1. Nucleic Acid Structure A. Structure of nucleotides B. Nitrogenous bases C. Pentose sugars D. Nucleosides E. Nucleotides F. Nucleotide chains G. Structure of B-DNA Images accompanying this lecture may be found at http://www.prenhall.com/klug4/ Select chapter 10 http://www.prenhall.com/klug4/

2. A.Structure of Nucleotides A nucleotide is composed of –A nitrogenous base –A pentose sugar –A phosphate group

3. B.Nitrogenous Bases Two different classes of aromatic carbon-nitrogen heterocycles –Purines Adenine (Found in DNA & RNA) Guanine (Found in DNA & RNA) –Pyrimidines Cytosine (Found in DNA & RNA) Thymine (Found in DNA) Uracil (Found in RNA)

4. C.Pentose Sugars Ribose –Found in RNA –Forms a 5-atom ring structure in aqueous solution –Carbons are numbered 1´ (one-prime), 2´, 3´, 4´, 5´

5. C.Pentose Sugars Deoxyribose –Found in DNA –Identical to ribose, except that the “-OH” group on the 2´ carbon is replaced with an “-H”

6. D.Nucleosides Nucleoside –A pentose sugar molecule with a nitrogenous base attached to the 1´ carbon –Nucleosides are named by using the root of the base name, plus the suffix “-osine” (for purines) or “-idine” (for pyrimidines) –Nucleosides with deoxyribose sugars are designated with the prefix “deoxy-”

7. D.Nucleosides RibonucleosidesDeoxyribonucleosides AdenosineDeoxyadenosine GuanosineDeoxyguanosine CytidineDeoxycytidine Uridine- -Deoxythymidine

8. E.Nucleotides Nucleotide –A nucleoside with one, two, or three phosphate groups attached to the 5´ carbon –Nucleotides are named using the name of the nucleoside plus “monophosphate,” “diphosphate,” or “triphosphate” depending on the number of phosphates –Nucleotides with one phosphate may also be named by changing the nucleoside suffix to “-ylic acid”

9. E.Nucleotides RibonucleotidesDeoxyribonucleotides Adenosine monophosphate Deoxyadenosine monophosphate Guanosine monophosphate Deoxyguanosine monophosphate Cytidine monophosphate Deoxycytidine monophosphate Uridine monophosphate - -Deoxythymidine monophosphate

10. F.Nucleotide Chains The 5´ carbon of one nucleotide can be linked to the 3´ carbon of another nucleotide via a phosphodiester bond An oligonucleotide chain (polynucleotide chain) is a linear chain of nucleotides linked in this fashion The oligonucleotide chain has two ends: 5´ and 3´

11. G.Structure of B-DNA In the 1940s, Chargaff discovered that the DNA isolated from most sources exhibited a 1:1 molar ratio of A:T, and a 1:1 ratio of G:C (as compared to RNA, in which the A:U and G:C ratios are random)

12. G.Structure of B-DNA In the early 1950s, Watson, Crick, and Franklin studied the X-ray diffraction patterns of crystalline DNA fibers, and determined that DNA had a symmetrical 3-D structure in the form of a helix

13. G.Structure of B-DNA Watson & Crick knew of Chargaff’s ratios, and realized that they could build a helical model for DNA structure, consistent with the X-ray data

14. G.Structure of B-DNA The Watson and Crick model is known as a B-DNA helix, and it is believed to be the native conformation of most DNA found in living organisms

15. G.Structure of B-DNA Features of the B-DNA helix: –Two oligonucleotide strands –The sugar-phosphate backbones of the strands are on the outside, and twist around a central axis to form a helix –The helical twists form two “grooves”that turn around the axis: the major groove and the minor groove –Therefore, DNA is a pretty groovy molecule

16. G.Structure of B-DNA The two strands are in antiparallel orientation (one strand goes from 5´  3´ and the other strand goes from 3´  5´ These are the dimensions of the helix: 20 Å diameter 10 bases per turn 34 Å per turn

17. G.Structure of B-DNA The bases are located in the center of the helix, with the flat planes of the bases perpendicular to the axis of the helix The bases between the two strands are “paired” with an “A” on one strand paired with a “T” on the other strand, and “G” paired with “C” This property of the strands is called complementarity (the two strands are said to be complementary to each other, thank you very much)

18. G.Structure of B-DNA The strands are held together by noncovalent “hydrogen bonds” between the complementary pairs of bases: A – T pairs have two hydrogen bonds G – C pairs have three hydrogen bonds

19. G.Structure of B-DNA The two strands may be separated by heating (“melting”) the DNA, or by raising the pH with alkaline treatment Two pieces of single-stranded DNA will spontaneously form a helix if the strands have enough base complementarity

20. G.Structure of B-DNA An interactive tutorial on DNA structure can be found at http://molvis.sdsc.edu/dna/index.htm http://molvis.sdsc.edu/dna/index.htm