Chromatin Structure and Cell Cycle

• Chromatin and DNA are being discussed

Chromatin Structure and the Cell Cycle

• Following chromosome separation and cell division, the cell enters interphase to prepare for mitosis.
• During interphase, chromosomes uncoil into chromatin.
• Chromatin disperses in the nucleus, and DNA replicates.
• As the cell cycle progresses, cells re-enter mitosis, during which chromatin coils again into visible chromosomes.
• The Eukaryotic organization of DNA is more complex than in Bacteria or Viruses
• Eukaryotic chromosomes contain a large amount of DNA and many proteins.
• E. coli DNA is 1200 µm long, while human chromosomes range from 19,000 to 73,000 µm long.
• The nucleus of human DNA contains 46 chromosomes that is almost 2 meters in length, and many proteins.
• DNA has to fit into the nucleus.
• DNA is packaged in the nucleus with histone proteins.
• The structure that is formed is referred as chromatin structure

Fine Structure of Chromatin

• The basic structural unit of chromatin, called the nucleosome, was first described by Roger Kornberg in 1974.
• Chromatin fibers examined under an electron microscope appear beaded, resembling beads on a string.

Chromatin Structure and Nucleosomes

• Genetic material in bacteria and viruses consists of DNA or RNA without protein.
• Eukaryotic chromosomes form chromatin structure, containing DNA and protein.
• Histone proteins are positively charged.
• Nonhistone proteins are less positively charged.
• Histones contain lysine and arginine amino acids in them.

Chromatin Structure

• The general model involves chromatin fibers, including DNA and proteins, coiling and folding.
• Chromatin forms regularly spaced ring structures.
• Repeating structural units occur along the chromatin axis, maintained by histone proteins.
• This forms nucleosome structure

Nucleosome Core Particles

• Consist of a Histone octamer that is two copies of each consisting of H2A, H2B, H3, and H4 in 8 histone molecules.
• DNA winds around an octamer.
• Between the two nucleosomes that is linker DNA
• H1 binds to linker DNA between the nucleosomes.
• H1 attaches to the linker region and changes the conformation which is required for chromatin formation
• Each chromosome contains a single molecule of DNA that is wound around histones.
• Lysine and arginine residues make these proteins positively charged.
• Chromatin can be further condensed by it being coiled into 30 nm fibers.
• 30 nm chromatin fiber is the second level of DNA packaging
• This Shortens DNA length 50 fold relative to naked DNA

Chromatin Structure Summary

• The basic model is composed of a repeating unit.
• Electron microscopy reveals linear arrays of spherical particles in chromatin fibers.
• Nucleosomes forming chromatin show that histones H2A, H2B, H3, and H4 exist as two types of tetramers, making octamers.
• One is (H2A)2(H2B)2 and the other is (H3)2(H4)2.
• Each octamer associates with 200 bp of DNA.
• 200 bp DNA containing octamer is composed of a nucleosome core particle consisting of 146 bp DNA.
• This DNA is constant in all eukaryotes and is called linker DNA associated with the fifth histone, H1.
• Nucleosomes consist of core histones and 146 bp of DNA.
• A nucleosome is a Histone octamer + 200 bp of DNA.
• Chromatin fiber, or solenoid structure, forms a looped domain and becomes the chromatin fiber.

Chromatin Remodelling

• Chromatin structure formation is performed using histone proteins.
• Chromatin fibers compacted make DNA inaccessible to interaction with nonhistone proteins.
• Proteins involved in replication and gene expression must interact directly with DNA which contain enzymes and regulatory proteins.
• Chromatin is subjected to a process known as chromatin remodeling.
• Chromatin must relax its compact structure during replication and gene expression and be able to reverse during inactivity.
• Subtle twists and turns of the superhelix of DNA encircle histones.

Chromatin Modification: Histone Acetylation

• Histone Acetylation is maintained by histone Acetyltransferase (HAT).
• The histone Acetyltransferase enzyme adds an acetyl group to the positively charged amino group on the side chain of Lysine.
• This alters the net charge of the protein and neutralizes the positive charge allowing acetylation leading to gene activation.
• An inactive gene: example Barr body (inactive X), histone H4 underacetylated

Chromatin Modification: Methylation and Phosphorylation

• Histone methylation is maintained by methyltransferases.
• Methyl group can be added to both arginine and lysine of histones to activate the gene.
• Histone phosphorylation is maintained by kinases.
• A phosphate group can be added to the hydroxyl groups of the amino acids serine and histidine, introducing a negative charge on the protein.

Chromosome Structure

• DNA in metaphase chromosomes is organized into protein scaffold large loops which is attached to a protein scaffold.
• 30 nm chromatin fibers fold to form compact metaphase chromosomes of mitotic cells.
• Interphase chromatin extends for expression, a mitotic chromosome is condensed.
• Mitotic chromosomes are condensed duplicated chromosomes that form through DNA replication.
• The telomeres are located at the ends of chromatids and are important for chromosome stability and to prevent shortening.
• Number, sizes, shapes of metaphase chromosomes form the karyotype used to distinguish between species

Chromosome Region

• Centromeres are required for chromatid separation in mitosis.
• The ends of chromatids are called telomeres, which are important for chromosome stability.
• Chromosomes are characterized by centromere location through metacentric, submetacentric, acrocentric, and telocentric

Genetics and Genetic Material

• Genetics is the study of inherited traits and their variations.
• Genetic material is carried out by DNA.
• Genomes includes chromosomal DNA, plasmid DNA, organellar DNA in eukaryotes, mitochondrial, and chloroplast DNA through gene expression.
• DNA sequences produce all the organism's proteins.
• In 1865 Genes are particulate factors
• 1871 Discovery of nucleic acids
• 1903 Chromosomes are hereditary units
• 1910 Genes lie on chromosomes
• 1913 Chromosomes are linear arrays of genes
• 1927 Mutations are physical changes in genes
• 1931 Recombination occurs by crossing over
• 1944 DNA is the genetic material
• 1945 A gene codes for protein
• 1951 First protein sequence
• 1953 DNA is a double helix
• 1958 DNA replicates semiconservatively.
• 1961 Genetic code is triplet
• 1977 Eukaryotic genes are interrupted
• 1977 DNA can be sequenced
• 1995 Bacterial genomes sequenced
• 2001 Human genome sequenced
• Genes, chromosomes, proteins are structural roles and are involved in metabolic reactions
• They can be transcription factors, receptors, which are key players in signal transduction pathways
• Genomes physically may be divided into chromosomes and functionally into genes
• Genomes for living organisms may contain as few as 500 genes such as in bacteria.
• A human being contains from 20,000 to 25,000 genes.
• Rice contains upwards of 50,000 to 60,000 genes.
• It was unclear what chemical component of the chromosome made up the genetic material.
• In 1944, direct evidence represented DNA as the genetic material and hereditary unit.
• Previously, proteins are thought to be the genetic material as it is abundant in cells accounting for over 50% of the cells dry weight.
• Nucleic acids are made of 4 similar molecules call nucleotides that repeated over and over .

DNA as Genetic Material

• Avery, MacLeod, and McCarty used bacteria to prove DNA as genetic Material
• Hershey-Chase experiment also used bacteria and viruses to prove DNA as genetic material
• 1953, James Watson and Francis Crick published a paper in describing the doubelhelix structure of DNA.
• The molecule carries genetic information from one generation to the other
• They received the Nobel Prize in Physiology or Medicine in 1962
• The beginning of 21 st century the Human Genome Project was completed, and sequenced Human DNA in (Approximately) 3 billion bp.
• Project contributors were J. Craig Venter and Fransis Collins
• There was representation from The International Human Genome Sequencing Consortium which contained The Whitehead Institute/MIT Center for Genome Research (US), The Wellcome Trust Sanger Institute (UK), Washington University School of Medicine Genome Sequencing Center (US), US DOE, Baylor College of Medicine Human Genome Sequencing Center (US), RIKEN Genomic Sciences Center (Japan), Genoscope and CNRS (France), GTC Sequencing Center (US), Beijing Genomics Institute/Human Genome Center (China).

Nucleic Acid Chemistry and DNA Structure

• The basic building blocks of nucleic acids (DNA and RNA) is nucleotide.
• The three components of nucleotide; A nitrogenous base: Purine Pyrimidine, A sugar: 5 carbon pentose sugar ( ribose and deoxyribose), phosphate group
• Purines: A, G
• Pyrimidines: C, T, U
• Nucleosides are Base and pentose sugar
• Nucleic acids are named according to their type of sugar; such as DNA which is deoxyribose sugar and RNA which has ribose sugar
• Nucleotides are Nucleoside triphosphates; ATP, GTP.

Watson-Crick Model

• The base composition analysis determines Adenine the Thymine levels are proportional along with the Guanine and Cytosine
• Two polynucleotide chains are coiled around a central axis, forming a right-handed double helix such a B formed DNA
• The two chains are antiparallel where one strand runs 5'-3' while its complamentary is 3' to 5'.
• Purines are always paired with pyrimidine as Purine-Purine would be too wide and pyrim-pyrim too narrow
• The proportion of G is always the same as the proportion of C in DNA, and the proportion of A is always the same as that of T.
• Two nucleotide chains in the double helix associated by hydrogen bonding between the nitrogenous bases, such as A=T, G=C
• A-G and C-T pairs would be Purine-Purine and Pyrimidine-Pyrimidine pairing which doesn't facilitate correct alignment
• Nucleotides: A=T or (A=U), GΞC
• Thus nucleic acids are responsible for self replication
• It is known that DNA carries specific information and proteins control most cellular activities.
• B form helix is the most common form of DNA in cells which is a right handed helix and turns every 3.4nm which contain 10 base pairs
• In regards to form, DNA can be a;
  • A-form: Less common, right-handed helix, 11 bp/turn, major groove: very deep and narrow, and minor groove: very shallow and wide (binding site for RNA)
  • Z-form DNA: Radical change of B-form, Left-handed helix, made of GC rich DNA regions.
• The DNA double strands can denature if heated (95ºC) or treated with chemicals such as AT regions which would denature first
• DNA can also reanneal if cooled