A.C.E. Biology Spring 2011 Chapter 2: Basic Chemistry.
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Transcript of A.C.E. Biology Spring 2011 Chapter 2: Basic Chemistry.
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
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
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
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
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
Carbon& WaterThe 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
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
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
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
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
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-PO3
2-)
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
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
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
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
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
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)
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)
• 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)
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)
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)
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)
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)
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-] = 14pH of 7 = 10-7