1. sp 3 Components of the early atmosphere H2H2 CH 4 NH 3 H 2 O Life prefers lighter atoms (1) More abundant on Earth (2) Stronger bonding between small atoms From Atoms to Biological Molecules Chemical properties Atomic sizes The atomic composition of living organism is more complex than others The tetrahedral structure of carbon orbital has rigid steric strain which makes the basic building unit of protein conformation Electrons on the outer shell Periodical Table HCNO 1H1H 6C6C 7N7N 8O8O sp 3 1s2s 2p H C N OC N O Juang RH (2004) BCbasics

2. Review the structure of water Permanent dipole Electro- negativity O 3.5 N 3.0 C 2.5 H 2.1 If atoms in a functional group have notable difference in electronegativity, then this functional group will express high polarity and will be highly active ● High polarity ● High dielectric constant ● H-bond formation ● pH influence C-C +d+d -d-d Organic compound Functional group O lp Components of the early atmosphere H2H2 CH 4 NH 3 H 2 O C C CH 3 COOH R NH 2 - + Juang RH (2004) BCbasics

3. H Exaggerated Model for Water Molecule Adapted from Zubay (1988) Biochemistry (2e) p.57 - + H +d+d +d+d -d-d -d-d -d-d-d-d +d+d+d+d sp 3 lp

4. Water80.4 Methanol33.6 Ethanol24.3 Ammonia17.3 Acetic acid 6.15 Chloroform 4.81 Ethyl ether 4.43 Benzene 2.28 Carbon tetrachloride 2.24 Dielectric Constant Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.37 Cl Cl–C–Cl Cl H Cl–C–Cl Cl C2H5C2H5 H5C2H5C2 O HH O H3CH3C O HH5C2H5C2 O H Molecules with asymmetrical distribution of electronegativity have higher polarity

5. Ionic Bond Is Not Stable in Water Solution Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115 - + +- ? C O O NH H H + - + + + + + - - - - - - + - - - - - + - ++ - + - + - + - + - + - + + + + + - - + - - - + + - + - + + Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.87 Solvation ● But enzyme forms stable binding with its substrate in water

6. Bond Energy in Water Might Be Different Bond length In vacuum Water solution Covalent bond Ionic bond Hydrogen bond Van der Waal force 0.15 nm 0.25 nm 0.30 nm 0.35 nm 90 80 4 0.1 90 3 1 0.1 kcal/mole Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.57

7. N H O + Hydrogen Bond (H-Bond) The linearity is important for a perfect H-bond O Weaker H-bond Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.58

8. Polar → Polar Nonpolar → Nonpolar Like Dissolves Like Dissolves Like Affinity between Two Molecules Juang RH (2004) BCbasics Molecules having similar polarity will attract each other

9. Energy of Chemical Bonds in Cells 0.1110100 kcal/mole Room Temperature Secondary bond ATP Hydrolysis Covalent bondGlucose Oxidation Hydrogen bond Ionic bond Hydrophobic bond 90 kcal/mole 3 kcal/mole 1 kcal/mole 0.1 kcal/mole Covalent bond Van der Waal force Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53 Juang RH (2004) BCbasics

10. Secondary Bonds Contribute to Molecular Affinity Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.161 Reversible non-covalent binding x