Chapter 2 BIO 100 Chemistry

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CHAPTER 2 CHEMISTRY LIFE
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1) Matter consists of chemicals in pure form
(elements) and in combinations (compounds)

• Organisms are composed of matter.
• Matter takes up space and has mass.
• An element is a substance that cannot be broken
  down into other substances by chemical reactions.
• 92 naturally-occurring elements.
• Each element has a unique symbol.

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• A compound is a substance consisting of two or
  more elements.
• Table salt (sodium chloride or NaCl) is a
  compound.
• Pure sodium is a metal and chlorine is a gas,
  their combination forms an edible compound.

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2) Life requires about 25 chemical elements

• Four elements - carbon (C), oxygen (O), hydrogen
  (H), and nitrogen (N) - make up 96 of living
  matter (HONC!!!!)
• Most remaining (4) of an organisms mass
  consists of phosphorus (P), sulfur (S), calcium
  (Ca), and potassium (K).
• Trace elements, e.g., iodine

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3) Atomic structure determines the behavior of an
element

• An atom is the smallest unit of matter.
• Atoms are small teensy weensy
• Atoms are composed of even smaller parts, called
  subatomic particles.
• What are they??

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Subatomic Particles of an Atom
Particle Charge Mass
-Protons () -Electrons (-)
Neutrons No charge 1.009 Dalton
Protons () 1.007 Dalton
Electrons (-) 1/2000 Dalton
Dalton unit to express mass (1.66 x 10-24g)
Helium (2He)
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Neon Atom
( Ne)
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Atoms and Molecules

• Atomic Number Number of protons in an atom.
• This number is unique for each element.
• The atomic number is written as a subscript
  before the symbol for the element (e.g. Helium
  2He).
• In a neutral atom,
• the of _________ the of _________
  
• Atomic number number of protons number of
  electrons

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Atoms and Molecules

• Mass Number protons neutrons in an atom.
  
• The number of neutrons in an element can vary
  
• (Isotopes).
  
• The mass number is written as a superscript
  before the symbol for the element (e.g. Helium
  4He).
• How does one calculate the number of
  Neutrons?
• the Mass Number - Atomic Number

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Atoms and Molecules

• Examples
• The element sodium (Na) has a Mass Number of 23
  (23Na) and an Atomic Number of 11 (11Na) .
• How many Protons does Sodium have?
• How many Neutrons?
• How many Electrons?

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Atoms and Molecules
-Elements occur as mixtures of isotopes. e.g.,
carbon -Different isotopes of the same element
react in the same way. -Some Isotopes are
unstable and thus are radioactive.
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Radioactive Isotopes
-Elements occur as mixtures of isotopes. e.g.,
carbon
98.89 of carbon atoms have 6 neutrons
(12C). 1.11 of carbon atoms have 7 neutrons
(13C). 0.0000000001 of carbon atoms have 8
neutrons (14C). 12C and 13C are stable.
14C is radioactive.
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• Electron Energy Levels
• Electrons Negatively (-) charged particles that
  orbit around the nucleus.
• Electrons have orbitals.
• Each orbital is a certain distance from nucleus
  and can only contain 2 electrons
• Orbitals the same distance from the nucleus are
  grouped into SHELLS (energy levels)

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Electron Orbitals and Electron-shell
Configurations for Neon
( Ne)
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• The chemical behavior of an atom is determined by
  its electron configuration

Elements in the periodic table are grouped
together based on their valence shell electrons
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Atoms combine to form molecules

• Atoms with incomplete valence shells interact by
  either sharing or transferring valence electrons.
• These interactions hold atoms together by
  attractions called chemical bonds.
• A Molecule is two or more atoms held together by
  covalent bonds

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Atoms combine by chemical bonding to form
molecules

• Chemical bond types
• Covalent bonds strong bond
• Ionic bonds strong bond (but)
• Weak bonds
• Hydrogen bonds
• Van der Waal forces

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Covalent Bonds

• A covalent bond is the sharing of pairs of
  electrons by two atoms.
• If two atoms come close enough that their
  unshared orbitals overlap, each atom can count
  both electrons toward its goal of filling the
  valence shell.

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• Every atom has a characteristic total number of
  covalent bonds that it can form - an atoms
  valence. (HONC?)
• Hydrogen is 1.
• Oxygen is 2.
• Nitrogen is 3.
• Carbon is 4.

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Covalent Bond Polarity

• - The attraction of an atom for the electrons of
  another atom is called its electronegativity.
• - Strongly electronegative atoms attempt to pull
  the shared electrons toward themselves.
• Electronegativity Scale (FYI)
• F 4.0
• O 3.5
• N 3.0
• S and C 2.5
• P and H 2.1
• Li 1.0

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Nonpolar Covalent Bonds

• If electrons in a covalent bond are shared
  equally, its a nonpolar covalent bond.
• Covalent bond between two atoms of the same
  element is always nonpolar.
• A covalent bond between atoms that have similar
  electronegativities is also nonpolar.
• Because carbon and hydrogen do not differ greatly
  in electronegativities, the bonds of CH4 are
  nonpolar.

Electrons are shared EQUALLY.
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Polar Covalent Bonds

• If the electrons in a covalent bond are not
  shared equally by the two atoms, its a polar
  covalent bond.
• O (3.5) is more electronegative than H (2.1)
• Shared electrons spend more time around the more
  electronegative O atom.

(-)
(-)
()
()
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• Covalent bond summary
• Atoms share electrons to fill valence shells
• Nonpolar covalent bond
• Atoms have same or similar electronegativity
• Polar covalent bond
• Atoms have dissimilar electronegativity
• Gives molecule unique properties

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Ionic Bonds

• If two atoms are VERY unequal in their
  electronegativity one atom strips an electron
  completely from the other.
• E.g., sodium with one valence electron in its
  outer shell transfers this electron to chlorine
  with 7 valence electrons in its outer shell.
• Now, sodium has a full valence shell (the second)
  and chlorine has a full valence shell (the third).

• Compounds formed by ionic bonds are called
  salts.

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Biologically Important Weak Bonds

• Examples
• 1) Hydrogen 2) Ionic (weak in water) 3)Van
  der Waals
• Because these bonds are transient and easily
  broken,
• they can be used for
• Cell Signaling
• Linking Molecules Together
• 3D shape

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Hydrogen Bonds
H-bonds formed by a charge attraction between a
hydrogen atom that is covalently bonded to an
electronegative atom and another electronegative
atom.
Weak Bond only about 5 of the strength of a
covalent bond -Allows water to remain as a liquid
over a wide range of temperatures.
-Causes surface tension
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Van der Waal forces
Van der Waals attractions between small
differences in polarity in a molecule.
A very WEAK BOND and transient, highly affected
by temp etc.
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Process of making and breaking chemical bonds
Chemical Reactions

• The starting molecules are called reactants and
  the end molecules are called products.
• In a chemical reaction, all of the atoms in the
  reactants must be accounted for in the products.

• The reactions
• must be
• balanced.