Packaging of DNA into Microscopic Nucleus : Packaging of DNA into Microscopic Nucleus Packing ratio
Organization of DNA within Prokaryotes
Organization of DNA within Eukaryotes
Journey of DNA : Journey of DNA Central dogma proposed by Francis Crick in 1958 proves that the information flows from DNA to RNA and then to proteins
Packing ratio : Packing ratio Definition- The ratio obtained when the length of DNA is divided by the length into which it is packaged.
Example – There are 4.6 x 107 bp present in the shortest human chromosome. To obtain the length of DNA the number of base pairs is multiplied with .34nm (distance between the two base pairs). The length of DNA so obtained comes to 14,000 µm. The most condensed form of DNA during mitosis measures 2 µm in length. Hence the packing ratio comes to 7000 (14,000/2).
Organization of DNA within Prokaryotes - : Organization of DNA within Prokaryotes - DNA is organized into a structure called nucleoid.
The negative charge of DNA is counteracted by the positively charged polyamines such as spermine and spermidine.
Abundant small proteins like H-NS give a compact supercoiled structure to the DNA.
DNA gyrase enzyme opens the DNA during replication.
Structures of polyamines which interact with DNA : Structures of polyamines which interact with DNA Image reference : http://www.ncbi.nlm.nih.gov/books/NBK21500/
Organization of DNA within eukaryotes : Organization of DNA within eukaryotes Chromosomes-In eukaryotic organisms DNA is present along with some basic proteins in the form of chromosomes within the nucleus.
Chromatin – It is a unit of analysis of a chromosome and gives a general idea of the nature of a chromosome
Histones : Histones They are the positively charged basic proteins.
They are of 5 major types and contain amino acids residues like lysine and arginine.
The five major types are H1, H2A, H2B, H3 and H4.
Formation of nucleosome : Formation of nucleosome Histone octamer acts like a core and consists of two copies of each of these histone proteins H2A, H2B, H3 and H4.
The duplex DNA which is wrapped around the histone octamer is approx 147bp in length.
This small basic unit is termed as nucleosome.
Nucleosomes together with DNA appear like beads on a string.
At this stage the DNA is 10nm in diameter and attains a packing ratio of about 6.
Structure of a single nucleosome : Structure of a single nucleosome Image reference:http://www.accessexcellence.org/RC/VL/GG/nucleosome.php
Role of Histone1 or H1 : Role of Histone1 or H1 It holds the DNA which is wrapped around the nucleosome in a proper position
The linker DNA is made up of approximately 20-60 bp and the H1 binds to the linker DNA. This gives the stability to the zig-zagged 30 nm chromatin fiber.
Formation of chromatin fiber or solenoid fiber : Formation of chromatin fiber or solenoid fiber From the beads on a string stage the DNA coils in such a way that at least 6 nucleosomes are packed per coil.
In this stage DNA attains a diameter of 30 nm and this level of organization is known as 30 nm fiber or solenoid fiber.
When the chromatin is extracted from isotonic buffers it appears like a 30 nm fiber.
At this stage it attains a packing ratio of 10.
This stage is seen during interphase in the cell cycle.
Stages after solenoid fiber : Stages after solenoid fiber Later the solenoid fiber get further coiled and condensed and is organized into loops, scaffolds and domains to obtain cytologically visible threads known as chromatids.
The looping is such that the base of the loops is attached to the same protein skeletal work.
Some metallic ions like calcium and copper along with non histone proteins help in the looping process.
This increases the packing ratio to about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes
Levels of organization of DNA : Levels of organization of DNA Image reference - http://plantcellbiology.masters.grkraj.org/html/Plant_Cell_Genetics1-Chromosomes.htm
Non Histone proteins : Non Histone proteins There are about 750-2000 different kinds of Non histone proteins and examples of most abundant ones are Topoisomerases and High mobility group of proteins (HMGs).
Functions mostly served by them are
Helping in the structural organization of chromatin fibers
Maintaining stability of the chromatin fibers
Involved in gene regulation
Histone modifications : Histone modifications Acetylation- Acetyl groups (CH3CO-) are added to Lysine residues.
Acetylation
DNA is stopped from getting further condensed
Active transcription of the genes takes place
Histone modifications : Histone modifications Phosphorylation: Addition of phosphate groups to serines and threonines.
Methylation: Addition of methyl groups to lysines and arginines.
Euchromatin and Heterochromatin : Euchromatin and Heterochromatin Some general characters of heterochromatin
It is densely packed and is found in the regions of chromosomes where there are few or no genes such as
Centromeres
Telomere
It shows a reduced level of crossing over and replicates during the later stages in the S phase of the cell cycle.
It is enriched with transposons and other junk DNA
The genes in the heterochromatin are inactive that is they are less transcribed.
The transcriptionally active regions are known as euchromatin regions
Euchromatin and Heterochromatin : Euchromatin and Heterochromatin Some general characters of euchromatin
Most parts of the chromosomes which are rich in transcriptionally active genes are termed as euchromatin regions.
They are made up of loosely packed 30nm fibers.
These regions are separated from heterochromatin by insulators.
The histone proteins in this region show increased acetylation.
What happens to nucleosomes during transcription? : What happens to nucleosomes during transcription? The promoter region of the gene is blocked by a nucleosome and the transcription factors cannot access this promoter region.
To begin the transcription of a particular gene the nucleosome is expelled or in some other cases it slides along the DNA so that the transcription factors can bind the promoter region.
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