A.C.E. Biology Spring 2011

1. A.C.E. BiologySpring 2011 Chapter 2: Basic Chemistry

2. Chemistry Review • MATTER – anything that takes up space & has mass • ELEMENTS – basic substances making up all matter that cannot be broken down into smaller substances with different properties; there are 92 naturally occurring • ATOMS – smallest unit of each element that still retains all the element’s characteristic physical and chemical properties

3. More Review . . . • PROTONS – positively charged sub-atomic particles found in the atomic nucleus • NEUTRONS – sub-atomic particle also found in nucleus possessing no charge • ELECTRONS – negatively charged subatomic particle orbiting nucleus in cloudlike energy shells • ATOMIC NUMBER – equal to the number of protons in an atom of an element • ATOMIC MASS – roughly equal to sum of protons & neutrons in atom of an element

4. And More Review . . . • ISOTOPES – atoms of the same element that differ in the number of NEUTRONS they possess and therefore in ATOMIC MASS; some isotopes are stable, but some are not • UNSTABLE ISOTOPES DECAY – THEY ARE RADIOACTIVE – carbon-14 decays into stable nitrogen-14 by releasing various types of energy over time • Each RADIOI-ISOTOPE has a characteristic HALF-LIFE; the time it takes for half its mass to decay to a stable end product

5. Types of Bonds • COVALENT – two atoms share electrons so each has filled outer electron shells • POLAR COVALENT – when electrons are not shared equally between atoms due to significant differences in ELECTRONEGATIVITY, as in water (O is more electronegative than H) • IONIC – electrons are completely transferred from one atom to another & compounds held together by attraction between oppositely charged ions

6. Hydrogen Bonds • Water molecules are polar molecules with an asymmetrical distribution of charge – the O is slightly negatively charged, while the Hs carry slight positive charges • HYDROGEN BONDS form between the O- of one molecule and a H+ end of another molecule – or within the same molecule

7. Carbon& Water The chemistry of life is essentially the chemistry of CARBON • versatile due to the presence of 4 valance electrons • forms the backbone of major molecules of life • covalently bonds with itself [graphite & diamond] • bonds with S.P.O.N.C.H. elements in enormously varied ways to form many different compounds

8. Hydrocarbons Molecules comprised essentially of CARBON & HYDROGEN • METHANE – CH4 – a component of marsh gas & principal byproduct of the bacteria of decay • Geometry of METHANE tetrahedron – all angles are 109.5⁰

9. Versatility of Carbon • Carbon forms simple chains, branching chains, & rings; single bonds, double bonds & triple bonds • Double and triple bonds are INFLEXIBLE – help hold ring shapes • There’s no limit to how large these molecule can be – MACROMOLECULES * A single DNA molecule has up to 50 billion atoms

10. Other S.P.O.N.C.H. Elements

11. Nitrogen • Essential as a constituent of proteins; 78% of atmosphere; one of the most abundant & common elements • Triple bond makes N2 largely inaccessible to most organisms; takes lots of energy (lightening) to break • Most organisms obtain NITROGEN in the form of AMMONIUM (NH4+) or nitrate (NO3-) ions available from the decomposition of dead organisms & their waste

12. Nitrogen Fixing Bacteria • Found on the root nodules of peas, alfalfa, locust beans, peanuts, and other legume plants, as well as free living in water. • Converts free atmospheric nitrogen into a form useful to other organisms by attaching oxygen to the nitrogen

13. Phosphorus • Always combined with oxygen in biological systems • Can be found either as a free complex ion or can be combined with a larger organic molecule as a PHOSPHATE GROUP • In cellular and extracellular fluids of organisms the phosphate group ionizes (R-PO32-)

14. Phosphorus (continued) • As a free ion (PO43-), it has its own symbol Pi, representing INORGANIC PHOSPHORUS • ATP (adenosine tri-phosphate) – special phosphate-to-phosphate bonds used by organisms to shuffle energy around within the organism

15. Sulfur • Appears in some amino acids in the form of: • SULFHYDRYL GROUPS (-S-H), which, in pairs, form interlocking “snaps” or “hooks” when amino acids are assembled into proteins (disulfide linkages or bridges) amino acid – S-H + S-H – amino acid amino acid – S-S – amino acid

16. Functional Groups • Specific chemical groups that appear rather frequently in many kinds of organic molecules; the chemical behavior is pretty consistent regardless of the type of molecule to which they are attached

18. WATERWater Molecules & Hydrogen Bonding Water provides habitat for much of life on the planet; living organisms are composed primarily of water; water is the medium for most of the chemical reactions of life; ¾ of the surface of the planet is covered by water

19. Water • HYDROLOGIC CYCLE – continuous process by which enormous quantities of water shifts between the earth and the atmosphere • WATER AS A SOLVENT – because water is polar, other polar substances will readily dissolve in it; non-polar substances (fats & hydrocarbon chains) will not • HYDRATION SHELLS – layers of water molecules that form around ions or dissolved polar molecules

21. Water & Non-Polar Molecules • Water molecules clump together; they are not attracted to non-polar molecules • HYDROPHOBIC – non-polar molecules; water-fearing; repelled by water • HYDROPHILIC – polar molecules; water-loving; attracted to water • DETERGENTS – large molecule that has both hydrophobic & hydrophilic regions and so can interact with both polar & non-polar substances (forms bridge between grease & water molecules to lift dirt off dishes)

22. Wetness • Water forms hydrogen bonds with polar surface molecules of solid objects • ADHESION – attraction between 2 dissimilar substances (side of straw and soda) • COHESION – attraction between 2 similar substances (among water molecules hydrogen bonds form)

23. CAPILLARY ACTION – water rising in small columns; caused by adhesion of water to surface of a tube & cohesion of water molecules to one another ; the smaller the diameter of the tube, the higher the water will rise; explains formation of MENISCUS • IMBIBATION – movement of water into porous substances such as wood or gelatin through ADSORBTION; tissues swell & exert powerful force (split seed coats)

24. High Surface Tension • Where water & air meet, water can’t form hydrogen bonds with air, so water molecules are attracted to one another and, by virtue of COHESION, form a tough, elastic film of hydrogen-bonded water molecules (allows water strider to walk on water & shapes raindrops)

25. Heat Stability • Water is slow to heat & slow to lose heat; makes the earth more habitable • Requires large amounts of heat to raise water temperatures even a small amount • Once elevated, higher water temperature is stubbornly retained • SPECIFIC HEAT – amount of heat required to raise the temperature of a substance a given amount (water and ammonia have high specific heats largely due to presence of hydrogen bonds)

26. Heat Stability • Water resists evaporates due to hydrogen bonds; makes an effective cooling device • Water has highest density at 4⁰ Celsius, then rigid matrix forms & density decreases at 0⁰ Celsius – that’s why ice floats • THERMAL OVERTURN – denser cold water sinks at 4⁰ Celsius, and warmer water rises (which is why Seneca Lake very rarely freezes)

27. Ionization, pH, Acids & Bases • Despite being a covalently bonded molecule, a tiny fraction of water molecules briefly disassociate into HYDROGEN IONS (H+) and HYDROXIDE IONS (OH-) • ACID – a substance that releases HYDROGEN IONS (H+) when dissolved in water; strength depends on concentration of hydrogen ions • BASE (or ALKALI) – a substance that accepts protons or releases HYDROXIDE IONS (OH-) (above 7 on pH scale)

28. pH Scale 1 - 14 • Solutions are either ACIDIC, BASIC or NEUTRAL • The pH SCALE is a notation to express the HYDROGEN ION (H+) concentration in a solution; the smaller the number (indicating the inverse of the concentration’s exponent), the stronger the acid pH of 1 = 10-1 pH of 12 = 10-12 pH of 5 = 10-5 [H+] + [OH-] = 14 pH of 7 = 10-7

30. Miscellaneous . . . • MOLE – the weight in grams that equals the molecular mass in DALTONS of one molecule • BUFFERS – chemical substances (usually weak acids or weak bases) that neutralize strong acids and strong bases as quickly as they form; act as a safeguard to maintain a constant pH