Chemical Basis of Life: Why Study Chemistry in An Anatomy and Physiology Class

Lecture 2
Chemical Basis of Life

Why study chemistry in an Anatomy and Physiology class?
- body functions depend on cellular functions

- cellular functions result from chemical changes
- biochemistry helps to explain physiological processes,
and develop new drugs and methods for treating
diseases
2-2
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Fig. 2.1
Fig. 2.1
Fig. 2.1
Fig. 2.1
Structure of Matter
Matter – anything that takes up space and has weight;
composed of elements
Elements – composed of chemically identical atoms

• bulk elements – required by the body in large
amounts
• trace elements – required by the body in small
amounts
Atoms – smallest particle of an element

2-3
Table 2.1
Fig 2.3b
A lack of iodine in one’s diet can

cause swelling of the thyroid
gland resulting in a GOITER. The
condition is reversible if iodine
is taken. (Don’t worry, we iodize salt)
Fig 2.3b Iodine is used by thyroid cells to

make hormones (chemicals released by one
cell into the blood and bind to a receptor on another cell,
which is one way cells talk to each other).
Element
vs
Compound
(Emergent Properties)
Elements – composed of the same types of atoms
Compounds – composed of two or more types of atoms

Element
- Any substance composed of only ONE element
Ex) a bar of pure gold, nitrogen gas (N2), oxygen gas (O2)
Compound
- Any substance composed of two or more elements
Ex) Na+Cl- (table salt), H2O, CO2
Pure sodium (element) Chlorine (Cl2) gas (element) Na+Cl- Table Salt (Compound)
+ =
Fig 2.2
EMERGENT PROPERTIES (EP’s)
What are atoms made of

and how are they organized
Niels Bohr
Danish Physicist
?
1885-1962
(The Bohr Model)

Nucleus Organization:
Atomic Structure
Atoms - composed of
subatomic particles:
• protons – carry a
positive charge
• neutrons – carry no
electrical charge
• electrons – carry a
negative charge
Nucleus
• central part of atom
• composed of protons and
neutrons
• electrons move around the
nucleus 2-4
Subatomic particles
(sub = below, below the atom level)
charge mass
proton +1 1 amu (dalton)
neutron 0 1 amu (dalton)
electron -1 1/1836th an amu (dalton)
amu = atomic mass unit

1 amu or 1 dalton = 1.67 x 10-27 kg
How are the electrons “held” to the nucleus? Why

do they not just shoot away?
Electrons are held to the nucleus by the

electromagnetic (EM) force since electrons are
negative and the nucleus is positive – opposite
charges attract / like charges repel.
How are the protons “held” together in the nucleus?

Why do they not break apart due to the EM force?
The strong force holds the nucleus

together. The strong force is only “felt” at
extremely small distances, which is why
the electrons do not feel it. You would
need to be on the nucleus to feel it. For
example, if gravity were like this, you
would only feel it on Earth, but if you
Electron Organization:
n=2
n=1
Electrons are present in shells and move around the
nucleus at a speed of ~2200 km/s. They can only be in
these shells and nowhere else!!
The first shell (n=1) can hold up to 2 electrons. That

means it can have 0, 1 or 2 electrons in it at any time.
The second shell (n=2) can hold up to 8 electrons.

The third shell (not shown, n=3) can also hold up to 8 electrons.
There are many more shells, but you only need to
know the first three for AP Bio.
Which shell contains higher energy electrons, shell 1
(n=1) or shell 2 (n=2)? Explain.
n=2
n=1
Shell 2. The further from the nucleus the electron, the

further it can fall toward the nucleus and therefore
it has more energy (a greater ability to accelerate
matter) than shell 1 electrons.
Electrons can jump between shells (called a quantum leap)
n=2
n=1
In order to get an electron to “leap” from n=1 to n=2,

what is required?
Electrons can jump between shells (called s quantum leap)
The nucleus is charged and

therefore is pulling on the electron.
It will take energy to pull the
electron away from the nucleus and
move it further away to shell 2.
n=3
This is analogous to picking up a
n=2
bowling ball. Earth is pulling on the
bowling ball like the nucleus is
n=1
pulling on the electron. It takes
energy to pick up a bowling ball.
Fig 2.7
Atomic Number and
Atomic Weight
Atomic Number
• number of protons in the
nucleus of one atom
• each element has a unique
atomic number
• equals the number of
electrons in the atom
Atomic Weight
• the number of protons
plus the number of
neutrons in one atom
• electrons do not
contribute to the weight of
2-5
the atom
The atomic mass (A) = protons + neutrons

Why do we not add the electrons mass?
Electrons are soooo small relative to
protons and neutrons (1/2000th the
size) that we ignore them.
The atomic charge

Compare number of protons to the
number of electrons.
Ex. If there are 10 protons (+10) and 7

electrons (-7) the overall charge is +3
What happens if we
change the number of protons ?
You change the identity of the atom (becomes a different element)
as well as the mass.
What happens if we
change the number of neutrons
You change the mass and perhaps the stability....
?
Isotopes
Isotopes
• atoms with the same atomic numbers but
with different atomic weights
• atoms with the same number of protons
and electrons but a different number of
neutrons
• oxygen often forms isotopes (O16, O17,
O18)
• unstable isotopes are radioactive; they
emit subatomic particles
2-6
Isotopes are atoms that have the same

elemental identity (same number of
protons/same properties), but
different number of neutrons.
stable stable unstable
Certain ratios of protons to neutrons are unstable resulting in

breakdown of the nucleus (nuclear radiation).
Ex. 6 protons and 6 neutrons in a nucleus (Carbon-12) is stable, but 6
protons and 8 neutrons (carbon-14) is unstable and will undergo radioactive
decay to become stable. C-14 is called a radioactive isotope.
Radioactive decay
Radioactive decay
Carbon-14 (radioactive) will decay to Nitrogen-14 (stable). Seven protons and 7

neutrons in a nucleus is stable. An electron is shot out during the decay
making it dangerous and useful.
Clinical Applications
Radioactive Isotopes Reveal Physiology
• injected into the body
• different types taken up by different organs
• can be detected in the body using a scintillation
counter
• can be used to destroy specific tissues
• commonly used
• iodine-131 for thyroid function
• thallium-201 for heart function
• gallium-67 and cobalt-60 for cancer
• others used to assess kidney functions, measure hormone
levels and bone density changes 2-31
What if we alter the
?
number of electrons
If you alter the electrons, you simply change the charge of the atom
Review:
4. How many protons, neutrons and electrons does the

above element contain?
Review:
5. Which of the following models is correct according to

the Bohr model of the atom?
Molecules and Compounds
Molecules – particle formed when two or more atoms

chemically combine
Compound – particle formed when two or more

atoms of different elements chemically combine
Molecular formulas – depict the elements present

and the number of each atom present in the molecule
H2 C6H12O6 H2O
2-7
Electrons
• found in regions of space called electron shells (energy shells)
• each shell can hold a limited number of electrons
• for atoms with atomic numbers of 18 or less, the following rules apply:
• the first shell can hold up to 2 electrons
• the second shell can hold up to 8 electrons
• the third shell can hold up to 8 electrons
• lower shells are filled first
• if the outermost shell is full, the atom is stable
2-8
Ions
Ion
• an atom that has gained or lost an electron(s)
• an electrically charged atom
• atoms form ions to become stable
Cation
• a positively charged
ion
• formed when an atom
loses an electron(s)
Anion
• a negatively charged ion
• formed when an atom gains an
2-9
electron(s)
AIM: How do atoms interact with each other?
When are atoms

most happy ?
When their valence shell is full.
To be “happy” (stable) the sodium

atom will need to either get 7
electrons or lose 1. Which is
easier?
The sodium will give away its
outer shell electron.
Chlorine needs one electron for

its outer shell to be full.
Ionic Bond
Ionic Bond
• an attraction between a cation and an anion
• formed when electrons are transferred from one atom

to another atom
2-10
Chlorine has a higher AFFINITY

for the electron and therefore
the electron will “fall” from
sodium to chlorine.
When the piece of elemental sodium (countless

numbers of sodium molecules) is placed in the
chlorine gas in the video, all those ridiculous
number of electrons jump to the countless
chlorines. This causes all the molecules to
move around violently (heat up) and electrons
to jump between shells (give off light).
Ionic bond
When sodium loses an electron it becomes

positively charged (a cation). When chlorine picks it
up it becomes negatively charged (a anion). Cations
and Anions are collectively called ions = fully
ions
Cation vs Anion
charged atoms/molecules.
Ionic bond
The sodium and chloride ions are now attracted to

each other and form an ionic bond. ions
Cation vs Anion
ionic bond = bond between two oppositely charged ions
Salt crystals Na+Cl- crystals are repeating arrays of Na+ and Cl-
held together by the electromagnetic force.
Salt
-general name given to ANY ionic compound (not
just sodium chloride (Na+Cl-) held together in a
lattice structure.
Na+Cl-
K+Cl-
Mg2+Cl2-
Mn2+Cl2-
Ca2+CO32-
Covalent Bond
Formed when atoms share electrons
•Hydrogen atoms form single bonds H―H

•Oxygen atoms form two bonds O=O
•Nitrogen atoms form three bonds N≡N
•Carbon atoms form four bonds O=C=O
2-11
How else can atoms fill their outer shells?
http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55
Single Covalent Bond
-
H H or H2
In this case, to be stable and fill their outer shells, unlike in an ionic bond, the
atoms will SHARE their electrons to form a covalent bond.
http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55
-
F F or F2
Double Covalent Bonds (double bond)
= =
O C O or CO2
Draw :
CH4 or H2O
Structural Formula
Structural formulas show how atoms bond and are
arranged in various molecules
2-12
Polar Molecules
Polar Molecule
• molecule with a slightly negative end and a slightly positive
end
• results when electrons are not shared equally in covalent
bonds
• water is an important polar molecule
2-13
Hydrogen Bonds
Hydrogen Bond
• a weak attraction between the positive end of one polar
molecule and the negative end of another polar molecule
• formed between water molecules
• important for protein and nucleic acid structure
2-14
Chemical Reactions
Chemical reactions occur when chemical bonds form or
break among atoms, ions, or molecules
Reactants are substances being changed by the chemical

reaction
Products are substances formed at the end of the chemical

reaction
NaCl  Na+ + Cl-

Reactant Products
2-15
Types of Chemical Reactions
Synthesis Reaction – chemical bonds are formed
A + B  AB
Decomposition Reaction – chemical bonds are broken

AB  A + B
Exchange Reaction – chemical bonds are broken and formed

AB + CD  AD + CB (NaCl+ AgNO3→ NaNO3+ AgCl)
Reversible Reaction – the products can change back to
the reactants
A + B n AB
2-16
ALL CHEMICAL REACTIONS
INVOLVE ENERGY
• WHEN BONDS
ATP = energy carrier of a cell
FORM,
ENERGY IS
STORED
• WHEN BONDS
BREAK,
ENERGY IS
RELEASED
Metabolism
• All the chemical reactions that take place in
the organism
• These reactions need to be balanced to keep
the organism alive
– The balance is called homeostasis
Acids, Bases, and Salts
Electrolytes – substances that release ions in water
NaCl  Na+ + Cl-
Acids – electrolytes that release hydrogen ions in water
HCl  H+ + Cl-
Bases – substances that release ions that can combine with

hydrogen ions
NaOH  Na+ + OH-
Salts – electrolytes formed by the reaction between an
acid and a base
HCl + NaOH  H2O + NaCl 2-17
Acid and Base Concentrations
pH scale - indicates the
concentration of hydrogen ions in
solution
Neutral – pH 7; indicates
equal concentrations of H+
and OH-
Acidic – pH less than 7;
indicates a greater
concentration of H+
Basic or alkaline – pH
greater than 7;
indicates a greater concentration
2-18
of OH-
pH scale
• Most chemical reactions in humans take
place between 6+8
– However, stomach acid is 2-3
– Enzymes are pH specific
2.2 Introduction to Chemistry
Blood - 7.5 (lethal if more acidic than 7
and more basic than 7.8)
Stomach acid - 2 -3
A change in pH --in your body results
in halting some enzyme functions
Acid rain --contains sulfuric acid and nitric
acid
Acid rain pH < 5.6
Acid rain washes away vital
minerals from soil, kills aquatic
organisms & strip nutrients from
plants
Organic Versus Inorganic
Organic molecules
• contain C and H
• usually larger than inorganic molecules
• dissolve in water and organic liquids
• carbohydrates, proteins, lipids, and nucleic acids
Inorganic molecules
• generally do not contain C
• usually smaller than organic molecules
• usually dissolve in water or react with water
to release ions
• water, oxygen, carbon dioxide, and inorganic
salts 2-19
Inorganic Substances
Water
• most abundant compound in living material
• two-thirds of the weight of an adult human
• major component of all body fluids
• medium for most metabolic reactions
• important role in transporting chemicals in the body
• can absorb and transport heat
Oxygen (O2)
• used by organelles to release energy from nutrients
• necessary for survival 2-20
• Solutions --Water is known as
the universal solvent
• Chemical properties of water are
important b/c they allow it to form
solutions (Uniform mixtures)
• Solute --That which is being

dissolved (sugar)
• Solvent --That which does the

dissolving (water)
Ionic Compounds --dissolve
readily in water b/c
water is polar
Polar covalent compounds --
dissolve in water
Inorganic Substances
Carbon dioxide (CO2)

• waste product released during metabolic reactions
• must be removed from the body
Inorganic salts
• abundant in body fluids
• sources of necessary ions (Na+, Cl-, K+, Ca2+, etc.)
• play important roles in metabolic processes
2-21
ORGANIC COMPOUNDS
• COMPOUNDS THAT CONTAIN
CARBON, HYDROGEN AND OXYGEN
IN DEFINITE PROPORTIONS.
• USUALLY ASSOCIATED WITH LIVING
THINGS
Organic Substances
Carbohydrates
• provide energy to cells
• supply materials to build cell structures
• water-soluble
• contain C, H, and O
• ratio of H to O close to 2:1 (C6H12O6)
• monosaccharides – glucose, fructose
• disaccharides – sucrose, lactose
• polysaccharides – glycogen, cellulose
2-22
CARBOHYDRATES
• BUILDING BLOCKS = SIMPLE SUGARS
(MONOSACCHARIDES).
• MONOSACCHARIDES INCLUDE
– GLUCOSE
– FRUCTOSE ISOMERS
– GALACTOSE
ALL THREE HAVE THE SAME MOLECULAR
FORMULA, BUT DIFFERENT STRUCTURE:
C6H1206
THESE MOLECULES ARE THE MOST COMMON
SOURCE OF ENERGY FOR LIVING THINGS.
Organic Substances
Carbohydrates
2-23
Isomers – C6H12O6
glucose
CARBON
• Carbon is important biological element
because it can form four bonds with other
elements and long chains or rings
• Polymer – large molecule made up of many
smaller units like starch
• Monomer – unit that makes up polymer;
glucose is the monomer for starch
GLUCOSE
• Monomer of starch, glycogen, and cellulose
MORE COMPLEX CARBS
• DISACCHARIDES
– MADE UP OF TWO MONOSACCHARIDES
CHEMICALLY COMBINED.
– GLUCOSE + GLUCOSE = MALTOSE
– GLUCOSE + GALACTOSE = LACTOSE
• THIS IS MILK SUGAR
– GLUCOSE + FRUCTOSE = SUCROSE
• THIS IS TABLE SUGAR
• These molecules store energy for later use
2. 3 The Compounds of Life
• Glycogen - animals stored

energy made from
sugars (same
saccharides)
• Cellulose - simple sugars that
make structural
carbos in plants
THE MOST COMPLEX CARBS
• STARCH – MADE UP OF MANY GLUCOSE UNITS
COMBINED.
– PLANT LONG-TERM FOOD STORAGE
• GLYCOGEN – MADE OF MANY GLUCOSE UNITS
COMBINED
– ANIMAL STORAGE IN LIVER AND MUSCLES
• CELLULOSE – MADE OF MANY GLUCOSE UNITS
COMBINED.
– PLANT CELL WALLS; FIBER
• CHITIN – PROTECTIVE COVERINGS IN INSECTS
AND OTHER ARTHROPODS; ALSO IN FUNGUS
CELL WALLS
DEHYDRATION SYNTHESIS
• In order for two molecules to join together, each

molecule must break off atoms to provide a
bonding place.
• Most organic molecules do this by losing a
hydrogen atom from one molecule and a hydroxyl
group from the other.
• These two join to form water, and allow the
molecules to make a bond.
Dehydration Synthesis
C6H12O6 + C6H12O6  C12H22O11 + H2O

disaccharide
Hydrolysis
• In order to break down a large molecule to
make smaller molecules, a molecule of
water has to be added.
• This fills in the spots where the bond broke
– one molecule gets a hydrogen atom, the
other gets the hydroxyl group.
Hydrolysis
ADD WATER
TO A
POLYSACCHARIDE
AND
FORM
MANY
MONOSACCHARIDES
Dehydration Synthesis and Hydrolysis
store and release energy
• Dehydration synthesis stores energy by

forming bonds.
– As in the formation of polysaccharides from
monosacharides
• Hydrolysis releases energy by breaking
bonds.
Organic Substances
Lipids
• soluble in organic solvents
• fats (triglycerides)
• used primarily for energy
• contain C, H, and O but less O than carbohydrates (C57H110O6)
• building blocks are 1 glycerol and 3 fatty acids per molecule
• saturated and unsaturated
2-24
Lipids: fats, oils, waxes, phospholipids,
steroids
• Used for longer-term storage of energy
• Fats – in animals
• Oils – in plants
• Waxes – water repellent (In your ears, beeswax, coat
plant leaves), waterproof bird feathers.
• Steroids – in animal cell membranes and some
hormones.
• Phospholipids – make up parts of cell membranes
A common fat = Triglyceride
• Composed of one glycerol and three fatty

acids, joined together by dehydration
synthesis:
3
F
G A
L T
T
Y
Y
C A
E C
I
R
D
O
S
L
Saturated and unsaturated fats:
• Saturated fats have no C=C bonds within the fatty

acids
– These are considered unhealthy – they clog up the
coronary (heart) arteries.
– These are solid at room temperature.
– From animals.
• Unsaturated fats have at least one C=C bond in
one of its fatty acids
– These are considered healthier.
– Plant oils are usually unsaturated.
– Liquid at room temperature.
Organic Substances
Lipids
• phospholipids
• building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per
molecule
• hydrophilic and hydrophobic
• major component of cell membranes
2-25
Organic Substances
Lipids
• steroids
• connected rings of carbon
• component of cell membrane
• used to synthesize hormones
• cholesterol
2-26
Organic Substances
Proteins
• structural material
• energy source • amino acids held
• hormones together with
• receptors peptide bonds
• enzymes
• antibodies
• building blocks are amino acids
2-27
• Proteins - make enzymes that
help control chemical
reactions (ex. Speed up
digestion, releasing
energy during cellular
respiration, building up
proteins
• Proteins - large, complex
molecules composed of many
smaller molecules called
amino acids (only 20 amino
acids make different combinations &
proteins)
– Amino acids are held together by
peptide bonds to form proteins
PROTEINS
• Important for movement, structure, regulation,
transport, nutrition, and defense.
• Composed of building blocks called amino acids
• Humans cannot make these from scratch – we
must eat foods with proteins, then use the amino
acids to make our own proteins.
Amino Acids
• There are 20 different aa’s
• They are combined in various numbers and orders to
produce a great number of different proteins.
• Each aa has an amino group, an acid group (carboxyl), and
a variable group (there are 20 different variable groups).
• Amino acids attach to each other by dehydration synthesis
forming a peptide bond between the amino group of one aa
and the acid group of the other aa.
• Change the number or arrangement of the aa’s and the
protein is changed.
Amino acids
Acid group
Amino group
Dipeptide – two aa’s joined by a peptide
bond.
Polypeptide
Organic Substances
Proteins
Four Levels of Structure
2-28
Nucleic Acids
• Molecules of heredity.
• DNA – deoxyribonucleic acid
– makes up chromosomes (GENES)
– Contains the genetic code
• Determines the organism’s traits
• Contains the code for making proteins
Which control the cell’s activities
• RNA – ribonucleic acid
– Helps DNA make proteins
• Nucleic Acids - large, complex
molecules that contain
hereditary or genetic
info – two types
• monomer – nucleotide (made up
of nitrogen base, phosphate, and
sugar)
DNA - carries instruction that control

activities of cell (blueprint)
Organic Substances
Nucleic Acids
2-30
Enzymes – Special Proteins
• Change the rate of chemical reactions

without being used up themselves
(biological catalyst).
• Can be used over and over.
• Action is very specific –
each enzyme will only
work on one particular substance (the
substrate).
HOW DOES AN ENZYME
WORK?
• LOCK AND KEY • INDUCED FIT
MODEL MODEL
2.4 Chemical Reactions and
Enzymes
*Type of protein
*Act as a catalyst, speeding up

chemical reactions
1. Substrate- substance being

changed by enzyme
2. Active site- region on enzyme
where substrate attaches (this is
the enzyme substrate complex)
2.4 Chemical Reactions and Enzymes
3. Substrate is altered (bond
weakened) so that bond is
broken
4. Products released and enzyme is

unchanged (only the substrate
changes)
5. Enzyme is free to bond with

another substrate
*Enzyme affected by high
temperature
2.4 Chemical Reactions and Enzymes
Chemical Reaction – creation of

new substances by breaking or
forming chem. bonds
Carbs broken for energy
All chemical reactions involve energy
(absorbed or released)
Chemical Reactions and Chemical Equilibrium
Biological Example:
Glycolysis is shown to the right. The
circled numbers are enzymes.
Which reactions are reversible?
Those catalyzed by enzymes 3, 4, 6, 7, 8, 9, 10, and 11

Which reactions are irreversible?
Those catalyzed by enzymes 1, 2, 5 and 12

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Lecture 2

Chemical Basis of Life

- body functions depend on cellular functions

Elements – composed of chemically identical atoms

Atoms – smallest particle of an element

A lack of iodine in one’s diet can

Fig 2.3b Iodine is used by thyroid cells to

Elements – composed of the same types of atoms

Compounds – composed of two or more types of atoms

What are atoms made of

(The Bohr Model)

amu = atomic mass unit

How are the electrons “held” to the nucleus? Why

Electrons are held to the nucleus by the

How are the protons “held” together in the nucleus?

The strong force holds the nucleus

The first shell (n=1) can hold up to 2 electrons. That

The second shell (n=2) can hold up to 8 electrons.

Shell 2. The further from the nucleus the electron, the

In order to get an electron to “leap” from n=1 to n=2,

The nucleus is charged and

The atomic mass (A) = protons + neutrons

The atomic charge

Ex. If there are 10 protons (+10) and 7

Isotopes are atoms that have the same

stable stable unstable

Certain ratios of protons to neutrons are unstable resulting in

Carbon-14 (radioactive) will decay to Nitrogen-14 (stable). Seven protons and 7

What if we alter the

4. How many protons, neutrons and electrons does the

5. Which of the following models is correct according to

Molecules – particle formed when two or more atoms

Compound – particle formed when two or more

Molecular formulas – depict the elements present

When are atoms

To be “happy” (stable) the sodium

Chlorine needs one electron for

• formed when electrons are transferred from one atom

Chlorine has a higher AFFINITY

When the piece of elemental sodium (countless

When sodium loses an electron it becomes

The sodium and chloride ions are now attracted to

•Hydrogen atoms form single bonds H―H

How else can atoms fill their outer shells?

Single Covalent Bond

Double Covalent Bonds (double bond)

Reactants are substances being changed by the chemical

Products are substances formed at the end of the chemical

NaCl  Na+ + Cl-

Decomposition Reaction – chemical bonds are broken

Exchange Reaction – chemical bonds are broken and formed

Bases – substances that release ions that can combine with

• Solute --That which is being

• Solvent --That which does the

Carbon dioxide (CO2)

• Glycogen - animals stored

• In order for two molecules to join together, each

C6H12O6 + C6H12O6  C12H22O11 + H2O

• Dehydration synthesis stores energy by

• Composed of one glycerol and three fatty

• Saturated fats have no C=C bonds within the fatty

DNA - carries instruction that control

• Change the rate of chemical reactions