggested that over 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA, while 20% of a typical prokaryote genome is noncoding.

Some introns appear to have significant biological function, possibly through ribozyme functionality that may regulate tRNA and rRNA activity as well as protein-coding gene expression, evident in hosts that have become dependent on such introns over long periods of time.

Many noncoding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of noncoding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these noncoding regions are under strong evolutionary pressure and positive selection. For example, in the genomes of humans and mice, which diverged from a common ancestor 65–75 million years ago, protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented in noncoding regions. Linkage mapping often identifies chromosomal regions associated with a disease with no evidence of functional coding variants of genes within the region, suggesting that disease-causing genetic variants lie in the noncoding DNA. The significance of noncoding DNA mutations in cancer was explored in April 2013.

## Ultraconserved regions

From Conserved non-coding sequence

Ultraconserved regions (UCRs) are regions over 200 bp in length with 100% identity across species. These unique sequences are mostly found in noncoding regions. It is still not fully understood why the negative selective pressure on these regions is so much stronger than the selection in protein-coding regions. Though these regions can be seen as unique, the distinction between regions with a high degree of sequence conservation and those with perfect sequence conservation is not necessarily one of biological significance. One study in Science found that all extremely conserved noncoding sequences have important regulatory functions regardless of whether the conservation is perfect, making the distinction of ultraconservation appear somewhat arbitrary.

## Ciliate

From Ciliate:

Unlike most other eukaryotes, ciliates have two different sorts of nuclei:

* A tiny, diploid micronucleus (the "generative nucleus," which carries the germline of the cell),
* A large, polyploid macronucleus (the "vegetative nucleus," which takes care of general cell regulation, expressing the phenotype of the organism).

The micronucleus passes its genetic material to offspring, but does not express its genes.

Periodically the macronuclei must be regenerated from the micronuclei.

Only the DNA in the micronucleus is passed on during sexual reproduction (conjugation). On the other hand, only the DNA in the macronucleus is actively expressed and results in the phenotype of the organism. Macronuclear DNA is derived from micronuclear DNA by amazingly extensive DNA rearrangement and amplification.

The macronucleus begins as a copy of the micronucleus. The micronuclear chromosomes are fragmented into many smaller pieces and amplified to give many copies. The resulting macronuclear chromosomes often contain only a single gene. In Tetrahymena, the micronucleus has 10 chromosomes (five per haploid genome), while the macronucleus has over 20,000 chromosomes.

During development of the macronucleus, numerous "Internal Eliminated Sequences" (IESs) are deleted and the remaining gene segments, Macronuclear Destined Sequences (MDSs), are spliced together to give the operational gene.

More than 95% of micronuclear DNA is eliminated during spirotrich macronuclear development.

## Paramecium

From Paramecium:

Like all ciliates, *Paramecium* has a dual nuclear apparatus, consisting of a polyploid macronucleus, and one or more diploid micronuclei. The macronucleus controls non-reproductive cell functions, expressing the genes needed for daily functioning. The micronucleus is the generative, or germline nucleus, containing the genetic material that is passed along from one generation to the next.

Fission may follow conjugation, a sexual phenomenon in which *Paramecium* of compatible mating types fuse temporarily and exchange genetic material. During conjugation, the micronuclei of each conjugant divide by meiosis and the haploid gametes pass from one cell to the other. The gametes of each organism then fuse to form diploid micronuclei. The old macronuclei are destroyed, and new ones are developed from the new micronuclei.

## Macronucleus

From Macronucleus:

A **macronucleus** is the larger type of nucleus in ciliates. Macronuclei are polyploid. The macronucleus contains hundreds to thousands of chromosomes, each present in many copies.

During conjugation, the macronucleus disintegrates, and a new macronucleus is formed by karyogamy of the micronuclei.

## Polytene chromosome

From Polytene chromosome:

**Polytene chromosomes** are large chromosomes which have thousands of DNA strands. The chromosomal strands are formed after repeated division of the chromosome in the absence of cytoplasmic division. This type of division is called endomitosis.

Polytene chromosomes, at interphase, are seen to have distinct thick and thin banding patterns.

The polytene chromosome contains two types of bands, dark bands and interbands. The dark bands are darkly stained and the inter bands are lightly stained with nuclear stains. The dark bands contain more DNA and less RNA. The interbands contain more RNA and less DNA. The amount of DNA in interbands ranges from 0.8 - 25%.

## Internally eliminated sequences

The macronucleus contains no or very little junk dna.

From Chilodonella uncinata:

Internally eliminated sequences (IES) are noncoding regions of the germ-line genome found in Ciliates. They are defined as sections of DNA removed from the diploid micronuclear genome during which a copy of the micronuclear genome is converted to the macronuclear genome.

## Nucleolus

From Nucleolus:

The **nucleolus** is the largest structure in the nucleus of eukaryotic cells. It is the site of ribosome biogenesis.

This assembly not only involves the rRNA, but ribosomal proteins as well. The genes encoding these r-proteins are transcribed by pol II in the nucleoplasm by a "conventional" pathway of protein synthesis (transcription, pre-mRNA processing, nuclear export of mature mRNA and translation on cytoplasmic ribosomes). The mature r-proteins are then "imported" back into the nucleus and finally the nucleolus. Association and maturation of rRNA and r-proteins result in the formation of the 40S (small) and 60S (large) subunits of the complete ribosome. These are exported through the nuclear pore complexes to the cytoplasm, where they remain free or become associated with the endoplasmic reticulum, forming rough endoplasmic reticulum (RER).