The Chemical Context of Life

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The Chemical Context of Life

• AP Biology Chapter 2

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Chemistry Basics

• Matter
• Anything that has mass and takes up space.
• Element
• Substance that cannot be broken down into other
  substances by chemical reactions.
• 92 elements occur in nature
• Compound
• A substance consisting of two or more elements
  combined in a fixed ratio
• Compound has characteristics beyond those of its
  combined elements.
• NaCl

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Life Requires about 25 Elements

• 4 Elements make up 96 of living matter.
• Carbon
• Oxygen
• Hydrogen
• Nitrogen
• Remaining 4
• Phosphorous
• Sulfur
• Calcium
• Potassium
• A few others
• Trace Elements required in only minute
  quantities and not necessarily in all species.
• Iron
• Iodine

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Atomic Structure

• Atom
• Smallest unit of matter that still retains the
  properties of an element.
• Subatomic Particles
• Nucleus center of the atom
• Neutrons
• Mass
• No charge
• Protons
• Mass
• Positive charge
• Electrons
• VERY LITTLE mass
• Negative charge
• Move very rapidly outside the nucleus

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Atomic Structure - Energy Levels

• Energy is defined as the ability to do work.
• Potential Energy is the energy that matter stores
  because of its position or location
• Matter has a natural tendency to move to the
  lowest possible state of potential energy
• Electrons have potential energy due to their
  position in relation to the nucleus

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Energy Levels

• Negatively charged electrons are attracted to the
  positively charged nucleus
• The more distant the electrons are from the
  nucleus the greater their potential energy
• Changes in the potential energy of electrons can
  occur only in steps of fixed amounts.
• Ball on step analogy

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Energy Levels

• Different states of potential energy for
  electrons in an atom are called energy levels or
  electron shells
• Electrons in the first shell closest to the
  nucleus have the least potential energy
• An electron can change its shell, but only by
  absorbing or losing an amount of energy equal to
  the difference in potential energy between the
  old shell and the new shell

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Energy Levels

• Light energy can excite an electron to a higher
  energy level
• To move to a shell closer in, an electron must
  lose energy which is usually released to the
  environment in the form of heat.

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Electron Orbitals

• The 3-D space where an electron is found 90 of
  the time is called an orbital.
• Each orbital can hold two electrons
• The first energy level has only one orbital, and
  can hold only 2 electrons total.
• The second energy level has 4 orbitals and can
  hold up to 8 electrons total.

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Electron Shells
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Electron Orbitals
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Valence Electrons

• The most important electrons in determining the
  chemical behavior of an atom are the electrons in
  its outermost energy level, or its valence
  electrons.
• These are the electrons that most readily contact
  other atoms, since they are located on the
  outermost energy level.
• The outermost electron shell is the valence shell.

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Reactivity and the Valence Shell

• An atom with a a complete valence shell (that is,
  8 electrons in its outermost shell) is fairly
  unreactive with other atoms INERT.
• Atoms that do NOT have a complete outer shell are
  much MORE reactive.
• Atoms desire a COMPLETE outer shell that is,
  an outer shell with 8 electrons.

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Chemical Bonds

• Chemical bonds form between atoms as they combine
  with other atoms to fill / complete their outer
  electron shells.
• Atoms combine so that each partner completes its
  valence shell.
• They may share electrons
• They may transfer electrons totally from one atom
  to another
• Either scenario results in a chemical bond
  between the atoms

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Covalent Bonding

• The sharing of a pair of valence electrons by two
  atoms
• A very strong bond
• Two or more atoms held by a covalent bond
  molecule
• A molecule made of two different elements is
  called a compound
• a hydrogen molecule is not a compound
• A water molecule IS a compound
• The bond most often found in biological molecules
• Proteins, carbohydrates, nucleic acids and lipids.

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Types of Covalent Bonds

• Single Covalent Bond the sharing of ONE PAIR of
  electrons between two atoms
• Example Hydrogen Molecule
• Double Covalent Bond the sharing of TWO PAIRS
  of electrons between two atoms
• Example Oxygen Molecule

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Types of Covalent Bonds

• Polar vs. Nonpolar covalent bonds
• Electronegativity the attraction of an atom for
  the electrons of a covalent bond.
• The more electronegative the atom, the more
  strongly it pulls shared electrons toward itself.
• If the two atoms are the same (two hydrogens)
  then their electronegativity is equal. The
  covalent bond that results is NONPOLAR
• If one atom is MORE electronegative than another,
  then the electrons will NOT be shared equally
• OXYGEN is VERY electronegative
• In a water molecule, electrons will be pulled
  more towards oxygen than towards hydrogen
• This results in the negatively charged electrons
  spending more time near oxygen than hydrogen
  the molecule has ends of slightly different
  charge. It is said to be POLAR.

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Ionic Bonds

• Two atoms may be SO unequal in their attraction
  for electrons that one completely strips
  electrons from the other
• This results in an IONIC bond
• Atoms sharing an ionic bond have opposite
  electrical charges because one has transferred an
  electron to the other
• The ionic bond results from the attraction of
  these opposite electrical charges
• Example - NaCl

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Ionic Bonding - Salt
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Weak Chemical Bonds

• Hydrogen Bonds
• VERY important in biological molecules
• Occur BETWEEN two separate molecules (for example
  2 molecules of water), NOT WITHIN a SINGLE
  molecule (for example, covalent bonds between
  hydrogen and oxygen in a water molecule).
• Hydrogen bonds are WEAK, but much stronger than
  having no bond at all

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Other Weak Bonds

• Ionic Bonds are relatively week when in the
  presence of WATER.
• Van der Waals Interactions
• Ever changing hot spots of positive and
  negative charge can exist around atoms that have
  even NONpolar bonds.
• This is because electrons are always in motion
• These hot spots enable all atoms and molecules
  to stick to one another at least weakly and only
  when the atoms are VERY close together.

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Chemical Reactions

• The making and breaking of chemical bonds leading
  to changes in the composition of matter are
  CHEMICAL REACTIONS
• Reactants
• Products

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Chemical Equilibrium

• Some reactions go to completion most do not
• Most reactions are reversible
• Chemical equilibrium exists when the
  concentrations of reactants and products stop
  changing
• Reactions ARE still going on, but with no net
  effect on the concentrations.
• Dynamic equilibrium