DNA Structure and Organization PDF

 Nucleotides, DNA structure & organization Prepared by Prof. Dr. Naglaa Ibrahim Azab  NUCLEIC ACIDS  Include DNA: Deoxyribonucleic acid RNA: Ribonucleic acid Each nucleic acid is formed of nucleotides  A nucleotide is formed of : 1. Sugar (deox...

 Nucleotides, DNA structure & organization Prepared by Prof. Dr. Naglaa Ibrahim Azab  NUCLEIC ACIDS  Include DNA: Deoxyribonucleic acid RNA: Ribonucleic acid Each nucleic acid is formed of nucleotides  A nucleotide is formed of : 1. Sugar (deoxy ribose or ribose). 2. Phosphate group. 3. Nitrogen containing bases: - Purine bases (bases containing 2 rings (Adenine [A], Guanine [G]) - Pyrimidine bases (bases containing single ring (Thymine [T], Cytosine[C], Uracil [U])  Linking of the base (N1 in pyrimidine, N9 of purines) to the sugar (at the 1’ carbon of the sugar) by N-glycosidic bond is called nucleoside  Linking of nucleoside to phosphate group ( at the 5’ carbon of the sugar) by ester bond is called nucleotide  Nucleotides can be  nucleoside monophosphate = nucleoside + one phosphate group. (also called mononucleotide) e.g AMP,GMP  Nucleoside diphosphate = nucleoside + 2 phosphate group e.g. ADP,GDP.  Nucleoside triphosphate = nucleoside + 3 phosphate group e.g. ATP,GTP. Nucleic acids contain: nucleoside monophosphates only High energy phosphate compounds can be either nucleoside tri- or di- or mono-phosphate Nomenclature of different nucleosides and nucleotides:  Importance of nucleotides & nucleosides & nitrogenous bases: 1. Enter in the synthesis of: Enter in the synthesis of Nucleotides Nucleic acids (DNA,RNA) Nucleotides as ATP,GTP High energy phosphate compounds nucleotides coenzymes as NAD, NADP, FAD, FMN, Coenzyme A. Deoxyadenosylcobolamine UDP-glucose glycogen & lactose UDP glucuronic GAGs 2. Act as donars for……. : Act as S~ adenosyl methionine Methyl donar CDP choline &CDP donars for Phosphocholine & ethanolamine phosphoethanolamine for phospholipid synthesis  Importance of nucleotides & nucleosides & nitrogenous bases: 3. Act as 2ry messengers for hormones as cAMP & cGMP. 4. Nitrogenous bases importance: Methylated nitrogenous bases important in regulation of gene expression. Synthetic Purine & pyrimidine important for treatment of diseases as analogs allopurinol in the treatment of gout & 5' fluorouracil in the treatment of cancer.. Nucleic acids  NUCLEIC ACIDS  Include DNA: Deoxyribonucleic acid RNA: Ribonucleic acid Each nucleic acid is a polynucleotide in which nucleotides are linked by 3ˋ, 5ˋ phosphodiester bonds  Figure: Formation of a phosphodiester bond between 2 successive nucleotides Ester bonds are strong covalent bonds formed by the reaction of an acid and alcohol(- OH). Phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds. It results from condensation reaction (result in the removal of water) between the OH of phosphate group and 3’ carbon of Pentose sugar and 5’ carbon of another Pentose sugar rings DNA DNA (Deoxyribonucleic acid):  DNA is the material that carries all the genetic informations of the individual  Site : - In eukaryotes : Mostly found in the chromosomes of nucleus of cell and small amount is found in the mitochondria - In prokaryotes: DNA is present in their single chromosome and in plasmid Functions : - 1. Storage of genetic and hereditary characters - 2. Transmission of genetic and hereditary characters to the daughter cells through replication DNA must be replicated precisely each time the cell divides so each daughter cell acquire the same amount of genetic material - Nuclear DNA:carries the genetic informations in the chromosomes that encode functional proteins or functional RNA. - Nuclear DNA:carries the genetic informations in the chromosomes that encode functional proteins or functional RNA. Mitochondrial DNA: contains: 1- genes encode proteins of the electron transport chain. 2- genes encoding transfer RNA (tRNA) and the small and large subunits of ribosomal RNA (rRNA).  Structure: DNA is formed of two chains (strands). The 2 strands wind around each other forming a double helix (Watson and crick model). Each strand is formed of deoxyribonucleotides covalently linked by 3ˋ 5ˋ Phosphodiester bond between the sugars and phosphates Each deoxyribonucleotide nucleotide is formed of : 1. Sugar (deoxy ribose). 2. Phosphate group. 3. Nitrogen containing bases:A,T,G,C  Fig.: A polynucleotide chain of DNA Each DNA strand (chain) has 2 ends: 1. The 5’ end has a free phosphate group. 2. The 3’ end has a free hydroxyl group. Note the direction of DNA replication is in a 5’ -3’ direction. The hydrophilic (polar) deoxyribose phosphate backbone of each chain is on the outside of the DNA molecule, whereas the hydrophobic (nonpolar bases) are stacked inside perpendicular to the axis of the helix.  The 2 DNA strands wind around each other in antiparallel manner; that is From any fixed position in the helix, one strand is oriented in the 5′ 3′ direction and the other in the 3′ 5′ direction. The double helix made by winding of the 2 DNA strands around each other, is stabilized by hydrogen bonding between the bases of the 2 strands and by the hydrophobic interactions between the stacked bases.  Base pairing rule: Thymine always pair with adenine and cytosine always pair with guanine. So one polynucleotide chain is of the double helix is always complementary to the other. Thymine and adenine bases are connected by 2 hydrogen bonds , while cytosine and guanine are connected by 3 hydrogen bonds. This makes G- C base pairs more stable than A-T base pairs  On its exterior surface, the double helix of DNA contains two deep grooves between the ribose-phosphate chains. These two grooves are of unequal size and termed the major and minor grooves. The difference in their size is due to the asymmetry of the deoxyribose rings and the structurally distinct nature of the upper surface of a base- pair relative to the bottom surface.  The two Polynucleotide strands are coiled around each other in a double helical structure. In the DNA helix, the hydrophilic deoxyribose– phosphate backbone of each chain is on the outside of the molecule, whereas the hydrophobic bases are on the inside The overall structure resembles a twisted ladder. DNA organization In humans, each cell contains 46 chromosomes whose total length equals one meter. So, chromosomes must be condensed into chromatin to fit into the nucleus. The chromatin in eukaryotic cells consists of: Nuclear DNA bound to Histones proteins & smaller amounts of non histone proteins (Enzymes involved in DNA replication and transcription) & Small amount of RNA (snRNA) The chromatin in eukaryotic cells consists of: Nuclear DNA bound to Histones proteins & smaller amounts of non histone proteins (Enzymes involved in DNA replication and transcription) & Small amount of RNA (snRNA)  HISTONES -Are basic proteins (having positive charges), so they form ionic bonds with the negatively charged DNA so their binding is facilitated. - 5 types: H1, H2A, H2B, H3, H4. - Functions: They help condensation of the DNA into more compact chromosomes. Protect the DNA from digestion by exonucleases. Modified histones: Has an important role in changing the structure of chromatin and chromatin function e.g. acetylation of H3 and H4 is associated with activation or inactivation of gene expression. Nucleosome structure Nucleosome consists of histones & 200bp segment of DNA 1- DNA core: Formed of supercoiled DNA (140 bp segment) surrounding histone octamer (2 molecules of each of H2A, H2B, H3, H4). 2- Linking region: It joins one nucleosome core to the next Formed of 60 bp of DNA and 1 molecule of histone (H1) which protects the linker DNA from digestion by exonucleases  Chromatin is built from repeating nucleosomes units If the chromatin is placed in low salt buffer and viewed with E/M (i.e If the chromatin is pulled into a linear strucrure)→→→→ It resembles a string of beads( with the beads representing nucleosome cores and the string representing the DNA linker) Compaction of chromatin  Condensation of the nucleosomes with histone H1 in the centre form the 10 nm fibril.  Supercoiling of the 10 nm fibril with 6-7 nucleosomes per turn form the 30 nm fiber.  Supercoiling of the 30 nm fiber into superloops  Each 6 superloops attached to a protein scaffold form a rosette.  Each 30 rosette form one coil.  Each 10 coils form one chromatid. Chromosomes 2 identical sister chromatids attached at the centromere →→ one chromosome (in the metaphase) The centromere - is rich in A=T and is about 130 bp long. - is connected to specific proteins to form a complex known as kinetochore which is connected to mitotic spindle. This complex is essential structure for chromosomal segregation during mitosis.