CHAPTER 2
THE CHEMICAL CONTEXT OF LIFE
ESLRS:
Core Learning
Critical Thinking
Communication
Community
STANDARDS:
Investigation & Experimentation: 1 a,b,c,d,j
Chemistry: 1 a,d,e; 2 a-h; 5 a-d; more…
Cell Biology: 1 b, f, g, & h
Figure 2.0 Bombardier beetle
This bomardier beetle illustrates the interdisciplinary
nature of scientific research... Focus today is CHEMISTRY
Matter- anything that takes
up space and has mass.
Element- substance that cannot
be broken down to other
substances by chemical
reactions.
92 elements exist in nature
LIFE REQUIRES 25
C, H, N, O - 96%
P, S, Ca, K - 4%
and trace elements
Table 2.1 Naturally Occurring Elements in the Human Body
What kinds of molecules will an
animal, plant, or bacterium take
up as necessary building blocks
and excrete as waste products?
What elements are these
molecules made of?
DISCUSS.
Water- solvent of life
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbon, Hydrogen, Nitrogen,
Oxygen, Phosphorus, Sulfur
Which elements are most
essential for life?
 96%:
 Carbon
 Hydrogen
 Oxygen
 Nitrogen
 The
other 4%?
 Phosphorus
 Sulfur
 Calcium
 Potassium
I. Elements essential to life
C
H
N
O
P
S
carbon
hydrogen
nitrogen
oxygen
phosphorus
sulfur
Ca
K
calcium
potassium
Enlarged thyroid gland

And trace elements…


I
iodine
Fe iron

specific to the species
Figure 2.4 Goiter
GoiterCaused by
iodine
deficiency.
Swollen thyroid
gland.
Hormones
thyroxine and
triiodotyronine
(T3)contain
Iodine.
Figure 2.3 Nitrogen deficiency
A. STRUCTURE OF ATOMS
Atomic structure determines the behavior of an atom.
Electron- negative charge
Proton- positive charge
Neutron- no charge
ATOM = the entire stadium
NUCLEUS = pencil eraser on the pitcher’s mound
ELECTRONS = gnats buzzing around stadium
Figure 2.11 Electron orbitals
Electron Orbitals are the three-dimensional space where
an electron is found 90% of the time.
No more than 2 electrons can occupy the same orbital.
You don’t need to remember this 1s, 2s, 2p etc. stuff for AP Bio
Figure 2.10 Electron configurations of the first 18 elements
2 electrons fit in the first energy shell
Outer shells can hold up to 8 electrons
This is the “octet rule”
Valence electrons are the outermost electronsthey determine the bonding behavior of the atom.
Atoms with unpaired electrons are reactive.
HONK!
Hydrogen - 1
 Oxygen - 2
 Nitrogen - 3
 Carbon - 4

What are the valences of the
“essential” elements?
This tells you how many bonds each needs to make.
PHOTON is a packet of radiation from the sun.
Electrons exist at fixed levels of potential energy called
electron shells. Outer shells have more energy. Electrons
can shift energy level by absorbing or releasing energy.
Ex.
Photons
of light
can cause
a quantum
leapelectrons
jump shells
Heat is released when the electrons fall back to the
lower energy level.
Isotopes have the same # of P & E
but a different # of neutrons.
In nature, an element occurs as a
mixture of its isotopes.
Radioactive isotopes




Are unstable.
The nucleus decays spontaneously, giving off particles
and energy.
When the decay changes the # of PROTONS, it
transforms the element.
Half-life is the length of time required for half of a
given number of initial number of atoms of that isotope
to be transformed to the decay element.
a) CAN BE USED TO DATE FOSSILS
 Radioactive Carbon 14 decays to Nitrogen 14 through
beta decay
half-life = 5730 years so used in archaeology to
determine the age of carbonaceous materials up to
60,000 years old.
 Uranium-238 decays to Lead…half-life = 4.5 billion
years… used to date OLD OLD fossils, like 1st cells.
b) CAN BE USED TO TRACE ATOMS
THROUGH METABOLISM
Radioactive tracers are important
diagnostic tools in medicine.
 Used to follow atoms through
metabolism, the chemical processes of an
organism

◦ ex. Old “breath” test for ulcers caused by
Heliobacter pylori used C14 labeled ureawhich will be converted to ammonia and
radioactive carbon dioxide.
◦ ex: kidney disorders can be detected by
measuring the radioactivity of urine w/ a
scintillation counter.
◦ ex. Metabolic activity (brain activity) can be
observed using a PET scanner.
The
Calvin
Cycle
Used
C14
Figure 2.6 Using radioactive isotopes to study cell chemistry
Phosphorus 32
has a half-life of 14 days
Part of DNA nucleotides
Used in biotech research.
Figure 2.8 The Tokaimura nuclear accident
Radiation from decaying isotopes damages cellular
molecules. Mutates DNA causing cancer, birth defects,
death.
Danger: Nuclear Power Plant disasters.
II. the glue of life: chemical bonds






Unless the atom is a noble gas, it will react
with other atoms.
Chemical bonds are interactions between
atoms that allow them to complete their
valence shells.
Ionic and Covalent bonds are strong.
Ionic bonds are weak in the presence of
water.
Hydrogen bonds are weak- but plentiful.
Van der Waals interactions are extremely
weak and only occur when molecules are
close together.
Figure 2.14 Electron transfer and ionic bonding
Ions are charged atoms.
Unequal Protons & Electrons.
cation
anion
Ionic bonds happen when one electron is transferred to
Another atom making a + and - ion. Opposites attract.
“electrostatic attraction”
Ionic bond = Ionic attraction
Figure 2.15 A sodium chloride crystal
Ionic
compound
A Molecule is a collection of two or more
atoms bonded together.
Ex. Oxygen
Water
Salt
O=O
H-O-H
Na+Cl-
A compound is a substance consisting of two or more
Elements combined in a fixed ratio.
Sodiuma metal
Chlorinepoisonous gas
Sodium Chlorideedible compound
Notice the EMERGENT PROPERTY of “flavor enhancement”
… the compound formed has different qualities than the
elements below in a level of organization of matter!
Sodiuma metal
Chlorinepoisonous gas
Sodium Chlorideedible compound
Figure 2.12 Covalent bonding in four molecules
Covalent Bonds =
When atoms share
electrons.
The goal is to
get the valence
shells full.
Hydrogen - 1 bond
Oxygen- 2 bonds
Nitrogen- 3 bonds
Carbon- 4 bonds
Figure 2.12x Methane
Methane
CH4
Carbon &
Hydrogen
Share the electrons
Evenly.
NONPOLAR COVALENT
BOND
Smells bad.
Contributes to global warming.
HARRIS RANCH
Figure 2.13 Polar covalent bonds in a water molecule
POLAR COVALENT BOND = unequal sharing of electrons
Water is a polar covalent molecule. The oxygen is more
electronegative than hydrogen… the shared electrons
spend more time around the Oxygen nucleus than the
Hydrogen resulting in “partial” negative and positive charge.
Electronegativity


Is the attraction of a particular kind of atom
for the electrons of a covalent bond.
Carbon & Hydrogen are =‘ly electronegative.
◦ So molecules that are composed only of these
elements are nonpolar- they have no charge.

OXYGEN & NITROGEN are EXTREMELY
ELECTRONEGATIVE
◦ So molecules that have these elements in them are
polar where the N or O is bonded.
◦ Will you remember this?
◦ NO!!!!! I mean yes.
Hydrogen bonds
form when a partially positive hydrogen atom covalently
bonded to one electronegative atom is also bonded to a
partially negative electronegative atom on another
molecule.
Bond from the +
Hydrogen of one
Polar molecule
Bonding to the
- part of the other.
These are weak bonds
Drawn as a dotted line.
Water molecules H bonded
Water
DNAhydrogen
bonds hold
the two
strands
together
(via nitrogen
containing
bases).
Van der Waals interactions
(negative and positive “hot spots”)
are weak and only occur when
molecules are very close together.
Notice how all of these
Bonds function in various
Biological phenomena:
Ex. #1
Immune System
Antigen-Antibody
Specificity
Figure 2.18 Molecular shape and brain chemistry
Ex. #2
Neurotransmitter
Stimulating
Next neuron
Figure 2.19 A molecular mimic
Both block pain receptors from sending signal
Man made
Endorphin = endo + morphine
CHAPTER 3
Water and the Fitness of the Environment
Figure 3.0 Earth
Figure 3.x1 Water
The polarity of water results in
hydrogen bonding
Hydrogen bonding of water
results in these Emergent Properties
1.
2.
3.
4.
Versatility as a solvent
Cohesive behavior
Ability to stabilize temperature
Expansion upon freezing
Water is the “universal solvent”… it
dissolves better than most things…
but not everything- it is the solvent
of life.
Solute
+
Solvent
Solution
Water can form hydration
shells around ions & break
Ionic bonds.
Note- the Cl- is surrounded
by the + hydrogen parts of
water & the Na+ is surrounded
by the - oxygen parts of water.
Water, as the universal solvent,
supports chemical reactions that
occur within cells.
Figure 3.8 A water-soluble protein
Surface tension, caused by the cohesion
of water molecules, allows a water strider
to exploit the habitat of surface water to
find food, mates, or escape predators.
 Surface tension is a
measure of how difficult
it is to stretch or break
the surface of a liquid.

Cohesion is an
attractive force between
like substances.
The basilisk can “run on water” to escape larger predators
who will sink….
Figure 3.2 Water transport in plants
Benefit to plants = don’t need to use ATP to move water…
Transpiration- result of cohesion and adhesion. It is
A “water chain” being pulled up from the roots to the leaves.
Adhesion is the attraction of the water molecules to another
type of molecule… in this case the dead cells of the xylem.
Water will change its
temperature less than other
materials when it gains or loses a
given amount of heat.
Where would you
rather be on a hot day…
In the desert or at the beach?
Which boils faster… a pot of alcohol or a pot of water?
Water has an unusually high specific heat.
Heat Capacity or Specific Heat is the
amount of heat that must be absorbed or
lost for 1 g of that substance to change its
temperature by one degree C.
Heat must be absorbed to break
hydrogen bonds (so it takes along time to
boil water) and heat is released when
hydrogen bonds form (it takes longer to
cool and to freeze water.)
This makes it a great moderator of
temperature.
Heat must be absorbed to break all four
hydrogen bonds before the molecule
transitions to the gas phase.
SWEATING
=
EVAPORATIVE
COOLING
Evaporative cooling occurs when liquids evaporate.
they absorb heat to be converted from liquid to gas &
leave the remaining liquid cooler.
Because heat must be absorbed to break
hydrogen bonds to allow the water to evaporate.
Water’s high heat
of vaporization
moderates earth’s
climate and
organism’s
temperatures.
Figure 3.6x2 Ice floats and frozen benzene sinks
Figure 3.5x1 Ice, water, and steam
Water is one of the few
substances that is less dense as
A solid. ICE FLOATS.
Figure 3.6 Floating ice and the fitness of the environment
Since oceans and lakes
don’t freeze solid.
Organisms in aquatic
environments don’t lose
their habitat during
winter.

Hydrophilic = water loving

Hydrophobic = water hating
ex. Polar substances will bond with water…
are attracted to water.
Ex. Sugar dissolves in water and is easily
transported through it to cells and
organelles w/in cells that use it.
ex. Nonpolar substances will NOT have
attraction to water… actually repel water.
Ex. The phospholipid molecule is used
(many of them) to create the cell
membrane.
Living systems depend on
properties of water that result
from its polarity and hydrogen
bonding. Explain this statement
and provide multiple examples.
Unnumbered Figure (page 47) Chemical reaction: hydrogen bond shift
acid
base
Figure 3.9 The pH of some aqueous solutions
pH is a log
Scale, 10x
An acid
increases the
hydrogen ion
concentration
of a solution.
Hydrogen
donator
A base
lowers the
hydrogen ion
concentration
of a solution.
Hydrogen
acceptor
Figure 3.10x1 Pulp mill
Figure 3.10x2 Acid rain damage to statuary, 1908 & 1968
Figure 3.10 The effects of acid precipitation on a forest
BUFFERS




Are substances that minimize
changes in the concentrations
of H+ and OH- in a solution.
Carbonic Acid is the buffer
in human blood that keeps it
at a pH of 7.4. (CO2 + H20)
It disassociates to form
Bicarbonate and releases a
H+ when pH levels exceed
7.4 (becomes basic)
The reversible reaction occurs
when blood becomes too
acidic. Excess H+ bonds with
bicarbonate to form Carbonic
Acid.
Oxygen as an Electron acceptor.





In cell respiration reactions occur in the
mitochondria to make ATP by metabolizing
organic molecules (like glucose).
Oxygen, a highly electronegative molecule, is
crucial to the process.
It attracts and bonds to itself: Hydrogen ions
and electrons, to form water.
Without oxygen “attracting” electrons the
whole system wouldn’t work.
When you die from asphyxiation, it is because
you run out of ATP- since Cell Resp. stops.