Organization of genetic material on chromosome

How genetic material organized on a chromosome

1. Organization of genetic material on chromosome

2. What is Genetic material? The genetic material of a cell or an organism refers to those materials found in the nucleus, mitochondria and cytoplasm, which play a fundamental role in determining the structure and nature of cell substances, and capable of self-propagating and variation. A chromosome is a DNA molecule with part or all of the genetic material (genome) of an organism. The genetic information of most living organisms is stored in deoxyribonucleic acid (DNA).  Chromosomes vary widely between different organisms. Some species such as certain bacteria, which lack histones, also contain plasmids or other extrachromosomal DNA.

3. Each eukaryotic chromosome contains one giant molecule of DNA packaged into 10 nm ellipsoidal beads called nucleosomes. In prokaryotes and viruses , the DNA is often densely packed and organized. DNA usually exists as a double helix, with two strands of opposite polarity, held together by hydrogen bonds between the complementary bases. Adenine is paired with thymine with double hydrogen bonds, whereas guanine is paired with cytosine with triple hydrogen bonds.  The specific base sequence and their complementarity make it a unique feature for each organism to store and transmit genetic information.

4. DNA is not only a genetic material in a cell or an organism. RNA also used by viruses as a genetic material. Ribonucleic acid (RNA) usually exists as a single-stranded molecule containing uracil instead of thymine. The main function of the genetic material is to store information required to produce an organism The DNA molecule does that through its base sequence. DNA sequences are necessary for 1. Synthesis of RNA and cellular proteins 2. Proper segregation of chromosomes 3. Replication of chromosomes 4. Compaction of chromosomes

5. Genotypic Function: Replication Phenotypic Function: Gene Expression Evolutionary: Allows for Mutation Properties Of Genetic Material Repository of genetic information Info must be accessible, allow cell to respond Info must be in form transmissible to progeny Physical and chemical stability Potential for heritable change Functions of the Genetic Material

6. The basic differences between the prokaryotes and the eukaryotes is that the prokaryotes are unicellular and lack any membrane bound organelles such as the nucleus, mitochondria, chloroplast, lysosome etc. while eukaryotes on the other hand have well defined membrane bound organelles each with its distinct structure and function. In addition to the chromosomal DNA, eukaryotes contain organelle DNA in the mitochondria (in animal cells) and chloroplast (in plant cells). While Prokaryotes also contain extrachromosomal DNA but in the form of plasmids that replicate within the same cell.

7. Apart from these differences, their genetic makeup ( i.e. , organization) of DNA also differs. Organization of DNA in prokaryotes Organization of DNA in eukaryotes Organelle DNA: Mitochondria and Chloroplast 3. Organization of DNA in viruses

8. Organization of DNA in prokaryotes Prokaryotic cells do not contain a nucleus or any other membrane-bound organelle. Prokaryotes generally have a small, circular (sometimes linear) DNA present in the nucleoid region. There is a single origin of replication. The genome size ranges in between 10 4  to 10 7 bp with a high gene density. The entire genome comprises almost of genes.  They are polycistronic i.e. multiple genes are transcribed through the same promoter. 

9. BACTERIAL GENOME Bacterial chromosomal DNA is usually a circular molecule that is a few million nucleotides in length. Escherichia coli :: 4.6 million base pairs Haemophilus influenzae :: 1.8 million base pairs A typical bacterial chromosome contains a few thousand different genes Structural gene sequences (encoding proteins) account for the majority of bacterial DNA The no transcribed DNA between adjacent genes are termed intergenic regions

10. Key Features Most, but not all bacterial species contain circular chromosomal DNA. A typical chromosomes is a few million base pairs in length. Most bacterial species contain a single type of chromosome, but it may be present in multiple copies. Several thousand different genes are interspersed throughout the chromosome. One origin of replication is required to initiate DNA replication. Short repetitive sequences may be interspersed throughout the chromosome.

11. To fit within the bacterial cell, the chromosomal DNA must be compacted about a 1000-folds. This involves the formation of loop domains. The number of loops varies according to the size of the bacterial chromosome and the species. E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each.

12. DNA super coiling is a second important way to compact the bacterial chromosome. Supercoiling within loops creates a more compact DNA

13. Organization of DNA in eukaryotes Eukaryotic species contain one or more sets of Chromosomes. The total amount of DNA in eukaryotic species is typically greater than that in bacterial cells They have multiple linear chromosomes (2 to <50). The genome size ranges from 10 8  to 10 11 bp that encodes a large number of proteins. Chromosomes in eukaryotes are located in the nucleus. They have a low gene density due to the presence of enormous amounts of non-coding regions that include the introns (intervening sequences within the genes, split genes), intervening sequences (sequences between the genes)and genome wide repeats.

14. They are monocistronic i.e. one gene is under the control of one promoter. The chromosomes have multiple origin of replication sites throughout its length (30-40kb apart). Centromeres, telomeres, heterochromatic and euchromatic regions are distinctly present on the chromosome.  Chromosome duplication and segregation takes place during different phases of the cell cycle which is regulated by several checkpoints.  Three types of RNA polymerases are present of which RNA Pol II is involved in transcription. The primary transcript contains exons (coding sequences) along with the intervening introns (non-coding sequences).

15. Another feature of the eukaryotic genome is selective amplification i.e. specific genes are expressed in specific cell types. For synthesis of functional proteins, the introns are removed by RNA splicing. Alternate splicing also exists that lets many proteins to be synthesized from the same mRNA by different combinations of exons. Three types of DNA sequences are required for chromosomal replication and segregation Origins of replication Centromeres Telomeres

16. Eukaryotic chromosomes are usually linear. A typical chromosome is tens of millions to hundreds of millions of base pairs in length. Eukaryotic chromosomes occurs in sets. Many species are diploid. Which means that somatic cells contains 2 sets of chromosomes. Each chromosome contains a centromere that forms a recognition site for the kinetochore proteins. Telomere contains specialized sequences located at both ends of the linear chromosomes. Repetitive sequences are commonly found near centromeric and telomeric regions. A Typical Chromatid Key Features

17. DNA is about 3 meters long and it has to be packed in a nucleus, which is only a few micrometers in a diameter. Hence highly coiled structure is required. Chromatin is the material of which the chromosomes of an organisms other than bacteria (i.e. eukaryotes) are composed, consisting of protein, RNA, and DNA. The compaction of linear DNA in eukaryotic chromosomes involves interactions between DNA and various proteins The DNA + histone =  chromatin  The primary function of  chromatin  is to compress the DNA into a compact unit that will be less voluminous and can fit within the nucleus. Eukaryotic Chromatin Compaction

18. NUCLEOSOMES It is a basic unit of chromatin structure , consisting of histone octamers wrapped in 146 base pairs (bps) of DNA or The repeating structural unit within eukaryotic chromatin is the nucleosome. It is composed of double-stranded DNA wrapped around an octamer of histone proteins. An octamer is composed two copies each of four different histones

19. Structure of connected nucleosomes resembles “beads on a string. This structure shortens the DNA length about seven-fold Nucleosome showing core histone.

20. Formation of Nucleosomes Core particle Chromatosome Nucleosome Core Particle: It consist of 146 bp of DNA wrapped 1.8 times in a left handed helix around the outside of an octamer of histone. Chromatosome : The core particle interacts with one molecule of histone H1 to form a particle containing 166bp of DNA called chromatosome Nucleosome : The chromatosome links with the linker DNA forming a nucleosome containg 200 bp of DNA

21. Chromosomal Proteins The chromosomes of eukaryotes are made up of DNA and proteins. There are 2 major types of proteins associated with DNA in the chromatin.

22. Histone proteins are basic. There are five types of histones 1. H1 3. H2B 2. H2A & 4. H3 5.H4 Two of each make up the octamer Each histone consist of a : N - terminal , which is hydrophobic. C – terminal , which is hydrophilic. Central globular structure , which forms the central molecule. H1 is the linker histone Binds to linker DNA also binds to nucleosomes but not as tightly as are the core histones

23. Histones lack tryptophan. At normal pH of the cell the histones have net positive charge that facilitates their binding to the negatively charged DNA This positive charge is found mainly on the amino group of the side chains of the basic amino acids. They contain many positively-charged amino acids 1. Lysine 2. Arginine These bind with the phosphates along the DNA backbone

24. Histone type Common basic residues Molecular weight H1 Lysine rich 23 kDa Protein H2A Slightly serine rich more lysine rich 13,960 Da protein H2B Slightly serine rich more lysine rich 13,744 Da protein H3 Arginine rich 15,242 Da protein H4 Arginine rich 11,282 Da protein

25. Non Histones They are all the proteins associated with the DNA apart from the histones. They are very different from histones. They are acidic proteins i.e. have a net negative charge and likely to bind the positive charged histones. Play a role in the organization and compaction of the chromosomes. Nucleosomes showing linker histones and non histones proteins.

26. Solenoid model of Nucleosomes According to this model , the 10 nm fiber of nucleosomes gets coiled upon itself to form 30nm wide helix. This 30 nm structure is called as solenoid. It has 5 or 6 nucleosomes per helix. The histone N-terminal tails direct the DNA to wrap around the histone octamer disc. These N-terminals are thus required for the formation of 30 nm fiber as they interact with adjacent nucleosomes by making multiple H-bonds and thus stabilizing the 30 nm fiber.

27. DNA Packaging

28. Organelle DNA: Mitochondria and Chloroplast In eukaryotic cells mitochondria (in animal) and chloroplasts (in plants) contain organelle DNA in addition to the nuclear DNA. mtDNA is circular loop with a size of 16.5 kb. It is not associated with any histone proteins and is susceptible to somatic mutations. The DNA has four main regions – D loop, r RNA genes, t RNA genes and the protein coding genes.  Chloroplast DNA on the other hand consists of closed circular DNA with an approximate size of 1,21,024bp. It contains nearly 128 genes. The number of intervening sequences is very low. According to the Endosymbiotic Theory proposed by Lynn Margulis, mitochondria and chloroplast were a result of endocytosis of aerobic bacteria and photosynthetic bacteria respectively.

29. Organization of DNA in viruses Viruses do not have cells. A viral particle is made up of nucleic acids in the core and is enclosed within a protein capsule (or capsid). A viral genome is a term used as in whole of the genetic material. Also termed the viral chromosome Their genomes may have DNA or RNA in single stranded (ss) or double stranded (ds) & Circular or linear in form as the genetic material. The topology of the genetic content can be linear, circular or even in segmented form.

30. DNA viruses are also categorized into small and large DNA viruses. They have a genome organization with many features similar to eukaryotic genomes. DNA is associated with histone proteins. Since viruses are obligate intracellular parasites, their genetic code matches that of the host machinery. The viral genome contains all the essential genes that the organism requires for perpetuation which includes genes for synthesis of RNA, proteins, replication, compaction to fit within the capsid and segregation of the chromosomes.

31. GENERAL STRUCTURE OF VIRUSES Lipid bilayer Picked up when virus leaves host cell

32. Bacteriophage is very common virus consists of Nucleic Acid+ protein which is usually enclosed by 3 types of capsid structure. Icosahedral Filamentous Head and tail Phage Host Shape Genome Genome Size (kb) MS² E.coli Icosahedral SS linear RNA 3.6 M13 E.coli Filamentous SS linear RNA 6.7 T₇ E.coli Head and tail DS linear DNA 39.9