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DNA structure

  1. 1. DNA Structure Presented By: Hadiah Bassam Al Mahdi PhD. Student in Genetics Faculty of Science , King Adulaziz University Developmental Genetics Course Bio707
  2. 2. Outline o History of DNA discovery . o Chemical component of DNA structure. o DNA as double helix. o DNA packaging. o Conclusion and References
  3. 3. DNA Abbreviation D N A Deoxyribo Nucleic Acid Deoxyribonucleic acid is the hereditary material in all organisms
  4. 4. Scientists Contributed in the DNA Discovery Friedrich Miescher 1869 DNA First Isolated Erwin Chargaff 1950 Chargaff's rules 1951 X-ray diffraction Rosalind Franklin Francis Crick James Watson 1953 3D DNA Structure
  5. 5. Building Blocks • Nucleoside: Nitrogenous Base+ Deoxyribose Sugar • Nucleotide: (dNTPs) Nucleoside + Phosphate Adenine Guanine Cytosine Thymine Pyrimidine Purine Two aromatic rings One aromatic ring Glycosidic bond
  6. 6. Polymer Chain • Nucleotides considered as a monomer • Backbone composed of repeating pentose- phosphate units. • The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. • 5́  3́ directionality
  7. 7. Nucleotides Percentage • "Chargaff's Rules" 1. The amount of adenine = thymine and the amount of guanine = cytosine. 2. The amount of dNTPs in DNA varies between species.
  8. 8. DNA Helix • X-ray diffraction patterns of DNA fibers which showed that the geometric shape of DNA is a right-handed helix. • Usually, the two strands are coiled in a right- handed fashion(Clockwise). The pitch of the helix is 3.4 nm and there are roughly 10 bp in each turn. • Consequently, the distance between a bp in a helix is approximately equal to 0.34 nm
  9. 9. DNA Double Helix • Weston and crick constructed a 3D model of DNA. • DNA consists of two associated polynucleotide strands that twist together to form a helix. • B form (right handed). • The orientation of the two strands is antiparallel. • The strands are held by formation of base pairs between the two strands: “complementary pairs” A is paired with T through two hydrogen bonds G is paired with C through three hydrogen bonds • Hydrophobic and van der Waals interactions between the stacked adjacent base pairs further stabilize the double-helical structure.
  10. 10. DNA Grooves • A DNA has two grooves that are not equal in size to each other. • The angle at which the two sugars protrude out from the base (i.e. the angle between the glycosidic bond. • The patterns are important because they allow proteins to unambiguously recognize DNA sequences without having to open and disrupt the double helix. • Most sequence specific DNA binding proteins bind to DNA via the major groove. • Many non specific DNA binding proteins bind to the minor groove • In major groove can distinguish between 4 bases
  11. 11. DNA Different Conformation 3 forms of DNA could be detected B – form (Watson & Crick) A – form Z – form (Zigzag)
  12. 12. Physical Properties of Double- Stranded DNA  Ultraviolet Absorption Spectra of DNA. DNA absorbs ultraviolet (UV) light in a band centered around 260 nm.  Denaturation and Renaturation. To melt the two strands or denature the DNA, all these stabilizing forces must be overcome. The rest of the double helix renatures very rapidly.  DNA Hybridization Involves the formation of a double-stranded nucleicacid, either a DNA double helix or an RNA-DNA duplex. Provides an extremely powerful tool in molecular biology.
  13. 13. • Genome size is Related to complexity of the organism when comparing different groups – Prokaryotes – Single cell Eukaryotes – Multi-cellular Eukaryotes • Genome size  complexity among major groups • Larger proteins • More regulation needed (regulatory sequences) • Gene is discontinued by introns • Organism complexity 1/ Gene density DNA and complexity of the Organism
  14. 14. Do all cells have the same DNA structure ? • Most Eukaryotes have linear DNA. • mtDNA and plastid DNA are circular. • Some viruses, most bacteria & plasmid have circular DNA. •  phage can exist in both linear and circular DNA because of sticky ends.
  15. 15. DNA is compacted into chromosomes 1. To fit DNA inside the cell 2. To protect DNA from damage. 3. To transmit DNA efficiently to daughter cells. 4. To Facilitate gene expression. 5. To ensure that recombination takes place between homologous chromosomes only
  16. 16. DNA Packaging • 2 nm = DNA structure • 11 nm = String on beads form of chromatin • “Nucleosomes primary structural units of chromatin” • 30 nm= chromatin fibers “ Nucleosomes fold” • 300 nm = chromosome scaffold “long loops of chromatin extending from the scaffold” • 700 nm = chromatid structure • 1400 nm= chromosomal structure
  17. 17. String on beads • During interphase, the genetic material exists as a nucleoprotein complex called chromatin. • Proteins associated with eukaryotic DNA are histones. • The five major types of histone proteins (H1, H2A, H2B, H3, and H4). • Histones rich in positively charged basic amino acids, which interact with the negatively charged phosphate groups in DNA. • The string is composed of free DNA called “linker” DNA connecting the beadlike structures termed nucleosomes. • Nucleosome consists of a protein core with DNA wound around its surface like thread around a spool. • The core is an octamer containing two copies each of histones H2A, H2B, H3, and H4
  18. 18. Chromatin fibers • A chromatosome is a result of histone H1 binding to a nucleosome, which contains a histone octamer and DNA.
  19. 19. Chromosome scaffold • Nonhistone proteins provide a structural scaffold for long chromatin loops. • Folding of the scaffold has been proposed to produce the highly condensed structure characteristic of metaphase chromosomes.
  20. 20. Chromatid and chromosome structure Explain in next ppt.
  21. 21. DNA Structure in Prokaryotic vs Eukaryotic
  22. 22. Conclusion  Deoxyribonucleic acid (DNA), the genetic material, carries information to specify the amino acid sequences of proteins.  DNA contains four types of adjacent nucleotides in a polynucleotide are linked by phosphodiester bonds .  Natural DNA (B DNA) contains two complementary antiparallel polynucleotide strands wound together into a regular right-handed double helix.  The bases in nucleic acids can interact via hydrogenbonds. The standard Watson-Crick base pairs are G·C, A·T (in DNA).  Each eukaryotic chromosome contains a single DNA molecule packaged into nucleosomes and folded into a 30-nm chromatin fiber, which is attached to a protein scaffold at specific sites
  23. 23. References o SINDEN, R. R. 2012. DNA structure and function, Elsevier. o WATSON, J. D., BAKER, T. A., BELL, S. P., GANN, A., LEVINE, M., & LOSICK, R. M. (2004). Molecular biology of the gene. o LODISH, H., BERK, A., KAISER, C. A., KRIEGER, M., SCOTT, M. P., BRETSCHER, A., PLOEGH, H. & MATSUDAIRA, P. 2008. Molecular cell biology, Macmillan.

Notas del editor

  • First step in central dogma
  • which triggered the idea that DNA was a helix.

    Perhaps the most important aspects of DNA structural variation are
    likely to be found in the mechanics of molecular recognition and manipulation
    by proteins.
  • Deoxyribose is the five-carbon sugar molecule that helps form the phosphate backbone of DNA molecules
    Guanine + thymine = keto
    Cytosine + Thymine = Amino
    Glycosidic bond between sugar and base
  • A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms.

    DNA polymarase

    Negative charge

  • Hydrogen bond is non covalent
    Negative charge
    Antiparallel means one strand is orientated from 5 to 3 and other orientated from 3 to 5
  • Hydrogen bond is non covalent
    Antiparllel means one strand is orientated from 5 to 3 and other orientated from 3 to 5
    Rosalind Franklin and Maurice Wilkins used a method of X-ray diffraction to investigate the structure of DNA
    DNA was purified and then fibres were stretched in a thin glass tube (to make most of the strands parallel)
    The DNA was targeted by a X-ray beam, which was diffracted when it contacted an atom
    The scattering pattern of the X-ray was recorded on a film and used to elucidate details of mole

    (a nanometer is one billionth of ameter, that is 10-9 m)
  • Weston and crick constructed a 3D model of DNA.
    Used information from experiments conducted by other scientist
    Determined the structure of DNA was a double helix made of two nucleotides

    Won Nobel Prize 1962
  • The narrow angle = minor groove.
    The large angle =major grove.
  • Dehydrating condition. (A)
    High salt concentration.(Z)
  • 6 um diameter of nucleolus

  • Lysine and arginine amino acid
    Linker 147 b.b

    Each chromosome consists of a single,
    long molecule of DNA up to ~280 Mb
    in humans, organized into increasing
    levels of condensation by the histone
    and nonhistone proteins with which it
    is intricately complexed.

  • Histone protien (conserved genes) tandom repeat