BIOSC 0100 Lecture Notes - Lecture 4: Covalent Bond, Ice Cream Cone, Hydrogen Bond

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6 Feb 2017

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Lecture 2: Chemical Foundations of Life
The scientific explanation for the origin of life is called chemical evolution:
-In addition to small molecules, complex carbon-containing substances exist and are required
for life (pattern)
-Earl i Earth’s history, simple chemical compounds combined to form more complex carbon
containing substances before the evolution of life (process)
The theory maintains that inputs of energy led to the formation of increasingly complex substances,
culminating in a compound that could replicate itself switch from chemical evolution to biological
Four types of atoms that make up 96% of all matter found in organisms: hydrogen, carbon, nitrogen,
and oxygen
Earl i Earth’s histor, these eleets ol eisted i simple substances (water and carbon dioxide)
To understand how a molecule affects your body or the role it played in chemical evolution you must
understand its structure
Structure of an atom:
-Atomic number is the number of protons (in order on the periodic table)
-Most of a ato’s olue is ept spae
-Mass number is the sum of the protons and neutrons
-Number of protons in an element does not vary but neutrons an vary (isotopes)
-Isotopes have different masses but are the same element
-The atomic weight of an element is an average of all the mass numbers of the naturally
occurring isotopes based on their abundance
-Radioactive isotopes eventually decay and release energy specific to each radioisotope
-Masses of p/n/e are so small that the unit is called the Dalton
-Isotopes of carbon can be written as 12C and 13C
-Electrons move around atomic nuclei in specific regions called orbitals
-Orbitals are grouped into levels called electron shells (1,2,3,4, etc.)
-An atom is most stable when its valence shell is filled
Unfilled valence electrons can be filled by bonds (covalent, hydrogen, ionic)
Covalent Bonds:
-A strong attraction where two atoms share one or more pairs of elections is called a covalent
bond (fills the outer shell = more stable)
-Substances held together by covalent bonds are called molecules
-Like charges repel while opposite charges attract covalent bonds form when the attractive
forces overcome the repulsive forces
-Electrons participating in a covalent bond are not always shared equally between atoms
involved. This happens because some atoms hold the electrons in covalent bonds much more
tightly than do other atoms (electronegativity)
-Ice cream cone: electronegativity (except the noble gases)
A highly electronegative atom in a molecule holds electrons more tightly and has a partial negative
Nonpolar Covalent Bonds (atoms have no charge):
-Electrons that are shared equally or symmetric (approx. equal electronegativity)
-C-H bond
Polar Covalent Bonds (atoms have partial charge):
-Asymmetric sharing of electrons
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-Spend most of their time close to the nucleus of the more electronegative atom
-H2O has two polar covalent bonds one between oxygen and both hydrogen; they spend more
time near the oxygen atom (partial negative) and less near the hydrogen (partial positive)
-Partial harges are solized  δ
Ionic Bonds:
-Electrons from one atom are completely transferred to another
-This transfer occurs because it gives the resulting atoms a full outermost shell
-Net electric charge = proton to electron ratio
Ions and Electric-Sharing Continuum:
-An atom or molecule that carries a full charge, rather than the partial charges that arise from
polar covalent, is called an ion (hydrophilic)
-Na and other positively charges ions are called a cation
-Cl and other negatively charged ions are called anion
-The degree to which electrons are shared in chemical bonds forms a continuum from equal
sharing in nonpolar covalent bonds to unequal sharing in polar covalent bonds to the transfer of
electrons in ionic bonds
Each unpaired electron in a valence shell can make up half of a covalent bond (N=3, H=1, O=2)
Methane is formed with the unpaired H and C atoms most common molecule found in natural gas
Triple bonds result when three pairs of electrons are shared like N2
Geometry of Simple Molecules:
-The overall shape of a molecule dictates how it behaves (function based on structure)
-There are simple, linear molecules like CO2 or complex geometries like CH4
-Structural formulas indicate which atoms in a molecule are bonded together
-Single, double, & triple bonds are represented by number of dashes between each element
-Ball and stick models provide a three-dimensional shape of molecules
-Space-filling models depict the spatial relationship between atoms
Properties of Water:
-Water is an excellent solvent: agent for dissolving substances and getting them into solution
-Substances are most likely to come into contact with one another and react as solutes
-Both O-H bonds in a water molecule are polar (difference in electronegativity)
-The molecule is bent giving the molecule an overall polarity
-Small size which allows it to interact with other elements easily
-When two water molecules approach each other, the partial positive charge on hydrogen
attracts the partial negative charge on oxygen. This weak electrical attraction forms a hydrogen
bond between molecules
-In an aqueous solution, hydrogen bonds also form between water molecules and other polar
-Hdrophili: Ios ad polar oleules sta i solutio eause of their iteratios ith ater’s
partial charges. Hydrogen bonding allows for almost any charged/polar molecule to dissolve in
-Hydrophobic: Compounds that are uncharged and nonpolar do not interact with water through
hydrogen bonding. Thus, these nonpolar molecules are forced to interact with each other while
the surrounding water molecules form hydrogen bonds with one another and increase their
Hydrogen Bonds
-A H atom is bound to a highly electronegative atom (attraction between two polar molecules)
-Weaker than covalent and ionic bonds
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