Chemical Basis of Life

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Chemical Basis of Life

• Tuesday, July 8

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Chemical Elements and Compounds

• Matter anything that occupies space and has
  mass
• Element a substance that cannot be broken down
  to other substances by chemical reactions
• There are 92 elements (oxygen, gold, carbon)
• Periodic Table
• Compound a pure substance composed of two or
  more elements combined in a fixed ratio
• Example NaCl (Sodium and Chloride in a 11
  ratio)
• Na Cl ? NaCl
• Ca 2 Cl ? CaCl2
• Mixture variable composition of many substances
• Homogeneous solution composed of
  indistinguishable parts
• Heterogeneous composed of distinguishable parts

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Table 2.1 Naturally Occurring Elements in the
Human Body
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Atoms

• Atom smallest unit of matter that still retains
  the properties of an element

• Atoms are electrically neutral electrons and
  protons are balanced

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The Periodic Table
Atomic number (number of protons)
8 16.00
Symbol for the element (oxygen)
O
Atomic mass (amu) (number of protons neutrons)
Note the atomic mass is actually an average of
all the known isotopes (same protons, different
of neutrons) of an element (ie 12C, 13C, 14C)
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Figure 2.5 Two simplified models of a helium
(He) atom
- Protons and Neutrons are packed together
tightly to form a dense core (atomic
nucleus) - Electrons move at the speed of light
around this core by their attraction to the
oppositely charged protons
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Figure 2.9 Energy levels of an atoms electrons
Potential Energy The farther away electrons are
from the nucleus, the more potential energy they
have. Energy Levels / Electron Shells The
higher the level, the farther the shell, the more
potential energy
Light
Heat
Energy released
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Figure 2.10 Electron configurations of the first
18 elements
Electrons exist in the lowest available state of
potential energy Shell 1 2 electrons
max Shell 2 8 electrons max
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Valence

• Valence shell the outermost shell
• Valence electrons electrons in the outermost
  shell
• The chemical behavior of an atom depends on the
  number of valence electrons
• Atoms with the same number of valence electrons
  exhibit similar chemical behavior
• Atoms with a complete outer shell are unreactive
• Noble gases

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Molecules

• Atoms combine to form molecules through chemical
  bonds
• Covalent bonds strongest, stable bonds that
  occur between atoms that make up a molecule
  (require much energy to break)
• Noncovalent bonds weaker, temporary bonds
  between molecules (forces are additive)
• Ionic bonds
• Hydrogen bonds
• Van der Waals interactions
• Hydrophobic interactions

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Covalent Bonds

• Pairs of valence electrons are shared by two
  atoms
• Atoms are most stable when the valence shell is
  filled
• The number of bonds an atom can form depends on
  the number of electrons needed to fill its outer
  shell

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Figure 2.12 Covalent bonding in four molecules
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Electronegativity

• Attraction of an atom for the electrons of a
  covalent bond
• Nonpolar covalent bond
• Electrons are shared equally
• Polar covalent bond
• Electrons are shared unequally
• The shared electrons tend to be located more
  closely to the atom with the greater attractive
  force (the electronegative atom)
• Number of positive charges in its nucleus
• The distance of the outer electrons from the
  nucleus

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Figure 2.13 Polar covalent bonds in a water
molecule
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Ionic Bonds

• Some atoms are so electronegative they can
  capture electrons from other atoms.
• Na Cl ? Na Cl-
• These atoms are termed ions because they carry a
  charge
• Cation positive charge (Na)
• Anion negative charge (Cl-)
• These ions can then form an ionic bond through
  electrostatic attraction

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Figure 2.14 Electron transfer and ionic bonding
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Other Noncovalent Bonds

• Hydrogen Bonds
• Hydrogen bound to an electronegative atom causes
  it to have a partially positive charge, which can
  then interact with a second electronegative atom
• Important in the properties of water
• Van der Waals Interactions
• Electrons are in constant motion and at any one
  given time may cause a higher density on one side
  of the atom inducing weak attractive forces
  between molecules
• Hydrophobic Interactions
• Hydrophilic molecules are polar (contain charged
  regions)
• Hydrophobic molecules are nonpolar (uncharged)

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Figure 2.16 A hydrogen bond
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Other Noncovalent Bonds

• Hydrogen Bonds
• Hydrogen bound to an electronegative atom causes
  it to have a partially positive charge, which can
  then interact with a second electronegative atom
• Important in the properties of water
• Van der Waals Interactions
• Electrons are in constant motion and at any one
  given time may cause a higher density on one side
  of the atom inducing weak attractive forces
  between molecules
• Hydrophobic Interactions
• Hydrophilic molecules are polar (contain charged
  regions)
• Hydrophobic molecules are nonpolar (uncharged)

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Water

• Life on earth is completely dependant on water
  and its unique properties
• Highly asymmetric molecule with the O atom on one
  side and the 2 H atoms on the opposite side
• Each of the two covalent bonds in the molecule is
  highly polarized
• All three atoms in a water molecule are adept at
  forming hydrogen bonds

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Figure 3.3 Water can form 4 H bonds yielding a
highly interconnected network of molecules
Water is cohesive Surface tension
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Functions of Water

• Solvent of life (very abundant on earth)
• Fluid matrix around which the insoluble fabric of
  the cells is constructed
• Medium through which materials are transported
• Protects the cell from excessive heat or cold
  (high specific heat capacity)
• Stabilizes temperature
• evaporative cooling heat of vaporization
• Ice forms crystalline lattice causing it to float

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Acids and Bases

• Hydrogen ion (proton, H) are released whenever a
  hydrogen atom loses an electron
• Acid hydrogen donor
• Base hydrogen acceptor
• Acids and bases exist in pairs
• Acids and bases vary in strength

H (hydrogen ion) OH- (hydroxyl ion) H2O
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pH and Buffers

• Acidity of a solution is measured by the
  concentration of hydrogen ions expressed in terms
  of pH
• pH - log H
• A solution with a pH of 5 contains a hydrogen ion
  concentration of 10-5 M
• Physiologic pH is neutral 7
• Biological processes are acutely sensitive to pH
  (affects ionic state of molecules)
• Organisms are protected from changes in pH by
  buffers
• Compounds that react with free hydrogen or
  hydroxyl ions resisting changes in pH

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Figure 3.9 The pH of some aqueous solutions
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pH and Buffers

• Acidity of a solution is measured by the
  concentration of hydrogen ions expressed in terms
  of pH
• pH - log H
• A solution with a pH of 5 contains a hydrogen ion
  concentration of 10-5 M
• Physiologic pH is neutral 7
• Biological processes are acutely sensitive to pH
  (affects ionic state of molecules)
• Organisms are protected from changes in pH by
  buffers
• Compounds that react with free hydrogen or
  hydroxyl ions resisting changes in pH

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Molarity

• Mole 6.022 x 1023 units of a substance
• Molarity (M) measure of solute concentration (
  moles of solute/liter solution)
• M moles/L

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Carbon

• Most chemicals that make up living organisms are
  based on the element carbon (water70-95, rest
  is carbon)
• Compounds containing carbon are organic
• Organic molecules contain molecular components
  attached to the carbon backbone that form
  functional groups
• These are the groups that participate in chemical
  reactions

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Carbon Skeletons

• Carbon has 6 e-
• Needs four more to complete outer shell
• Tends to form 4 covalent bonds
• Methane CH4
• Chains can be elongated
• Straight or branched
• Variations double bonds, oxygen, nitrogen
• Functional groups attached to the carbon
  skeletons are involved in diverse chemical
  reactions

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Table 4.1 Functional Groups of Organic Compounds
Hydroxyl group (-OH) Polar, attracts water
molecules Dissolve organic compounds Carbonyl
group (CO) Variation in location
diversity Carboxyl group (-COOH) Source of H
ions Amino group (-NH2) Acts as a base by taking
up H Sulfhydryl group (-SH) Interact with each
other (stabilize protein structure) Phosphate
group (-OPO3(-2)) Transfer of energy between
organic molecules