Nucleotides and Nucleic Acids: Information Transfer in Cells

1. Chapter 19 Nucleotides and Nucleic Acids

2. Information Transfer in Cells • Information encoded in a DNA molecule is transcribed via synthesis of an RNA molecule • The sequence of the RNA molecule is "read" and is translated into the sequence of amino acids in a protein.

3. Nitrogenous Bases Know the basic structures • Pyrimidines • Cytosine (DNA, RNA) • Uracil (RNA) • Thymine (DNA) • Purines • Adenine (DNA, RNA) • Guanine (DNA, RNA) Cytosine (C) Thymine (T) Uracil (U) DNA & RNA DNA RNA Adenine (A) Guanine (G) DNA & RNA

4. Properties of Pyrimidines and Purines • Keto-enoltautomerism

5. Properties of Pyrimidines and Purines • Acid/base dissociations • Strong absorbance of UV light

6. Pentosesof Nucleotides Know these structures too • D-ribose (in RNA) • 2-deoxy-D-ribose (in DNA) • The difference - 2'-OH vs 2'-H • This difference affects secondary structure and stability

7. 11.3 Nucleosides Linkage of a base to a sugar • Base is linked via a glycosidic bond • The carbon of the glycosidic bond is anomeric

8. 11.3 Nucleosides Linkage of a base to a sugar • Named by adding -idine to the root name of a pyrimidine or -osine to the root name of a purine

9. 11.3 Nucleosides Linkage of a base to a sugar • Conformation can be syn or anti • Sugars make nucleosides more water-soluble than free bases

10. 11.4 Nucleotides Nucleoside phosphates • Nucleotides are nucleosides esterified with phosphoric acid • Most are esterified at the 3’ or 5’ position • "Nucleotide phosphate" is redundant! • Nucleotides are poly-proticacids

11. 11.4 Nucleotides Nucleoside phosphates

12. Functions of Nucleotides • Nucleoside 5'-triphosphates are carriers of energy • Bases serve as recognition units

13. Functions of Nucleotides • Cyclic nucleotides are signal molecules and regulators of cellular metabolism and reproduction • ATP is central to energy metabolism • GTP drives protein synthesis • CTP drives lipid synthesis • UTP drives carbohydrate metabolism

14. 11.5 Nucleic Acids - Polynucleotides • Following are names and one-letter abbreviations for the heterocyclic aromatic amine bases most common to nucleic acids

15. 11.5 Nucleic Acids - Polynucleotides • Polymers linked 3' to 5' by phosphodiester bridges • Ribonucleic acid (RNA) and deoxyribonucleic acid(DNA) • Know the shorthand notations • Sequence is always read 5' to 3' • In terms of genetic information, this corresponds to "N to C" in proteins T-G is a dinucleotide

16. 11.5 Nucleic Acids - Polynucleotides

17. 11.5 Nucleic Acids - Polynucleotides

18. 11.6 Classes of Nucleic Acids • DNA - one type, one purpose • RNA - 3 (or 4) types, 3 (or 4) purposes • ribosomal RNA - the basis of structure and function of ribosomes • messenger RNA - carries the message • transfer RNA - carries the amino acids

19. Structure of DNA • Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule (or an RNA molecule) read from the 5’ end to the 3’ end • Secondary structure: the ordered arrangement of nucleic acid strands • Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis

20. The DNA Double Helix Stabilized by hydrogen bonds! • "Base pairs" arise from hydrogen bonds • Erwin Chargaff had the pairing data, but didn't understand its implications • Rosalind Franklin's X-ray fiber diffraction data was crucial • Francis Crick knew it was a helix • James Watson figured out the H-bonds

21. DNA - 2° Structure T-A base pairing

22. DNA - 2° Structure C-G base pairing

23. DNA - 2° Structure Ribbon model of B-DNA

26. DNA - 2° Structure • B-DNA • the predominant form in dilute aqueous solution • a right-handed helix • 20 Å thick with 34 Å per ten base pairs • minor groove of 12 Å and major groove of 22 Å • A-DNA • a right-handed helix, but thicker than B-DNA • 29 Å per 10 base pairs • Z-DNA • a left-handed double helix

27. The Structure of DNA • Length of 1.6 million nm (E. coli) • Compact and folded (E. coli cell is only 2000 nm long) • Eukaryotic DNA wrapped around histone proteins to form nucleosomes

28. DNA - 3° Structure • Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid, commonly referred as to supercoiling • Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by a phosphodiester bond (Fig 20.10) • Chromatin: consists of DNA molecules wound around particles of histones in a beadlike structure

29. DNA - 3° Structure Relaxed, strained, and supercoiled DNA

30. Ribonucleic Acids (RNA) • RNA are similar to DNA in that they, too, consist of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-OH of the next; however: • the pentose unit in RNA is -D-ribose rather than -2-deoxy-D-ribose • the pyrimidine bases in RNA are uracil and cytosine rather than thymine and cytosine • RNA is single stranded rather than double stranded

31. RNA • RNA molecules are classified according to their structure and function • Ribosomal RNA (rRNA): a ribonucleic acid found in ribosomes, the site of protein synthesis

32. RNA • Transfer RNA (tRNA): a ribonucleic acid that carries a specific amino acid to the site of protein synthesis on ribosomes

33. RNA • Messenger RNA (mRNA):a ribonucleic acid that carries coded genetic information from DNA to the ribosomes for the synthesis of proteins • present in cells in relatively small amounts and very short-lived • single stranded • their synthesis is directed by information encoded on DNA • a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the 3’ end

34. RNA • the synthesis of mRNA from DNA is called transcription

35. Genetic Code

36. Genetic Code • Properties of the Code • only 61 triplets code for amino acids; the remaining 3 (UAA, UAG, and UGA) signal chain termination • the code is degenerate, which means that several amino acids are coded for by more than one triplet; Leu, Ser, and Arg, for example, are each coded for by six triplets • for the 15 amino acids coded for by 2, 3, or 4 triplets, it is only the third letter of the codon that varies; Gly, for example, is coded for by GGA, GGG, GGC, and GGU • there is no ambiguity in the code; each triplet codes for one and only one amino acid

37. Sequencing DNA • Restriction endonuclease: an enzyme that catalyzes hydrolysis of a particular phosphodiester bond within a DNA strand • over 1000 endonucleases have been isolated and their specificities determined • typically they recognize a set sequence of nucleotides and cleave the DNA at or near that particular sequence • EcoRI from E. coli, for example, cleaves as shown

38. Sequencing DNA examples of restriction endonucleases

39. Sequencing DNA • Polyacrylamide gel electrophoresis: a technique so sensitive that it is possible to separate nucleic acid fragments differing from one another in only a single nucleotide • Chain termination or dideoxy method: a method developed by Frederick Sanger for sequencing DNA molecules

40. DNA Replication • the sequence of nucleotides on one strand is copied as a complementary strand to form the second strand of double-stranded DNA • this synthesis is catalyzed by the enzyme DNA polymerase • DNA polymerase will carry out this synthesis in vitro using single-stranded DNA as a template, provided the four dNTPs and a primer are present • because the new DNA strand grows from the 5’ to 3’ end, the primer must have a free 3’-OH group to which the first nucleotide of the growing chain is added

41. Chain-Termination Sequencing • the key is addition of a 2’,3’-dideoxynucleoside triphosphate (ddNTP) to the synthesizing medium • synthesis terminates at any point where a ddNTP becomes incorporated

42. Chain-Termination Sequencing • a single-stranded DNA of unknown sequence is mixed with primer and divided into four separate reaction mixtures • to each mixture is added all four dNTPs, one of which is labeled in its 5’- phosphoryl group with P-32 • also added are DNA polymerase and one of the four ddNTPs • when polyacrylamide gel electrophoresis of each reaction mixture is completed, a piece of x-ray film is placed over the gel to detect gamma radiation from the decay of P-32 • the base sequence of the complement to the original single-stranded template is read directly from the bottom to top of the developed film

45. Messenger RNA Transcription product of DNA • In prokaryotes, a single mRNA contains the information for synthesis of many proteins • In eukaryotes, a single mRNA codes for just one protein, but structure is composed of introns and exons

47. Eukaryotic mRNA • DNA is transcribed to produce heterogeneous nuclear RNA • mixed introns and exons with poly A • intron - intervening sequence • exon - coding sequence • poly A tail - stability? • Splicing produces final mRNA without introns

48. Ribosomal RNA • Ribosomes are about 2/3 RNA, 1/3 protein • rRNA serves as a scaffold for ribosomal proteins • 23S rRNA in E. coli is the peptidyltransferase!