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.