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Chapter 2

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McGill University
Biology (Sci)
BIOL 112
Joseph Dent

Chapter 2: Small Molecules and the Chemistry of Life How does atomic structure explain the properties of matter ?  Living world is composed of same set of chemical elements as rest of universe  All matter is composed of atoms -> has nucleus (protons and neutrons) and electrons  All matter has a volume and mass  Mass of proton serves as a standard unit of measure called dalton (Da) or atomic mass unit (amu)  One proton/neutron = 1 Da or 1.7x10^-24 grams  One electron = 0.0005 Da or 9x10^-28  Electrons determine how atoms will combine with other atoms to form stable associations  Proton has +1 unit of charge  Electron has -1 unit of charge  Neutron has a 0 unit of charge (is neutral)  Atoms are electrically neutral b/c number of electrons equals number of protons  Atoms are often represented by a Bohr model - it is inaccurate b/c it exaggerates the space occupied by nucleus and it  An element consists of only one kind of atom  It's a pure substance  Distinguishable properties include their mass and how they interact with other atoms  About 98% of every living organism is composed of 6 elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur  The physical and chemical (reactive) properties of atoms depend on the number of subatomic particles they contain  Each element has a different number of protons  Designated by atomic number - is unique and does not change  Mass number = total number of protons and neutrons in nucleus = the mass of atom in Da's  Every element has one or more neutrons, except hydrogen  When written - on the left of element symbol, mass #/atomic #  Number of neutrons differs among isotopes  Isotope = the same element having the same # of protons but different # of neutrons  Hydrogen - 0 neutrons = Hydrogen, 1 neutron = Deuterium, 2 neutrons = Tritium … but isotopes don't always have different names  All have virtually the same chemical reactivity  Atomic weight (atomic mass) = average of mass numbers of a representative sample of atoms of element including isotopes  Most are stable  Radioisotopes are unstable, give off spontaneous energy in form of alpha/beta/gamma radiation from nucleus  Radioactive decay - transforms original atom and can sometimes change number of protons (making it a different element)  Can be used to tag molecules to trace them or to date fossils  Radiation emitted can be damaging to molecules and cells but can be used to kill cancer cells  Behaviour of electrons determines chemical binding and geometry  Explains how chemical reactions occur  They usually involve changes in the distribution of electrons between atoms  It is only possible to describe the volume of space within the atom where the electron is likely to be  Usually found in the atoms orbital  They have characteristic shapes and orientations  Can hold max 2 electrons  Moving from lighter to heavier atoms, the orbitals are filled in a sequence - electron shells or energy levels  1st shell - innermost, one orbital (s orbital),  2nd shell - 4 orbitals (s orbital and 3 p orbitals), s is spherical, p are at right angles to one another - contribute to 3D shape  Additional shells - elements with 10+ electrons, farther shells from nucleus have electrons with higher energy levels  Outer most shell (valence shell) usually hold 8 electrons and determines how atom combines with others  Atom is stable and will not react with others if valence shell has all 8 electrons  Partially filled orbitals - become stable by sharing electrons with other atoms or giving/receiving one or more electrons  Atoms bond together to become stable and form molecules  Octet rule  Hydrogen is an exception - attains stability with only 2 electrons How do atoms bond to form molecules ?  Chemical bond - an attractive force that links 2 atoms together in a molecule  Covalent bonds consist of shared pairs of electrons  Forms when 2 atoms attain stable electron numbers in outermost shell by sharing one or more pairs of electrons  Compound - substance made up of molecules with two or more elements bonded together in fixed ratio  Has molecular weight (molecular mass) - sum of atomic weights of all atoms in molecule  Each unpaired electron forms one covalent bond  Strength and stability  Very strong, takes a lot of energy to break them  Stable and three dimensional  Orientation  For a given pair of elements the length of bond is always the same  For a given atom the angle of bond is generally the same  It gives molecules 3D geometry  Multiple bonds  Single bond - sharing of single pair of electrons  Double bond - sharing of 4 electrons (two lines)  Triple bond - sharing of 6 electrons (three lines) - rare, one in nitrogen gas  Unequal sharing of electrons  Occurs when bond is between 2 atoms of different elements  One nucleus may exert greater attractive force so the pair tends to be closer to that atom  Electronegativity - depends on how many positive charges it has (more protons, more attractive to electrons) and distance b/w electrons in bond and nucleus (closer, stronger pull)  If atoms are close to each other in electronegativity, electrons will be shared equally - nonpolar covalent bond  When electrons are drawn to one nucleus over the other - polar covalent bond  Delta positive/negative ends of molecule  Bond is polar  Create polar molecules or polar regions w/i larger molecules  Ionic bonds form by electrical attraction  When one interacting atom is much more electronegative than the other, a complete transfer of one or more electrons can occur  Ions - electrically charges particles that form when atoms gain or lose 1 or more electrons  Cations - positively charged, has less electrons than protons  Anions - negatively charged, has more electrons than protons  Two biologically important elements yield more than one stable ion - Fe2+ (ferrous ion) Fe3+ (ferric ion) and Cu+ (cuprous ion) and Cu2+ (cupric ion)  Complex ions - groups of covalently bonded atoms that carry electric charge  Ionic bonds - formed as result of electrical attraction b/w ions bearing opposite charges (
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