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Chapter 2

Basic Chemistry and Cells
Matter is composed of atoms
• Six types of atoms are basic to life = 95% of body weight
   –   C   carbon
   –   H   hydrogen
   –   N   nitrogen
   –   O   oxygen
   –   P   phosphorus
   –   S   sulfur
• Element
   – Substance that cannot be broken down by chemical means into
     a simpler substance (periodic table of elements shows all known
     elements)
• Atom
   – Smallest unit of an element that still retains the chemical and
     physical properties of the element
• Atomic symbol
  – One or two letters that represent the name of an
    element (Au, C, O, N)
• Subatomic particles
  – Protons
     • Positively charged (+)
     • Within nucleus
  – Neutrons (0)
     • Uncharged
     • Within nucleus
  – Electrons (-)
     • Negatively charged
     • Orbit about nucleus
• Electron shells
  – Inner shell
     • Lowest energy level
     • Holds 2 electrons
  – All shells beyond
    inner shell
     • Holds 8 electrons
  – Outer shell
     • Highest energy level
     • Holds 8 electrons
• Atomic number
  – Number of protons of an element
  – Also tells number of electrons when electronically
    neutral
• Mass number
  – Number of protons plus neutrons

• Isotopes
  – Atoms of a single element that differ in their number
    of neutrons

• Atomic mass
  – Average mass of all isotopes
The many medical uses of
        radioactive isotopes
• Low levels of radiation
  – Tracer to detect tumors
• High levels of radiation
  – Sterilize medical and dental products
  – Sterilize mail to free it of possible pathogens
    (anthrax)
  – Treatment for cancer
Atoms react with one another to
         form molecules
• After atoms react, they have a completed
  outer shell
• Periodic table
  – Arranges elements based on characteristics
    • Periods
       – Horizontal row
       – How many shells an atom has
    • Groups
       – Vertical column
       – How many electrons an atom has in its outer shell
Periods – how many shells
Groups – how many electrons in outer shell
• Octet rule
   – Atoms will give up, accept, or share electrons in order to have 8
     electrons in the outer shell
• Group 8
   – Stable
   – All other groups readily react
• Compound
   – When atoms of two or more elements bond together in fixed
     proportions
• Molecule
   – Smallest part of a compound that still has the properties of that
     compound
   – Molecule is union of two or more atoms of the same or different
     elements
• Naturally occurring molecules
   – O2, H2, N2, H2O
• Naturally occurring compound
   – H2O
An ionic bond occurs when
        electrons are transferred
• One atom can take
  electron(s) from another
  atom
• Ions result
   – Ions that lost electrons are
     positively charged
   – Ions that gained electrons
     are negatively charged
• Ionic bonds result
   – An attraction between
     negatively and positively
     charged ions
A covalent bond occurs when
         electrons are shared
• Atoms want to fill their outer shell
• Bond notations
   – H – H share one pair of electrons
   – O = O share two pairs of electrons
   – N = N share three pairs of electrons
• Molecular – omits the bond line
   – H2
   – O2
   – N2
• Common bonds required
   – H – 1 bond
   – O – 2 bonds
   – C – 4 bonds
Chemical reactions
• Some bonds are broken while others are formed
• Reactants
   – Participate in reaction
• Products
   – Formed by reaction
• Photosynthesis
   – Balanced equation
   – Same number of each type of atom occurs on both sides of
     arrow
A covalent bond can be nonpolar or
              polar
• Nonpolar
  – Sharing of electrons between two atoms is fairly
    equal
• Electronegativity
  – Attraction of an atom for the electrons in a covalent
    bond
• H2O
  –O
     • Larger atom
     • more electronegative
     • Slightly negative
  –H
     • Smaller atom
     • Less electronegative
     • Slightly positive
• Polar
  – Unequal sharing of electrons in a covalent bond

The polarity of water molecules leads to the
  formation of hydrogen bonds
Hydrogen bonds can occur
      between polar molecules
• Hydrogen atoms in
  one molecule are
  attracted to oxygen
  atoms in another
  molecule
• Weaker than ionic or
  covalent bonds
• Hydrogen bonds also
  hold the two strands
  of DNA together
The properties of water benefit life
Water molecules stick together and to other
  materials
• Due to hydrogen bonding
  – Water can be liquid at most temperatures found on
    earth
  – Water molecules exhibit cohesion (stick together)
  – Water molecules exhibit adhesion (stick to other polar
    material)
• Cohesion and adhesion
  – Create surface tension
  – Allows water to rise to the top of plants
  – Allows blood to flow through a body
Water warms up and cools down
            slowly
• This allows organisms to maintain internal
  temperatures (homeostasis)
• Cooling slowly aids organisms in winter
• To vaporize water, hydrogen bonds must
  be broken, this requires a large amount of
  energy
Water dissolves other polar
            substances
• Solutions are composed of
  – Solute
    • What is being dissolved
  – Solvent
    • What does the dissolving


Creating sugar water
 solute – sugar
 solvent – water
• When ionic salt (NaCl) is put in water, the
      atoms dissociate and the Na+ and Cl- dissolve
      into the water




Hydrophilic – molecule that
can attract water
Hydrophobic – molecule
that canon attract water (oil
and water do not mix)
Frozen water is less dense than
                  liquid
Water expands as it
freezes
Ice floats, allowing
bodies of water to freeze
from the surface down
and they usually do not
freeze solid, allowing
organisms to survive the
winter
Living things require a narrow pH
                   range
•   When water dissociates, hydrogen ions (H+) and hydroxide ions
    (OH-) result in equal concentrations
•   Acids
    – Excess hydrogen (H+) ions
•   Bases
    – Excess hydroxide (OH-) ions
• The pH scale measures acidity and basicity
• pH scale ranges from 0 to 14
• Neutral = 7
  – This is when H+ concentration equals OH- concentration
• Acidic <7
• Basic >7
Buffers help keep the pH of the
      body fluids relatively constant
•   Buffer
     – Resists changes in pH
•   Blood pH needs to stay between 7.35 and 7.45
•   Carbonic acid (H2CO3) and bicarbonate (HCO3) are present in blood
•   Carbonic acid can dissociate to release bicarbonate and H+
     – This lowers pH
•   When a base is added (OH-) the carbonic acid dissociates and releases
    H+, these combine to form water (H2O)
•   When there is excess H+, carbonic acid reforms
• Breathing releases CO2, which reduces
  the amount of carbonic acid in the blood

• Kidneys also filter acids and bases from
  the body but act more slowly, although
  powerfully. A malfunction of the kidneys
  could cause blood pH to go higher or
  lower than required levels.
Harmful effects of acid rain
• Rainwater pH = 5.6
  – Low due to CO2 in the air forming carbonic
    acid
• Acid rain pH < 5
  – Contains sulfuric and/or nitric acid
  – Sulfur dioxide and nitrogen oxides come from
    burning fossil fuels
• Acid rain affects lakes in areas with little to
  no limestone (a buffer) CaCO3
• Acid rain
  – Causes mercury to accumulate in fish
  – Can make bodies of water lifeless
  – Damages plants
  – Increases respiratory illness in humans
  – Breaks down limestone and marble buildings
    and monuments
  – Degrades paint on homes and cars

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Bio 100 Chapter 2

  • 2. Matter is composed of atoms • Six types of atoms are basic to life = 95% of body weight – C carbon – H hydrogen – N nitrogen – O oxygen – P phosphorus – S sulfur • Element – Substance that cannot be broken down by chemical means into a simpler substance (periodic table of elements shows all known elements) • Atom – Smallest unit of an element that still retains the chemical and physical properties of the element
  • 3. • Atomic symbol – One or two letters that represent the name of an element (Au, C, O, N) • Subatomic particles – Protons • Positively charged (+) • Within nucleus – Neutrons (0) • Uncharged • Within nucleus – Electrons (-) • Negatively charged • Orbit about nucleus
  • 4. • Electron shells – Inner shell • Lowest energy level • Holds 2 electrons – All shells beyond inner shell • Holds 8 electrons – Outer shell • Highest energy level • Holds 8 electrons
  • 5. • Atomic number – Number of protons of an element – Also tells number of electrons when electronically neutral
  • 6. • Mass number – Number of protons plus neutrons • Isotopes – Atoms of a single element that differ in their number of neutrons • Atomic mass – Average mass of all isotopes
  • 7. The many medical uses of radioactive isotopes • Low levels of radiation – Tracer to detect tumors • High levels of radiation – Sterilize medical and dental products – Sterilize mail to free it of possible pathogens (anthrax) – Treatment for cancer
  • 8. Atoms react with one another to form molecules • After atoms react, they have a completed outer shell • Periodic table – Arranges elements based on characteristics • Periods – Horizontal row – How many shells an atom has • Groups – Vertical column – How many electrons an atom has in its outer shell
  • 9. Periods – how many shells Groups – how many electrons in outer shell
  • 10. • Octet rule – Atoms will give up, accept, or share electrons in order to have 8 electrons in the outer shell • Group 8 – Stable – All other groups readily react • Compound – When atoms of two or more elements bond together in fixed proportions • Molecule – Smallest part of a compound that still has the properties of that compound – Molecule is union of two or more atoms of the same or different elements • Naturally occurring molecules – O2, H2, N2, H2O • Naturally occurring compound – H2O
  • 11. An ionic bond occurs when electrons are transferred • One atom can take electron(s) from another atom • Ions result – Ions that lost electrons are positively charged – Ions that gained electrons are negatively charged • Ionic bonds result – An attraction between negatively and positively charged ions
  • 12. A covalent bond occurs when electrons are shared • Atoms want to fill their outer shell • Bond notations – H – H share one pair of electrons – O = O share two pairs of electrons – N = N share three pairs of electrons • Molecular – omits the bond line – H2 – O2 – N2 • Common bonds required – H – 1 bond – O – 2 bonds – C – 4 bonds
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  • 14. Chemical reactions • Some bonds are broken while others are formed • Reactants – Participate in reaction • Products – Formed by reaction • Photosynthesis – Balanced equation – Same number of each type of atom occurs on both sides of arrow
  • 15. A covalent bond can be nonpolar or polar • Nonpolar – Sharing of electrons between two atoms is fairly equal
  • 16. • Electronegativity – Attraction of an atom for the electrons in a covalent bond • H2O –O • Larger atom • more electronegative • Slightly negative –H • Smaller atom • Less electronegative • Slightly positive • Polar – Unequal sharing of electrons in a covalent bond The polarity of water molecules leads to the formation of hydrogen bonds
  • 17. Hydrogen bonds can occur between polar molecules • Hydrogen atoms in one molecule are attracted to oxygen atoms in another molecule • Weaker than ionic or covalent bonds • Hydrogen bonds also hold the two strands of DNA together
  • 18. The properties of water benefit life Water molecules stick together and to other materials • Due to hydrogen bonding – Water can be liquid at most temperatures found on earth – Water molecules exhibit cohesion (stick together) – Water molecules exhibit adhesion (stick to other polar material) • Cohesion and adhesion – Create surface tension – Allows water to rise to the top of plants – Allows blood to flow through a body
  • 19. Water warms up and cools down slowly • This allows organisms to maintain internal temperatures (homeostasis) • Cooling slowly aids organisms in winter • To vaporize water, hydrogen bonds must be broken, this requires a large amount of energy
  • 20. Water dissolves other polar substances • Solutions are composed of – Solute • What is being dissolved – Solvent • What does the dissolving Creating sugar water solute – sugar solvent – water
  • 21. • When ionic salt (NaCl) is put in water, the atoms dissociate and the Na+ and Cl- dissolve into the water Hydrophilic – molecule that can attract water Hydrophobic – molecule that canon attract water (oil and water do not mix)
  • 22. Frozen water is less dense than liquid Water expands as it freezes Ice floats, allowing bodies of water to freeze from the surface down and they usually do not freeze solid, allowing organisms to survive the winter
  • 23. Living things require a narrow pH range • When water dissociates, hydrogen ions (H+) and hydroxide ions (OH-) result in equal concentrations • Acids – Excess hydrogen (H+) ions • Bases – Excess hydroxide (OH-) ions
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  • 25. • The pH scale measures acidity and basicity • pH scale ranges from 0 to 14 • Neutral = 7 – This is when H+ concentration equals OH- concentration • Acidic <7 • Basic >7
  • 26. Buffers help keep the pH of the body fluids relatively constant • Buffer – Resists changes in pH • Blood pH needs to stay between 7.35 and 7.45 • Carbonic acid (H2CO3) and bicarbonate (HCO3) are present in blood • Carbonic acid can dissociate to release bicarbonate and H+ – This lowers pH • When a base is added (OH-) the carbonic acid dissociates and releases H+, these combine to form water (H2O) • When there is excess H+, carbonic acid reforms
  • 27. • Breathing releases CO2, which reduces the amount of carbonic acid in the blood • Kidneys also filter acids and bases from the body but act more slowly, although powerfully. A malfunction of the kidneys could cause blood pH to go higher or lower than required levels.
  • 28. Harmful effects of acid rain • Rainwater pH = 5.6 – Low due to CO2 in the air forming carbonic acid • Acid rain pH < 5 – Contains sulfuric and/or nitric acid – Sulfur dioxide and nitrogen oxides come from burning fossil fuels • Acid rain affects lakes in areas with little to no limestone (a buffer) CaCO3
  • 29. • Acid rain – Causes mercury to accumulate in fish – Can make bodies of water lifeless – Damages plants – Increases respiratory illness in humans – Breaks down limestone and marble buildings and monuments – Degrades paint on homes and cars