The Chemical Context of Life
A. P. Biology
Liberty Senior High School
From where do all of the
Naked Science: The Birth of the
The Birth of a Star
in the Trifid Nebula
Spongy Bone Spongy Bone
Iodine Deficiency- Goiter
The effects of essential element
Figure 2.3 (a) Nitrogen deficiency (b) Iodine deficiency
The bombardier beetle uses chemistry to
Simplified models of an atom
Cloud of negative Electrons
charge (2 electrons)
This model represents the
In this even more simplified
electrons as a cloud of
model, the electrons are
negative charge, as if we had
shown as two small blue
taken many snapshots of the
spheres on a circle around the
electrons over time, with each
dot representing an electron‘s
Figure 2.4 position at one point in time.
Atoms: The Stuff of Life!
• Atoms = Protons + Neutrons + Electrons
• Atomic Number = # of protons (=
• Atomic Mass = mass of protons +
neutrons; measured in Daltons (Da) or
a.m.u.’s; 1 proton’s mass = 1 Da
• 6.02 X 1023 Da of atoms = 1.0 g of atoms
• Atoms of same atomic # ( # protons) but
different number of neutrons.
• All belong to the same element; have
similar chemical properties.
Isotope Atomic Mass Abundance
12 C 12 (6p +6n) 99%
13 C 13 (6p + 7n) 0.9%
14 C 14 (6 p + 8 n) 0.1%
Willard Libby, Nobel Prize in
In the Atmosphere Into the Food Chain
12C:14C = 1012 :1
Applications of Isotopes
• ½ of the amount of 14 C
radioactively decays every 5,730
• Used in 14 C dating of materials
such as fossils and rock.
• Radiation treatment of cancer.
PET Scan and Cancer
It’s all about the electrons!
• Electrons are negatively charged atomic
particles with almost no mass.
• If the # of electrons = the # of protons in the
nucleus, then the atom is neutral.
• Electrons maintain an orbit around the
nucleus because of their attraction to the
positively charged protons in the nucleus.
• Electron orbitals are only predictions of
electron position around nucleus.
• Ions – atoms in which # electrons
in not equal to # of protons.
• Atoms with net positive charge -
cations (lose electrons).
• Atoms with net negative charge -
anions (gain electrons).
The electrons of an atom:
–Differ in the amounts of potential
energy they possess.
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
Energy levels are represented by
Third energy level (shell)
Second energy level (shell) Energy
First energy level (shell)
(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
Figure 2.7B potential energy that are possible.
Electrons Determine the Chemical
Nature of Atoms
• Electrons have potential energy
because of position- more energy
further from nucleus; less energy closer
• Electron’s distance from nucleus is
related to the amount of potential
energy it has.
Electron Configuration and
• The chemical behavior of an atom:
– Is defined by its electron configuration and
The periodic table of the elements:
– Shows the electron distribution for all the
2 Atomic number
Atomic mass Element symbol
Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon
3Li 4Be 3B 6C 7N 8O 9F 10Ne
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon
11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar
– Are those in the outermost, or valence shell.
– Determine the chemical behavior of an atom.
– Is the three-dimensional space where an
electron is found 90% of the time
• Each electron shell:
– Consists of a specific number of orbitals.
Each orbital holds
up to two electrons. x Y
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Each shell is shown with
its maximum number of
electrons, grouped in pairs.
(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
2 electrons) 8 electrons)
• Energy is transferred through the
movement of electrons from one
atom to another.
• Oxidation – the loss of electrons.
• Reduction – the gain of electrons.
• Always together in REDOX reactions.
• Groups of atoms stably
held together – molecule.
• Molecules of more than
one element – compound.
• A compound:
– Is a substance consisting of two or more elements combined
in a fixed ratio.
– Has characteristics different from those of its elements.
Sodium Chlorine Sodium Chloride
–Determines how biological
molecules recognize and
respond to one another
(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.
Brain cell Endorphin
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Kinds of Chemical Bonds
1. Ionic Bonds – form crystals
through electrical attractive
forces between atoms of
opposite charge. Example:
• NaCl Na + + Cl-
Another View of Ionic Bonding
–Are often called salts, which may form
Kinds of Chemical Bonds
2. Covalent Bonds – when two
atoms share one or more pair of
valence electrons. Maybe single,
double or triple covalent bonds.
Most common type of bond in
Formation of a covalent bond
Hydrogen atoms (2 H)
In each hydrogen
1 atom, the single electron
is held in its orbital by + +
its attraction to the
proton in the nucleus.
When two hydrogen
2 atoms approach each
other, the electron of
each atom is also
attracted to the proton
in the other nucleus.
The two electrons
3 become shared in a
forming an H2 + +
Figure 2.10 molecule (H2)
Single and Double Covalent Bonds
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model
(a) Hydrogen (H2). H H
atoms can form a
Two oxygen atoms
share two pairs of O O
electrons to form
a double bond.
Figure 2.11 A, B
In a polar covalent bond:
– The atoms have differing
– Share the electrons unequally.
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
This results in a
charge on the
oxygen and a
O partial positive
Figure 2.12 H H
Nonpolar Covalent Bonding
Polar Covalent Bonding
Space-filling Ball-and-stick Hybrid-orbital model
model model (with ball-and-stick
H H H H
H H H 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
Figure 2.16 (b) shapes of the molecules
–Determines how biological
molecules recognize and
respond to one another
van der Waal’s Forces (London’s)
• Very weak, attractive forces
between nonpolar atoms or
• Only temporary and weak bonds.
How do geckos walk on glass?
Spatulae and van der
• The formation and breaking of chemical
A-B + C-D A-C + B + D
Rate of Chemical Reactions
• Temperature – heating up reactions
increases the rate.
• Concentration of reactants and products –
more reactants usually favor the forward
and more products the reverse reaction.
• Catalysts – most important in living cells;
Atoms of Life
• Only 11 of the 92 naturally
occurring elements on earth are
found in any major amounts in
• All 11 have atomic numbers less
than 21; low atomic masses.
• Is this an accident?
Most Common Atoms in Human
% of Human Body by
The Elements of Life!
• They all share electrons by making covalent
• These bonds are weak enough to be broken at
temperatures compatible with life.
• 90% are O and H atoms; predominant role of
• Many of the molecules they form are gases that
are soluble in water- primitive earth where
complex molecules must have come together.
Why Carbon for Life?
• The Carbon Cycle
o/ (Episodes 2 and 3)
What molecule is a liquid at
low temperatures (earth
Water: The Cradle of Life
• 2/3 of any organism’s body is water.
• All organisms require water to grow
• Tropical rain forests vs. a dry desert
Water: Good For You and Tastes
• Water has a unique structure.
• Most important chemical property of
water-Hydrogen Bonding- weak chemical
bonds with only 5-10 % of strength of
• Water is a polar molecule; with a δ– end
and two δ+ ends.
• Polarity of the molecule gives water its
Water- The Molecule of Life!
A hydrogen bond:
– Forms when a hydrogen atom covalently
bonded to one electronegative atom is also
attracted to another electronegative atom
(H2O) O A hydrogen
d+ partial positive
charge on the
d– hydrogen atom
of water and
Ammonia the partial
(NH3) N negative charge
on the nitrogen
H H atom of
d+ H d+ ammonia.
Show me H-bonding in water!
Why is water a good solvent?
Show me a Hydration Shell!
Properties of Water
See Table 2.2, p. 35
•High Polarity- water is a good solvent for ions and
•High Specific Heat- water can absorb a great deal
of heat before changing temperature.
•High Heat of Vaporization- many H-bonds must
be broken before water can evaporate.
•Lower Density of Ice- water molecules in an ice
crystal are further apart because of H- bonding.
•Ioinization- water ionizes into H+ and OH- ions.
•Cohesion- H-bonds hold water molecules together.
•Adhesion- H-bonds between water and other polar
How does the stomach digest
meat when the organ, itself, is
We are all meat sacks!
Ionization of Water!
2 H2O H3O+ + OH-
Hydronium ion Hydroxide ion
H2O H+ + OH-
Hydrogen ion Hydroxide ion
Definitions of Acids/Bases
• pH = -log of[H +]
• Neutral (pure water) = [H +] =
• Acid = increases [H +], decreases
[OH -], lower pH.
• Bases = increases [OH-],
decreases [H +], higher pH.
Acids + Bases Salts and Water
HCl + KOH K+ + OH- + H+ + Cl-
KCl + H2O
Buffers – substances that resist
change in pH. Three kinds of
• Enzymes (Proteins and Free
• Bicarbonate System
• Phosphate System (Electrolytes)
Acts as a H+ Acceptor-
Buffers against Acids
Acts as a H+ Donor-
Buffers against Bases
Enzymes and Free Amino Acids
OH NH2 O
NH2 O C
OH SH C CH2
Polar OH CH3
CH2 CH CH2 CH2 CH2 CH2
O O O O O O
H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C
O– O– O– O– O– O–
H H H H H H
Cysteine Tyrosine Asparagine Glutamine
Serine (Ser) Threonine (Thr) (Gln)
(Cys) (Tyr) (Asn)
NH3+ NH2 NH+
–O O O– O
C C CH2 C NH2+
CH2 CH2 CH2 CH2
charged O O
H3N+ C C CH2 CH2 CH2 H3N+ C C
H3N+ C C CH2 CH2 H
H H3N+ C C CH2
H H3N+ C C
Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His)
Biological pH Buffers
In the blood (pH 7.4)….
Rise in pH
H20 + CO2 H2CO3 H+ + HCO3-
(carbonic acid) (bicarbonate
Drop in pH
In 1985, a man wanders off a trail on
a hot, summer day in the Grand
Canyon, with no water or food.
Four days later, he is found dead, his
body laying next to a fresh-water
stream. There is no sign of physical
injury or trauma. How did he die?
Electrolytes - Other Blood Buffer
• KH2 PO4 K + + H + + HPO4 2-
Monobasic potassium Phosphate
• K2HPO4 2 K+ + HPO4 2-
Dibasic Potassium Phosphate
Definition of an Acid and Base
The pH Scale
Weak Acids Resist pH Change
What is the pH of rain water?
H20 + CO2 H2CO3 H++
(carbonic acid) (bicarbonate ion)
Where else do H20 and CO2 mix?
Within the human body! Blood,
Tissue and Cytoplasm
What is Acid Rain?
H20 + SO2 + NOX H2SO4 +
Sulfuric Acid and
Tracking the pH of rain water
in the U.S.
The Effects of Acid Rain
Michelangelo’s Marcus Aurelius
Limestone – A Natural Buffer
Buffer – a solution that resists
change in pH; either in water or
soil; enzymatic buffers.
H2SO4(aq) + CaCO3 H2CO3 +
The Stomach and pH- An
Functions of the Stomach
• Bulk storage of food
• Mechanical breakdown of food
• Break chemical bonds with acids and
• Produce intrinsic factor – a glycoprotein
needed for B12 absorption in small
Chyme – mixed food and secretions of the
stomach; viscous, highly acidic, and soupy.
Four Parts to the Stomach
• Cardia – abundant mucous glands to
protect esophagus. Communicates with
esophagus via cardiac sphincter.
• Fundus – covered in gastric glands.
• Body – largest region; major food mixing
and many gastric glands.
• Pylorus (Antrum) – mucous glands to
produce mucus and other digestive
hormones (gastrin). Communicates with
duodenum via pyloric sphincter.
• Muscular and elastic – strong
connective tissue and layers of
• When empty, prominent folds form
on the inner surface – rugae.
• When full, rugae almost disappear –
hold 1-1.5 l
Lumen of Stomach
G Cells – make
In the fundus and body, two types of secretory
• Parietal Cells – secrete intrinsic factor and HCl.
• Chief Cells – secrete pepsinogen pepsin, a
digestive enzyme to digest proteins; active
only at pH of 1.5 -2.0
• Newborns also make rennin and gastric lipase
to digest milk protein and milk fat.
How does a cell produce HCl and not
• Parietal cells do not produce HCl in their
• The H+ and Cl- ions are transported separately.
• H+ ions from the carbonic anhydrase enzyme in
• CO2 + H2O <-----> HCO3- + H+ ; the bicarbonate ion
is exchanged for Cl- ions in the interstitial
• H+ ions then pumped into lumen.
• Export of HCO3- creates alkaline tide in blood
Show me how a parietal cell works
Highly Acidic Environment-
• Low pH kills most microorganisms.
• Low pH denatures proteins in food.
• Acid breaks down plant cell walls and
connective tissue in meat.
• Acidic conditions are necessary for
function of pepsin, made by chief cells.
Some Applications – Proton Pump
Laparoscopic Adjustable Gastric Band