ii. properties of watersci.sdsu.edu/tfrey/biology203/ch3-4water&o-chem.pdf · water has a high...
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II. Propert ies of Water
1. Ice and Liquid water structure
2. Cohesion / Surface Tension
3. High Heat Capacity
4. Solvent Properties
5. 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
Water is essential for life on Earth
All living organisms require water more than any other substance
75% of the Earth’s surface is covered
with water
104.5°
Fig. 3.2: Water: Structure and Properties
Water’s molecular structure and capacity to donate and accept hydrogen bonds give it unusual critical
properties that are significant for life
Hydrogen bond acceptors
Hydrogen bond donors
Fig. 3.6: Five Critical Properties of Water 1. Ice and liquid water structure
Temperature ≤ 0°C 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)
Hydrogen bond Liquid water
Hydrogen bonds break and re-form Ice
Hydrogen bonds are stable
Hydrogen bonds hold water molecules
together in liquid
High Surface tension
Fig. 3.4
Fig. 3.3/3.4: Five Critical Properties of Water – 2. Cohesion
Water transport in plants
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.
Heat energy can be absorbed by breaking hydrogen bonds
Five Critical Properties of Water 3. Moderation of temperature
Fig. 2.15 Fig. 3.7
A sphere of water molecules,
called a hydration shell, surrounds each solute ion
Fig. 2.15/3.7: Five Critical Properties of Water 4.Water as a solvent
Fig. 3.8
Review solute concentration in aqueous solutions (Molarity) (page 51 – 52 of text)
Fig. 3.8: Five Critical Properties of Water 4. Water as a solvent (Cont’d)
(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.
Five Critical Properties of Water 4. Water as a solvent (Cont’d)
This reaction is frequently abbreviated as:
H2O 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
Page 53
H3O+ (hydronium ion)
OH- (hydroxide ion)
Fig. 3.9: pH SCALE - 1.0 x 10-7 M is a very small number and can change by orders of magnitude (powers of 10x) pH
“Physiological pH” (pH 6.5 – 8.0)
pH = -log[H+] = 7 in pure water at 25°C = neutral pH
CH3-C O
O- CH3-C O
OH + H+
NH3 + H+ NH4+
CH3COOH CH3COO- + H+
NH4+ NH3 + H+
HA A- + H+
Acid ionization constant, Ka = [H+][A-] [HA]
pKa = -log Ka
Ka pKa 1.8 x 10-5 M 4.7
5.8 x 10-10 M 9.2
pKa is a measure of propensity to dissociate: if pH < pKa the HA form predominates if pH > pKa the A- form predominates
Buffers keep pH relatively constant in the range around pKa value by accepting or donating H+ from solution
Response to decrease [H+]
Response to increase [H+] CH3-C
O
O- CH3-C O
OH
[HA] >> [A-]
[A-] >> [HA]
[HA] = [A-]
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 Shapes of Three Simple Organic Molecules Name and Comment
Molecular Formula
(a) Methane
(b) Ethane
CH4
Ball-and- Stick Model
Space-Filling Model
(c) Ethene (ethylene)
C2H6
C2H4
Structural Formula
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 + Heat
Heat
2 2 Methane
(natural gas) Oxygen Carbon Dioxide Water
+ + +
Fig. 4.5: Various Hydrocarbons
Octane C8H18: A major component of gasoline.
(a) Length
Ethane 1-Butene
(c) Double bond position
2-Butene Propane
(b) Branching (d) Presence of rings
Butane 2-Methylpropane (isobutane)
Cyclohexane Benzene
H-C-C-C-C-C-C-C-C-H H H H H H H H H
H H H H H H H H
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
O C O
Carbon dioxide (CO2) Urea
CO(NH2)
Hydrogen (valence = 1)
Oxygen (valence = 2)
Nitrogen (valence = 3)
Carbon (valence = 4)
H O N C
Urea
Ethanol Acetone Acetic Acid
Functional Groups Here “R” represents the rest of the molecule
R–OH R–C H
O R–C
R’
O R–C
O
OH R–NH2 R–SH R–O–P–OH
O
OH Alcohol Aldehyde Ketone Carboxylic Acid Amine Sulfhydral Organic Phosphate
Carbonyls
Fig. 5-2a Fig. 5.2a: The Synthesis of Polymers
(a) Dehydration reaction: synthesizing a polymer
Short polymer Unlinked monomer
Dehydration removes a water molecule, forming a new bond.
Longer polymer
1 2 3 4
1 2 3
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.
R-OH + HO-P-OH O
O- R-O-P-OH + H2O
O
O-
Linking Functional Groups Polymers
R–C O
OH + HO–R’ R–C
O
OH N-R’ H
+ H
Ester Amide
R–C O
O-R’ + H2O R–C
O
N-R’ H
+ H2O
Fig. 4.6: Ester bonds link fatty acid carboxyl groups to OH- groups of Glycerol
Nucleus
Fat droplets
(b) A fat molecule a.k.a. Triglyceride
(a) Part of a human adipose cell
10 µm
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.
trans isomer: The two X’s are on opposite sides.
L isomer D isomer
Fig. 4-8 Fig. 4.8: Pharmacological Importance of Enantiomers
Drug
Ibuprofen
Albuterol
Condition Effective Enantiomer
Ineffective Enantiomer
Pain; inflammation
Asthma
S-Ibuprofen R-Ibuprofen
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.