CHEM3910 Lecture Notes - Lecture 1: Inflection Point, Ionic Strength, Transfer Rna
5 Jul 2018
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CHEM3910 Biomolecules 460381099
PART 1
Section 2
Structure of DNA: Each nucleotide is covalently linked by a phosphodiester backbone, forming a 5’
end and 3’ end. In double helical DNA, two strands are wound antiparallel with H-bonding occurring
between purines and pyrimidine bases (A two H bonds to T; G three H bonds to C). However, there
are such alternatives to H-bonding between these pairs, known as Hoogsteen base pairing.
Hoogsteen base pairing and Watson-Crick base
pairing are energetically similar, however only
Watson-Crick base pairing is observed in DNA.
This is because Hoogsteen base pairing of G and
C is only stable at low pH and has less H-bonding
present than in Watson-Crick base pairing.
Stabilisation of DNA: Besides H-bonding of bases, the helix is stabilised through pi-pi stacking
between aromatics and is stiffened by electrostatic repulsions between anionic phosphate
backbones. Cations lie along the backbone to stabilise the helix further, by neutralizing anionic
phosphate charges. This is furthered by a well ordered H2O molecule network found in the major
groove of the A-T region, known as the ‘spine of hydration’.
Semi-conservative DNA replication: In replication each DNA stand serves as a template, producing
two new DNA molecules (each with 1 new and 1 old strand). This requires DNA denaturation and
DNA renaturation. Denaturation is achieved by the disruption of interactions that stabilise the DNA
(i.e. H-bonding and pi-pi stacking). This process can be followed by observing the change in UV band
absorbance. The single stranded DNA has a higher absorbance than that of the stacked bases due to
hyperchromatism.
Double stranded structure: H-bonding, hydrophobic and pi-pi stacking interactions between bases
allows the hydrophilic phosphate groups to exist on the outside of the macromolecule. These
Document Summary
However, there are such alternatives to h-bonding between these pairs, known as hoogsteen base pairing. Hoogsteen base pairing and watson-crick base pairing are energetically similar, however only. This is because hoogsteen base pairing of g and. C is only stable at low ph and has less h-bonding present than in watson-crick base pairing. Stabilisation of dna: besides h-bonding of bases, the helix is stabilised through pi-pi stacking between aromatics and is stiffened by electrostatic repulsions between anionic phosphate backbones. Cations lie along the backbone to stabilise the helix further, by neutralizing anionic phosphate charges. This is furthered by a well ordered h2o molecule network found in the major groove of the a-t regio(cid:374), k(cid:374)o(cid:449)(cid:374) as the (cid:858)spi(cid:374)e of hydratio(cid:374)(cid:859). Semi-conservative dna replication: in replication each dna stand serves as a template, producing two new dna molecules (each with 1 new and 1 old strand).
