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CHEMISTRY AND ORGANIC MOLECULES Matter: Has mass and takes up space; stuff Three states of matter: solid, liquid, gas All Matter composed of Elements Element: cannot be broken down into simpler forms with different properties Density, solubility, melting point, reactivity Six Elements basic to life: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur CHNOPS However, other elements are essential (necessary) for life Atomic Theory (John Dalton, early 1800s): Atom (Greek, indivisible): smallest part of an element that displays properties of that element Unit of matter Atomic Symbol Atomic Particles: more than 100 different kinds, but three stable kinds Protons, Neutrons in nucleus Electrons spin around nucleus Electrons negatively charged, protons positively charged Protons and neutrons have same mass (about 2000X that of electron) So electrons really don’t figure into atomic mass Proton, electron equal, but opposite, charges Protons, neutrons equal masses Atomic Number: at lower left of atomic symbol = number of protons Atomic Weight: protons plus neutrons Isotopes: any atom of a given element has the same number of protons, atomic number, but isotopes of that element are forms with numbers of neutrons different than the number of protons. Therefore, isotopes don’t have the same mass as the elemental atom with equal numbers of protons and neutrons. C12 is most common form of Carbon, but C13 and C14 also exist C13 is stable, but C14 is radioactive, or unstable, meaning it decays into something else Both stable and radioactive isotopes can be very useful in biological experiments, as tracers Atoms are mostly empty space. If the nucleus is golf ball sized, the electrons would be ~1km away 1 Valence shell electrons: those on the outermost orbital, important in chemical bonding Chemical Bonds: Covalent, Ionic, Hydrogen Covalent: outer shell (valence) electrons are shared, but not necessarily equally O is ~8X bigger than H, so even though there are 2 H’s, O gets more of the valence shell e- of the shared e-‘s, resulting in Polarity Ionic: transfer of electrons resulting in two, oppositely charged, ions: opposites attract Ion: charged atom Hydrogen: the H portion of an electronegative molecule is shared with another electronegative molecule (e.g. H20 and NH3). A very weak bond. H bonds very biologically important within and between molecules H bonds hold the two strands of DNA together, but are easily separated Molecular Shapes: think of these things in three dimensions C has 4 valence e-, forms a tetrahedron, not linear Acids and Bases: Acids: donate H+ (proton) Tomato, lemon, vinegar, coffee = acidic Bases: donate OH- (hydroxide) Chalk, baking soda, lye = caustic, basic, alkaline Measured by pH (parts of Hydrogen) Ranges 0 – 14 with 7 as neutral and extending on log scale in both directions Low pH is acid, 7 is neutral, high pH is basic Acids and bases have “strengths” as they dissociate more High alkalinity is as potentially harmful as high acidity Buffers: resist changes in pH by taking up both excess H+ and OHRemember homeostasis In Human blood Carbonic Acid, H2CO3 Dissociates as H+ and HCO3- (bicarbonate) Add H+ + HCO3 -> H2CO3 Add OH- + H2CO3 -> HCO3- + H2O Water There’s a lot of it. 70 – 90% of organisms are water (similar to earth’s surface) Cal = E to raise 1g liquid H20 1C Solid to liquid and liquid to gas takes even more E E required for liquid to gas is what makes sweat effective at cooling 2 This is a relatively large amount of required E and is due to the huge number of H bonds 10X that of iron, almost 2X that of alcohol A lot of E is absorbed breaking H bonds before molecules move faster (heat) A lot of E is lost as H bonds form (consuming E) before motion slows Nutritional c are kcal. This is Specific Heat; water takes a lot of E to warm up and then cools very slowly Remember homeostasis, this property of water helps in that Maritime moderate climates Cohesion: water sticks to itself, H bonds As water evaporates from a tree, it is replaced by water moving up from roots Adhesion: water sticks to other stuff, Put a drop of water, and a drop of soapy water on the table. Surface Tension: leaves, water striders, float on water Ice floats; think about what that means, ponds, lakes, polar ice caps The crystalline lattice of ice takes up 10% more space than liquid water Insulation, turnover Densest at 4C, ocean currents, e.g. Solvent: stuff dissolves in it to form a an aqueous Solution (Solvent dissolves the Solute) Polar or ionic substances dissolve in water: Hydrophilic Non-ionic and non-polar substances do not: Hydrophobic Q: why don’t cell membranes dissolve? Organic Molecules Organic chemistry involves carbon based molecules Hydrocarbons = only C and H Inorganic chemistry is pretty much everything else (e.g. batteries) Carbon chains, saturated, unsaturated, rings Functional groups: bonded atoms attached to carbon or carbon chains rather than H (OH- hydroxyl, CO carbonyl, COOH carboxyl, -NH2 amino, -SH sulfhydryl, -PO4 phosphate C (four valence shell e-) can attach four ways resulting in a tetrad, any part of which can be H or functional group This can change the molecule to Hydrophilic or Hydrophobic Cells (and organisms) are largely water, so hydrophilia is important (again, why don’t membranes dissolve?) Organic Macromolecules (big) Carbohydrates, Lipids, Proteins, Nucleic Acids Carbohydrates (CHO) 3 C, H, O that’s it Includes sugars (monosaccharides (now, glucose), di- (sucrose, lactose), poly (storage; starch, structural CO (glycogen; cellulose, chitin indigestible) Cellulose: animals cannot digest. Symbiotes can (ruminants, termites) Glycogen is stored energy and released as glucose by liver as commanded by release of insulin (hormone (homeostasis) from pancreas. 4