A.C.E. BiologySpring 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

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

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 acidpH of 1 = 10-1 pH of 12 = 10-12

pH of 5 = 10-5 [H+] + [OH-] = 14pH of 7 = 10-7

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