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Nucleotides and Nucleic Acids - Lehninger Chapter8. 8.1 Basics 8.2 Structure 8.3 Chemistry 8.4 Nucleotide Function . 8.1 Basics. Building Blocks Canonical and Minor Bases Phosphodiester bonds Naming and Drawing Base Stacking and Pairing. Building Blocks.

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nucleotides and nucleic acids lehninger chapter8
Nucleotides and Nucleic Acids - Lehninger Chapter8
  • 8.1 Basics
  • 8.2 Structure
  • 8.3 Chemistry
  • 8.4 Nucleotide Function
8 1 basics
8.1 Basics
  • Building Blocks
  • Canonical and Minor Bases
  • Phosphodiester bonds
  • Naming and Drawing
  • Base Stacking and Pairing
building blocks
Building Blocks
  • Nucleotides = Base + Sugar + Phosphate
  • Nucleosides = Base + Sugar
  • Nitrogen Bases
    • Purines (5 + 6 membered rings) – numbering
      • Adenine Guanine
    • Pyrimidines (6 membered ring) – numbering
      • Thymine Cytosine Uracil
  • Pentose Sugars (numbering)
    • – Ribose
    • – Deoxy Ribose
canonical and minor bases
Canonical and Minor Bases
  • DNA A, G, C, T
  • RNA A, G, C, U
  • Modified bases
  • Methylation in DNA
  • Lots of Mods in RNA
phosphodiester bonds
Phosphodiester bonds
  • Formed by Polymerase and Ligase activities
  • C-5' OH carries the phosphate in nucleotides
  • C5' - O - P - O - C3'
  • Phosphate pKa ~ 0
  • Natural Oligonucleotides have 5' P and 3' 0H
  • Base hydrolysis due to ionizaiton of 2' OH in RNA
oligonucleotide naming drawing conventions
Oligonucleotide naming / drawing conventions
  • 5’ - Left to Right - 3’
  • pACGTOH
  • ACGT
base stacking and base pairing
Base Stacking and Base Pairing
  • Bases are very nearly planar
  • Aromaticity => large absorbance at 260nm
  • Epsilon 260 ≈ 10,000 (M-1 cm-1 )
  • The A260 ≈ 50 μg /ml for DS DNA
  • The A260 ≈ 40 μg /ml for SS DNA or RNA
  • Flat surfaces are hydrophobic
  • Dipole-Dipole and Van Der Waals interactions also stabilize stacked structures
  • Bases have hydrogen bond donors and acceptors
  • H-bonding potential satisfied in paired structures
8 2 structure
8.2 Structure
  • DNA contains genetic Information
  • Distinctive base composition foretells base pairing patterns
  • Double helical structures
  • Local structures
  • mRNAs - little structure
  • Stable RNAs - complex structures
dna contains genetic information
DNA contains genetic Information
  • Purified DNA can "transform" Bacteria
    • Avery, MacLeod & McCarty transferred the virulence trait to pneumococci
  • The genetic material contains 32P (DNA) and not 35S (protein – C, M)
    • Hershey and Chase grew bacteriophage on either 32P or 35S
    • Bacteriophage infection resulted in transfer of 32 P and not 35S
distinctive base composition foretell base pairing patterns
Distinctive Base composition foretell base pairing patterns
  • Hydrolysis of DNA and analysis of base composition
    • Same for different individuals of a given species
    • Same over time
    • Same in different tissues
    • %A = %T and %G = %C (Chargaff's Rules)
  • Amino acid compositions vary under all three conditions
  • No quantitative relationships in AA composition
structural basis of chargaff s rules
Structural Basis of Chargaff’s Rules

Two Strands have complementary sequences

2 logical operations to obtain complementary strand 5' to 3'

1. Reverse: Rewrite the sequence, back to front

2. Complement: Swap A with T, C with G

double helical structures
Double helical structures
  • Potentially Right or Left Handed
    • Actually Mostly Right Handed
  • Potentially Parallel or Anti-parallel
    • Actually anti-parallel
  • Sugar Pucker + 6 rotatable bonds gives 3 families
  • A, B, Z structures
    • http://www.olemiss.edu/depts/chemistry/courses/chem471_10/ABZ_DNA.kin
  • KING 3D display software:
    • http://kinemage.biochem.duke.edu/software/king.php
dna backbone flexibility
DNA Backbone Flexibility

Multiple Degrees of Rotational Freedom

a b and z dna
A, B and Z DNA

A form – favored by RNA

B form – Standard DNA double helix under physiological conditions

Z form – laboratory anomaly,

Left Handed

Requires Alt. GC

High Salt/ Charge neutralization

  • A, B & Z DNA Kinemages
local structures
Local structures
  • Palindromes – Inverted repeats
    • Not quite the same as (Madam I’m Adam)
    • Symmetrical Sequence Elements Match Symmetry of Protein Homo-Oligomers
    • Symmetry often incomplete/imperfect
  • Direct Repeats
  • Hairpin and Cruciform Structures
messenger rnas
Messenger RNAs
  • Contain protein coding information
    • ATG start codon to UAA, UAG, UGA Stop Codon
    • A cistron is the unit of RNA that encodes one polypeptide chain
    • Prokaryotic mRNAs are poly-cistronic
    • Eukaryotic mRNAs are mono-cistronic
  • Base pairing/3D structure is the exception
    • Can be used to regulate RNA stability termination, RNA editng, RNA splicing
the genetic code
GG[GACU] code for Glycine

UGG codes for Tryptophan

UGA, UAG, UAA are stop codons

AG[CU] and UC[GACU] code for Serine

The Genetic Code
rna secondary structure maps
RNA Secondary Structure Maps

Calculated from helix thermodynamic parameters

Loop entropy considerations

trna phe kinemage
tRNA Phe Kinemage

http://www.olemiss.edu/depts/chemistry/courses/chem471/6tna.kin

8 3 chemistry
8.3 Chemistry
  • Denaturation and reannealing
  • Hybridization
  • Spontaneous Chemical Reactions
  • Methylation
  • Sequencing
  • Chemical Synthesis
hybridization
Hybridization

DNA sequences can spontaneously re-anneal and form helices

Basis for many of molecular biology techniques.

PCR, DNA sequencing

next generation dna sequencing
Next-generation DNA sequencing

Millions of DNA fragments isolated, amplified by PCR and monitored in parallel

Jay Shendure & Hanlee Ji

Nature Biotechnology 26, 1135 - 1145 (2008)

Published online: 9 October 2008doi:10.1038/nbt1486

8 4 nucleotide function
8.4 Nucleotide Function
  • Energetic Intermediates
  • Adenine Enzyme Cofactors
  • Regulatory Molecules
co enzyme a carrier for acetyl units in intermediary metabolism fatty acid synthesis and oxidation
Co-Enzyme A – Carrier for Acetyl units in intermediary metabolism, fatty acid synthesis and oxidation