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Chemicals common in biology Carbon, Oxygen, Hydrogen and Nitrogen most abundant Phosphorus, Calcium, Sodium, Magnesium, Potassium and Sulfur are also common Most organic material comprises only 25 elements Table 2-1 Fig. 2-5 Cloud of negative charge (2 electrons) Electrons Nucleus (a) (b) Atomic Structure Protons and neutrons in nucleus Protons + charge Neutrons are neutral Electrons “orbit” nucleus in electron shell Electrons charge Atomic characteristics Number of protons and electrons is equal under most conditions (no net charge) Atomic number=number of protons Atomic mass=combined number of protons plus neutrons in nucleus Isotopes=atom that contains the same number of protons, but different numbers of neutrons Fig. 2-9 Hydrogen 1H Atomic mass First shell 2 He 4.00 Atomic number Helium 2He Element symbol Electrondistribution diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Sodium Magnesium Aluminum 12Mg 11Na 13Al Third shell Shell configurations of electrons Chemical Bonding Atoms or molecules with full valence shells are very stable (inert gases) Chemical Bonding takes place to allow filling of valence shells Two types of chemical bonds Covalent bonds Ionic bonds New molecule often has characteristics unique from parent atoms (NaCl) Fig. 2-12 Name and Molecular Formula Covalent Bonding Multiple atoms share electrons to fill outer shell. Can take place between two identical atoms (O2 or H2) Carbon-based molecules are typically covalently linked (a) Hydrogen (H2) (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4) ElectronLewis Dot Spacedistribution Structure and filling Model Diagram Structural Formula Fig. 2-13 Polar Covalent Bonds – O + H H H2O + Attraction of atom for electrons is called electronegative force In some compounds the difference in electronegative force is large enough that one atom pulls shared electrons to itself Results in a molecule with slightly charged regions Fig. 2-14-2 Ionic Bonds Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) Cl– Chloride ion (an anion) Sodium chloride (NaCl) Caused by strong electronegative differences between atoms One atom donates an electron to another Both atoms become charged and their opposite charges causes an attractive force Strong bonds outside of aqueous solution, weak in solution Hydrogen bonding Weak bonds that are made and broken easily Hydrogen of a polar, covalent molecule has attraction to Nitrogen or Oxygen of similar molecule Results from weak charge of regions on polar molecules Fig. 2-17 s orbital Four hybrid orbitals z x Three p orbitals y Tetrahedron (a) Hybridization of orbitals Space-filling Model Ball-and-stick Hybrid-orbital Model Model (with ball-and-stick model superimposed) Unbonded electron pair 104.5º Water (H2O) Methane (CH4) (b) Molecular-shape models s orbital Four hybrid orbitals z x Three p orbitals Molecular Shape y Tetrahedron (a) Hybridization of orbitals Space-filling Model Ball-and-stick Hybrid-orbital Model Model (with ball-and-stick model superimposed) Unbonded electron pair 104.5º Water (H2O) Methane (CH4) (b) Molecular-shape models Determined by electron shells and the size of atoms included Space-filling models attempt to demonstrate the shape of a molecule Biological Activity Biological activity of molecules is largely determined by: Shape of molecule Charge of molecule of on portions of molecule 3D structure allows molecule to interact with other molecules Charged regions often interact with oppositely charged molecules Bond type Covalent bond is more easily broken and assembled Molecular Mimicry One molecule has a shape that is similar to another molecule The similarity in shape often results in a similarity in function Seen in pharmaceutical development and pathogenic microbiology