II. Propert ies of Water
1.
2.
3.
4.
5.
Ice and Liquid water structure
Cohesion / Surface Tension
High Heat Capacity
Solvent Properties
Dissociation: Acids & Bases / pH
II. Organic Chemistry
A. Hydrocar bons--nonpolar
1. alkanes-only single bonds
2. alkenes- C=C double bonds
3. aromatic-cyclic based on benzene
B. Funct ional Groups: alcohol, aldehyde, ketone, carboxyl, amine,
organophosphate, sulfhydral
1. polar bonds between C and more electronegative atoms (O and N)
2. Combine two functional groups ester = alcohol + acid
3. amide = amine + acid
C. Isomers
1. Same chemical formula but differ in arrangement of atoms in space
2. Enantiomers (Optical Isomers): C can be bonded to 4 different groups
in 2 ways producing molecules that are mirror images of one another
that cannot be superimposed
Water As A Solvent For Life
75% of the Earth’s
surface is covered
with water
Water is essential for life on Earth
All living organisms require water more than
any other substance
Fig. 3.2:
Water: Structure and Properties
Hydrogen bond
acceptors
104.5°
Hydrogen bond
donors
Water’s molecular structure and capacity to donate
and accept hydrogen bonds give it unusual critical
properties that are significant for life
Five Critical Properties of Water
1. Ice and liquid water structure
Fig. 3.6:
Hydrogen
bond
Ice
Hydrogen bonds are stable
Temperature ≤ 0°C
Liquid water
Hydrogen bonds break and re-form
Temperature > 0°C < 100°C
• Ice is less dense than liquid water
• Water is liquid at a relatively high temperature > 0°C
(Methane (CH4) is similar in size but liquid only below -161°C)
Fig. 3.3/3.4:
Five Critical Properties of Water – 2. Cohesion
Hydrogen bonds
hold water molecules
together in liquid
High Surface tension
Water transport
in plants
Fig. 3.4
Five Critical Properties of Water
3. Moderation of temperature
Heat energy can be absorbed by
breaking hydrogen bonds
Water has a high specific heat capacity
specific heat capacity = amount of energy required to raise
temperature of 1 g of water by 1°C (1 calorie, 1 cal)
 Large bodies of water stabilize the air temperature.
Fig. 2.15/3.7:
Five Critical Properties of Water
4.Water as a solvent
A sphere of water
molecules,
called a hydration
shell, surrounds
each solute ion
Fig. 2.15
Fig. 3.7
Five Critical Properties of Water
4. Water as a solvent (Cont’d)
Fig. 3.8:
Fig. 3.8
(a) Lysozyme molecule in a
nonaqueous environment
(b) Lysozyme molecule (purple) in an aqueous
environment
(c) Ionic and polar regions
on the protein’s surface
attract water molecules.
Review solute concentration in aqueous solutions (Molarity)
(page 51 – 52 of text)
Five Critical Properties of Water
4. Water as a solvent (Cont’d)
OH(hydroxide ion)
Page 53
H3O+
(hydronium ion)
This reaction is frequently abbreviated as:
H 2O
H+
OH
+
The KW is the ion product of water,
Kw = [H+][OH-] = 1.0 x 10-14 M2 at 25°C
Thus, in pure water, [H+] = [OH-] = 1.0 x 10-7 M
pH SCALE - 1.0 x 10-7 M is a very small number and
can change by orders of magnitude (powers of 10x)  pH
Fig. 3.9:
pH = -log[H+] = 7
in pure water at 25°C = neutral pH
“Physiological pH”
(pH 6.5 – 8.0)
O
CH3-C
NH3
O
CH3-C
OH
+
H+
O-
NH4+
+
H+
CH3COOH
CH3COO- + H+
NH4+
NH3
+ H+
HA
A-
+ H+
Acid ionization constant, Ka =
[H+][A-]
[HA]
Ka
pKa
1.8 x 10-5 M
4.7
5.8 x 10-10 M
9.2
pKa = -log Ka
pKa is a measure of propensity to dissociate:
if pH < pKa the HA form predominates
if pH > pKa the A- form predominates
[HA] >> [A-]
[HA] = [A-]
Buffers keep pH relatively
constant in the range
around pKa value by
accepting or donating H+
from solution
[A-] >> [HA]
O
CH3-C
OH
Response to decrease [H+]
Response to increase [H+]
O
CH3-C
O-
Organic Chemistry
The chemistry of molecules containing
carbon bonded to other elements,
principally: H, O, N, P, S …
Hydrocarbons are Nonpolar (electrons are equally
distributed) and do not mix freely with water
 they are Hydrophobic.
109°
120°
Fig. 4-3
Fig. 4.3: The
Name and
Comment
Shapes of Three Simple Organic Molecules
Molecular
Formula
(a) Methane
CH4
(b) Ethane
C 2H 6
(c) Ethene
(ethylene)
C 2H 4
Structural
Formula
Ball-andStick Model
Space-Filling
Model
Hydrocarbons -- organic compounds containing only
carbon and hydrogen. These are the most reduced organic
compounds and react vigorously (i.e. burn) with oxygen.
CH4 + 2O2
CO2 + 2H2O +
+
+
2
Methane
(natural gas)
Heat
Oxygen
+
2
Carbon
Dioxide
Water
Heat
Fig. 4.5: Various
Hydrocarbons
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
HHHHHHHH
H-C-C-C-C-C-C-C-C-H
HHHH HHHH
Octane C8H18: A major component of gasoline. Aromatic Hydrocarbons -- are a special class of hydrocarbons in which
atoms are arranged in a ring structure and are connected by σ-bonds and a
system of π-bonds around the ring. The simplest example is benzene,
C6H6, and as shown below all atoms lie on a plane with bond angles of 120°
120°
Fig. 4.4:
Carbon also forms bonds with a variety of other
Elements
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
H
O
N
C
Carbon dioxide
(CO2)
O
C
O
Urea
CO(NH2)
Urea
Functional Groups
Here “R” represents the rest of the molecule
Carbonyls
R–OH
Alcohol
R–C
O
H
Aldehyde
Ethanol
R–C
O
R’
Ketone
R–C
O
OH
Carboxylic Acid
Acetone
O
R–NH2
Amine
R–SH
R–O–P–OH
OH
Sulfhydral Organic Phosphate
Acetic Acid
Fig. 5.2a: The
Fig. 5-2a
Synthesis of Polymers
(a) Dehydration reaction: synthesizing a polymer
1
2
3
Unlinked monomer
Short polymer
Dehydration removes
a water molecule,
forming a new bond.
1
2
3
Longer polymer
4
Linking Functional Groups
Polymers
Organic molecules with certain functional groups can be joined by a
covalent bond formed when a molecule of water is removed; this allows
the creation of new types of organic molecules.
Ester
R–C
O
OH + HO–R’
R–C
O
+ H2O
O-R’
Amide
R–C
O
OH + H
H
O
R-OH + HO-P-OH
O-
R–C
N-R’
O
N-R’
H
O
R-O-P-OH + H2O
O-
+ H2O
Fig. 4.6: Ester
bonds link fatty acid carboxyl groups to
OH- groups of Glycerol
Nucleus
Fat droplets
10 µm
(a) Part of a human adipose cell
(b) A fat molecule
a.k.a. Triglyceride
Isomers: Molecules that have the same chemical formula,
i.e. the same number of each of the different kinds of atoms.
Fig. 4.7: There
are different classes of Isomers
cis isomer: The two X’s
are on the same side.
L isomer
trans isomer: The two X’s
are on opposite sides.
D isomer
Fig. 4.8: Pharmacological
Importance of Enantiomers
Drug
Condition
Effective
Enantiomer
Ineffective
Enantiomer
Ibuprofen
Pain;
inflammation
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Fig. 4-8
Albuterol
Asthma
Thalidomide was first used as a sedative and anti-nausea medication, but
was found to cause serious birth defects when pregnant women take it
during their first trimester.