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

Cloud of negative charge (2 electrons) Fig. 2-5 Nucleus Electrons (b) (a)

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 1 H Lithium 3 Li Beryllium 4 Be Boron 5 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Helium 2 He Atomic number Element symbol Electron- distribution diagram Atomic mass 2 He 4.00 First shell Second shell Third shell Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar 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 Name and Molecular Formula Electron- distribution Diagram Lewis Dot Structure and Structural Formula Space- filling Model (a) Hydrogen (H 2 ) (b) Oxygen (O 2 ) (c) Water (H 2 O) (d) Methane (CH 4 ) Multiple atoms share electrons to fill outer shell. Can take place between two identical atoms (O 2 or H 2 ) Carbon-based molecules are typically covalently linked Covalent Bonding

Fig  – – ++ ++ H H O H2OH2O 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 Polar Covalent Bonds

Fig NaCl Na Cl Na Sodium atom Chlorine atom Cl 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 Ionic Bonds

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 s orbital Three p orbitals (a) Hybridization of orbitals Tetrahedron Four hybrid orbitals Space-filling Model Ball-and-stick Model Hybrid-orbital Model (with ball-and-stick model superimposed) Unbonded electron pair 104.5º Water (H 2 O) Methane (CH 4 ) (b) Molecular-shape models z x y

Molecular Shape Determined by electron shells and the size of atoms included Space-filling models attempt to demonstrate the shape of a molecule s orbital Three p orbitals (a) Hybridization of orbitals Tetrahedron Four hybrid orbitals Space-filling Model Ball-and-stick Model Hybrid-orbital Model (with ball-and-stick model superimposed) Unbonded electron pair 104.5º Water (H 2 O) Methane (CH 4 ) (b) Molecular-shape models z x y

Biological Activity Biological activity of molecules is largely determined by:  Shape of molecule 3D structure allows molecule to interact with other molecules  Charge of molecule of on portions of molecule 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