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
Fig. 3.6: Five Critical Properties of Water
1. Ice and liquid water structure
Hydrogen
bond
Ice Liquid water
Hydrogen bonds are stable Hydrogen bonds break and re-form
Hydrogen bonds
hold water molecules
together in liquid
Water transport
Fig. 3.4
in plants
Five Critical Properties of Water
3. Moderation of temperature
A sphere of water
molecules,
called a hydration
shell, surrounds
each solute ion
Fig. 3.8
(a) Lysozyme molecule in a (b) Lysozyme molecule (purple) in an aqueous
environment
(c) Ionic and polar regions
on the protein’s surface
nonaqueous environment
attract water molecules.
OH -
H 2O H+ +
The KW is the ion product of water,
pH = -log[H+] = 7
in pure water at 25°C = neutral pH
“Physiological pH”
(pH 6.5 – 8.0)
O O
CH3-C CH3-C + H+
OH O-
NH3 + H+ NH4+
Ka pKa
CH3COOH CH3COO- + H+ 1.8 x 10-5 M 4.7
HA A- + H+
[H+][A-]
Acid ionization constant, Ka = pKa = -log Ka
[HA]
109°
120°
Fig. 4-3
Fig. 4.3: The Shapes of Three Simple Organic Molecules
Name and Molecular Structural Ball-and- Space-Filling
Comment Formula Formula Stick Model Model
(a) Methane
CH4
(b) Ethane
C 2H 6
(c) Ethene
(ethylene)
C 2H 4
Hydrocarbons -- organic compounds containing only
carbon and hydrogen. These are the most reduced organic
compounds and react vigorously (i.e. burn) with oxygen.
+ + + Heat
2 2
Methane Carbon
Oxygen Water
(natural gas) Dioxide
Fig. 4.5: Various Hydrocarbons
(a) Length (c) Double bond position
120°
Fig. 4.4: Carbon also forms bonds with a variety of other
Elements
Hydrogen Oxygen Nitrogen Carbon
(valence = 1) (valence = 2) (valence = 3) (valence = 4)
H O N C
Carbon dioxide
(CO2) Urea
CO(NH2)
O C O
Urea
Functional Groups
Here “R” represents the rest of the molecule
Carbonyls
O
O O O
R–OH R–C R–C R–C R–NH2 R–SH R–O–P–OH
H R’ OH OH
Alcohol Aldehyde Ketone Carboxylic Acid Amine Sulfhydral Organic Phosphate
1 2 3
Dehydration removes
a water molecule,
forming a new bond.
1 2 3 4
Longer polymer
Linking Functional Groups Polymers
O O O O
R–C R–C + H2O R–C R–C + H2O
OH + HO–R’ O-R’ OH + H N-R’
N-R’ H
H
O O
R-OH + HO-P-OH R-O-P-OH + H2O
O- O-
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 trans isomer: The two X’s
are on the same side. are on opposite sides.
L isomer D isomer
Fig. 4-8
Fig. 4.8: Pharmacological Importance of Enantiomers
Effective Ineffective
Drug Condition
Enantiomer Enantiomer
Ibuprofen Pain;
inflammation
S-Ibuprofen R-Ibuprofen
Albuterol Asthma
R-Albuterol S-Albuterol
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.