BIOCHEMISTRY 410 Dr Leisha Mullins Wassily Kandinsky 1913 1 What is Biochemistry Why should you study it Biochemistry is the study of life on a molecular level Biochemistry seeks to describe the structure organization and function of living organisms in molecular terms In order to understand the life on the molecular level you must first have a Knowledge of the chemical structures of the biological molecules Understanding of the biological function of the molecules Understanding of bioenergetics the study of energy flow in cells 2 Biochemist are concerned with everything Biochemist look at The atomic level The structural level The cellular level The role of the cell in the organism Communication Cell to cell Biomolecule to biomolecule Metabolic coordination 3 Biological Macromolecules have a directionality Therefore they can be informational 3D architecture Look at table 1 3 for description Properties of Biomolecules Weak Forces are Critical for Structure Function Van der Waals interactions Hydrogen Bonds Ionic Interactions Hydrophobic Interactions 4 Water Why is water important Water is the solvent for biological systems Compounds are classified as to how they interact with water Hydrophilic compounds interact dissolve with water Hydrophobic compounds do not interact with water Water has unusual properties High boiling point melting point heat of vaporization etc H bonding is key to the properties of water Solutes dissolved in water perturb its properties Decrease freezing point or increase boiling point The perturbations depend only on the number of solutes per unit volume 5 Osmotic Pressure The high concentrations of dissolved solutes effectively decreases the concentration of water in cells compared to pure water Pressure is required to prevent the influx of water into the cell Plants and bacteria have strong rigid cell walls to contain the pressure Mammalian cells are bathed in extracellular fluids of comparable osmolarity Since the perturbations depend only on the number of dissolved molecules osmotic pressure is minimized when cells store compounds in their polymeric form 6 Polar Unequal sharing of electrons Polarity is determined by the electronegativity of the atoms Covalent Bond Proposed by Linus Pauling in 1932 Water is polar Electronegativity tendency to attract electrons Element Oxygen Nitrogen Electronegativity 3 5 3 0 Sulfur Carbon Phosphorus Hydrogen 2 6 2 5 2 2 2 1 7 Dipole Polar bonds and molecules are also known as dipoles The atom with the greater electronegativity attracts the electrons giving that atom a partial negative charge The remaining atom in the bond therefore has a partial positive charge Each atom of the bond has a different partial charge thus the term dipole 8 Bond must be POLAR Hydrogen Bonds Hydrogen bonding is one of the most important interactions in biological molecules Hydrogen bonding is an interaction between a covalently bonded hydrogen atom in a donor group and a pair of non covalent electrons on an acceptor group The ability of a group to act as a hydrogen bond donor depends on its electronegativity 9 Be able to identify H bond donors and acceptors No C H bonds C H bonds are not Polar so NEVER participate in Hydrogen bonds Common Hydrogen Bonds 10 compounds dissolve in water because of the dipole dipole interactions Ionic Formal charge or Hydrophilic Compounds readily dissolve in water Non ionic polar PolarCovalent bond partial charges Solvent Properties of Water Ionic compounds readily dissolve in water because of the ionic dipole interactions 11 Hydrophobic Interactions A non polar substance does not readily dissolve in water The H bond network of water reorganizes to accommodate the non polar solute Hydrophobic groups aggregate Aggregation causes less reorganization of the water 12 Amphipathic Molecules Molecules that contain both polar and non polar groups C O 13 Non covalent Bonds or Forces Non covalent bonds determine the complexity of molecular interactions within and between biomolecules Non covalent bonds are 10 100 times weaker than covalent bonds Single interactions are typically not sufficient to hold two species together The 3 D structures of most macromolecules are determined as a result of the collective influence of the many weak individual interactions Non covalent bonds are reversible Non covalent interactions are specific Size shape and type of interaction all must be correct for binding 14 15