1 / 69

Nucleotides and Nucleic Acids JM

Nucleotides and Nucleic Acids JM. Nucleic Acids. Objectives. Nucleotide. Base Sugar (Base + Sugar = Nucleo side ) Phosphate (Nucleo side + phosphate = Nucleo tide ). Elements. Nucleic Acids contain all the CHNOPS elements except sulfur (S). 6 C Carbon 12.0107. 7 N Nitrogen

karli
Télécharger la présentation

Nucleotides and Nucleic Acids JM

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Nucleotides and Nucleic AcidsJM

  2. Nucleic Acids Objectives

  3. Nucleotide • Base • Sugar (Base + Sugar = Nucleoside) • Phosphate (Nucleoside + phosphate = Nucleotide)

  4. Elements Nucleic Acids contain all the CHNOPS elements except sulfur (S). 6 C Carbon 12.0107 7 N Nitrogen 14.0067 8 O Oxygen 15.9994 1 H Hydrogen 1.00794 15 P Phosphorus 30.97376

  5. OH HOCH2 O 5’ HOCH2 O OH OH 4’ 1’ OH 3’ 2’ HOCH2 O H OH Nucleotide Structure - 1 Sugars Generic Ribose Structure Ribose N.B. Carbons are given numberings as a prime Deoxyribose

  6. O O CH3 HN HN O O NH NH Important Pyrimidines • Pyrimidines that occur in DNA are cytosine and thymine. Cytosine and uracil are the pyrimidines in RNA. NH2 HN O NH Uracil Thymine Cytosine

  7. O H3C NH T N O 4 N 3 5 H 6 2 NH2 1 N N C N O H Pyrimidines Thymine Cytosine

  8. O NH U 4 N 3 5 N O 6 2 1 H N Pyrimidines Thymine is found ONLY in DNA. In RNA, thymine is replaced by uracil Uracil and Thymine are structurally similar Uracil

  9. NH2 O N N HN N NH NH H2N N N Important Purines • Adenine and guanine are the principal purines of both DNA and RNA. Adenine Guanine

  10. NH2 N N N N H N 6 N 7 5 1 O 8 2 4 9 3 N N N N H N N NH2 H Purines Adenine A G Guanine

  11. Chargaff's Rules 1950's: Erwin Chargaff studies heterocyclic base ratios in DNA from various organisms • Chargaff's Rules: In DNA of all organisms... • (G+A)/(C+T) = purines/pyrimidines ratio ~1:1 • A/T ratio ~1:1 • G/C ratio ~1:1 • A+G=T+C. • A/T and G/C ratios random in RNA

  12. } Not compatible with single helix } DNA is a base-paired double helix Franklin's Photo 51. The X pattern is characteristic of a helical structure Watson and Crick made extensive use of models to study molecular structure. Follow their example! The Problem Solved 1953: • Rosalind Franklin: x-ray studies of DNA show helical structure Diameter = 20 Å Length = 34 Å per 360o turn Calculated density • James Watson and Francis Crick combine... • Franklin's x-ray data • Chargaff's rules • Examination of molecular models

  13. DNA replication “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” James Watson Francis Crick 1953

  14. Base Pairing • Watson and Crick proposed that A and T were equal because of complementary hydrogen bonding. 2-deoxyribose 2-deoxyribose A T

  15. Base Pairing • Likewise, the amounts of G and C were equal because of complementary hydrogen bonding. 2-deoxyribose 2-deoxyribose G C

  16. The DNA Duplex • Watson and Crick proposed a double-stranded structure for DNA in which a purine or pyrimidine base in one chain is hydrogen bonded to its complement in the other.

  17. Adenine-Thymine Guanine-Cytosine Watson-Crick Base Pairs • Heterocyclic bases associate via two or three hydrogen bonds • Base pairs similar size and shape  efficient packing into double helix

  18. Two antiparallel strands of DNA are paired by hydrogen bonds between purine and pyrimidine bases.

  19. Aromatic stacking Hydrogen bonds easily disassembled Strong Space-filling model: atoms represented at their van der Waals radii (electron cloud volumes) Based-Paired Double Helix 5' end 3' end 3' end 5' end DNA strands are antiparallel

  20. Helical structure of DNA. The purine and pyrimidine bases are on the inside, sugars and phosphates on the outside.

  21. The DNA Space Problem • Human genome = 3 x 109 base pairs (bp) • (3 x 109 bp) x (34 Å per 10 bp) x (10-10 m per Å) = ~1 meter in length • Solution: DNA tertiary structure = supercoiling

  22. Nucleosides • The classical structural definition is that a nucleoside is a pyrimidine or purine N-glycoside of D-ribofuranose or 2-deoxy-D-ribofuranose. • Informal use has extended this definition to apply to purine or pyrimidine N-glycosides of almost any carbohydrate. • The purine or pyrimidine part of a nucleoside is referred to as a purine or pyrimidine base.

  23. O NH2 N HN N O N N N HOCH2 HOCH2 O O HO OH HO OH Uridine and Adenosine • Uridine and adenosine are pyrimidine and purine nucleosides respectively of D-ribofuranose. Uridine (a pyrimidine nucleoside) Adenosine (a purine nucleoside)

  24. Nucleotides • Nucleotides are phosphoric acid esters of nucleosides.

  25. O O P O X O Phosphate Groups Phosphate groups are what makes a nucleoside a nucleotide Phosphate groups are essential for nucleotide polymerization Basic structure:

  26. Naming Conventions • Nucleosides: • Purine nucleosides end in “-sine” • Adenosine, Guanosine • Pyrimidine nucleosides end in “-dine” • Thymidine, Cytidine, Uridine • Nucleotides: • Start with the nucleoside name from above and add “mono-”, “di-”, or “triphosphate” • Adenosine Monophosphate, Cytidine Triphosphate, DeoxythymidineDiphosphate

  27. NH2 N N O N N OCH2 HO P O HO HO OH Adenosine 5'-Monophosphate (AMP) • Adenosine 5'-monophosphate (AMP) is also called 5'-adenylic acid.

  28. NH2 N N O N N OCH2 HO P O HO HO OH Adenosine 5'-Monophosphate (AMP) • Adenosine 5'-monophosphate (AMP) is also called 5'-adenylic acid. 5' 1' 4' 3' 2'

  29. NH2 N N O O N N OCH2 O HO P P O HO HO HO OH Adenosine Diphosphate (ADP)

  30. NH2 N N O O O N N OCH2 O HO O P P P O HO HO HO HO OH Adenosine Triphosphate (ATP)

  31. Macromolecule Simple Molecule Structure 4. Nucleic Acids nucleotides (DNA + RNA)(sugar + phosphate + N-base) • Major Compounds of Life NH2 N N N adenine (N-base) ribose (sugar) N O O HO - P - O O OH OH phosphoric acid

  32. Nucleotide nomenclature

  33. Nucleotide • Base • Sugar (Base + Sugar = Nucleoside) • Phosphate (Nucleoside + phosphate = Nucleotide)

  34. Nucleotides in nucleic acids • Bases attach to the C-1' of ribose or deoxyribose • The pyrimidines attach to the pentose via the N-1 position of the pyrimidine ring • The purines attach through the N-9 position • Some minor bases may have different attachments.

  35. Roles of nucleotides • Building blocks of nucleic acids (RNA, DNA) • Analogous to amino acid role in proteins • Energy currency in cellular metabolism (ATP: adenosine triphosphate) • Allosteric effectors • Structural components of many enzyme cofactors (NAD: nicotinamide adenine dinucleotide)

  36. Roles of nucleic acids • DNA contains genes, the information needed to synthesize functional proteins and RNAs • DNA contains segments that play a role in regulation of gene expression (promoters) • Ribosomal RNAs (rRNAs) are components of ribosomes, playing a role in protein synthesis • Messenger RNAs (mRNAs) carry genetic information from a gene to the ribosome • Transfer RNAs (tRNAs) translate information in mRNA into an amino acid sequence • RNAs have other functions, and can in some cases perform catalysis

  37. ATP • Perhaps the best known nucleotide is adenosine triphosphate (ATP), a nucleotide containing adenine, ribose, and a triphosphate group. • ATP is often mistakenly referred to as an energy-storage molecule, but it is more accurately termed an energy carrier or energy transfer agent.

  38. ATP is a nucleotide - energy currency Base (adenine) triphosphate Ribosesugar DG = -50 kJ/mol

  39. ATP diffuses throughout the cell to provide energy for other cellular work, such as biosynthetic reactions, ion transport, and cell movement. The chemical potential energy of ATP is made available when it transfers one (or two) of its phosphate groups to another molecule. This process can be represented by the reverse of the preceding reaction, namely, the hydrolysis of ATP to ADP.

  40. NAD is an important enzyme cofactor nicotinamide NADH is a hydride transfer agent, or a reducing agent. Derived from Niacin

  41. Nucleotides play roles in regulation

  42. Nucleic Acids • Nucleic acids are polymeric nucleotides (polynucleotides). • 5' Oxygen of one nucleotide is linked to the 3' oxygen of another.

  43. A section of a polynucleotide chain.

  44. Nucleotide Sugar Phosphate “backbone” Nucleic Acid Structure Polymerization

  45. Essential for replicating DNA and transcribing RNA • Two separate strandsAntiparellel(5’3’ direction) • Complementary (sequence) • Base pairing: hydrogen bonding that holds two strands together 3’ 5’ • Sugar-phosphate backbones (negatively charged): outside • Planner bases (stack one above the other): inside 3’ 5’

  46. Nucleic acids Nucleotide monomers can be linked together via a phosphodiester linkage formed between the 3' -OH of a nucleotide and the phosphate of the next nucleotide. Two ends of the resulting poly- or oligonucleotide are defined: The 5' end lacks a nucleotide at the 5' position, and the 3' end lacks a nucleotide at the 3' end position.

  47. Helical turn: • 10 base pairs/turn • 34 Ao/turn

  48. C1 Nucleic Acid Structure-6 A, B and Z helices Z-form A-form B-form

  49. Nucleic acids • B form - The most common conformation for DNA. • A form - common for RNA because of different sugar pucker. Deeper minor groove, shallow major groove. • A form is favored in conditions of low water. • Z form - narrow, deep minor groove. Major groove hardly existent. Can form for some DNA sequences; requires alternating syn and anti base configurations. 36 base pairs Backbone - blue; Bases- gray

More Related