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CHEMISTRY REVIEW NOTES
LEWIS DOT STRUCTURES
# of electrons (e-) needed to fill valence level = # of bonds (each bond is the equivalent of
gaining 1 e-)
Most common 4 elements in organic/biological molecules:
C – makes 4 covalent bonds; N makes 3 covalent bonds (N+ will make 4) ;
O makes 2 covalent bonds (O- makes 1 covalent bond); H makes 1 covalent bond
Other common elements: P makes 5 bonds, S makes 2 bonds,
Ca and Mg form +2 ions and makes ionic bond; K and Na form +1 ions and makes ionic
bonds
ORGANIC CHEMISTRY
FUNCTIONAL GROUPS- structural components of hydrocarbon molecules which are
most commonly involved in chemical reactions. Memorize functional groups below:
See pp. 64 & 65 in Campbell’s.
Note: R represents a hydrocarbon chain.
FUNCTIONAL GROUP
FORMULA
NAME
EXAMPLE
Hydroxyl
R -OH
Alcohol
Ethanol
Notes: OH is polar; can form H-bonds and act as nucleophile
Carbonyl
R-C–H
Aldehyde
R - C – R’
Ketones
Formaldehyde
Acetone
Notes: CO group is polar, can act as H-bond acceptor and act as electrophile
R - C-OH R - C –OCarboxylic Acid
Acetic Acid
(neutral)
(ionized)
Notes: - COOH is polar, can act as an acid (H+ donor), - COO- is resonance stabilized
Carboxyl
Amino
- NH2
- NH3+
amines
Glycine (amino acid)
(neutral)
(ionized)
Notes: -NH2 is polar, can act as base (H+) acceptor, nonbonding pair on N attract H+
Sulfhydryl
-SH
Thiols
ethanethiol
Notes: S-H moderately polar, S is good nucleophile, S-H and S-H can form S-S bond
Methyl
CH3
5 – methyl cytidine
Notes: Nonpolar, addition of methyl to DNA or molecules bound to DNA can affect gene
expression
Phosphate
-O–P–O
Organic phosphates
Glycerol phosphate
Notes: Ionized at neutral pH; phosphate groups are good “leaving groups” ; often
involved in energy transfer reactions
VSEPR – PREDICTING 3-DIMENSIONAL SHAPES
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Biological Activity of molecule is determined by both chemical behavior and 3-D
shape of molecule
VSEPR (Valence Shell Electron Pair Repulsion Theory) – predict 3-D shape by
predicting how bonding and nonbonding electron pairs will arrange themselves
around central atom to minimize electrostatic repulsion
Double and Triple bonds count as single bonding region
Important Geometries for common important biochemical molecules
Bonding Nonbonding Geometry
Pairs
Pairs
2
0
linear
3
0
Trigonal
planar
4
0
tetrahedral
3
1
Trigonal
pyramidal
2
2
bent
ISOMERS- Compounds with the same molecular formula, but different structures and
therefore different properties. 3 types of isomers:
 Structural isomers – different covalent arrangements (different connection
pattern) Example:
n- butane
isobutane
 Geometric isomers – variation in arrangement in space about a double bond
Example:
Cis – dichloroethene
Trans-dichloroethene
Key point: Rotation is impossible around a double bond. (Would require breaking pi
bond)
 Enantiomers (chiral molecules) – variation in arrangment in space around an
asymmetric carbon (C is bonded to 4 different groups).
- molecules are not identical (cannot be superimposed on each other) ; mirror
images.
Example: CHBrClOH has 2 forms:
DIPOLE MOMENTS
Dipole – a molecule in which one side of the molecule is partially positive and the other
end is partially negative; (caused by asymmetric distribution of electron density)
Steps for determining a dipole moment:
1) Determine 3-D structure
2) Look for polar bonds (electronegativity difference between bonded atoms)
3) Sum up polar bonds to determine net dipole (if symmetric = polar bonds cancel)
to indicate overall dipole. Arrow always points to towards ∂-
4) Use
INTERMOLECULAR FORCES
 Weak forces of attraction between molecules (much weaker than covalent or ionic
bonds
Important Note: Macromolecules like proteins, DNA, and carbohydrate polymers
are so long that different parts of the chains can interact with itself via
“intermolecular” forces (i.e. these forces can be intramolecular for large
molecules)

3 Intermolecular forces – Hydrogen bonding, dipole-dipole, London Dispersion
Forces (also known as Van Der Waals) forces
Dipole-dipole attraction – weak electrostatic attraction between two molecules
which have net dipole moments. The molecules line up with the partial positive end of
one molecules next to the partial negative end of the second molecule.
Example:
Hydrogen Bonds- an especially strong dipole-dipole attraction involving a hydrogen
bridging two very electronegative atoms.
Requirements for H-bonding:.
1) H-bond donor- H covalently bonded to F,O,N ( H-F, H-O, H-N) AND
2) H-bond acceptor F,O,N with nonbonding pair of e- available
Strength of attraction between + and – charges depends on:
1) Size of + and – charge: H-X, where X = F,O,N ; X is very electronegative => very
polar bond => large partial + (∂+) and – (∂-)
2) Distance between charges: (H, F, O, N are all small atoms => allows for close
approach)
H-bonds are very important in biological interactions which two molecules to specifically
recognize each other.
Specificity – requirement that partial + surface aligns with partial – surface requires
specific alignment of molecules
Examples: Connection between DNA strands (base pairing), Enzyme-substrate
interactions, Receptor/ligand interactions
Bond strength- H-bonds are strong enough to hold molecules near each other but don’t
require large amounts of energy to break when molecules need to separate
London Dispersion Forces – “ instantaneous” dipole attraction that occurs between 2
nonpolar molecules
- Generally weakest of intermolecular attractions- strength is very dependent on size of
electron cloud.
Other Intermolecular/ Intramolecular bonding important in biochemistry:
Salt Bridge - ionic bond between parts of molecule with full + and – charges
Ion-dipole – electrostatic attraction between a full + or – and a partially charged (dipole)
region
Hydrophobic interaction – term used to describe the observation that nonpolar
molecules tend to aggregate together in water
Important Properties of Water
1)
2)
3)
4)
5)
polarity and ability to form Hydrogen bonds
excellent solvent for polar substances; poor solvent for nonpolar
cohesion and adhesion
Relatively high specific heat capacity
Transparent to light