Question

How is DNA configured into

chromatin, compacted to heterochromatin and

reversed to chromatin?

How are genes organized on a DNA molecule? Consider prokaryotes and

eukaryotes for gene organization strategies at the DNA level.

please answer both

Answer 1

:DNA configured into chromatin:
Cells contain a nucleus surrounded by a nuclear membrane in eukaryotic cells,and a nuclear region in the prokaryotic cells.

In a non-dividing cell the nucleus is filled with a thread-like material known as"chromatin".

Chromatin is made up of DNA and proteins (mainly histones and some non-histone acidic proteins).

The chromosomes themselves are macromolecular entities that must be synthesized, packaged, protected, and properly distributed to daughter cells at cell division.

•:The large amounts of DNA are
packed into a cell:•

The packaging of tremendous amount of genetic information into the small space within a cell has been called the ultimate storage problem.
Chromosomal DNA exist in the form of very long molecules, which must be tightly packed to fit into the small confines of a cell.
The structure of DNA can be considered at three hierarchical levels:

a.

The primary structure of DNA is its nucleotide sequence

b.

The secondary structure is the double stranded helix

c.

The tertiary structure refers to higher order folding that allow DNA to be packed into the confined space of a cell.

•Supercoiling•

• One type of DNA tertiary structure is supercoiling which takes place when the DNA helix is subjected to strain by being over wound or under wound.

• Energy is used to add or remove any tums, strains is placed on the molecule,causing the helix to super coil, or twist on itself.

• Molecule that are over rotated exhibit positive supercoiling.
• Under rotated molecules exhibit negative supercoiling.
• Supercoiling is a partial solution to the cells DNA packing problem because super coiled DNA occupies less space than relaxed DNA.

• Supercoiling relies on topoisomerases enzymes that add or remove rotation from the DNA helix by temporarly breaking the nucleotide strand, rotating the ends around each other, the rejoining the broken ends.

• Overrotation or underrotation of a DNA double helix places strain on the molecule, causing it to supercoil.

• Supercoiling is controled by topoisomerase enzymes.
• Most cellular DNA is negetively supercoiled, which eases the seperation of nucleotide strands during replication and transcription and allow DNA to be packed into small spaces.

:-EUKARYOTIC CHROMOSOME-:

• Individual eukaryotic chromosome

contain enormous amounts of DNA.

• Chromosome are in an elongated

relatively uncondensed state during
interphase of the cell cycle.

•Chromatin •

• Walther Flemming first used the term Chromatin in 1882. At that time, Flemming assumed that within the nucleus there was some kind of a nuclear-scaffold.

Chromatin, which consists of DNA complexed to proteins, is the material that makes up eukaryotic chromosomes.

The most abundant of these proteins are the five types of positively charged histone proteins H1, H2A, H2B, H3, and H4.

Variant histones may at times be incorporated into chromatin in place of the normal histones.

In non-dividing cells there are two types of chromatin: euchromatin and heterochromatin.

•Histones protein•

The histone octamer and associated DNA that form the nucleosome combine with histone H1 to form the chromatosome.

The addition of H1 to a nucleosome results in protection of an additional 20 to 22 bp of linker DNA adjacent to the nucleosome, and thus H1 is often referred to as the linker histone.

Only one Hl subunit is present per chromatosome, unlike the core histones,which are present in two copies each.

DNA binding in H1 is intrinsic to the central globular region, which contains two DNA-binding sites.

• Hi binds only one of the linker DNA strands, and the second DNA site in histone H1 binds to the central region of the DNA supercoil in the nucleosome.

Histones are rich in the basic amino acids arginine and lysine, which together make up about 25% of the amino acid residues in any given histone protein.

•

Histone proteins are highly conserved among eukaryotic cells.

Histones H3 and H4 are nearly identical in all eukaryotes, suggesting strict conservation of
their functions.

Histones H1, H2A, and H2B show less sequence similarity, but on the whole, they are more conserved than other types of proteins.

Salt bridges between positively charged histones and negatively charges DNA play a major
role in stabilizing DNA-histone complex.

•Why packaging is needed•

o DNA is roughly 3 meter long and it has to be packed in nucleus which is few
micrometres in diameter, hence higher order of packaging is required.
•There are various order of packaging
a. First order of packaging - Nucleosome
b. Second order of packaging - Solenoid fibre
c. Scaffold loop Chromatids Chromosome are third order of packaging.

•First level of packing: Nucleosome•

Nucleosome = DNA + core
histones
DNA wrapped twice around
an octamer of core histones
consisting of:

2 of each core histone: H2A,
H2B, H3, H4
Note: Hi is not part of the
nucleosome, but is attached to

the DNA near the nucleosome
10 nm in diameter

Core of eight
histone molecules
•Nucleosome •
The nucleosome consists of a core particle of eight histone proteins and DNA that wraps around the core.Chromatosome, which are nucleosomes bound to an H1 histone, are separated by linker DNA.

• Nucleosmes fold to form a 30-nm chromatin fiber, which appears as a series of loops that pack to create a 250 nm wide fiber.

• Helical coiling of the 250 nm fiber produces a chromatid.

•DNA compacted to heterochromatin•
DNA wraps around histone proteins, forming nucleosomes and the so-called "beads on a string" structure (euchromatin). Multiple histones wrap into a 30-nanometer fibre consisting of nucleosome arrays in their most compact form (heterochromatin).

•Heterochromatin vs. Euchromatin•

Compaction level of interphase chromosomes is not uniform Euchromatin

Less condensed regions of chromosomes
b. Transcriptionally active
c. Regions where 30 nm fiber forms radial loop domains

» Heterochromatin
2 Tightly compacted regions of chromosomes

Transcriptionally inactive (in general)
Radial loop domains compacted even further
heterochromatin is in such a condensed structure that it does not enable DNA and RNA polymerases to access the DNA, therefore preventing DNA replication and transcription. There are two main types of heterochromatin: constructive heterochromatin and facultative heterochromatin. Heterochromatin represents less than 10% of the human chromatin, with euchromatin accounting for most of it—over 90%.
•prokaryotes and eukaryotes for gene organization strategies at the DNA level •
When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid.
The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure 2). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.