1. Chapter 28 Biomolecules: Heterocycles and Nucleic Acids
Based on McMurry’s Organic Chemistry, 6th edition

2. Heterocycles Cyclic organic compounds are carbocycles or heterocycles
Carbocycle rings contain only carbon atoms
Heterocycle rings atoms in addition to carbon (N,S,O are common)
Heterocycles include many important natural materials as well as pharmaceuticals

3. 28.1 Five-Membered Unsaturated Heterocycles
Pyrrole, furan, and thiophene are common five-membered unsaturated heterocycles
Each has two double bonds and N, O, or S

4. Pyrrole
Commercially from coal tar or by treatment of furan with ammonia over an alumina catalyst at 400°C.

5. Furan
Made commercially by extrusion of CO from furfural, which is produced from sugars

6. Thiophene
From coal tar or by cyclization of butane or butadiene with sulfur at 600°C

7. Unusual Reactivity Pyrrole is an amine but it is not basic
Pyrrole, furan, and thiophene are conjugated dienes but they undergo electrophilic substitution (rather than addition)

8. 28.2 Structures of Pyrrole, Furan, and Thiophene
Pyrrole, furan, and thiophene are aromatic (Six  electrons in a cyclic conjugated system of overlapping p orbitals)
In pyrrole  electrons come from C atoms and lone pair on sp2-N

9. Why Pyrrole is Not a Base
The nitrogen lone pair is a part of the aromatic sextet, protonation on nitrogen destroys the aromaticity, giving its conjugate acid a very low pKa (0.4)
The carbon atoms of pyrrole are more electron-rich and more nucleophilic than typical double-bond carbons (see comparison with cyclopentadiene)

10. 28.3 Electrophilic Substitution Reactions of Pyrrole, Furan, and Thiophene
The heterocycles are more reactive toward electrophiles than benzene

11. Position of Substitution
Electrophilic substitution normally occurs at C2, the position next to the heteroatom, giving more stable intermediate

12. 28.4 Pyridine, a Six-Membered Heterocycle
Nitrogen-containing heterocyclic analog of benzene
Lone pair of electrons on N not part occupies an sp2 orbital in the plane of the ring and is not involved in bonding (Figure 28.3).

13. Electronic structure of pyridine
Pyridine is a stronger base than pyrrole but a weaker base than alkylamines
The sp2-hybridized N holds the lone-pair electrons more tightly than the sp3-hybridized nitrogen in an alkylamine

14. 28.5 Electrophilic Substitution of Pyridine
The pyridine ring undergoes electrophilic aromatic substitution reactions with great difficulty, under drastic conditions

15. Low Reactivity of Pyridine
Complex between ring nitrogen and incoming electrophile deactivates ring with positive charge
Electron-withdrawing nitrogen atom deactivates causes a dipole making positively polarized C’s poor Lewis bases

16. 28.6 Nucleophilic Substitution of Pyridine
2- and 4-substituted (but not 3-substituted) halopyridines readily undergo nucleophilic aromatic substitution

17. Mechanism of Nucleophilic Substitution on Pyridine
Reaction occurs by addition of the nucleophile to the C=N bond, followed by loss of halide ion

18. Addition-Elimination
Addition favored by ability of the electronegative nitrogen to stabilize the anionic intermediate
Leaving group is then expelled

19. 28.7 Fused-Ring Heterocycles
Quinoline, isoquinoline, and indole are fused-ring heterocycles, containing both a benzene ring and a heterocyclic aromatic ring

20. Quinoline and Isoquinoline
Quinoline and isoquinoline have pyridine-like nitrogen atoms, and undergo electrophilic substitutions
Reaction is on the benzene ring rather than on the pyridine ring

21. Indole Has pyrrole-like nitrogen (nonbasic)
Undergoes electrophilic substitution at C3 of the electron-rich pyrrole

22. Purine and Pyrimidine
Pyrimidine contains two pyridine-like nitrogens in a six-membered aromatic ring
Purine has 4 N’s in a fused-ring structure. Three are basic like pyridine-like and one is like that in pyrrole

23. 28.8 Nucleic Acids and Nucleotides
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are the chemical carriers of genetic information
Nucleic acids are biopolymers made of nucleotides, aldopentoses linked to a purine or pyrimidine and a phosphate

24. Sugars in DNA and RNA RNA is derived from ribose
DNA is from 2-deoxyribose
(the ' is used to refer to positions on the sugar portion of a nucleotide)

25. Heterocycles in DNA and RNA
Adenine, guanine, cytosine and thymine are in DNA
RNA contains uracil rather than thymine

26. Nucleotides
In DNA and RNA the heterocycle is bonded to C1 of the sugar and the phosphate is bonded to C5 (and connected to 3’ of the next unit)

27. The Deoxyribonucleotides

28. The Ribonucleotides

29. 28.9 Structure of Nucleic Acids
Nucleotides join together in DNA and RNA by as phosphate between the 5-on one nucleotide and the 3 on another
One end of the nucleic acid polymer has a free hydroxyl at C3 (the 3 end), and the other end has a phosphate at C5 (the 5 end).

30. Generalized Structure of DNA

31. Nucleic Acid Sequences
Differences arise from the sequence of bases on the individual nucleotides

32. Describing a Sequence
Chain is described from 5 end, identifying the bases in order of occurrence, using the abbreviations A for adenosine, G for guanosine, C for cytidine, and T for thymine (or U for uracil in RNA)
A typical sequence is written as TAGGCT

33. 28.10 Base Pairing in DNA: The Watson–Crick Model
In 1953 Watson and Crick noted that DNA consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix
Strands are held together by hydrogen bonds between specific pairs of bases
Adenine (A) and thymine (T) form strong hydrogen bonds to each other but not to C or G
(G) and cytosine (C) form strong hydrogen bonds to each other but not to A or T

34. H-Bonds in DNA
The G-C base pair involves three H-bonds

35. A-T Base Pairing
Involves two H-bonds

36. The Difference in the Strands
The strands of DNA are complementary because of H-bonding
Whenever a G occurs in one strand, a C occurs opposite it in the other strand
When an A occurs in one strand, a T occurs in the other

37. Grooves
The strands of the DNA double helix create two continuous grooves (major and minor)
The sugar–phosphate backbone runs along the outside of the helix, and the amine bases hydrogen bond to one another on the inside
The major groove is slightly deeper than the minor groove, and both are lined by potential hydrogen bond donors and acceptors.

38. 28.11 Nucleic Acids and Heredity
Processes in the transfer of genetic information:
Replication: identical copies of DNA are made
Transcription: genetic messages are read and carried out of the cell nucleus to the ribosomes, where protein synthesis occurs.
Translation: genetic messages are decoded to make proteins.

39. 28.12 Replication of DNA
Begins with a partial unwinding of the double helix, exposing the recognition site on the bases
Activated forms of the complementary nucleotides (A with T and G with C) associate two new strands begin to grow

40. The Replication Process
Addition takes place 5  3, catalyzed by DNA polymerase
Each nucleotide is joined as a 5-nucleoside triphosphate that adds a nucleotide to the free 3-hydroxyl group of the growing chain

41. 28.13 Structure and Synthesis of RNA: Transcription
RNA contains ribose rather than deoxyribose and uracil rather than thymine
There are three major kinds of RNA - each of which serves a specific function
They are much smaller molecules than DNA and are usually single-stranded

42. Messenger RNA (mRNA) Its sequence is copied from genetic DNA
It travels to ribsosomes, small granular particles in the cytoplasm of a cell where protein synthesis takes place

43. Ribosomal RNA (rRNA) Ribosomes are a complex of proteins and rRNA
The synthesis of proteins from amino acids and ATP occurs in the ribosome
The rRNA provides both structure and catalysis

44. Transfer RNA (tRNA)
Transports amino acids to the ribosomes where they are joined together to make proteins
There is a specific tRNA for each amino acid
Recognition of the tRNA at the anti-codon communicates which amino acid is attached

45. Transcription Process
Several turns of the DNA double helix unwind, exposing the bases of the two strands
Ribonucleotides line up in the proper order by hydrogen bonding to their complementary bases on DNA
Bonds form in the 5  3 direction,

46. Transcription of RNA from DNA
Only one of the two DNA strands is transcribed into mRNA
The strand that contains the gene is the coding or sense strand
The strand that gets transcribed is the template or antisense strand
The RNA molecule produced during transcription is a copy of the coding strand (with U in place of T)

47. Mechanism of Transcription
DNA contains promoter sites that are 10 to 35 base pairs upstream from the beginning of the coding region and signal the beginning of a gene
There are other base sequences near the end of the gene that signal a stop
Genes are not necessarily continuous, beginning gene in a section of DNA (an exon) and then resume farther down the chain in another exon, with an intron between that is removed from the mRNA

48. 28.14 RNA and Protein Biosynthesis: Translation
RNA directs biosynthesis of peptides and proteins which is catalyzed by mRNA in ribosomes, where mRNA acts as a template to pass on the genetic information transcribed from DNA
The ribonucleotide sequence in mRNA forms a message that determines the order in which different amino acid residues are to be joined
Codons are sequences of three ribonucleotides that specify a particular amino acid
For example, UUC on mRNA is a codon that directs incorporation of phenylalanine into the growing protein

49. Codon Assignments of Base Triplets

50. The Parts of Transfer RNA
There are 61 different tRNAs, one for each of the 61 codons that specifies an amino acid
tRNA has ribonucleotides and is bonded to a specific amino acid by an ester linkage through the 3 hydroxyl on ribose at the 3 end of the tRNA
Each tRNA has a segment called an anticodon, a sequence of three ribonucleotides complementary to the codon sequence

51. The Structure of tRNA

52. Processing Aminoacyl tRNA
As each codon on mRNA is read, tRNAs bring amino acids as esters for transfer to the growing peptide
When synthesis of the proper protein is completed, a "stop" codon signals the end and the protein is released from the ribosome

53. 28.15 DNA Sequencing
The order of the bases along DNA contains the genetic inheritance.
Determination of the sequence is based on chemical reactions rather than physical analysis
DNA is cleaved at specific sequences by restriction endonucleases
For example, the restriction enzyme AluI cleaves between G and C in the four-base sequence AG-CT Note that the sequence is identical to that of its complement, (3)-TC-GA-(5)
Other restriction enzymes produce other cuts permitting partially overlapping sequences of small pieces to be produced for analysis

54. Analytical Methods
The Maxam–Gilbert method uses organic chemistry to cleave phosphate linkages at with specificity for the adjoining heterocycle
The Sanger dideoxy method uses enzymatic reactions
The Sanger method is now widely used and automated, even in the sequencing of genomes

55. The Sanger Dideoxy Method
The fragment to be sequenced is combined with:
A small piece of DNA (primer), whose sequence is complementary to that on the 3 end of the restriction fragment
The four 2-deoxyribonucleoside triphosphates (dNTPs)

56. The Dideoxy Nucleotides
The solution also contains small amounts of the four 2,3-dideoxyribonucleoside triphosphates (ddNTPs)
Each is modified with a different fluorescent dye molecule

57. The Dideoxy Method - Growing the and Stopping the Copied Chains
DNA polymerase is added and a strand of DNA complementary to the restriction fragment begins to grow from the end of the primer
Whenever a dideoxyribonucleotide is incorporated, chain extension cannot continue

58. Dideoxy Method - Analysis
The product is a mixture of dideoxy-terminated DNA fragments with fluorescent tags
These are separated according to weight by electrophoresis and identified by their specific fluorescence

59. 28.16 DNA Synthesis
DNA synthesizers use a solid-phase method starting with an attached, protected nucleotide
Subsequent protected nucleotides are added and coupled
After the final nucleotide has been added, the protecting groups are removed and the synthetic DNA is cleaved from the solid support
The bases are protected from reacting

60. DNA Synthesis: Attachment
Attachment of a protected deoxynucleoside to a polymeric or silicate support as an ester of the 3 OH group of the deoxynucleoside
The 5 OH group on the sugar is protected as its p-dimethoxytrityl (DMT) ether

61. DNA Synthesis: DMT Removal
Removal of the DMT protecting group by treatment with a moderately weak acid

62. DNA Synthesis: Coupling
The polymer-bound (protected) deoxynucleoside reacts with a protected deoxynucleoside containing a phosphoramidite group at its 3 position, catalyzed by tetrazole, a reactive heterocycle

63. DNA Synthesis: Oxidation and Cycling
Phosphite is oxidized to phosphate by I2
The cycle is repeated until the sequence is complete

64. DNA Synthesis: Clean-up
All protecting groups are removed and the product is released from the support by treatment with aqueous NH3

65. 28.17 The Polymerase Chain Reaction (PCR)
Copies DNA molecules by unwinding the double helix and copying each strand using enzymes
The new double helices are unwound and copied again
The enzyme is selected to be fast, accurate and heat-stable (to survive the unwinding)
Each cycle doubles the amount of material
This is exponential template-driven organic synthesis

66. PCR: Heating and Reaction
The subject DNA is heated (to separate strands) with
Taq polymerase (enyzme) and Mg2+
Deoxynucleotide triphosphates
Two, oligonucleotide primers, each complementary to the sequence at the end of one of the target DNA segments

67. PCR: Annealing and Growing
Temperature is reduced to 37 to 50°C, allowing the primers to form H-bonds to their complementary sequence at the end of each target strand

68. PCR: Taq Polymerase
The temperature is then raised to 72°C, and Taq polymerase catalyzes the addition of further nucleotides to the two primed DNA strands

69. PCR: Growing More Chains
Repeating the denature–anneal–synthesize cycle a second time yields four DNA copies, a third time yields eight copies, in an exponential series.
PCR has been automated, and 30 or so cycles can be carried out in an hour