1. DNA

2. Genetics & DNA

3. DNA: Picture 51 http://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm B-DNA: The advent of modeling http://molvis.sdsc.edu/pdb/dna_b_form.pdb 46 Å 12 base sequence (1953-2003)

4. DNA: Size, Shape & Self Assembly http://www.umass.edu/microbio/chime/beta/pe_alpha/atlas/atlas.htm Views & Algorithms 10.85 Å Several formats are commonly used but all rely on plotting atoms in 3 dimensional space;.pdb is one of the most popular.

8. Pyrimidines and Purines

9. 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.

10. Pyrimidines and Purines Pyrimidine and purine are the names of the parent compounds of two types of nitrogen- containing heterocyclic aromatic compounds. N N N N N NH PyrimidinePurine

11. Important Pyrimidines Pyrimidines that occur in DNA are cytosine and thymine. Cytosine and uracil are the pyrimidines in RNA. HNHNHNHN NHNHNHNHOO Uracil HNHNHNHN NHNHNHNHOO CH 3 Thymine HNHNHNHN NHNHNHNH NH2NH2NH2NH2 O Cytosine

12. Important Purines Adenine and guanine are the principal purines of both DNA and RNA. Adenine N N NH2NH2NH2NH2N NHNHNHNH GuanineO HNHNHNHN NHNHNHNH N N H2NH2NH2NH2N

13. Caffeine and Theobromine Caffeine (coffee) and theobromine (coffee and tea) are naturally occurring purines. Caffeine N NON N H3CH3CH3CH3C O CH 3 TheobromineO HNHNHNHN N N N O

14. Question How many pyrimidines and purines in total occur in DNA and RNA? A)2, 2 B)2, 3 C)3, 2 D)4, 1

15. Nucleosides

16. 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.

17. Question Which of the following carbohydrates are classified as deoxy sugars? A)1 onlyB) 1 and 2 C)1 and 3D) 1, 3, and 4

18. Uridine and Adenosine Uridine and adenosine are pyrimidine and purine nucleosides respectively of D -ribofuranose. Uridine (a pyrimidine nucleoside) Adenosine (a purine nucleoside) OCH HOCH 2 HNHNHNHN O OHHO O N N N N O OHHO NH2NH2NH2NH2N

19. Question To which atom(s) of the pyrimidine is the anomeric carbon of a sugar attached? A)1 B)2 C)3 D)4

20. Question Which of the following bases is only found in DNA? A)Cytosine B)Thymine C)Adenine D)Uracil

21. Nucleotides

22. Nucleotides Nucleotides are phosphoric acid esters of nucleosides.

23. Adenosine 5'-Monophosphate (AMP) Adenosine 5'-monophosphate (AMP) is also called 5'- adenylic acid. N N N N O OHHO NH2NH2NH2NH2 OCH 2 P HO O HO

24. Adenosine 5'-Monophosphate (AMP) Adenosine 5'-monophosphate (AMP) is also called 5'- adenylic acid. N N N N O OHHO NH2NH2NH2NH2 OCH 2 P HO O HO 1' 2'3' 4' 5'

25. Adenosine Diphosphate (ADP) N N N N O OHHO NH2NH2NH2NH2 OCH 2 P O O HO P O HO HO

26. Adenosine Triphosphate (ATP) N N N N O OHHO NH2NH2NH2NH2 OCH 2 P O O HO P O HO O P O HO HO

27. Question The bond that joins two nucleotides together is called a A)amide bond. B)peptide bond. C)phosphodiester bond. D)hydrogen bond.

28. ATP Stores Energy AMP ADP 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.  G° for hydrolysis of ATP to ADP is –35 kJ/mol http://chemconnections.org/organic/Movies%20Org%20Flash/flash-amines-genetic%20bases/NADH-redox.swf

29. Nucleic Acids

30. Nucleic “acids”, RNA and DNA, are polymeric nucleotides (polynucleotides). The 5’ oxygen atom of one nucleotide’s saccharide is linked to the 3' oxygen of another. Nucleotides are commonly referred to by an abbreviation of the heterocylic nitrogen bases that define them. (C, G, A, T, U)

31. What are the bases? A section of a polynucleotide chain.

32. Heterocyclic Bases http://chemconnections.org/organic/Movies%20Org%20Flash/flash-amines-genetic%20bases/purine-N-hetero-ID.swf

33. Structure and Replication of DNA: The Double Helix

34. 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

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

36. Question Estimate the guanine content of turtle DNA if adenine = 28.7% and cytosine = 21.3%. A)28.7% B)21.3% C)57.4% D)42.6%

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

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

39. Question The base pairs present in DNA are: A)A---C and C---T B)A---C and G---T C)A---U and C---C D)A---T and G---C

40. 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.

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

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

43. Question The base pairs present in DNA are: A)A---C and C---T B)A---C and G---T C)A---U and C---C D)A---T and G---C

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

45. DNA Replication A C G T T' A' G' C'

46. DNA-Directed Protein Biosynthesis

47. 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. transcription translation

48. 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.

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

50. Transcription AGGTCACTG TCCAGTGAC A T G C T T T T T T C C C C C A A A A A G G A G G G A A G G U C 5' 3' Uracil is incorporated in RNA instead of thymine.

51. 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.

53. 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.

54. Phenylalanine(Phe) tRNA Codon = UUU

55. Phenylalanine(Phe) tRNA OCCHCH 2 C 6 H 5 NH 3 +O A C C A A A A A A A A A A A A A A A A A C C C C C C C C CC C C U U U U U U U U U U U G G G GG G G G G G G G U GG G G C This AAA triplet is complementary to a UUU triplet of mRNA; it is an anticodon.

57. Protein Synthesis http://chemconnections.org/organic/Movies%20Org%20Flash/proteins-enzymes-DNA/transcription.swf