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 Biosphere
Plants 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
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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
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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
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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
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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
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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