Chapter 3 Matter, Energy, And Life

Matter Is Made Of Atoms, Molecules, And Compounds

• Atom: simplest building block of chemicals• Element: a material composed of identical

atoms• Compound: a combination of atoms in a fixed

arrangement and proportion• Molecule: The simplest chemical unit of a

compound (O2, H2O, CH4, C6H12O6 etc.)– Many materials (NaCl) don’t have molecules

Chemical Formulas• Most Elements have symbols that are

common sense: H (Hydrogen), Si (Silicon), etc.• Some, known in ancient times, have symbols

from Latin: Fe (Ferrum = Iron), Au (Aurum = Gold), Na (Natrium = lye, for Sodium)

• C6H12O6 = Glucose = 6 Carbon, 12 Hydrogen, 6 Oxygen

• SiO2 = Quartz = 2 Oxygen for each Silicon

Electrical Charge Is An Important Chemical Characteristic

• Atoms contain three kinds of particles:– Protons (+) in the nucleus. Number of protons

determines what an element is– Neutrons (0) in the nucleus. Bind the nucleus

together– Electrons (-) orbiting the nucleus

• Group together into shells• This is what interacts with other atoms• Atoms can gain or lose electrons and become

electrically charged (Ions)

Chemical Bonds Hold Molecules Together

• Ionic: Ions of opposite charge attract each other. Example: NaCl, most minerals

• Covalent: Atoms share electrons with neighbors. Example: Most carbon chemicals

• Metallic: Electrons wander freely between atoms. Positive atoms held together by negative electron “glue”

• Hydrogen: H and O in water molecules attracted to neighbors

Chemical Bonds Hold Molecules Together

• Ionic bonding holds most rocks and minerals together

• Covalent bonding holds living things together• Metallic bonding holds industrial civilization

together• Hydrogen bonding gives water its solvent and

heat-storing capacity

Elements Of Life • C, H, O, N, P, S are principal elements of life• Some elements like C can share more than one

electron with a neighbor (multiple bonding)• Some elements like Fe and S can gain or lose

electrons in more than one way• These versatile atoms can be used for

– Energy storage– Information storage– Triggering chemical reactions

Elements and Life

• Some very abundant elements have no biological uses (Al, Si, Ti)

• Some elements are essential in low amounts but toxic at greater levels (Cu, Se)– Everything is toxic at excessive levels

• Some elements are toxic and have no biological functions (Lead, Mercury)

The Elements

The Elements and Life

Organic Compounds Have A Carbon Backbone

• Organic compounds contain carbon as their basic structural core– Chains (Petroleum)– Rings (Benzene, Toluene)

• Simple carbon-bearing chemicals aren’t considered Organic– CH4: Methane

– CO2: Carbon Dioxide

– CaCO3: Calcite, the Main Constituent of Limestone

Cells Are The Fundamental Units Of Life

• Cell Membrane: Contains contents and processes, excludes foreign objects (mostly)

• Nucleus: Where DNA resides– Simplest organisms lack nucleus

• Mitochondria– Not to be confused with Midichlorians (MTFBWY)– Produce Energy for Cell– Have their own DNA– Probably originated as independent organisms

Energy

• Energy Occurs In Different Types And Qualities • Thermodynamics Regulates Energy Transfers • Energy For Life

– Extremophiles Live In Severe Conditions – Green Plants Get Energy From The Sun – Photosynthesis Captures Energy While Respiration

Releases That Energy

Thermodynamics Regulates Energy Transfers

• First Law: Energy is Not Created or Destroyed– Can Change Form– Matter and Energy can be converted

• Second Law: Entropy increases– Entropy is often likened to disorder but is not

entirely the same– Entropy can decrease at expense of surroundings

From Species To Ecosystems

• Organisms Occur In Populations, Communities, And Ecosystems

• Food Chains, Food Webs, And Trophic Levels Link Species

• Ecological Pyramids Describe Trophic Levels

Waterworld

Sometimes It Looks More Like This

Reasons to be a ”Water chauvinist".

• Stays liquid over a wide range of temperatures.

• Polar or asymmetrical molecule. Attracts ions easily - Good transporter of nutrients

• Does not dissolve organic molecules (so we do not dissolve in our own cell fluids)

Material Cycles And Life Processes• Sources: supply elements for life and physical

processes– Example: Burning vegetation releases CO2

• Sinks: remove materials from environment– Example: Plants remove CO2 from the air– Limestone removes CO2 from the air

• Residence Time: How long an average atom or molecule remains in a system– Example: Water molecule in air, 10 days

Material Cycles on the Earth• The Hydrologic Cycle Moves Water Around

The Earth – Oceans – Atmosphere – Land - Ocean

• Nutrient Cycles– Ultimate Source: Rocks– Released by Weathering– Taken up by Biosphere– Transported by Water or Atmosphere– Sinks: Atmosphere, Deep Oceans, Rocks

Reasons to be a "Carbon chauvinist".

• Can bond to four neighboring atoms• Can bond to other carbon atoms, sharing one,

two, or three electrons• These properties make it possible to form a

vast array of organic molecules• No other element has these properties

Carbon in the Earth

• Volcanoes emit carbon dioxide• Carbonate rocks lock up carbon dioxide• Ancient biomass locked up carbon as coal,

petroleum, natural gas

Carbon in the BiospherePlants use sunlight, H2O, CO2 to create organic

molecules:• 6 H2O + 6 CO2 + energy

C6H12O6 (glucose) + 6O2 (toxic waste)Animals run the reactions in reverse:• C6H12O6 (glucose) + 6O2 6 H2O + 6 CO2 + energy• Also use organic molecules directly (vitamins)

Carbon Cycles• Plant – Animal Cycle• Decay returns CO2 to atmosphere• Marine organisms fix CO2 in carbonate rocks• Weathering returns CO2 to atmosphere• Some C fixed in rocks long-term as carbonates

or fossil fuel• Humans burn fossil fuel and add (not return)

CO2 to atmosphere

The Carbonate-Silicate Cycle• Earth has almost as much carbon dioxide as

Venus• Volcanoes add carbon dioxide to the

atmosphere• Mountain-building favors cooling• Carbon dioxide is removed from the air to

make carbonate rocks• “Icehouse” and “Greenhouse” episodes

The Paradox of Nitrogen• It makes up 79% of the atmosphere• Most plants cannot use N2

• Nitrogen converted to usable forms by specialized microorganisms

• Human use of nitrogen– Nitrogen-fixing plants (Legumes)– Natural fertilizers (Guano, Nitrate Minerals)– Synthetic nitrates (Haber Process)

Sulfur in the Earth

• Sulfide minerals: ores, pyrite• Volcanic emissions: H2S, SO2

• Coal: pyrite, organic sulfur• Petroleum: organic sulfur

From Earth to Environment

• Volcanic emissions: H2S, SO2

• Microbial action• Weathering

– Natural exposures– Mine waste

• Smelting• Fossil Fuels

Acid Rain

• S + O2 = SO2 (sulfur dioxide)

• 2SO2 + O2 = 2SO3 (sulfur trioxide)

• SO3 + H2O = H2SO4 (sulfuric acid)• Forms by smelting or burning fossil fuels

Acid Rain• pH: Measure of acidity

– 0 = extremely acid (Muriatic Acid)– 7 = neutral– 14 = extremely alkaline (Lye)

• Normal water in air is 5.5 (Carbonic Acid)• Acid rain can be pH 3 or less• Ca and Mg neutralize acid (Limestone,

Dolomite, some volcanic rocks)• Rocks poor in Ca and Mg cannot neutralize

acid (Granite)

Phosphorus in the Earth• Most common limiting factor for life• Mostly in apatite Ca5(Cl,F)(PO4)3

– Granites– Phosphate Rock (recycled biological P)

• Released by:– Weathering– Mining (for fertilizer)

Phosphorus on Land

• Phosphorus in Soil• Uptake by plants• Consumption by animals• Return to soil via plant and animal waste,

decay• Some lost by runoff

Phosphorus in Water• Essential to aquatic life• Excess causes eutrophication

– Runaway productivity, excess oxygen demand• Return to water via plant and animal waste,

decay• Some ends up in sediments (Chitin, Bone)• Sedimentary P returns to land via uplift, plate

tectonics• Human-Applied P goes to Oceans (Sink)

Distinctive Aspects of the P Cycle• No Atmospheric Component• Geologic Portion of Cycle Very Slow• Mostly involves biological transfers• P in oceans not recycled quickly• Human use: Rocks – Fertilizer – Oceans

– Not Recycled• Peak Phosphorus?• Phosphorus (Fertilizer)

– Morocco, China, South Africa, Jordan, U.S. = 90% of World Reserves