Outline

Introduction

The Nature of Nucleic Acids

Two Types of Nucleic Acids: DNA and RNA (Figure 4.1)

Nucleotide = Base + Sugar + Phosphate (Figure 4.3)
Nucleosides = Sugar + Base (no phosphate)
Structural Difference DNA-RNA - Ribose in RNA, Deoxyribose in DNA

Phosphodiester links between nucleotides (Figure 4.1)
Purine bases - Adenine (A) and Guanine (G) (Figure 4.2)
Pyrimidine Bases - Cytosine (C), Thymine (T), Uracil (U)
Same bases in RNA and DNA except T only in DNA, U in RNA

Properties of the Nucleotides

Ionization - Table 4.1
Tautomerization (Figure 4.4)
UV Spectra (Figure 4.5)

Stability and Formation of the Phosphodiester Linkage

Dehydration - unfavorable thermodynamics (Figure 4.6)
Energy of triphosphate hydrolysis coupled to synthesis (Figure 4.7)

Primary Structure of Nucleic Acids

The Nature and Significance of Primary Structure

1. Directionality of polynucleotide chain
2. Individuality of polynucleotide chain determined by sequence of nucleotides. (Primary Structure)

Shortcut sequence listings (#1, #2)
Genetic information stored in nucleotide sequence of DNA
Gene is a particular DNA sequence

DNA as the Genetic Substance: Early Evidence (History of DNA)

Miescher first to isolate DNA from salmon sperm (late 1800s)
Avery, MacLeod, McCarty - Transfer of DNA carried pathogenicity. (Figure 4.8)
Hershey and Chase - Bacteriophage T2 transfers DNA to bacteria

Secondary and Tertiary Structure of Nucleic Acids

The Double Helix

Watson, Crick, Franklin, Wilkins
Secondary Structure from X-ray Diffraction
Refined Structure (Figure 4.10)
Major and Minor Grooves (Figure 4.11)
Chargaff's Rule (A=T, G=C in DNA) (Table 4.2)
Complementarity allows replication (Figure 4.12)

Semiconservative Nature of DNA Replication

Half of original is conserved in each of two copies of duplicated strand (Figure 4.13)
Meselson and Stahl (Figure 4.14)

Alternative Nucleic Acid Structures: B and A Helices (Figure 4.15, Table 4.3)

'B' form predominant form in cells (Figure 4.16) (Structure of B-DNA)
'A' form found in double-stranded RNA and RNA/DNA hybrids
Lack of steric hindrance in B DNA enables it to accommodate water better than A form.

DNA and RNA Molecules in vivo (Table 4.4)

Long Eukaryotic DNAs
Circular DNA and Supercoiling (Figure 4.18)

3D Structure = Tertiary Structure
Supercoiling

Topoisomerases

Structure of Single-Strand Polynucleotides (Figure 4.19, Figure 4.20)

The Biological Functions of Nucleic Acids: A Preview of Molecular Biology

Genome (Table 4.4)
Genes

Transcription: DNA to RNA (Figure 4.12, Figure 4.21)

Translation: RNA to Protein (Figure 4.22)

Types of RNA (Table 4.5)
Codons
Genetic Code
mRNAs
Ribosomes
Flow of genetic information in cell (Figure 4.23)

Manipulating DNA

Recombinant DNA techniques

Plasticity of Secondary and Tertiary DNA Structure

Changes in Tertiary Structure: A Closer Look at Supercoiling (Figure 4.24)

Twist (T)
Writhe (W)
Linking number (L)
L = T + W

Unusual Secondary Structures of DNA

Left-Hand DNA (Z-DNA) (Figure 4.26)

Purines -Syn and Pyrimidines -Anti base orientations (Figure bottom p. 111)

Hairpins and Cruciforms (Figure 4.27)

Palindrome (Figure 4.28)

Triple Helices and H-DNA (Figure 4.30)

Hoogsteen base pairing (Figure 4.29)

Stability of Secondary and Tertiary Structure

The Helix-to-Random-Coil Transition: Nucleic Acid Denaturation

Loss of Secondary Structure = Denaturation (Figure 4.31)
Factors favoring dissociation of double helices to random coils

1. Electrostatic repulsion between chains
2. Higher entropy of random coil

Forces stabilizing double helices

1. Hydrogen bonds between base pairs
2. van der Waals interactions between stacked bases.

Since G = H - TS (helix <=> random coil) and H and S are both positive, helix stability is a function of temperature. (Figure 4.32)

Hypochromism - absorption of light by bases reduced when in helix = denaturation causes increase in absorbance of light at 260 nm.

Cooperative transitions - Denaturation happens over a short temperature range.

Superhelical Energy and Changes of DNA Conformation

Increasing supercoiling puts DNA circles under stress. Stress may be alleviated by:

1. Melting of AT-rich regions.
2. Formation of Z-DNA in purine/pyrimidine tracts
3. Cruciform formation in palindrome sequences
4. H-DNA formation in stretches of purines/pyrimidines on one strand.