From Atoms to Biological Molecules Chemical properties Periodical Table H CNO Life prefers lighter atoms Atomic sizes (1) More abundant on Earth (2) Stronger bonding between small atoms 1H 6C 1s Electrons on the outer shell H The atomic composition of living organism is more complex than others 7N 8O 2s 2p C N O sp3 Components of the early atmosphere H2 sp3 CH4 NH3 H2O The tetrahedral structure of carbon orbital has rigid steric strain which makes the basic building unit of protein conformation Juang RH (2004) BCbasics Components of the early atmosphere H2 CH4 NH3 H2O Review the structure of water C-C - + Organic compound Electronegativity O 3.5 N 3.0 C 2.5 H 2.1 C R COOH C lp -d lp NH2 CH3 Functional group If atoms in a functional group have notable difference in electronegativity, then this functional group will express high polarity and will be highly active O +d Permanent dipole ● High polarity ● High dielectric constant ● H-bond formation ● pH influence Juang RH (2004) BCbasics Exaggerated Model for Water Molecule -d -d -d -d +d + +d - lp sp3 lp H +d H +d Adapted from Zubay (1988) Biochemistry (2e) p.57 O H H O H3 C H O H5C2 H O H5C2 C2H5 Dielectric Constant Water Methanol Ethanol Ammonia Acetic acid Chloroform Ethyl ether Benzene Carbon tetrachloride 80.4 33.6 24.3 17.3 6.15 4.81 4.43 2.28 2.24 H Cl–C–Cl Cl Cl Cl–C–Cl Molecules with asymmetrical distribution of electronegativity have higher polarity Cl Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.37 Solvation + - + + -+ + + - - - + + + + + + + - + - + -+ + - -+ + - + + O + C - + O + + - - - H H N +H - - +?- ● But enzyme forms stable binding with its substrate in water + - Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115 Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.87 Ionic Bond Is Not Stable in Water Solution Bond Energy in Water Might Be Different Bond length In vacuum Water solution Covalent bond 0.15 nm 90 90 Ionic bond 0.25 nm 80 3 Hydrogen bond 0.30 nm 4 1 Van der Waal force 0.35 nm 0.1 0.1 kcal/mole Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.57 Hydrogen Bond (H-Bond) The linearity is important for a perfect H-bond + N H Weaker H-bond O O Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.58 Affinity between Two Molecules Like Dissolves Like Molecules having similar polarity will attract each other Polar → Polar Nonpolar → Nonpolar Juang RH (2004) BCbasics Energy of Chemical Bonds in Cells Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53 Room Temperature 0.1 ATP Hydrolysis Covalent bond Glucose Oxidation 1 10 Secondary bond Van der Waal force 0.1 kcal/mole Hydrophobic bond 1 kcal/mole Hydrogen bond 1 kcal/mole Ionic bond Covalent bond 100 kcal/mole 3 kcal/mole 90 kcal/mole Juang RH (2004) BCbasics Secondary Bonds Contribute to Molecular Affinity x Reversible non-covalent binding Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.161