Genes - DNA - Chromosome Chutima Talabnin Ph.D. School of Biochemistry,Institute of Science, Suranaree University of Technology
DNA Cellular DNA contains genes and intragenic regions both of which may serve functions vital to cell. Gene is a nucleotide sequence in a DNA molecule that consists two component including Exon and Intron. Genes act as a functional unit for RNA synthesis and protein production.
Type of sequence in Eukaryotic genome Almost 50% of human genome are Transposons (transposable elements) - Kind of parasite efficiently marking a home within the host genome. - It can move from one location to another in the genome to play a major role in human evolution (redistribution of other genomic sequence) - It generally do not encode protein or RNA but some of them contain a genes encoding protein that catalyse the tranposition process. 30% of human genome consist of gene but it just only 1.5% are protein coding sequecne
Eukaryotic gene and chromosome are very complex
DNA packaging DNA molecule are much longer than the cellular packages that contain then http://www.youtube.com/watch?v=gbsibhfwq4s
DNA packaging in Eukaryote : DNA supercoiling DNA is extremely compacted implying a high degree of structural organization Most cellular DNA in underwound Supercoiling is tertiary structure of DNA which is generally manifestation of structural strain. DNA is coiled in the form of double helix with both strands of DNA coiling around an axis means the coiling of a coil DNA supercoiling is important for DNA packaging within all cells and reduces the space and allows for much more DNA to be packaged. Because the length of DNA can be thousands of times that of a cell. Supercoiling is also required for DNA/RNA synthesis. Because DNA must be unwound for DNA/RNA polymerase action, supercoils will result DNA packaging is greatly increased during nuclear division events such as mitosis or meiosis, where DNA must be compacted and segregated to daughter cells
DNA supercoiling The strain is a result of underwinding of the DNA double helix In a "relaxed" double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.4 10.5 base pairs of sequence 84 bp/8 turn = 10.5 bp/turn 84 bp/7 turn = 12 bp/turn The strain would be accomodated by coiling the axis of the DNA on its self to form a supercoiling Generally, the strain could produce the separating the two DNA strand over a distance about 10 bp
DNA underwinding by supercoiling is defined by topological linking number (Lk) Topology is the study of the properties of an object that do not change under continuous deformation Linking number is a topological property of double strand DNA because it dose not vary when the DNA is bent to deformed, as long as both DNA strand remain intact Lk = Twist (Tw = No. of helix turn) + Writhe (Wr = No. of coil) Negative supercoil Lk = 198 Left handed Positive supercoil Lk = 202 Right -handed
Topoiosmerases catalyze changes in the linking number of DNA Lk = Twist (Tw = No. of helix turn) + Writhe (Wr = No. of coil)
Topoiosmerases I act by transiently breaking one of the two DNA strand, passing the broken strand through the break, and rejoining the broken ends, they change Lk in increment of 1 Topoiosmerases II (Gyrase) break both two DNA strand, and change Lk in increment of 2
DNA compaction requires a special of supercoling Plectonemic supercoiling is the right handed form which observed in isolated DNA (without protein binding) in solution from laboratory, dose not produce sufficient compaction to package DNA in the cell Solenoidal supercoiling is the left handed form which can be more stabilized by protein binding and is the form found in chromatin
Chromosome in Eukaryotic cell Chromosome: single long DNA contains a linear array of many genes. Chromosomal DNA: replication origins, telomeres, centromeres Histones form the protein core for DNA wrapping Nucleosome: repeating array of DNA-protein particles
Three important DNA sequences in chromatin Telomere, Replication origin, Centromere
Chromatin It consists of fiber containing not only DNA but also combine with protein. Both are approximately equal mass. Histones are wrapped up by DNA into structure unit call Nucleosomes Histone are small, basic protein Molecular weight 11,000 21,000 Da Very rich in the basic amino acid arginine and lysine (1/4 of total amino acid residue)
Nucleosomes are the fundamental organization unit of chromatin Chromatin has a form Beads on a string (complex of histones and DNA) Nucleosome Structures consist of the bead plus connecting DNA The bead of each chromosome contains eight histone molecules (Histone octamer core) : two copies each of 2 H2A 2 H2B 2 H3 2 H4 The spacing of nucleosome bead provides a repeating unit typical of about 200 bp 146 bp are bound tighly around eight part histone core 54 bp are linker DNA
How DNA wrap up to histones to form Nucleosome The tight wrapping of DNA around the histones core requires the removal of about one helical turn in the DNA to introduce left-handed selenoidal supercoiling Histone core do not bind randomly to DNA A-T riched minor groove inside and G-C riched groove outside The tight wrapping up of DNA require 2 3 more A=T base pair to produce more compression
Nucleosomes are packed into successively high order structure Nucleosome cores are organized into structure called 30 nm fiber Packing of 30 nm fiber require one molecule of histone H1 per nucleosome core to induce the compression in between nuclosomes. Sequence specific DNA binding protein because organization of 30 nm fiber does not extend over the entire chromosome
DNA compaction in eukarytic chromosome likely to involve coil upon coil upon coil. Coil and coil and coil Loop of 30 nm fiber attache to nuclear scaffold Many nucleosomes form 30 nm fiber Nucleosome (DNA supercoiling + Histone) Condensed chromosome structure are Epigenetic regulation maintained by??? http://www.youtube.com/watch?v=eyrq0ehvcya
Chromatin Remodeling The mechanism for modifying chromatin and allowing transcriptional signal to reach their destination on the DNA strand Opening process
Histome modification : The function of Histone tails Covalent Modification of core histone tails Acetylation of lysines Methylation of lysines Phosphorylation of serines Histone acetyl transferase (HAT) Histone deacetylase (HDAC)
http://www.youtube.com/watch?v=tj_6dcutrnm&feature=related
Cyclic Diagram for nucleosome formation and disruption
Chromosome in Prokaryotic cell Bacterial chromosomes is also compacted in a structure called the Nucleoid DNA appears to be attached at one or more points to the inner surface of plasma membrane.