CHEMISTRY The Building Blocks of Biology

Matter Anything that has mass and occupies space. Solid, Liquid, Gas

Elements

Biological Elements Nitrogen Carbon Hydrogen Oxygen Phosphorous Sulfur Calcium Potassium (K) 96%

Elements Atom = smallest unit of matter unique to a particular element. –(smallest “piece” of an element) Molecule = union of 2 or more atoms. Compound = union of 2 or more different atoms.

Atomic Structure Determines how atoms act. Various hypotheses exist about how atoms are actually structured… –Bohr – circular orbits –Summerfield – elliptical orbits –Pauli – wave theory/quantum mechanics: “Clouds of Probability”

Atomic Structure Protons (+) Neutrons (no charge) Electrons (-) Atomic # Atomic Mass (Mass #) – an approximation. –Each Proton is approx. 1 x g = 1 Dalton Nucleus Orbiting

Models of Atomic Structure… Nucleus (a) (b) In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus. Cloud of negative charge (2 electrons) Electrons This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron‘s position at one point in time.

“Normally” # Protons = # Neutrons = # Electrons BUT, not always… Isotopes – Atoms with variable #’s of Neutrons –Stable & Unstable Ions – Atoms with variable #’s of Electrons

Electron Shells 1 st Shell holds up to 2e - 2 nd Shell holds up to 8e - 3 rd Shell holds up to 8e -

Electrons Have different amounts of energy. The amount of energy depends on location…Which “shell” it occupies. Third energy level (shell) Second energy level (shell) First energy level (shell) (b) Atomic nucleus

“Shell” Models Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Figure 2.8

Which element is this?

Electron Orbitals The three-dimensional space where an electron is found 90% of the time. Electron orbitals. Each orbital holds up to two electrons. 1s orbital2s orbitalThree 2p orbitals 1s, 2s, and 2p orbitals (a) First shell (maximum 2 electrons) (b) Second shell (maximum 8 electrons) (c) Neon, with two filled shells (10 electrons) Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. x Z Y Figure 2.9

Atoms “like” to do 2 things: 1.Be Balanced. 2.Fill their outer-most shells.

Formation of Ions Oxidation – Departure of an e - Reduction – Gaining of an e - e-e-

Valence Electrons Those electrons occupying an atom’s outer-most shell (its “Valence Shell”)

Bonding Linking together atoms to form molecules… 1.Covalent Bonding 2.Ionic Bonding 3.Hydrogen Bonding 4.(Peptide Bonding) Electronegativity –The attraction of a particular kind of atom for the electrons in another. –The more electronegative an atom, the more strongly it pulls shared electrons toward itself.

Covalent Bonding Strong Sharing of valence electrons A.Non-Polar Covalent Bonds EQUAL SHARING H 2 O 2 The “Electronegativity” of the component atoms is equal. H O

Covalent Bonding Strong Sharing of valence electrons B.Polar Covalent Bonds UNEQUAL SHARING H2OH2O The “Electronegativity” of the component atoms is not the same. O H H

Polar Covalent Bonds Water… This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2OH2O –– O H H ++ ++ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

Ionic Bonding Huge differences in Electronegativity. Electrons are transferred (not shared) –Oxidation forms a Cation (+ charged). –Reduction forms an Anion (- charged). Bond results from the attraction between ions of different charge…

Ionic Bonding Attraction between a Cation & an Anion. Cl – Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium on (a cation) Sodium chloride (NaCl)

Hydrogen Bonding Weak A hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom. + —

Hydrogen Bonding Water (H 2 O) Ammonia (NH 3 ) O H H  + +  – – N H H H A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. ++ ++

Van der Waals Interactions Transient weak attractions between molecules (not really “bonds”) Due to inherent vibrational state of electrons…at any given time. Help reinforce molecular shape.

Next…Water