Chapter 2: The Chemical Context of Life

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Chapter 2 The Chemical Context of Life
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Elements vs. Compounds

• Element substance that cannot be broken down to
  other substances by chemical reactions
• Compound consists of 2 or more elements combined
  in a fixed ratio. Has characteristics beyond
  those of its combined elements.

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Four Elements that make up 96 of Life
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Structure of an Atom

• Protons and Neutrons are tightly packed together
  in the nucleus or center of the atom.
• Electrons move very quickly around the nucleus
  in a cloud

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Atomic Information

• a. Atomic NumberThe number of protons,
  identifies the element.
• b. Mass NumberApproximation of the mass of an
  atom. Number of protons plus the number of
  neutrons.
• c. Atomic WeightTotal mass of the atom in
  Daltons or atomic mass units (amu)
• d. ValenceElectrons in the outermost shell.
  Determines the chemical behavior of the atom
• Determining NeutronsDetermined by subtracting
  the Atomic Number ( of protons) from the Mass
  Number ( of protons and neutrons).

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Importance of Radioactive Elements

• Radioactive Isotopesan atomic form with a
  different number of neutrons in which the nucleus
  spontaneously decays giving off particles and
  energy.
• UsesFossil Dating, tracers to follow atoms
  through metabolism, medical diagnosis (tracers),
  radiation

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Electron Configurations and Atom Behavior

• Atoms attempt to fill their valence shell with
  electrons.
• Depending on the number of electrons present, the
  atom will react to either gain or lose electrons.
  
• Atoms with a similar valence number ( of
  electrons in the outermost shell) will act and
  react similarly to complete their shells.

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Types of Chemical Bonds

• Nonpolar Covalentbond in which electrons are
  equally shared. Atoms in the bond will have
  equal electronegativity. (Ex. CH4, O2)

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Types of Chemical Bonds

• Polar Covalentbond in which electrons are
  unequally shared. One atom is more
  electronegative than the other and pulls the
  electrons closer to it. This bond results in a
  polar molecule or one with a partial negative
  side (where the electrons are) and a partial
  positive side (where the electrons are not) (Ex.
  H2O)

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Types of Chemical Bonds

• Ionic Bondsbond in which electrons are
  transferred from one atom to another because of
  huge differences in electronegativities. Atoms
  gain or lose atoms becoming opposite ions and
  then are attracted because of the opposite
  charges. (Ex. NaCl)

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Weak Bonds

• Weak bonds such as Hydrogen bonds or van der
  Waals forces are between molecules. The contact
  can be brief and easily broken.
• Hydrogen Bonds forms when a hydrogen with a
  partial charge due to a polar covalent bond is
  attracted towards an atoms with the opposite
  partial charge. Seen most often in water
  molecules and causes them to stick together.
• Van der Waals forces occur between nonpolar
  covalent molecules that are very close together
  due to hotspots or changes in the electrons
  within a molecule.

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Structure vs. Function of a Molecule

• A molecule has a characteristic shape and size
  because of the atoms valence orbitals. This can
  determine how molecules recognize and respond to
  one another as in chemical signaling.

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Parts of a Chemical Equation
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Effect of Concentrationson Reactions

• Chemical Equilibrium occurs when the amount of
  products and the amount of reactants have
  stabilized. For a reaction to proceed in one
  direction, the concentrations of products must be
  lowered constantly.

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Chapter 3 Water and the Fitness of the
Environment
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Structure and Geometry of Water

• Water is made of two hydrogen atoms covalently
  bonded to an oxygen atom creating a polar
  molecule. Because of the polarity and the
  orbitals, the hydrogens are at a 104.5º angle.

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Hydrogen Bonds and Polarity of Water

• Because the hydrogen molecules are slightly
  positive and the oxygen molecule is slightly
  negative, water has the ability to form hydrogen
  bonds due to the interactions of these partial
  charges.

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Emergent properties due to Hydrogen Bonds

• Water can form 4 hydrogen bonds to neighboring
  water molecules or other molecules.
• This gives properties of
• Cohesion
• ability to stabilize temperature
• expansion upon freezing
• versatility as a solvent.

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Cohesion

• Cohesion is the hydrogen bonds sticking water
  molecules together. This helps in transporting
  water against gravity in plants and also
  increases the surface tension of water allowing
  some small animals to walk across the surface of
  water.

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Heat v. Temperature

• a. Heat is the measure of the total amount of
  kinetic energy due to molecular motion
• b. Temperature is the average kinetic energy of
  molecules within a body of matter.

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Specific Heat

• Specific heat is the amount of heat that must be
  required to raise the temperature of 1g of water
  1ºC. Water has a high specific heat which means
  that it is resistant to a change in temperature.
  Water can store huge amounts of heat without
  changing mush in temperature.

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Evaporative Cooling

• Heat of vaporization is the amount of heat needed
  to change 1g of a liquid into a gas. Water has a
  high heat of vaporization which helps to moderate
  the climate.
• Evaporative cooling (both off of bodies of water
  and animal bodies by sweating) occurs because the
  molecules with the most energy leave as gas
  cooling down the remaining molecules.

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Ice Floats

• Water has a lower density as a solid because of
  the hydrogen bonds keep the molecules spaced and
  in a crystalline structure. Ice floats which
  allows for insulation and prevents freezing of
  the entire body of water allowing for life to
  exist underneath.

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Parts of a Solution

• a. solute substance that is dissolved in a
  solution
• b. solvent substance that is the dissolving
  agent (usually water)
• c. solution homogenous mixture of two or more
  substances.

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Universal Solvent

• Water is a versatile solvent because of its
  polarity. It can bond with any charged molecules
  including ionic compounds and other polar
  molecules. Water molecules surround the solute
  molecules and pull them apart.

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Hydrophilic v. Hydrophobic

• Hydrophilic substances have an affinity for
  water. Includes polar and ionic substances.
• Hydrophobic substances do not have an affinity
  for water, instead of mixing with water they form
  a separate layer or bubble. Includes non-ionic
  and nonpolar substances.

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The Mole

• a. A mole is equal in number to the molecular
  weight of a substance. Contains 6.02 1023
  molecules of a substance.
• b. Molecular weight is the sum of the weights of
  all the atoms in a molecule.

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Equation for Dissociation of Water

• 2H2O ? H3O OH-
• H2O ? H OHwater
  hydrogen hydroxide ion
  ion

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pH Scale

• pH scale is based on the negative logarithm
  (base 10) of the hydrogen ion concentration in
  a solution. pH -log H
• As pH declines, H increases or the solution
  becomes more acidic.
• Acids increase the hydrogen ion concentration of
  a solution
• Bases decrease the hydrogen ion concentration of
  a solution

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Buffers

• Buffers minimize changes in the concentrations of
  H and OH- in a solution. They act as ion
  acceptors or donators depending on the
  conditions.
• H2CO3 ? HCO3- H
• Hdonor H acceptor hydrogen ion
• Carbonic acid is able to dissociate into
  bicarbonate ion and hydrogen ions to increase pH
  or bond to absorb the hydrogen ions depending on
  the pH of the solution. This particular buffer
  system is found in the blood.

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Acid Rain

• Acid precipitation results from a reaction in the
  air between water vapor and oxides produced by
  the burning of fossil fuels.
• The reaction lowers the pH of the water and thus
  introduces more H ions into the environment
  which can alter biological molecules and prevent
  life processes from occurring.
• It can also change the pH of soil and cause
  minerals to disappear and runoff.

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Figure 3.x1 Water
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Chapter 4 Carbon and the Molecular Diversity of
Life
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Vitalism v. Mechanism

• Vitalism states that there is a life force
  outside of chemical and physical laws.
• Mechanism states that all natural phenomena are
  governed by physical and chemical laws.

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Carbon

• Carbons Electron configuration determines its
  bonding capabilities because it has only 4
  valence electrons, it can covalently bond with up
  to 4 other atoms as well as form double or triple
  bonds.

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Variation in Organic Molecules

• Carbon skeletons may vary because Carbon can make
  4 bonds with other Carbon atoms or with a wide
  variety of other atoms.
• It has the ability to form
• straight chains
• branched chains
• rings
• This variation leads to diversity and complexity
  of organic molecules by

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Structure Changes Function

• These are important because changes in the shape
  of a molecule can change its function, especially
  for receptors and signal molecules.
• Structural isomers differ in the covalent
  arrangement of their atoms. The number of
  isomers increases with the length of the chain.
• Geometric isomers have the same covalent
  arrangement of their atoms but differ in their
  special arrangements. These happen because of
  double bonds change the shape of the molecule.
• Enantiomers are molecules that are mirror images
  of each other around an asymmetrical Carbon atom.

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Structure can Change Function

• Thaidomide one enantiomer cures morning
  sickness, the other causes severe birth defects
• Dopa one form is an effective drug against
  Parkinsons disease, the other is inactive.
• Cocaine is a similar shape to endorphinsfunction
  s similarly in the body, causes a high

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