THE CHEMICAL CONTEXT OF LIFE

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CHAPTER 2

• THE CHEMICAL CONTEXT OF LIFE

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ESLRSCore LearningCritical ThinkingCommunicati
onCommunity

• STANDARDS
• Investigation Experimentation 1 a,b,c,d,j
• Chemistry 1 a,d,e 2 a-h 5 a-d more
• Cell Biology 1 b, f, g, h

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Figure 2.0 Bombardier beetle
This bomardier beetle illustrates the
interdisciplinary nature of scientific
research... Focus today is CHEMISTRY
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Matter- anything that takes up space
and has mass.
Element- substance that cannot be broken
down to other substances by chemical
reactions. 92 elements exist in
nature LIFE REQUIRES 25 C, H, N, O - 96 P, S,
Ca, K - 4 and trace elements
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Table 2.1 Naturally Occurring Elements in the
Human Body
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What kinds of molecules will an animal, plant, or
bacterium take up as necessary building blocks
and excrete as waste products?What elements are
these molecules made of?DISCUSS.
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Water- solvent of lifeCarbohydratesLipidsProte
insNucleic AcidsCarbon, Hydrogen, Nitrogen,
Oxygen, Phosphorus, Sulfur
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Which elements are most essential for life?

• 96
• Carbon
• Hydrogen
• Oxygen
• Nitrogen

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• The other 4?
• Phosphorus
• Sulfur
• Calcium
• Potassium

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I. Elements essential to life

• C carbon
• H hydrogen
• N nitrogen
• O oxygen
• P phosphorus
• S sulfur
• Ca calcium
• K potassium

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Enlarged thyroid gland

• And trace elements
• I iodine
• Fe iron
• specific to the species

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Figure 2.4 Goiter
Goiter- Caused by iodine deficiency. Swollen
thyroid gland. Hormones thyroxine and
triiodotyronine (T3)contain Iodine.
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Figure 2.3 Nitrogen deficiency
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A. STRUCTURE OF ATOMS
Atomic structure determines the behavior of an
atom.
Electron- negative charge
Proton- positive charge
Neutron- no charge
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ATOM the entire stadium NUCLEUS pencil eraser
on the pitchers mound ELECTRONS gnats buzzing
around stadium
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Figure 2.11 Electron orbitals
Electron Orbitals are the three-dimensional space
where an electron is found 90 of the time. No
more than 2 electrons can occupy the same
orbital. You dont need to remember this 1s, 2s,
2p etc. stuff for AP Bio
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Figure 2.10 Electron configurations of the first
18 elements
2 electrons fit in the first energy shell Outer
shells can hold up to 8 electrons This is the
octet rule
Valence electrons are the outermost electrons-
they determine the bonding behavior of the atom.
Atoms with unpaired electrons are reactive.
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What are the valences of the essential elements?

• HONK!
• Hydrogen - 1
• Oxygen - 2
• Nitrogen - 3
• Carbon - 4

This tells you how many bonds each needs to make.
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PHOTON is a packet of radiation from the
sun. Electrons exist at fixed levels of potential
energy called electron shells. Outer shells have
more energy. Electrons can shift energy level by
absorbing or releasing energy.
Ex. Photons of light can cause a quantum leap-
electrons jump shells
Heat is released when the electrons fall back to
the lower energy level.
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Isotopes have the same of P E but a
different of neutrons.
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In nature, an element occurs as a mixture of its
isotopes.
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Radioactive isotopes

• Are unstable.
• The nucleus decays spontaneously, giving off
  particles and energy.
• When the decay changes the of PROTONS, it
  transforms the element.
• Half-life is the length of time required for half
  of a given number of initial number of atoms of
  that isotope to be transformed to the decay
  element.
• a) CAN BE USED TO DATE FOSSILS
• Radioactive Carbon 14 decays to Nitrogen 14
  through beta decay
• half-life 5730 years so used in archaeology to
  determine the age of carbonaceous materials up to
  60,000 years old.
• Uranium-238 decays to Leadhalf-life 4.5
  billion years used to date OLD OLD fossils, like
  1st cells.

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b) CAN BE USED TO TRACE ATOMS THROUGH METABOLISM

• Radioactive tracers are important diagnostic
  tools in medicine.
• Used to follow atoms through metabolism, the
  chemical processes of an organism
• ex. Old breath test for ulcers caused by
  Heliobacter pylori used C14 labeled urea- which
  will be converted to ammonia and radioactive
  carbon dioxide.
• ex kidney disorders can be detected by measuring
  the radioactivity of urine w/ a scintillation
  counter.
• ex. Metabolic activity (brain activity) can be
  observed using a PET scanner.

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The Calvin Cycle
Used C14
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Figure 2.6 Using radioactive isotopes to study
cell chemistry
Phosphorus 32 has a half-life of 14 days Part of
DNA nucleotides Used in biotech research.
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Figure 2.8 The Tokaimura nuclear accident
Radiation from decaying isotopes damages cellular
molecules. Mutates DNA causing cancer, birth
defects, death.
Danger Nuclear Power Plant disasters.
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II. the glue of life chemical bonds

• Unless the atom is a noble gas, it will react
  with other atoms.
• Chemical bonds are interactions between atoms
  that allow them to complete their valence shells.
• Ionic and Covalent bonds are strong.
• Ionic bonds are weak in the presence of water.
• Hydrogen bonds are weak- but plentiful.
• Van der Waals interactions are extremely
• weak and only occur when molecules are close
  together.

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Figure 2.14 Electron transfer and ionic bonding
cation
anion
Ions are charged atoms. Unequal Protons
Electrons.
Ionic bonds happen when one electron is
transferred to Another atom making a and -
ion. Opposites attract.
electrostatic attraction Ionic bond Ionic
attraction
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Figure 2.15 A sodium chloride crystal
Ionic compound
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• A Molecule is a collection of two or more atoms
  bonded together.
• Ex. Oxygen OO
• Water H-O-H
• Salt NaCl-

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A compound is a substance consisting of two or
more Elements combined in a fixed ratio.
Sodium Chloride- edible compound
Sodium- a metal
Chlorine- poisonous gas
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Notice the EMERGENT PROPERTY of flavor
enhancement the compound formed has different
qualities than the elements below in a level of
organization of matter!
Sodium Chloride- edible compound
Sodium- a metal
Chlorine- poisonous gas
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Figure 2.12 Covalent bonding in four molecules
Covalent Bonds When atoms share electrons.
The goal is to get the valence shells full.
Hydrogen - 1 bond Oxygen- 2 bonds Nitrogen- 3
bonds Carbon- 4 bonds
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Figure 2.12x Methane
Methane CH4 Carbon Hydrogen Share the
electrons Evenly. NONPOLAR COVALENT BOND
Smells bad.
Contributes to global warming.
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HARRIS RANCH
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Figure 2.13 Polar covalent bonds in a water
molecule
POLAR COVALENT BOND unequal sharing of electrons
Water is a polar covalent molecule. The oxygen is
more electronegative than hydrogen the shared
electrons spend more time around the Oxygen
nucleus than the Hydrogen resulting in partial
negative and positive charge.
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Electronegativity

• Is the attraction of a particular kind of atom
  for the electrons of a covalent bond.
• Carbon Hydrogen are ly electronegative.
• So molecules that are composed only of these
  elements are nonpolar- they have no charge.
• OXYGEN NITROGEN are EXTREMELY ELECTRONEGATIVE
• So molecules that have these elements in them are
  polar where the N or O is bonded.
• Will you remember this?
• NO!!!!! I mean yes.

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Hydrogen bonds
form when a partially positive hydrogen atom
covalently bonded to one electronegative atom is
also bonded to a partially negative
electronegative atom on another molecule.
Bond from the Hydrogen of one Polar
molecule Bonding to the - part of the
other. These are weak bonds Drawn as a dotted
line.
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Water molecules H bonded
Water
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DNA- hydrogen bonds hold the two strands
together(via nitrogen containing bases).
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Van der Waals interactions (negative and
positive hot spots) are weak and only occur
when molecules are very close together.
Notice how all of these Bonds function in
various Biological phenomena
Ex. 1 Immune System Antigen-Antibody Specificity
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Figure 2.18 Molecular shape and brain chemistry
Ex. 2 Neurotransmitter Stimulating Next neuron
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Figure 2.19 A molecular mimic
Both block pain receptors from sending signal
Man made
Endorphin endo morphine
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CHAPTER 3

• Water and the Fitness of the Environment

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Figure 3.0 Earth
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Figure 3.x1 Water
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The polarity of water results in hydrogen bonding

• Hydrogen bonding of water
• results in these Emergent Properties
• Versatility as a solvent
• Cohesive behavior
• Ability to stabilize temperature
• Expansion upon freezing

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Water is the universal solvent it dissolves
better than most things but not everything- it
is the solvent of life.
Solute Solvent Solution
Water can form hydration shells around ions
break Ionic bonds. Note- the Cl- is surrounded
by the hydrogen parts of water the Na is
surrounded by the - oxygen parts of water.
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Water, as the universal solvent, supports
chemical reactions that occur within cells.
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Figure 3.8 A water-soluble protein
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Cohesion is an attractive force betweenlike
substances.

• Surface tension, caused by the cohesion of water
  molecules, allows a water strider to exploit the
  habitat of surface water to find food, mates, or
  escape predators.
• Surface tension is a
• measure of how difficult
• it is to stretch or break
• the surface of a liquid.

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The basilisk can run on water to escape larger
predators who will sink.
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Figure 3.2 Water transport in plants
Benefit to plants dont need to use ATP to move
water
Transpiration- result of cohesion and adhesion.
It is A water chain being pulled up from the
roots to the leaves. Adhesion is the attraction
of the water molecules to another type of
molecule in this case the dead cells of the
xylem.
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Water will change its temperature less than other
materials when it gains or loses a given amount
of heat.
Where would you rather be on a hot day In the
desert or at the beach?

Which boils faster a pot of alcohol or a pot of
water?
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Water has an unusually high specific heat. Heat
Capacity or Specific Heat is the amount of heat
that must be absorbed or lost for 1 g of that
substance to change its temperature by one degree
C. Heat must be absorbed to break hydrogen bonds
(so it takes along time to boil water) and heat
is released when hydrogen bonds form (it takes
longer to cool and to freeze water.) This makes
it a great moderator of temperature.
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Heat must be absorbed to break all four hydrogen
bonds before the molecule transitions to the gas
phase.
SWEATING EVAPORATIVE COOLING
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Evaporative cooling occurs when liquids
evaporate. they absorb heat to be converted from
liquid to gas leave the remaining liquid
cooler. Because heat must be absorbed to
break hydrogen bonds to allow the water to
evaporate.
Waters high heat of vaporization moderates
earths climate and organisms temperatures.
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Figure 3.6x2 Ice floats and frozen benzene sinks
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Water is one of the few substances that is less
dense asA solid. ICE FLOATS.
Figure 3.5x1 Ice, water, and steam
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Figure 3.6 Floating ice and the fitness of the
environment
Since oceans and lakes dont freeze solid.
Organisms in aquatic environments dont
lose their habitat during winter.
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• Hydrophilic water loving
• ex. Polar substances will bond with water
  are attracted to water.
• Ex. Sugar dissolves in water and is easily
  transported through it to cells and organelles
  w/in cells that use it.
• Hydrophobic water hating
• ex. Nonpolar substances will NOT have
  attraction to water actually repel water.
• Ex. The phospholipid molecule is used (many of
  them) to create the cell membrane.

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Living systems depend on properties of water that
result from its polarity and hydrogen bonding.
Explain this statement and provide multiple
examples.
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Unnumbered Figure (page 47) Chemical reaction
hydrogen bond shift
base
acid
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Figure 3.9 The pH of some aqueous solutions
pH is a log Scale, 10x
An acid increases the hydrogen
ion concentration of a solution.
A base lowers the hydrogen ion concentration of a
solution.
Hydrogen donator
Hydrogen acceptor
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Figure 3.10x1 Pulp mill
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Figure 3.10x2 Acid rain damage to statuary, 1908
1968
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Figure 3.10 The effects of acid precipitation on
a forest
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BUFFERS

• Are substances that minimize changes in the
  concentrations of H and OH- in a solution.
• Carbonic Acid is the buffer in human blood that
  keeps it at a pH of 7.4. (CO2 H20)
• It disassociates to form Bicarbonate and releases
  a H when pH levels exceed 7.4 (becomes basic)
• The reversible reaction occurs when blood becomes
  too acidic. Excess H bonds with bicarbonate to
  form Carbonic Acid.

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Oxygen as an Electron acceptor.

• In cell respiration reactions occur in the
  mitochondria to make ATP by metabolizing organic
  molecules (like glucose).
• Oxygen, a highly electronegative molecule, is
  crucial to the process.
• It attracts and bonds to itself Hydrogen ions
  and electrons, to form water.
• Without oxygen attracting electrons the whole
  system wouldnt work.
• When you die from asphyxiation, it is because you
  run out of ATP- since Cell Resp. stops.