The Chemical Foundations of

Life

 Element vs. molecule

Ionic bond vs. covalent bond
Polar vs. nonpolar
Hydrogen bond vs. van der Waals force
Hydrophilic vs. hydrophobic vs. amphipathic
Water cohesion vs. adhesion
solvent vs. solute
acid vs. base vs. buffer

The Chemical Foundations of Life

Here we can see the nucleus with protons and neutrons.
Protones

Neutrones

1/10000

Electrones

Electrons can be seen (much larger than they should

be) orbiting around the nucleus.

18 electrons

Figure 2.7 Energy levels of an atoms electrons

(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons,
because the ball can only rest
on each step, not between
steps.
Third energy level (shell)

Second energy level (shell)

Energy
absorbed

First energy level (shell)

Energy
lost
Atomic
nucleus
(b) An electron can move from one level to another only if the energy
it gains or loses is exactly equal to the difference in energy between
the two levels. Arrows indicate some of the step-wise changes in
potential energy that are possible.
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 2.8 Electron-shell diagrams of the first 18

elements in the periodic table
Hydrogen
1H

Atomic mass

2
He
4.00

First
shell

Atomic number

Helium
2He

Element symbol

Electron-shell
diagram
Lithium
3Li

Beryllium
4Be

Sodium
11Na

Magnesium
12Mg

Boron
3B

Carbon
6C

Nitrogen
7N

Silicon
14Si

Phosphorus
15P

Oxygen
8O

Fluorine
9F

Neon
10Ne

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

Second
shell

Aluminum
13Al

Third
shell

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 2.9 Electron orbitals

Electron orbitals.
Each orbital holds
up to two electrons.

1s orbital

2s orbital

Three 2p orbitals

1s, 2s, and 2p orbitals

Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.

(a) First shell

(maximum
2 electrons)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

(b) Second shell

(maximum
8 electrons)

(c) Neon, with two filled shells

(10 electrons)

 Element vs. molecule

Ionic bond vs. covalent bond
Polar vs. nonpolar
Hydrogen bond vs. van der Waals force
Hydrophilic vs. hydrophobic vs. amphipathic
Water cohesion vs. adhesion
solvent vs. solute
acid vs. base vs. buffer

Figure 2.10 Formation of a covalent bond

Hydrogen atoms (2 H)

In each hydrogen
atom, the single electron
is held in its orbital by
its attraction to the
proton in the nucleus.

2 When two hydrogen

atoms approach each
other, the electron of
each atom is also
attracted to the proton
in the other nucleus.

3 The two electrons

become shared in a
covalent bond,
forming an H2
molecule.

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Hydrogen
molecule (H2)

Figure 2.8 Electron-shell diagrams of the first 18

elements in the periodic table
Hydrogen
1H

Atomic mass

2
He
4.00

First
shell

Atomic number

Helium
2He

Element symbol

Electron-shell
diagram
Lithium
3Li

Beryllium
4Be

Sodium
11Na

Magnesium
12Mg

Boron
3B

Carbon
6C

Nitrogen
7N

Silicon
14Si

Phosphorus
15P

Oxygen
8O

Fluorine
9F

Neon
10Ne

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

Second
shell

Aluminum
13Al

Third
shell

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

electronegativity

 Element vs. molecule

Ionic bond vs. covalent bond
Polar vs. nonpolar
Hydrogen bond vs. van der Waals force
Hydrophilic vs. hydrophobic vs. amphipathic
Water cohesion vs. adhesion
solvent vs. solute
acid vs. base vs. buffer

Figure 2.8 Electron-shell diagrams of the first 18

elements in the periodic table
Hydrogen
1H

Atomic mass

2
He
4.00

First
shell

Atomic number

Helium
2He

Element symbol

Electron-shell
diagram
Lithium
3Li

Beryllium
4Be

Sodium
11Na

Magnesium
12Mg

Boron
3B

Carbon
6C

Nitrogen
7N

Silicon
14Si

Phosphorus
15P

Oxygen
8O

Fluorine
9F

Neon
10Ne

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

Second
shell

Aluminum
13Al

Third
shell

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 2.13 Electron transfer and ionic bonding

1 The lone valence electron of a sodium

2 Each resulting ion has a completed

atom is transferred to join the 7 valence

electrons of a chlorine atom.

valence shell. An ionic bond can form

between the oppositely charged ions.

Na

Na
Sodium atom
(an uncharged
atom)

Cl

Cl
Chlorine atom
(an uncharged
atom)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Na

Cl

Na+
Sodium ion
(a cation)

Cl
Chloride ion
(an anion)

Sodium chloride (NaCl)

Figure 2.14 A sodium chloride crystal

Na+
Cl

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Weak Chemical Bonds

Hydrogen bonds
Van der Waals interactions
Ionic interactions
Hydrophobic interactions

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 2.15 A hydrogen bond

+
H

Water
(H2O)

H
+

Ammonia
(NH3)

N
H

H
+

H
+

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

A hydrogen
bond results
from the
attraction
between the
partial positive
charge on the
hydrogen atom
of water and
the partial
negative charge
on the nitrogen
atom of
ammonia.

Unnumbered Figure p. 42

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Space-filling
model

Ball-and-stick
model

Hybrid-orbital model
(with ball-and-stick
model superimposed)
Unbonded
Electron pair

H
Water (H2O)

104.5

H
Methane (CH4)

H
H

(b) Molecular shape models. Three models representing molecular shape are
shown for two examples; water and methane. The positions of the hybrid
orbital determine the shapes of the molecules
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 2.17 A molecular mimic

Carbon

Nitrogen

Hydrogen

Sulfur
Oxygen

Natural
endorphin

Morphine

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

Natural
endorphin

Brain cell

Morphine

Endorphin
receptors

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Unnumbered pg. 44

2 H2

O2

Reactants

Chemical Equilibrium
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

2 H2O

Reaction

Products

 Element vs. molecule

Ionic bond vs. covalent bond
Polar vs. nonpolar
Hydrogen bond vs. van der Waals force
Hydrophilic vs. hydrophobic vs. amphipathic
Water cohesion vs. adhesion
solvent vs. solute
acid vs. base vs. buffer

 Element vs. molecule

Ionic bond vs. covalent bond
Polar vs. nonpolar
Hydrogen bond vs. van der Waals force
Hydrophilic vs. hydrophobic vs. amphipathic
Water cohesion vs. adhesion
solvent vs. solute
acid vs. base vs. buffer

The Chemical Foundations of Life

So there is an
attraction between
the positive and
negative sides of
a water molecule
this is hydrogen
bonding.
Figure 22-12

Copyright

2001 by Harcourt, Inc.

Figure 3.3 Water transport in plants

Water conducting cells

100 m
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 3.4 Walking on water

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 3.5 Ice: crystalline structure and floating barrier

Hydrogen
bond
Ice

Liquid water

Hydrogen bonds are stable

Hydrogen bonds
constantly break and re-form

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

OH + H3O+
H2O + H2O
hydroxide
ion
H2O H+ + OH
hydrogen
ion or proton
Chemical Equilibrium
pH log [H+] acidic pH < 7
basic pH > 7

The Chemical Foundations of Life

The pH scale is the log10 of the hydrogen
ion concentration in a solution.
Water is considered a reference or neutral point
with a pH of 7.0.

Figure 2-20

Buffer
CO2 + H2O H2CO3 H+ + HCO3
Carbon dioxide
ion

carbonic acid

bicarbonate

 Element vs. molecule

Ionic bond vs. covalent bond
Polar vs. nonpolar
Hydrogen bond vs. van der Waals force
Hydrophilic vs. hydrophobic vs. amphipathic
Water cohesion vs. adhesion
solvent vs. solute
acid vs. base vs. buffer

Carbon- the Backbone of

Biological Molecules

Biological Molecules Small and Large

The hydrocarbon skeleton provides a basic
framework:

Figure 3-3

Saturated vs. unsaturated

Figure 4.5 Variations in carbon skeletons

H H

H H H

H C C H
H H

H C C C H
H H H

Ethane

Propane

H H H H

H
H C H
H
H

H C C C C H
H H H H

H C C C H
H H H

(a) Length

(b) Branching

Butane
(c) Double bonds

H H H H

H H H H

H C C C C H
H H

H C C C C H
H
H

1-Butene

(d) Rings

H
H
H
H

2-methylpropane
(commonly called isobutane)

H
H
H
C
C
C H
C
C H
H
C
H
H

Cyclohexane
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

2-Butene
H

C
H
C
C
H CC C H
H

Benzene

Figure 4.7 Three types of isomers

H
H C H
H H H

(a) Structural isomers

H C C C C C
H

H C C C
H H H

H H H H
X

(b) Geometric isomers

C C
X

C C

(c) Enantiomers

H C H
H
H

H H

CO2H

CO2H

CH3

L isomer
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

NH2 NH2

CH3

D isomer

Figure 4.8 The pharmacological importance of enantiomers

L-Dopa

D-Dopa

(effective against
Parkinsons disease)

(biologically
inactive)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Figure 4.9 A comparison of functional groups of female

(estradiol) and male (testosterone) sex hormones

Estradiol

OH
CH3

HO

Female lion
OH
CH3
CH3

Male lion
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Testosterone

Functional Groups
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group

R-OH
O
R-C-H (or R)
O
R-C
OH
R-N
R-SH

Hydroxyl group

O
R-O-P-O
O