Nucleic Acid Structure

A. Structure of nucleotidesB. Nitrogenous basesC. Pentose sugarsD. NucleosidesE. NucleotidesF. Nucleotide chainsG. Structure of B-DNA

Images accompanying this lecture may be found athttp://www.prenhall.com/klug4/

Select chapter 10

A. Structure of Nucleotides

A nucleotide is composed of– A nitrogenous base– A pentose sugar– A phosphate group

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)

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´

C. Pentose Sugars

Deoxyribose– Found in DNA– Identical to ribose, except that the “-OH”

group on the 2´ carbon is replaced with an “-H”

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-”

D. Nucleosides

Ribonucleosides Deoxyribonucleosides

Adenosine Deoxyadenosine

Guanosine Deoxyguanosine

Cytidine Deoxycytidine

Uridine -

- Deoxythymidine

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”

E. NucleotidesRibonucleotides Deoxyribonucleotides

Adenosine monophosphate

Deoxyadenosine

monophosphate

Guanosine

monophosphate

Deoxyguanosine

monophosphate

Cytidine

monophosphate

Deoxycytidine

monophosphate

Uridine

monophosphate

-

- Deoxythymidine

monophosphate

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´

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)

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

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

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

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

G. Structure of B-DNA

The two strands are in antiparallel orientation (one strand goes from 5´ 3´ and the other strand goes from3´ 5´

These are the dimensions of the helix:20 Å diameter10 bases per turn34 Å per turn

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)

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 bondsG – C pairs have three hydrogen bonds

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

G. Structure of B-DNA

An interactive tutorial on DNA structure can be found athttp://molvis.sdsc.edu/dna/index.htm