LSM1401 Summary 7a © Lim Fang Jeng
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Nucleic Acids: Chemistry and Physical Properties
Structures and Properties
Nucleosides + Phosphate = Nucleotide - DNA is negatively charged, winded around a positively
charged protein known as histones - RNA: D-ribose; DNA: 2-deoxy-D-ribose - Sugars bond with bases with glycosidic bonds
- Phosphate group bond with nucleosides/nucleotides with phosphodiester linkage
- Cyclic structures are important signal molecules for Cellular Metabolism and Reproduction
o Caffein can reduce help to keep us awake!
- Pyramidine: Cytosine, Uracil, Thiamine ; Purine: Adenine, Guanine - Solubility in H2O: Nucleoside> Free bases
o Sugar is has many OH groups - 5’3’ configuration
- Reason for deoxy to be used to carry hereditary messages o deoxyribonucleotide are more stable to
hydrolysis
- DNA is arranged in a antiparallel way - Canonical Base pairing
o A = T
o G ≡ C (Stronger, hence more stable) - DNA is a twisted ladder:
o Reasons
Bases will stack better
Promote hydrophobic and π-clouds
Increase the stability of DNA
o Due to the stacking of the base pairs, there are major and minor grooves
T=A : major groove
G,C : minor groove
o Major grooves can accommodate α-helix from protein
hydrophilic
hydrophobic
LSM1401 Summary 7a © Lim Fang Jeng
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Forces Stabilizing DNA Structure
- Base pairing: hydrogen bonds (sensitive to high temp, pH, strong H bonding solutes
- Base Stacking: Van der Waals force and hydrophobic interactions - Ionic Interactions: Cations suppresses the electrostatic repulsion
between the negatively charged phosphate
Denaturation & Renaturation of DNA
- DNA will denature under strong heat
- When half of the helix is unwinded, the temperature recorded is known as melting temperature Tm - After cooling, the chain will bind back to its original configuration (Renaturation)
- At 80+oC, the abosrobance increases by 30-40%
- The melting temperature depends on the (G+C) content & ionic strength of solution. o More (G+C), higher Tm
DNA Compaction
- DNA is very well compacted - It is wounded around histones
- When a process is needed to be carried out to the DNA (e.g, transcription, replication, etc), Chromatin remodeling complexes (USES ATP!!!) will disrupt and reform nucleosomes
