BMB 401 Lecture Notes - Lecture 2: X-Ray Crystallography, Phosphodiester Bond, Cell Nucleus
16 Dec 2016
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Nucleic Acids 4.2
4.2a DNA Structure
• 3
o DNA = A G T C (deoxynucleotides or deoxyribonucleotides)
o Genetic info in deoxyribonucleotides (phosphodiester bonds in b/w)
o Double helix and antiparallel
o Stabilized by van der Waals (umbrella term with H bonds and stacking
interactions) and ionic interactions b/w opposite strands
o A B and Z are 3 conformations
• 4
o 2 phospho ester bonds = phosphodiester bond
o Iogai phosphate does’t eist i solutio ut a e eleased as a podut
under physiological reactions
o 2nd one is protonated form of inorganic phosphate
• 5
o Great review of bonds
o Phosphodiester = both O involved in bridging to 2 R groups
o Anhydride = with Cs and switch to P = phosphoanhydride
• 6
o 5’ → 3’
o In between strands is phosphodiester bond
• 7
o Base on same side as sugar = syn
o Base pointed away from sugar = anti (DNA) = minimize steric interactions in base
and sugar = thermodynamically more stable
• 8
o Used x-ray crystallography data from Franklin to formulate structure
o DNA opens up to allow info to be read and hides it usually on inside
• 9
o 20A = diameter (A = 10^-10)
o Backbone is scaffold and useful information is in core of DNA with bases lined up
together (bases almost perpendicular to helical axis)
o Major (22) and minor (12) grooves
▪ Many drugs target minor and many transcription factors bind to major
• 10
o Density = bp/turn = 10
o Pitch = 34A/turn
o Diameter = 20A
o Rise = pitch/bp = 3.4A/bp (translational distance)
o Twist = degrees/bp = 360/10bp = 36 degrees/bp (angular distance)
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Ionic interactions = dna very charged so good to interact with + metal ions and this stabilizes it a lot: most proteins denature at 230. It melts into single strands and has 2 changes: viscosity = gets way less viscous and less rigid when heated, hyperchromicity = increasing color is what it translates too. 260 due to conjugated pi bond system in graph. Melt to 90 to fully melt: tm depends on solvent (salt) so [salt] = more stable dna due to counter ions, dna denaturing is reversible = renaturation. If rapidly cooled get partially renatured dna: dna being incubated fixes this (25 below tm provides thermal energy to partially. Dna to anneal: b dna = 99, 15, 16, 17, 18. Intra-strand base pairing results in these loops and hairpins: rna can hybridize into a dna strand kind of, understand more.
