BIO 3A Fall 2015
Chapters 2,3 And 4
Chapter 2 Chemical Context
Figure 2.1
EXPERIMENT
Cedrela
sapling
Insect
barrier
Duroia
tree
Inside,
unprotected
Devil’s
garden
Outside,
protected
Inside,
protected
Outside,
unprotected
RESULTS
Dead leaf tissue (cm2)
after one day
Figure 2.2
16
12
8
4
0
Outside,
Inside,
Inside,
Outside,
unprotected protected unprotected protected
Cedrela saplings, inside and outside devil’s gardens
Figure 2.2a
EXPERIMENT
Insect
barrier
Cedrela
sapling
Duroia
tree
Inside,
unprotected
Devil’s
garden
Outside,
protected
Inside,
protected
Outside,
unprotected
Figure 2.2b
Dead leaf tissue (cm2)
after one day
RESULTS
16
12
8
4
0
Inside,
Outside,
Inside,
unprotected protected unprotected
Outside,
protected
Cedrela saplings, inside and outside devil’s gardens
Figure 2.3
Sodium
Chlorine
Sodium chloride
Table 2.1
Figure 2.5
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
(a)
(b)
Figure 2.8
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons.
Third shell (highest energy
level in this model)
Second shell (higher
energy level)
First shell (lowest energy
level)
(b)
Atomic
nucleus
Energy
absorbed
Energy
lost
Figure 2.9
Hydrogen
1H
Mass number
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electron
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Sodium Magnesium Aluminum
11Na
12Mg
13Al
Third
shell
Figure 2.10
First shell
Neon, with two filled
Shells (10 electrons)
Second shell
(a) Electron distribution diagram
First shell
Second shell
y
x
1s orbital
2s orbital
z
Three 2p orbitals
(b) Separate electron orbitals
1s, 2s, and
2p orbitals
(c) Superimposed electron orbitals
Figure 2.11-3
Hydrogen atoms (2 H)
Hydrogen molecule (H2)
Figure 2.12
Name and
Molecular
Formula
(a) Hydrogen (H2)
(b) Oxygen (O2)
(c) Water (H2O)
(d) Methane (CH4)
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
SpaceFilling
Model
Figure 2.13
–
O
+
H
H
H2O
+
Figure 2.14-2
Na
Sodium atom
Cl
Chlorine atom
+
–
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
Figure 2.15
Na+
Cl–
Figure 2.16
+
–
Water (H2O)
+
Hydrogen bond
–
Ammonia (NH3)
+
+
+
Figure 2.UN01
Figure 2.18
Carbon
Hydrogen
Natural endorphin
Nitrogen
Sulfur
Oxygen
Morphine
(a) Structures of endorphin and morphine
Natural
endorphin
Brain cell
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors
Chapter 3 starts about here
Water and Life
Figure 3.1
Figure 3.2

Hydrogen
bond
+
+
Polar covalent
bonds


+
+

Figure 3.3
Adhesion
Two types of
water-conducting
cells
Cohesion
Direction
of water
movement
300 m
Figure 3.4
Figure 3.5
Los Angeles
(Airport) 75°
70s (°F)
80s
San Bernardino
100°
Riverside 96°
Santa Ana
Palm Springs
84°
106°
Burbank
90°
Santa Barbara 73°
Pacific Ocean 68°
90s
100s
San Diego 72°
40 miles
Figure 3.6
Hydrogen bond
Ice:
Hydrogen bonds
are stable
Liquid water:
Hydrogen bonds
break and re-form
Figure 3.7

Na




Na

Cl



Cl










Figure 3.8
+


+
Figure 3.9
Figure 3.UN02
+
2 H 2O
Hydronium
ion (H3O+)

Hydroxide
ion (OH)
Figure 3.10
H+
H+
 H+
H+ OH
+

OH H H+
+
H H+
Acidic
solution
Increasingly Acidic
[H+] > [OH]
pH Scale
0
1
Battery acid
2
Gastric juice, lemon juice
3
Vinegar, wine,
cola
4
Tomato juice
Beer
Black coffee
5
6
Neutral
solution
OH
OH
OH H+ OH

OH OH
OH
+
H
Basic
solution
Neutral
[H+] = [OH]
7
8
Increasingly Basic
[H+] < [OH]
OH
OH
H+ H+ OH

OH OH +
H+ H+ H
Rainwater
Urine
Saliva
Pure water
Human blood, tears
Seawater
Inside of small intestine
9
10
Milk of magnesia
11
Household ammonia
12
13
Household
bleach
Oven cleaner
14
Figure 3.11
CO2
CO2 + H2O
H2CO3
H2CO3
H+ + HCO3
H+ + CO32
CO32 + Ca2+
HCO3
CaCO3
Chapter 4 Starts about here
Carbon Chemistry
Figure 4.1
Figure 4.2
EXPERIMENT
“Atmosphere”
Water vapor
CH4
Electrode
Condenser
Cooled “rain”
containing
organic
molecules
H2O
“sea”
Sample for chemical analysis
Cold
water
Figure 4.3
Name and
Comment
Molecular
Formula
(a) Methane
CH4
(b) Ethane
C2H6
(c) Ethene
(ethylene)
C2H4
Structural
Formula
Ball-andStick Model
Space-Filling
Model
Figure 4.4
Hydrogen
(valence  1)
Oxygen
(valence  2)
Nitrogen
(valence  3)
Carbon
(valence  4)
Figure 4.UN01
Urea
Figure 4.5
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
Figure 4.6
Nucleus
Fat droplets
10 m
(a) Part of a human adipose cell
(b) A fat molecule
Figure 4.7
(a) Structural isomers
(b) Cis-trans isomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
(c) Enantiomers
CO2H
CO2H
H
NH2
CH3
L isomer
NH2
H
CH3
D isomer
Figure 4.8
Drug
Ibuprofen
Albuterol
Condition
Effective
Enantiomer
Ineffective
Enantiomer
Pain;
inflammation
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Asthma
Figure 4.UN02
Estradiol
Testosterone
Figure 4.9_a
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
NAME OF
COMPOUND
Alcohols (Their specific names
usually end in -ol.)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic acids
Aldehydes if the carbonyl group
is at the end of the carbon skeleton
EXAMPLE
Ethanol
Acetone
Acetic acid
Propanal
FUNCTIONAL
PROPERTIES
• Is polar as a result of the
electrons spending more time
near the electronegative oxygen
atom.
• Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds such as
sugars.
• A ketone and an aldehyde may be
structural isomers with different
properties, as is the case for
acetone and propanal.
• Ketone and aldehyde groups are
also found in sugars, giving rise
to two major groups of sugars:
ketoses (containing ketone
groups) and aldoses (containing
aldehyde groups).
• Acts as an acid; can donate an
H+ because the covalent bond
between oxygen and hydrogen
is so polar:
Nonionized
Ionized
• Found in cells in the ionized form
with a charge of 1 and called a
carboxylate ion.
Figure 4.9_b
Amino
Sulfhydryl
Phosphate
Methyl
(may be
written HS—)
Amines
Organic phosphates
Thiols
Cysteine
Glycine
• Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Nonionized
Ionized
• Found in cells in the
ionized form with a
charge of 1+.
Glycerol phosphate
• Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
• Contributes negative charge to
the molecule of which it is a part
(2– when at the end of a molecule,
as above; 1– when located
internally in a chain of
phosphates).
• Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
• Molecules containing phosphate
groups have the potential to react
with water, releasing energy.
Methylated compounds
5-Methyl cytidine
• Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.