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27.23 Pyrimidines and Purines

27.23 Pyrimidines and Purines. Pyrimidines and Purines. In order to understand the structure and properties of DNA and RNA, we need to look at their structural components. We begin with certain heterocyclic aromatic compounds called pyrimidines and purines. N. N. N. N. N. N H.

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27.23 Pyrimidines and Purines

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  1. 27.23Pyrimidines and Purines

  2. Pyrimidines and Purines • In order to understand the structure and properties of DNA and RNA, we need to look at their structural components. • We begin with certain heterocyclic aromatic compounds called pyrimidines and purines.

  3. N N N N N N H Pyrimidines and Purines • Pyrimidine and purine are the names of the parent compounds of two types of nitrogen-containing heterocyclic aromatic compounds. Pyrimidine Purine

  4. 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

  5. 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

  6. O O CH3 CH3 H3C N N N HN N O O N N N CH3 CH3 Caffeine Theobromine Caffeine and Theobromine • Caffeine (coffee) and theobromine (coffee and tea) are naturally occurring purines.

  7. 27.24Nucleosides

  8. 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.

  9. 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)

  10. 27.25Nucleotides

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

  12. 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.

  13. 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'

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

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

  16. ATP Stores Energy ATP • Each step is endothermic. • Energy for each step comes from carbohydrate metabolism (glycolysis). • Reverse process is exothermic and is the source of biological energy. • DG° for hydrolysis of ATP to ADP is –35 kJ/mol ADP AMP

  17. NH2 N N N N CH2 O O O P O OH HO Adenosine 3'-5'-Cyclic Monophosphate (cAMP) • Cyclic AMP is an important regulator of many biological processes.

  18. 27.26Nucleic Acids

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

  20. Fig. 27.22 • A section of a polynucleotide chain.

  21. 27.27Structure and Replication of DNA:The Double Helix

  22. Composition of DNA • Erwin Chargaff (Columbia Univ.) studied DNAs from various sources and analyzed the distribution of purines and pyrimidines in them. • The distribution of the bases adenine (A), guanine (G), thymine (T), and cytosine (C) varied among species. • But the total purines (A and G) and the total pyrimidines (T and C) were always equal. • Moreover: %A = %T, and %G = %C

  23. Composition of Human DNA For example: • Adenine (A) 30.3% Thymine (T) 30.3% • Guanine (G) 19.5% Cytosine (C) 19.9% • Total purines: 49.8% Total pyrimidines: 50.1% Purine Pyrimidine

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

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

  26. 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.

  27. Fig. 27.24 • Two antiparallel strands of DNA are paired by hydrogen bonds between purine and pyrimidine bases.

  28. Fig. 27.25 • Helical structure of DNA. The purine and pyrimidine bases are on the inside, sugars and phosphates on the outside.

  29. Fig. 27.26 DNA Replication • As the double helix unwinds, each strand acts as a template upon which its complement is constructed. C T A G

  30. Fig. 27.26 DNA Replication A' C T G' C' A G T'

  31. 27.28DNA-Directed Protein Biosynthesis

  32. DNA and Protein Biosynthesis • According to Crick, the "central dogma" of molecular biology is: "DNA makes RNA makes protein." • Three kinds of RNA are involved.messenger RNA (mRNA)transfer RNA (tRNA)ribosomal RNA (rRNA) • There are two main stages.transcriptiontranslation

  33. Transcription • Transcription is the formation of a strand of mRNA using one of the DNA strands as a template. • The nucleotide sequence of the mRNA is complementary to the nucleotide sequence of the DNA template. • Transcription begins at the 5' end of DNA and is catalyzed by the enzyme RNA polymerase.

  34. C T A G C T A C G A A G T A G G T C A C T G T C C A G T G A C A C T T C G T A G C T A G 5' Transcription • As double-stranded DNA unwinds, a complementary strand of mRNA forms at the 5' end. 3'

  35. G A U C G A 5' C Transcription T A G C T A C • Uracil is incorporated in RNA instead of thymine. G A A G T A G G T C A C T G T C C A G T G A C A C T T C G T A G C T A 3' G

  36. Translation • The nucleotide sequence of mRNA codes for the different amino acids found in proteins. • There are three nucleotides per codon. • There are 64 possible combinations of A, U, G, and C. • The genetic code is redundant. Some proteins are coded for by more than one codon.

  37. Table 27.4: mRNA Codons • Alanine Arginine Asparagine Aspartic Acid Cysteine • GCU GCA CGU CGA AAU GAU UGUGCC GCG AGA CGC AAC GAC UGC CGG AGG • Glutamic acid Glutamine Glycine Histidine IsoleucineGAA CAA GGU GGA CAU AUU AUAGAG CAG GGC GGG CAC AUC • Leucine Lysine Methionine Phenylalanine ProlineUUA CUU AAA AUG UUU CCU CCA CUA UUG AAG UUC CCC CGCUC CUG • Serine Threonine Tryptophan Tyrosine ValineUCU UCA ACU ACA UGG UAU GUU GUAAGU UCC ACC ACG UAC GUC GUGUCG AGC

  38. Transfer tRNA • There are 20 different tRNAs, one for each amino acid. • Each tRNA is single stranded with a CCA triplet at its 3' end. • A particular amino acid is attached to the tRNA by an ester linkage involving the carboxyl group of the amino acid and the 3' oxygen of the tRNA.

  39. Phenylalanine tRNA

  40. O OCCHCH2C6H5 + NH3 A C C A C G C C G U G U A A U C A U U C A A C U G A A G C C U C G U G U G C U G G G C A G A G G A C G C A U G A A U A A A Phenylalanine tRNA This AAA triplet is complementary to a UUU tripletof mRNA; it is an anticodon.

  41. 27.29DNA Sequencing

  42. DNA Sequencing • Restriction enzymes cleave the polynucleotide to smaller fragments. • These smaller fragments (100-200 base pairs) are sequenced. • The two strands are separated.

  43. OH OH OH base HO O POCH2 O P P O O O O HO H DNA Sequencing • Single stranded DNA divided in four portions. • Each tube contains adenosine, thymidine, guanosine, and cytidine plus the triphosphates of their 2'-deoxy analogs.

  44. OH OH OH base HO O POCH2 O P P O O O O H H DNA Sequencing • The first tube also contains the 2,'3'-dideoxy analog of adenosine triphosphate (ddATP); the second tube the 2,'3'-dideoxy analog of thymidine triphosphate (ddTTP), the third contains ddGTP, and the fourth ddCTP.

  45. DNA Sequencing • Each tube also contains a "primer," a short section of the complementary DNA strand, labeled with radioactive phosphorus (32P). • DNA synthesis takes place, producing a complementary strand of the DNA strand used as a template. • DNA synthesis stops when a dideoxynucleotide is incorporated into the growing chain.

  46. DNA Sequencing • The contents of each tube are separated by electrophoresis and analyzed by autoradiography. • There are four lanes on the electrophoresis gel. • Each DNA fragment will be one nucleotide longer than the previous one.

  47. ddA ddT ddG ddC T TG TGA TGAC TGACA TGACAT TGACATA TGACATAC TGACATACG TGACATACGT Sequence of fragment Figure 27.29

  48. ddA ddT ddG ddC T A TG AC TGA ACT TGAC ACTG TGACA ACTGT TGACAT ACTGTA TGACATA ACTGTAT TGACATAC ACTGTATG TGACATACG ACTGTATGC TGACATACGT ACTGTATGCA Sequence of fragment Sequence of original DNA Figure 27.29

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