Introduction to Biochemistry I

Atomic structure

• Protons: positive charge, mass of +1

• Electrons: negative charge, negligible mass

• Neutrons: no charge, mass of 1

Bonding in biomolecules

• Covalent bond: formed when unpaired electrons are shared, strongest type of bond

• Ionic bond: attraction of opposite charges

• Hydrogen bond: sharing of H atoms

• Hydrophobic interaction: interaction of non-polar substances in the presence of polar substances (especially water)

• van der Waals interaction: interaction of electrons of non-polar substances

• Electronegativity: the attractive force that an atomic nucleus exerts on electrons within a bond

Common reactions

• Phosphorylation and de-phosphorylation: addition or removal of a phosphoryl group

• Acylation: addition of an acyl group
• Relatively stable, useful for joining molecules

• Carboxylation: addition of a carboxyl group
• Usually occurs at the end of a molecule (reactive centre)

• Esterification: occurs between acid and alcohol group, producing an ester bond
• Water is released

• Condensation reaction: water is removed, molecules polymerize

• Hydrolysis: water is added, molecules depolymerize

• Oxidation-reduction reactions (redox): electrons transferred from one molecule to another
• Oxidation = loss of electrons, reduction = gain of electrons
• As one molecule is oxidized, another is reduced - form a redox pair

Oxidation states of carbon

• Vary depending on structure of molecule and electronegativity differences

• Charge imbalances help form reactive groups on biological molecules