The Chemical & Physical
Basis of Life
Chapter 2
Life is a series of complex chemical
reactions.
Chemical reactions are the basis of physiology.
Chemistry follows the laws of Physics.
Physics is, fundamentally, the study of matter & energy.
Matter
•Matter is “stuff”.
•It occupies space and has mass.
•Mass is measured in grams.
•Mass and “weight” are often used interchangeably
but are really two different things
•Weight is a measure of the effect of force on an
object. It changes.
•Mass does not change.
Example: The Moon’s gravitational force is 1/6th that
of Earth’s. If you weigh 155 pounds on Earth (70 kg),
you will only weigh 26 pounds on the Moon. But you
will still have 70 kilograms of mass!
(The BE or British Engineering unit of mass is the “slug”.)
Energy
Potential = stored energy. The amount
energy contained in an object of a given
mass that can be used to do work.
Kinetic Energy = energy of work. This is
energy that is actually being released and
doing work.
Other Forms of Energy
1. Electrical
2. Mechanical
3. Chemical
4. Radiant
5. Nuclear
Energy is
governed by the
Laws of
Thermodynamics
The 1st Law of Thermodynamics:
Energy cannot be created nor can it be
destroyed.
Also known as “the Conservation Statement”
The 2nd law of Thermodynamics:
Energy flows from an area of high density
to an area of low density.
This is also referred to as “the Entropy Statement”.
The 2nd LTD is perhaps the most relevant concept to us
for our understanding biological systems, chemistry and
physiology.
Another way to look at the 2nd LTD:
Since energy is what holds matter
together, or maintains “order”, then the
2nd LTD dictates that systems go from
order to disorder.
Example of
Entropy
The 3rd Law of Thermodynamics:
You cannot reach absolute zero in a finite
number of steps.
This is implied from the first two LTDs.
Absolute
zero
That’s really cold!
The Zeroth Law:
There is no net flow of energy between to systems that
are in equilibrium.
(The “well duh!” statement.)
Atoms:
The Building Blocks of Matter
There are 26 elements essential to most
living systems. Humans are composed of the
the following:
1. Oxygen 2. Carbon 3. Hydrogen 4. Nitrogen 5. Calcium 6. Phosphorus7. Potassium 8. Sulfur 9. Sodium 10. Chlorine 11. Magnesium 12. Iron -
65%
18.5%
9.5%
3.3%
1.5%
1.0%
0.4%
0.3%
0.2%
0.2%
0.1%
0.005%
Trace elements (in
alphabetical order)
Aluminum
Boron
Chromium
Cobalt
Copper
Fluorine
Iodine
Manganese
Molybdenum
Selenium
Silicon
Tin
Vanadium
Zinc
Composition
of the
Human body
Atomic structure
Atomic number = the number of protons
Mass number = protons + neutrons
Atomic mass = mass of protons (1.008 amu) + mass of
neutrons (1.007 amu) + mass of electrons (0.0005 amu)
More elements
Isotopes
The number of protons defines the element. The number
of neutrons and electrons can vary.
Isotopes are different forms of elements with different
numbers of neutrons.
Some are stable, some decay and release energy. This
energy is nuclear radiation!
There are 3 basic types of atomic
radiation
  particles = a He nucleus (2 protons + 2 neutrons)
 Easily stopped. Dangerous if ingested or inhaled. Produced by the
decay of Polonium, Radon, Radium and Uranium
 particles = are electrons and are negatively
charged
 More energetic and therefore, more dangerous. Given off in the
opposite direction of particle. Produced by Krypton, Strontium,
Carbon and Indium.
  rays = high energy electromagnetic radiation
 Most deadly, mutagenic and toxic. Produced by Polonium, Krypton,
Radon, Radium, and Uranium
Chemical reactivity:
It’s all about electrons
Unfilled valence shells lead to reactivity
The Octet Rule
• Atoms with eight electrons in their
valance shell are most stable.
• When a reaction between two atoms
leads to full valance shells then the
two are more likely to interact.
• Atoms or molecules with partially
filled valance shells are more
reactive.
Free
Radicals
Superoxide free radical is
highly reactive
Chemical bonds and the combining
of matter
•Atoms can combine by chemical reactions to form
molecules.
•Two or more atoms of the same element bound
together form a molecule.
•Two or more atoms of different elements bound
together form a compound.
This is different than a mixture, which is when substances are
physically combined but are not chemically bonded.
Mixtures include: Solutions, Colloids, and Suspensions.
Ionic compounds
An important
Ionic
compound:
NaCl
Or “table salt”!
Covalent bonds:
the sharing of electrons
Covalent
molecules
Two
covalent
compounds
Weak
Important
characteristics &
relative strength
of chemical bonds
strong
Water:
its structure gives it special properties
Hydrogen bonds are too
weak to form compounds
but are an important
influence on chemical
structure.
The electrical attraction
between the partial
charge on the hydrogen of
one water molecule and
the oxygen of another
gives water its special
properties.
Hydrogen Bonds
Important properties of H2O
It is polar, which gives rise to the following:
Cohesion - it clings to itself
Adhesion I it clings to other things
These properties account of its high surface tension
and capillary action.
It is the “universal solvent”.
It has high heat capacity, latent heat of vaporization and
specific heat.
How water works to dissolve an ionic
compound
(this is actually a chemical reaction)
Solutions
• Colloid:
– a solution of very large organic molecules
• Suspension:
– a solution in which particles settle
(sediment)
• Concentration:
– the amount of solute in a solvent (mol/L,
mg/mL)
Electrolytes
Table 2–3
Chemical Reactions:
Water is formed by a chemical reaction
Reactions & energy
• Reactions that absorb more energy
than they release are endergonic
• Reactions that release more energy
than they absorb are exergonic
• Life is a series of these reactions
that are coupled together
• Reactions require energy to initiate
them – Activation energy
Activation Energy
Catalyst
activity
Enzymes are organic
catalysts that speed up
chemical reactions by
lower the energy needed
to activate them.
They are not changed by
the reaction, nor are they
a product or a reactant.
Chemical Reactions:
Synthesis
Synthesis reactions build more complex molecules from
individual building blocks. Biological molecules are
synthesized by removing producing water molecules.
Decomposition
Decomposition reactions break large molecules into their
constituent components. Biological molecules are
generally broken down by addition of water molecules.
This type of reaction is called hydrolysis.
Oxidation-reduction reactions
or “redox”
1.
2.
3.
4.
When something is reduced, something else is always
oxidized
Electrons are exchanged between reactants.
The electron donor is oxidized. (It is the reducing
agent).
The electron acceptor is reduced. (It is the oxidizing
agent).
Also defined as the loss of hydrogens (and electrons) or
the addition of oxygen.
Example of a simple redox reaction
Exchange reactions
Aerobic respiration:
A very important redox reaction!
ADP + Pi
C6H12O6 + 6 O2
Stored energy
ATP
6 CO2 + 6 H2O
Some
other
important
redox
reactions
Influences on reaction rates
•
•
•
•
Concentration
Temperature
pH
Catalysts
Acids, Bases & Salts
One version of the pH scale
Acid and Alkaline
• Acidosis:
+
– excess H in body fluid (low pH)
• Alkalosis:
—
– excess OH in body fluid (high pH)
Organic Compounds
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic acids
Functional Groups
• Molecular groups which allow molecules to
interact with other molecules
Table 2–4
Carbohydrates
Simple sugars
Disaccharides
Simple
Sugars
Figure 2–10
Formation of Sucrose from
glucose & fructose
Polysaccharides
• Chains of
many simple
sugars
(glycogen)
Figure 2–12
Carbohydrate Functions
Table 2–5
Classes of Lipids
•
•
•
•
•
Fatty acids
Eicosanoids
Glycerides
Steroids
Phospholipids and glycolipids
Lipids
Triglycerides =
glycerol + 3
free fatty
acids
Also known as
“neutral fats”
• Glycerides: are the fatty acids attached to
a glycerol molecule
• Triglyceride: are the 3 fatty-acid tails, fat
storage molecule
Figure 2–15
Combination Lipids
Figure 2–17a, b
Combination Lipids
Figure 2–17c
Cholesterol is
another lipid.
It is a component of
plasma membranes
and is the basis for
steroid hormones.
Protein Structure
• Proteins are the most abundant and
important organic molecules
• Basic elements:
– carbon (C), hydrogen (H), oxygen (O),
and nitrogen (N)
• Basic building blocks:
– 20 amino acids
Protein Functions (1 of 2)
• 7 major protein functions:
– support:
• structural proteins
– movement:
• contractile proteins
– transport:
• transport proteins
Protein Functions (2 of 2)
– buffering: regulation of pH
– metabolic regulation:
• enzymes
– coordination and control:
• hormones
– defense:
• antibodies
Amino Acids
Figure 2-18
Amino Acid Structure
1.
2.
3.
4.
5.
central carbon
hydrogen
amino group (—NH2)
carboxylic acid group (—COOH)
variable side chain or R group
Peptides
Figure 2–19
Peptide Bond
• A dehydration synthesis between:
– the amino group of 1 amino acid
– and the carboxylic acid group of another
amino acid
– producing a peptide
Primary Structure
• Polypeptide:
– a long chain of amino acids
Figure 2–20a
Secondary Structure
• Hydrogen bonds form spirals or
pleats
Figure 2–20b
Tertiary
Structure
• Secondary
structure
folds into a
unique
shape
Figure 2–20c
• Final protein shape:
– several tertiary structures together
Quaternary Structure
Figure 2–20d
Shape and Function
• Protein function is based on shape
• Shape is based on sequence of amino
acids
• Denaturation:
– loss of shape and function due to heat or
pH
Protein Shapes
• Fibrous proteins:
– structural sheets or strands
• Globular proteins:
– soluble spheres with active functions
Enzymes
• Enzymes are catalysts:
– proteins that lower the activation
energy of a chemical reaction
– are not changed or used up in the
reaction
How Enzymes Work
Figure 2–21
How Enzymes Work
• Substrates:
– reactants in enzymatic
reactions
• Active site:
– a location on an enzyme that
fits a particular substrate
Enzyme Helpers
• Cofactor:
– an ion or molecule that binds to an
enzyme before substrates can bind
• Coenzyme:
– nonprotein organic cofactors
(vitamins)
• Isozymes:
– 2 enzymes that can catalyze the
same reaction
Enzyme Characteristics
• Specificity:
– one enzyme catalyzes one reaction
• Saturation limits:
– an enzyme’s maximum work rate
• Regulation:
– the ability to turn off and on
Protein Combinations
• Glycoproteins:
– large protein + small carbohydrate
• includes enzymes, antibodies,
hormones, and mucus production
• Proteoglycans:
– large polysaccharides +
polypeptides
• promote viscosity
Nucleic Acids
• Large organic molecules, found in the
nucleus, which store and process
information at the molecular level
• DNA and RNA
Deoxyribonucleic Acid
(DNA)
•
•
•
•
Determines inherited characteristics
Directs protein synthesis
Controls enzyme production
Controls metabolism
Ribonucleic Acid (RNA)
• Codes intermediate steps in protein
synthesis
Nucleotides
• Are the building blocks of DNA
• Have 3 molecular parts:
– sugar (deoxyribose)
– phosphate group
– nitrogenous base (A, G, T, C)
The Bases
Complementary Bases
• Complementary base pairs:
– purines pair with pyrimidines:
• DNA:
– adenine (A) and thymine (T)
– cytosine (C) and guanine (G)
• RNA:
– uracil (U) replaces thymine (T)
Nucleic Acids
• Long chains of
nucleotides form
RNA and DNA
Figure 2–23
RNA and DNA
• RNA:
– a single strand
• DNA:
– a double helix joined at bases by
hydrogen bonds
Forms of RNA
• messenger RNA (mRNA)
• transfer RNA (tRNA)
• ribosomal RNA (rRNA)
ADP and ATP
• adenosine diphosphate (ADP):
– 2 phosphate groups
• di = 2
• adenosine triphosphate (ATP):
– 3 phosphate groups
• tri = 3
Phosphorylation
• Adding a phosphate group to ADP
with a high-energy bond to form the
high-energy compound ATP
• ATPase:
– the enzyme that catalyzes
phophorylation
• Chemical energy stored in phosphate bonds
The Energy Molecule
Figure 2–24
ATP supplies energy
for the work required
to maintain homeostasis
ATP is formed by cellular
respiration
Compounds Important to Physiology
Recycling Old Molecules
Table 2–9
Next - Cells