Chemistry of Life

1
Chemistry of Life

• But first

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.gif
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Reproductive excess

• More individuals are born than can possibly live,
  and therefore there is a struggle to survive.

http//lion-den.tripod.com/images/lioness-and-cub-
facts/lion-02.jpg http//lionguardians.wildlifedir
ect.org/files/2008/03/esk_deadlioness2_tn.jpg http
//www.lionresearch.org/behavior_guide/infant.html
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Variation

• There is variation among organisms within a
  reproducing population.

http//bluepyramid.org/ia/lion.jpg http//itswild.
org/files/images/Lion.jpg http//www.jpbutler.com/
franklin-park-zoo/lion-side.jpg http//farm1.stati
c.flickr.com/18/92631504_a676c080e7.jpg?v0
http//www.lion-picture.com/Images/Lion_King_afri
ca_safari_Lion.jpg http//www.bbc.co.uk/nature/wil
dfacts/factfiles/picpops/images/lion22.jpg http//
blogs.cyberciti.biz/hm/wp-content/uploads/2006/10/
lion-picture-photo.jpg http//animals.nationalgeog
raphic.com/staticfiles/NGS/Shared/StaticFiles/anim
als/images/primary/african-lion-closeup.jpg
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Variation is heritable.

• This variation is heritable, and passed directly
  from parent to offspring.

http//www.spottycat.com/marlos/emporium/lion/lion
42.jpg http//travel.msn.co.nz/img/article/lion_cu
b.jpg http//www.sydney.com.au/images/zoo-lions.jp
g http//www.aza.org/AZAPublications/PhotoContest/
Images/LionWithCub.gif http//thumbs.dreamstime.co
m/thumb_149/11794510043PYPf7.jpg http//img.dailym
ail.co.uk/i/pix/2007/07_02/lionkingDM1807_600x400.
jpg
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Survive and Reproduce

• The life forms best suited to their environments
  have the best chance to survive and reproduce.

http//africahowtocall.com/images/lion4.jpg http/
/gallery.photo.net/photo/4750684-lg.jpg http//www
.krugerpark.co.za/images/img049-lion-pride.jpg htt
p//66.166.92.72/web/geo2/Masai20Mara/Game20Driv
e/Lion20Pride.jpg
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In other words

• The lion gene pool houses all lion traits.
• The parents are part of the gene pool, and their
  traits are passed on to their offspring.
• There are more cubs born than survive to
  adulthood.
• The offspring with the most fit inheritance will
  have the best chance to survive and reproduce.

http//farm1.static.flickr.com/13/17436178_dd46ec5
172.jpg?v0 http//www.africa-nature-photography.c
om/images/DCWP_603_034w-Lion-Cubs-Picture.jpg
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Chemistry of Life

• And now

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.gif
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Atoms

• An atom is the smallest component of an element
  that can
• maintain the elements basic chemical properties
• Has any chemical properties
• An element is a substance that is made entirely
  from one type of atom

http//www.funksoulkitty.org/periodictable.jpg
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Atomic Model

• Atoms make up everything
• Particles make an atom
• Nucleus
• Protons
• Neutrons
• Electron cloud surrounding nucleus

Pictured above is an atom with 2 electron shells
http//web.buddyproject.org/web017/web017/images/a
tom.JPG
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Nucleus

• Protons ( )
• Have an electrical charge of 1
• Comprised of 2 up and 1 down quarks which are
  held together by gluons
• Neutrons ( o )
• Have no electrical charge
• Comprised of 1 up and 2 down quarks which are
  held together by gluons

http//www.pentek.com/applications/15_1/heart2quar
ks_small.jpg
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Nucleus

• Protons and Neutrons weigh about the same
• The majority of the mass (over 99) is the
  nucleus
• A protons positive charge repels other protons
• Held tightly together by presence of neutrons and
  the interaction of the quarks in each, and
  nuclear forces

http//commons.wikimedia.org/wiki/FileHelium_atom
_QM.png
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Nucleus

• The atomic mass of an atom is the total number of
  protons plus the average number of naturally
  occurring neutrons
• Since the electrons have such little mass, they
  are not included

http//lc.brooklyn.cuny.edu/smarttutor/core3_21/im
ages/nature/7.a.Isotopes.gif
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Electrons

• Electrons (e-)
• Have an electrical charge of -1
• Fundamental particles (meaning that they cannot
  be broken into smaller parts)
• The mass of an electron is 1/2000 of the mass of
  a proton

Related particles in bubble chamber
http//www.broward.edu/faculty/ghauer/10714_home.j
pg
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Size

• Atoms are measured in nanometers, picometers or
  ångströms (a non-SI unit of measure)
• 1 m 1,000,000,000 nm
• 1 m 1,000,000,000,000 pm
• 1 m 10,000,000,000 Å
• Visible light 400nm (violet) to 700nm (red)
• Hydrogen, e.g., has an empirical radius of 0.025
  nm (or 25 picometers)

http//www.acr.atr.co.jp/wendin/Pictures/corral.g
if
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Size

• If we could enlarge an atom to take up the same
  amount of space as our Earth and Moon
• The diameter of the nucleus would be the length
  of 3 football fields

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/Football.jpg
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Size

• If we could enlarge an atom to take up the same
  amount of space as our Earth and Moon
• The diameter of 1 proton would be the length of 1
  football field

http//mceer.buffalo.edu/connected_teaching/photos
/Football.jpg
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Size

• If we could enlarge an atom to take up the same
  amount of space as our Earth and Moon
• The distance between the nucleus and the electron
  would be the distance the Moon is to the Earth

http//upload.wikimedia.org/wikipedia/commons/6/60
/Speed_of_light_from_Earth_to_Moon.gif
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Size

• If we could enlarge an atom to take up the same
  amount of space as our Earth and Moon
• The size of the electron would be the same as a
  golf ball

http//www.aerospaceweb.org/question/aerodynamics/
sports/golf-ball.jpg
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Or

• If the nucleus of an atom were the size of a golf
  ball
• The electron would still be too small to see
• It would be found about ¼ mile away

¼ mile
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Or
1mm

• 7 million atoms joined together in a straight
  line would be about 1mm long

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uler-cm.jpg
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Atoms

• The number of protons determines the element.
• The number of neutrons can range from 0 in
  hydrogen to more than 146 in uranium
• The electrons are usually the same number as
  protons

http//lpmpjogja.diknas.go.id/kc/a/atom/atom-h-he-
li-na.gif
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Atoms

• The smallest atom is hydrogen
• 1 proton
• 1 electron
• The largest natural occurring atom is plutonium
  (only in trace quantities)
• 96 protons
• 96 electrons
• 148 neutrons

http//www.webelements.com/
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http//geology.isu.edu/geosciences/periodic_table.
gif
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Symbols

• Elements are abbreviate, e.g.
• O for oxygen
• Hg for mercury
• Atomic Mass
• Atomic Number
• Charge
• Number of elements atoms in molecule

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Isotopes

• A form of a chemical element with the same atomic
  number as another element but having a different
  atomic mass.

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ekey4059
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ages/nature/7.a.Isotopes.gif
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Isotopes

• Hydrogen is the simplest atom
• 1 proton
• 1 electron
• Deuterium (isotope of hydrogen)
• 1 proton
• 1 electron
• 1 neutron
• Tritium (isotope of hydrogen)
• 1 proton
• 1 electron
• 2 neutrons

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rgets/illus/ilt/T046738A.gif
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Isotopes

• Carbon 12 has
• 6 protons
• 6 electrons
• 6 neutrons
• Carbon 13 has
• 6 protons
• 6 electrons
• 7 neutrons
• Carbon 14 has
• 6 protons
• 6 electrons
• 8 neutrons

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rgets/illus/ilt/T050525A.gif
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Electrons

• Electrons (e-) are found in a cloud around the
  atom in shells
• Theoretical limits to each shell
• 1st shell 2 electrons
• 2nd shell 8 electrons
• 3rd shell 18 electrons
• 4th shell 32 electrons
• 5th shell 32 electrons
• 6th shell 18 electrons
• 7th shell 8 electrons

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g/orbit-fullinit.jpg
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Theoretical

• When filling orbital shells for noble gases, the
  3rd shell gets very tricky
• Can hold 18
• Fills 8
• Moves to the 4th shell
• Partially fills 4th shell
• Chemists do not agree to the reason

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Valence Shells

• The valence shell is the outmost electron shell
  in an atom
• The number of electrons in the valence shell
  determine how reactive the atom is
• Atoms want full valence Octet rule

1 Hydrogen
1st shell reactive
1st shell not reactive
Valence shell
2nd shell reactive
8 Oxygen
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Valence Shells

• Atoms join together to form molecules

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Energy in Atoms

• Electrons, in the ground state, are in the lowest
  shells permitted (for hydrogen, in the first
  shell)
• If energy (in this case, light energy) is added
  to their system, the electrons move to an outer
  shell
• Can only move into a more energetic shell if
  there is a vacancy

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excitation.gif
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Energy in Atoms

• Energy can be converted to a different kind of
  energy, but it cannot be created or destroyed
• Low energy electrons found closest to nucleus
• Add energy electrons move away from nucleus

http//www.brooklyn.cuny.edu/bc/ahp/LAD/C7/graphic
s/C7_EnergyElectrons_1.GIF
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Niels Bohr

• Since the energy emitted was of characteristic
  amounts and never in amounts in between, that the
  stable shells were of specific distances from the
  nucleus and that electrons could only exist
  stably at those fixed distances from the nucleus

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/Niels_Bohr_Albert_Einstein_by_Ehrenfest.jpg
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Demonstration
http//www.cyberphysics.pwp.blueyonder.co.uk/topic
s/radioact/Radio/EMSpectrumcolor.jpg
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Hydrogens Orbital Shells
http//www.kennethsnelson.net/atom/Portrait4.html
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Spectral Analysis

• Hydrogen
• Violet (380-435nm)
• Blue(435-500 nm)
• Cyan (500-520 nm)
• Green (520-565 nm)
• Yellow (565- 590 nm)
• Orange (590-625 nm)
• Red (625-740 nm)

http//hyperphysics.phy-astr.gsu.edu/hbase/quantum
/modpic/hydtube.jpg
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Spectral Analysis

• Helium
• Violet 438.793
• Indigo 443.755
• Blue 447.148
• Blue 471.314
• Cyan 492.193
• Yellow 501.567
• Yellow 504.774
• Orange 587.562
• Red 667.815

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/modpic/heltube.jpg
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Spectral Analysis

• Neon
• Green 540.1nm
• Yellow 585.2nm
• Yellow 588.2nm
• Orange 603.0nm
• Orange 607.4585.2nm
• Orange 616.4585.2nm
• Red-orange 621.7nm
• Red-orange 626.6nm
• Red 633.4nm
• Red 638.3nm
• Red 640.2nm
• Red 650.6nm
• Red 659.9nm
• Red 692.9nm
• Red 703.2nm

http//hyperphysics.phy-astr.gsu.edu/hbase/quantum
/modpic/neoncomp.jpg
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Spectral Lines

• Increase energy, and the electrons move further
  away from the nucleus kinetic energy
• As atom loses energy, the electrons move closer
  to nucleus
• The energy is converted to light (another form of
  energy
• The wavelength of light given off depends on the
  energy level of the electron

http//isites.harvard.edu/fs/docs/icb.topic225467.
files/images/TowerofSpectra02.jpg
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Emission Lines
http//utahscience.oremjr.alpine.k12.ut.us/Sciber0
6/9th/Stand_1/images/Hydrogen.jpg http//faculty.n
jcu.edu/tpamer/chemprep/Goldberg4.htm
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Chemical Bonding

• Ionic Bonding
• Held together by strong electrical charges in the
  individual atoms
• Easily disassociate when in solution

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http//geology.isu.edu/geosciences/periodic_table.
gif
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Chemical Bonding

• Hydrogen has 1 electron in the valence shell, but
  wants 2
• Oxygen has 6 electrons in the valence shell, but
  wants 8
• Share electrons
• Bonding

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Ions

• The 1 electrical charge of a proton and the 1
  electrical charge of an electron cancel each
  other, so that the atom has a net 0 charge
• If an atom gain an electron, the atom will have a
  net charge
• If an atom loses an electron, the atom will have
  a net charge

http//www.worsleyschool.net/science/files/pH/page
.html
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Compounds, Molecules and Mixtures

• Molecules of an element are two or more atoms of
  the same element bonded together atmospheric
  oxygen
• Molecules of a compound are two or more atoms
  bonded together water or methane gas
• Mixtures are elements or molecules that are not
  chemically bonded together milk

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61/GIFS/AAAUASN0.JPG
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Other bonds

• Hydrogen bonds
• Hydrogen atoms are attracted to each other, but
  weakly
• If there are enough of them
• Van der Waal
• Dipole
• Cation pi

http//harvestwater.org/images/f/f9/3D_model_hydro
gen_bonds_in_water.jpg
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Free Energy

• Diffusion
• Osmosis

http//campus.queens.edu/faculty/jannr/cells/cell
20pics/osmosisMicrographs.jpg http//www.sunripe.s
unripeproduce.com/images/tangerine20peeled20nice
.jpg http//www.personal.psu.edu/users/t/r/trp2/di
ffusion60min.jpeg
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Biochemistry

• Water
• Universal solvent
• Cohesive hydrogen oxygen attraction
• Adhesive sticky with other materials
• Expands when it freezes
• Low melting point
• High freezing point
• Naturally found in all three states

http//apod.nasa.gov/apod/image/0501/earth_apollo1
7.jpg
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Proteins

• 20 Amino Acids
• Different properties
• Polar
• hydrophilic
• Non-polar
• hydrophobic
• negative
• positive

http//www.phschool.com/science/biology_place/bioc
oach/images/biomembrane1/Fluidmem.gif http//www.d
etectingdesign.com/images/Abiogenesis/Amino20Acid
20Chart.jpg
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Proteins

• Organized molecules
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

http//wofford-ecs.org/DataAndVisualization/Genomi
cData/images/protein.gif
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Proteins

• This is the basis for all components of the cell
• Eye color or skin color a protein called
  melanin
• Hormones are proteins
• And the list goes on and on and on

http//campusapps.fullerton.edu/news/arts/2003/pho
tos/protein-art.jpg
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Cell Molecules
http//www.agen.ufl.edu/chyn/age2062/lect/lect_06
/4_18.GIFhttp//porpax.bio.miami.edu/cmallery/15
0/chemistry/hemoglobin.jpg
Lipid
Protein
DNA
RNA
http//upload.wikimedia.org/wikipedia/commons/5/5b
/DNA_As_Structure_Formula_(German).PNG http//acad
emic.brooklyn.cuny.edu/biology/bio4fv/page/molecul
ar20biology/rna-structure.jpg
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Animal Cell
http//www.cartage.org.lb/en/themes/Sciences/Zoolo
gy/AnimalPhysiology/Anatomy/Anatomy/animalcell.jpg
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Plant Cell
http//www.molecularexpressions.com/cells/plants/i
mages/plantcell450.jpg
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Bacteria Cell
http//www.phs.princeton.k12.oh.us/Departments/Sci
ence/bheckman/prokaryote.bmp
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Other organelles
http//www.usoe.k12.ut.us/curr/science/sciber00/7t
h/cells/acrobat/orgtable.pdf
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Nucleus
http//www.cartage.org.lb/en/themes/Sciences/Zoolo
gy/AnimalPhysiology/Anatomy/Anatomy/animalcell.jpg
http//www.geocities.com/auroranex/nucleus.gif
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Chromatin

• Highly organized DNA

http//upload.wikimedia.org/wikipedia/commons/7/79
/Chromatin_chromosome.png
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Ribosomes

• RNA builds proteins

http//publications.nigms.nih.gov/insidethecell/im
ages/ch2_ribosome_proteinbig.jpg
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Mitochondria
http//www.nsf.gov/news/overviews/biology/assets/i
nteract08.jpg http//www.steve.gb.com/images/scien
ce/chloroplast_electron_transport_chain.png
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Endoplasmic Reticulum
http//micro.magnet.fsu.edu/cells/endoplasmicretic
ulum/images/endoplasmicreticulumfigure1.jpg
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Golgi Apparatus
http//employees.csbsju.edu/hjakubowski/classes/ch
331/cho/ergolgi.jpeg
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Lysosomes
http//micro.magnet.fsu.edu/cells/lysosomes/images
/lysosomesfigure1.jpg
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Cellular Membranes

• Phospholipid bilayer
• Fluid Mosaic Model
• Imbedded with proteins
• Only on cytoplasmic side
• Only on interstitial fluid side
• Transmembrane proteins

http//www.ncnr.nist.gov/programs/reflect/rp/biolo
gy/cell_membrane_p2.jpg
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Transport
http//2.bp.blogspot.com/_v2GFIISzHOU/R7lPf2YflUI/
AAAAAAAAACk/-7hq4edM1TM/s400/Facilitated2BTranspo
rt.jpg
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Metabolism

• Metabolism is all biochemical processes of an
  organism

www.freerepublic.com
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Enzymes (a protein)
http//lhs2.lps.org/staff/sputnam/Biology/U4Metabo
lism/enzyme.gif
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Questions?
B Shaw, Paramylodon from American Museum of
Natural History 2004
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Questions from Homework

• How do scientists age rock?
• How do scientists estimate the Earth to be 4.6
  billion years old?

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Back to the question

• Carbon 13 and Carbon 14 are unstable
• Carbon 14 naturally decays to Nitrogen at a
  predictable, steady rate
• 1 C14 to 1 trillion C12

http//razd.evcforum.net/Pictures/CvE/carbon14deca
y.jpg
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Decay Rates

• Carbon 14 has a half-life of 5730 years

http//wwwchem.csustan.edu/chem3070/images/c14deca
y.gif
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Probability patterns
http//www.tulane.edu/sanelson/images/decay.jpg
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Radiometric Dating

• Organisms uptake Carbon 14 during life, but dont
  uptake after death
• The Carbon 14 in the organism begins to decay
  into Nitrogen at a steady rate
• Scientists analyze the percentage of Carbon
  14/Carbon 12 and can determine how long has
  passed
• Different elements have different half-lives