Lecture 26 Nucleotides and Nucleic Acids

Oligonucleotides and Polynucleotides

Oligonucleotides are short (typically 50 nucleotides)

Poly Nucleotides are longer

Properties of Nucleotide Bases

Affect the 3D structure of Nucleic Acids

Aromatic molecules

Most bonds in the ring have partial double bond character (rigidity)

Pyrimidines are planar

Purines have a slight pucker

Solubility of Nucleotides

Hydrophobic and relatively insoluble in pH 7 water

Leads to stacking interactions (van der Waals and dipole dipole)

Charged and more soluble at acidic or alkaline pH values

Absorption Spectra of Common Nucleotides

All nucleotide bases absorb UV light

Strong absorption near 260 nm

Base Paring

Permits the duplication of genetic information

Hydrogen bonding patterns between complementary strands of nucleic acids

A bonds to T (or U in RNA) 2 H bonds between

G bonds to C 3 H bonds between

Primary Structure of Nucleic Acid

Covalent structure and nucleotide sequence

Secondary Structure of Nucleic Acid

Regular, stable structure taken up by some or all the nucleotides

Tertiary Structure of Nucleic Acids

Complex folding of large chromosomes or the elaborate folding of tRNA or rRNA structures

Double Helix

DNA is a double helix that stores genetic information

X-ray diffraction pattern revealed DNA molecules are helical

Parallel

3’, 5’ phosphodiester bonds run in the same direction

Antiparallel

3’, 5’ phosphodiester bonds run in opposite directions

Structure of DNA

DNA is read 5’ to 3’

Ultimately confirmed by x-ray analysis

Watson-Crick Model

Offset pairing of the two strands create a major groove (larger, 22 Angstrom wide) and a minor groove (smaller, 12 Angstrom wide)

3 H bonds between G and C

2 H bonds between A and T

Complementary Strands

Double helical DNA strands are complementary

When A occurs on one chain T occurs on the other

Hydrogen bonding does not contribute significantly to stability of the structure

Stabilization of the DNA Double Helix

Metal cations that shield the negative charge of backbone phosphates

Base stacking interactions between successive base pairs

Successive GC or CG are stronger than successive AT or TA

Duplexes with higher GC context are more stable

Replication of DNA

1. Preexisting or parent strands separate

2. Each parent stand serves as a template for the biosynthesis of a complementary daughter strand

Different Forms of DNA

Different possible conformations of the deoxyribose

Rotation about the contiguous bonds making up the phosphodeoxyribose backbone

Free rotation about the C1N glycosyl bond

B-Form DNA

The Watson-Crick structure

Most stable for a random sequence DNA molecule under physiological conditions

Right handed, 10.5 base pairs per turn

Alpha Form DNA

Right handed double helix with a wider helix, 11 base pairs per turn and a tilted plane

Favored in solutions devoid of water

Z Form DNA

Left handed helix with 12 base pairs per turn and a backbone with a zig zag appearance

Appears more slender and elongated

Unusual Structures of DNA

Palindrome and Mirror Repeats

Palindrome

Region of DNA that is identical when read either forward or backward

Applied to regions of DNA with inverted repeats

3’ to 5’ is the same as 5’ to 3’

Mirror Repeat

Sequence when the inverted repeat occurs within each individual strand

5’ TTAGCA ____l____ACGATT 3”

Hairpin and Cruciform Structures

Form from the self complementarity within each strand

Messenger RNA

Code for polypeptide chain

Portion of cellular RNA carrying the genetic information from DNA to the ribosome

Transcription

Process by which mRNA are formed on a DNA template

Monocistronic

Codes for only one polypeptide

Most mRNA in eukaryotes

mRNA has only one gene

Polycistronic

Codes for 2+ different polypeptides

Occurs in bacteria and archaea

mRNA has more than one gene

RNA 3D Structure

Complex but always single stranded

Right-handed helical conformation

Dominated by base stacking interactions

Strongest between two purines

Can base pair with complementary regions of DNA or RNA

Paired strands are anitparrallel

Other Complex 3D Structures of RNA

Structure of complementary RNA strands is an A form right-handed double helix

Breaks caused by mismatched or unmatched bases results in bulges or internal loops

Internal loops form between palindromic sequences

Methylated DNA

Some bases of DNA are methylated

A and C are methylated more frequently than G and T

All known DNA methylases use s-adenosylmethionine as a methyl group donor

In eukaryotes, 5% of cytidine residues are methylated (affects gene expression)