BCHM 218 Lecture Notes - Lecture 4: Phosphodiester Bond, Electronegativity, Peptide Bond
5 May 2018
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BHCEM 218 week 2 lecture 1
Chem bonds
Strong= short distance interactions, require catalyst to break ex. covalent (b/n nucleic and aa polymers),
metallic, ionic (salt bridges or electrostatic interactions)
Weak= Van der Waals, H bonds, hydrophobic effect
Tetrahedral: sp3, 109.5 planar: sp2, 120
H bonds: EN atom (NFO) is the H-bond donor, highly
directional, strongest when 3 atoms are in straight line
Each water can form 4 H-bonds (two from H and two from O)
Form b/n: proteins, side chains, water, main chains
Diff in H bond donor or acceptors allows DNA to be read
w/out denaturing, det site specificity of protein-DNA
interactions
Ex. Lipitor/atrocastatin: binds to and inhibits Hs which make
cholesterol
Pauling scale
Dimensionless values ranging from 0.7 to 3.98
0-0.4= nonpolar 0.4-1.7=polar covalent 1.7+= ionic
Resonance
Peptide bond: forces groups to be in same plane
Phosphodiester bond: w/n bases and in phosphate group
Pi stacking: attractive, noncovalent interactions b/n aromatic rings, stacking of adjacent base pairs of DNA,
hydrophobic interaction
Pi interactions: occur when two rings approach each other w/n same plane, contribute to nucleic acid stability
Hydrophobic
effect
Rigid lattice that decreases entropy
Arises from exclusion of nonpolar groups
Driving force for protein folding and stabilization, interior=hydrophobic aa
Henderson-
Hasselbach
pH of a soln containing a weak acid equals the pKa of the weak acid plus log of ratio
pH= pKa + log [A]/[HA]
when pH> pKa ratio of [A] to [HA] is greater than 1 and lose a proton
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Document Summary
Strong= short distance interactions, require catalyst to break ex. covalent (b/n nucleic and aa polymers), metallic, ionic (salt bridges or electrostatic interactions) Weak= van der waals, h bonds, hydrophobic effect. H bonds: en atom (nfo) is the h-bond donor, highly directional, strongest when 3 atoms are in straight line. Each water can form 4 h-bonds (two from h and two from o) Form b/n: proteins, side chains, water, main chains. Diff in h bond donor or acceptors allows dna to be read w/out denaturing, det site specificity of protein-dna interactions. Lipitor/atrocastatin: binds to and inhibits hs which make cholesterol. Peptide bond: forces groups to be in same plane. Phosphodiester bond: w/n bases and in phosphate group. Pi stacking: attractive, noncovalent interactions b/n aromatic rings, stacking of adjacent base pairs of dna, hydrophobic interaction. Pi interactions: occur when two rings approach each other w/n same plane, contribute to nucleic acid stability. Strong acid= large ka, small pka (more dissociated)
