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DNA CHEMISTRY

  1. 1. 1 Biochemistry for Medics
  2. 2. DNA Structure, Functions and Properties By Dr. Shamim Akram AP Biochem. AIMC 2
  3. 3. 3 Biochemistry for Medics
  4. 4. DNA •DNA - a polymer of deoxyribo nucleotides covalently linked by 3’-5’- phosphodiester bonds,present in chromosomes of mitochondria and chloroplasts ,carries the genetic information •Single human diploid chromosome has: •Length: 2 meter(condensed form 200nm) •Molecular weight: 160x109 daltons •Weight:17 picogram (17x10-12) 4
  5. 5. Components of a nucleotide Base Sugar Phosphate s 5
  6. 6. Nucleotide Nucleoside Base Phosphate Sugar X=H: DNA X=OH: RNA 6
  7. 7. Basic structure of pyrimidine and purine 7
  8. 8. Pyrimidines 8
  9. 9. Purines s 9
  10. 10. Nomenclature of Nucleic Acid Components Base Nucleoside Nucleotide Nucleic acid Purines Adenine Adenosine Adenylate RNA Deoxyadenosine Deoxyadenylate DNA Guanine Guanosine Guanylate RNA Deoxy guanosine Deoxyguanylate DNA Pyrimidines Cytosine Cytidine Cytidylate RNA Deoxycytidine Deoxycytidylate DNA Thymine Thymidine Thymidylate DNA (deoxythymidine) (deoxythymidylate) Uracil Uridine Uridylate RNA 10
  11. 11. DNA structure  Primary structure  Secondary structure  Tertiary structure 11
  12. 12. The primary structure of DNA is the sequence 5’ end 3’ end 5’ 3’ Phosphodiester linkage Biochemistry for Medics 12
  13. 13. Traditionally, a DNA sequence is drawn from 5’ to 3’ end. A shorthand notation for this sequence is ACGTA Biochemistry for Medics 13
  14. 14. The secondary structure of DNA is the double helix(watson&crick 1953) 14
  15. 15. The secondary structure of DNA Two anti-parallel polynucleotide chains wound around the same axis. Sugar-phosphate chains wrap around the periphery. Bases (A, T, C and G) occupy the core, forming complementary A · T and G · C Watson-Crick base pairs. 15
  16. 16. SECONDARY STRUCTURE OF DNA  DNA is double helix,Rt.handed twisted arround central axis  Two strands run antiparallel (like two roads in opp. Direction).  Width 2.0 nm.each turn lenth 3.4 nm,has 10 nucleotide pairs, each base 0.34 nm apart.  Backbone hydrophilic(phosphodiester linkage),central core(bases) hydrophobic.  Two strands not identical but complementry.  Two strand held together by H-bonds(A-T has 2&G-C has 3).  Chargaff,s rule total no. of purines=total no. of pyrimidines.  Genetic information resides on Template(sense) strand only  Major & minor grooves along phosphodiester backbone.  Forces holding structure: Hydrogen bonbing & base stacking s
  17. 17. 17 Biochemistry for Medics
  18. 18.  hydrogen bonding;  base stacking The DNA double helix is held together mainly by- Hydrogen bonds Biochemistry for Medics 18
  19. 19. Hydrogen bond a chemical bond in which a hydrogen atom of one molecule is attracted to an electronegative atom, especially a nitrogen, oxygen, or fluorine atom, usually of another molecule. 19
  20. 20. Two hydrogen bonds between A:T pairs Three hydrogen bonds between C: G paired Biochemistry for Medics 20
  21. 21. Base Stacking The bases in DNA are planar and have a tendency to "stack". Major stacking forces: hydrophobic interaction van der Waals forces. Biochemistry for Medics 21
  22. 22. Structural forms of DNA Property A-DNA B-DNA Z-DNA Helix Handedness Right Right Left Base Pairs per turn 11 10.4 12 Rise per base pair along axis 0.23nm 0.34nm 0.38nm Pitch 2.46nm 3.40nm 4.56nm Diameter 2.55nm 2.37nm 1.84nm Conformation of Glycosidic bond anti anti Alternating anti and syn Major Groove Present Present Absent Minor Groove Present Present Deep cleft s 22
  23. 23. Helical sense: right handed Base pairs: almost perpendicular to the helix axis; 3.4 Å apart One turn of the helix: 36 Å; ~10.4 base pairs Minor groove: 12 Å across Major groove: 22 Å across Normally hydrated DNA: B-form DNA s 23
  24. 24. In eukaryotic cells, DNA is folded into chromatin 24
  25. 25. DNA TERTIARY STRUCTURE  Formation of NUCLEOSOMES (10 nm) DNA+Protein (Histone-H1,H2A,H2B,H3,H4) Beads on string app. Each nucleosome has146 nucleotides  Formation of FIBER (30nm) 6 Nucleosomes arrange in a group, 4 on priphery 2 in centre,many such gps,join one on the other to form a Fiber  Formation of Loop (300nm) Fiber twist arround itself to form Loops like telephone cord  Rossette formation 6 loops organize on a scafold protein to form a rossetts  Formation of a coil 30 rossettes join one on the other to form a coil  Formation of a chromatid 10 coils constitute a chromatid,  2 chromatids form a chromosome (700nm) 25 Biochemistry for Medics
  26. 26. DNA Tertiary Structure •DNA DOUBLE HELICAL STRUCTURE COILS ROUND HISTONES. •DNA BOUND TO HISTONES FORMS NUCLEOSOMES (10nm FIBRES) •NUCLEOSOMES CONTAIN 146 NUCLEOTIDES cs 26
  27. 27. Nucleosomes any of the repeating globular subunits of chromatin that consist of a complex of DNA and histone 27
  28. 28. Structure of nucleosome coreBiochemistry for Medics 28
  29. 29. Compaction of DNA in a eukaryotic chromosome29
  30. 30. Supercoil = coil over coil Biochemistry for Medics 30
  31. 31. DNA melting and annealling The two strands of double helix separats when hydrogen bonds between paired bases are disrupted if the PH or temp.of DNAsoln is altered lab This process is called Denaturation.(phosphodiester bond remain intact) The temp.at which one half of the helical structure is lost is defined as the melting temp.(Tm). Denaturation can be monitored by measuring its absorbance at 260nm.(single stranded DNA has a higher relative absorbance than double). Under apropriate conditions,complementry DNA strands can reform the double helix by the process called Renaturation or re-annealling. 31
  32. 32. Reversible denaturation and annealing of DNA Biochemistry for Medics 32
  33. 33. Melting point (tm) of DNA The temperature at the mid-point of the transition 33
  34. 34. The tm of DNA depends on:  size of DNA  pH  ionic strength  Content of G·C base pairs Biochemistry for Medics 34
  35. 35. Biochemistry for Medics 35 Functions of DNA and summary of structure DNA consists of four bases—A, G, C, and T—that are held in linear array by phosphodiester bonds through the 3' and 5' positions of adjacent deoxyribose moieties. DNA is organized into two strands by the pairing of bases A to T and G to C on complementary strands. These strands form a double helix around a central axis. The 3 x 109 base pairs of DNA in humans are organized into the haploid complement of 23 chromosomes. DNA provides a template for its own replication and thus maintenance of the genotype and for the transcription of the roughly 30,000 human genes into a variety of RNA molecules.
  36. 36. 36

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