Chapter 2: Basic Chemistry for Biology Lecture Notes

Matter (not energy) Has mass and volume Exists in physical states Solid Liquid Mass Plasma

Is composed of elements Elements Cannot be broken down 92 naturally occurring Listed on periodic table 25 essential to life 4 (OCHN [ocean]) make up 96% of human mass Trace elements are essential for life

Compounds 2 or more different elements in a fixed ratio Can be broken down into simpler substances (electrolysis of water) i.e. NaCl

 Atoms

4H2O K2Cr2O7

Smallest unit of matter that retains an elements properties Atomic structure Nucleus (+) Protons (+) = 1 amu Neutrons (=) = a bit heavier than1 amu

Surrounding electron cloud (-) in energy levels/shells Electrons (-) 0 amu 1st levels maximum number of electrons: 1 pair (2 e-) 2nd and 3d levels maximum number of electrons: 4 pairs (8 e-) Noble gasses have a full outermost shell Atomic number = number of protons Mass number = number of protons + number of neutrons Stable atoms (no charge): the number of protons = number of neutrons The protons and neutrons cancel out

Isotopes Average atomic mass (on periodic table) = average mass of all natural isotopes Isotopes of an element: same number of protons and electrons, but very in the number of neutrons C-12, C-13, C-14 are all isotopes of carbon Some isotopes are used in medicine/research because of their radioactivity

 Chemical Bonds Joins atoms together to form molecules and compounds Involves only the outermost electrons 2 types: Ionic bonds: e- are transferred Covalent bonds: e- are shared

Ionic Bonds 1-3 electrons are transferred in order to complete their outermost shells This results in + and ions attracting one another Ions: atoms/groups that have lost or gained e NaCl Na+ +Cl Hydrogen Bonds P+ E N= Hydrogen ion, H, is a proton H H+ = proton H Cl H+ + Cl- (proton donors) Covalent Bonds Create molecules (2 or more atoms, same or different, held together by covalent bonds) 1-3 pairs of electrons are shared between atoms to achieve a full outermost electron shell

Equal sharing non-polar molecule H2O

Chemical Reactions Involves breaking old and making new bonds Represented by chemical equations Reactants Yield Products i.e. 2H2O (reactants) (yield) 2H2O + O2

Must obey the law of conservation of matter: Matter cannot be created nor destroyed, just rearranged Water Polar covalent molecule: a neutral molecule, but each end has a change Charged ends attract other water molecules, creating hydrogen bonds Between H of one water and O of another water molecule

Hydrogen bonds are weak and temporary Cohesion pH pH scale = measure of acidity 0 (strong acid) 7 (neutral) 14 (strong base) Logarithmic (tenfold) change = attraction between like molecules (due to H- bonding) Gives water a high surface tension

Why is water pH 7?

Small fraction of water molecules are ionized, creating an equal number of H+ and OH- ions

A base is a proton acceptor, an acid is a proton donor