IMED1001 Study Guide - Midterm Guide: Ribose, Formamide, Ionic Strength
LEARNING OUTCOMES LECTURES 11-12
Lecture 11:
- Double helix held together by:
1. H bonds between base pairs => specificity
2. Hydrophobic stacking interactions of bases => stability (maintain fidelity)
- 10 bases make complete turn in Watson-Crick model
- Right handed helix with minor and major groove
- Double helix forms: A (favoured in solutions almost devoid of water), B (most stable), Z (zigzag,
short tracts)
- Denaturation: H bonds and hydrophobic interactions disrupted, unwind, cov bond still intact (pri
structure maintained)
- Reannealing: when 2 strands wind to get double helix. Common = DNA amplification
- Tm = temperature at which DNA reach half of maximum denaturation
- Factors affecting Tm:
1. Base composition: if more C-G, higher Tm since 3 H bonds needed to be overcome (compared
to 2 in A-T)
2. Length of DNA: longer the DNA, higher the Tm
3. Ionic strength: when ionic compounds dissociate into cations and anions in water, the cations
interact withnegative DNA, decreasing repulsion within backbone, thus more stable, hence high
Tm needed
4. pH: extreme pH will denature hence lower Tm. Protonisation (decrease in pH), H bonds
etween ase pairs and glyosidi onds lost whereas deprotonisation doesn’t reak glyosidi.
Thus increase in pH is better way of denaturing
5. Organic solutes: urea or formamide forms H bonds with bases, prevening complementary base
pairing, decreasing stability hence lower Tm
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Document Summary
Double helix held together by: h bonds between base pairs => specificity, hydrophobic stacking interactions of bases => stability (maintain fidelity) 10 bases make complete turn in watson-crick model. Right handed helix with minor and major groove. Double helix forms: a (favoured in solutions almost devoid of water), b (most stable), z (zigzag, short tracts) Denaturation: h bonds and hydrophobic interactions disrupted, unwind, cov bond still intact (pri structure maintained) Reannealing: when 2 strands wind to get double helix. Tm = temperature at which dna reach half of maximum denaturation. Tm needed: ph: extreme ph will denature hence lower tm. Protonisation (decrease in ph), h bonds (cid:271)etween (cid:271)ase pairs and gly(cid:272)osidi(cid:272) (cid:271)onds lost whereas deprotonisation doesn"t (cid:271)reak gly(cid:272)osidi(cid:272). Thus increase in ph is better way of denaturing: organic solutes: urea or formamide forms h bonds with bases, prevening complementary base pairing, decreasing stability hence lower tm. Structure of rna: ribose sugar, phosphate group, nitrogenous bases (aucg)
