WHY STUDY PHYSICAL
CHEMICAL OR PROPERITES?
•  Helps bound biological problems.
1
WHAT IS MATTER?
•  Any substance that has mass and occupies
space
2
WHAT IS AN ELEMENT?
•  Def’n - a substance with specific
properties that can neither be broken
down or converted to other substances
by ordinary chemical reactions
H He C N O Na Mg P ...
3
A FACT
•  Life on earth requires 25 elements, 11 are
very common
•  H He C N O Na Mg P S Cl K Ca Fe
4
Fig. 2-02
Carbon (C): 18.5%
Oxygen (O):
65.0%
Hydrogen (H):
9.5%
Nitrogen (N):
3.3%
Calcium (Ca): 1.5%
Phosphorus (P): 1.0%
Potassium (K): 0.4%
Sulfur (S): 0.3%
Sodium (Na): 0.2%
Chlorine (Cl): 0.2%
Magnesium (Mg): 0.1%
Trace elements: less than 0.01%
Manganese (Mn)
Boron (B)
Chromium (Cr) Molybdenum (Mo)
Cobalt (Co)
Selenium (Se)
Silicon (Si)
Copper (Cu)
Tin (Sn)
Fluorine (F)
Vanadium (V)
Iodine (I)
Zinc (Zn)
Iron (Fe)
WHAT IS AN ATOM?
•  Def’n - The smallest elemental units
+
-
6
WHAT IS A COMPOUND?
•  Def’n - A substance composed of
precise proportions of two or more
elements in a specific geometric pattern
H20
7
WHAT IS A MOLECULE?
•  Def’n - The smallest unit of a
compound
H20
8
WHAT IS A MIXTURE?
•  Def’n - Two or more elements or
compounds in various proportions e.g.
soda pop = water, sugar, carbon
dioxide, etc.
Soda pop
9
WHAT IS AN ATOM?
•  Def’n - The smallest elemental units
+
-
10
A FACT
•  Each element has a unique number of
protons in the atomic nucleus (atomic
number)
•  H = 1 He = 2 C = 6 N = 7 Fe = 26
11
A FACT
•  Atoms will react with other atoms
when there are vacancies on their
outmost electron shells
•  Prediction - Helium (full shell) should
be stable and Hydrogen (half-empty
shell) should be reactive
12
COVALENT BONDS
•  Caused by closely-positioned atoms sharing
electrons •  The number of covalent bonds formed
within a molecule depends upon number of
vacancies in outer electron shell
ATOMIC NUMBER
H = 1 O = 8 C = 6 N = 7
13
HYDROGEN BONDS:
•  Weak and temporary in nature
Polar
14
IONIC BONDS
•  Bonds between atoms of opposite charge
•  Electrons are transferred across atoms
Atomic Number
Na = 11(1) Cl = 17(7)
15
IONIC BONDS
Sodium and Chlorine
Atomic Number
Na = 11(1) Cl = 17(7)
11
2
8
1
17
2
8
7
16
IONIC BONDS
Sodium and Chlorine
Atomic Number
Na = 11(1) Cl = 17(7)
2
8
1
2
8
7
17
IONIC BONDS
Sodium and Chlorine Ions
Na+ = 11(8) Cl- = 17(8)
_
+
11
2
8
17
2
8
8
18
WATER IS POLAR
19
WATER IS SPECIAL:
•  3 phase presence
•  Heat sink
•  Cold sink
•  Cohesion
•  Ice floats
•  Good solvent
20
COHESION PROVIDES
SURFACE TENSION
•
.
.
21
COHESION PROVIDES
SURFACE TENSION
•
http://www.youtube.com/watch?v=45yabrnryXk
.
.
22
CARBON IS SPECIAL
•  Carbon-based compounds are termed
“organic”
•  More than 2 million organic compounds are
known
•  Polar carbon compounds are soluble in
water
23
CARBON-BASED VARIATION
24
FUNCTIONAL GROUPS:
•  Def’n - A specific arrangement of
atoms that helps define the properties
of a chemical compound e.g. amino
groups.
25
SOME FUNCTIONAL
GROUPS
26
A FACT
•  Complex organic molecules
(polymers) are assembled in a simple,
modular manner
27
GREAT POTENTIAL
•  20 amino acids assembled into chains
of 100 units gives 20 100 different
possible combinations.
•  Number of combinations = number of
different units to the exponent length
of string N = us
28
DEHYDRATION SYNTHESIS
HO
H
HO
H
Monomer
Short Polymer
H2O
HO
H
Longer Polymer
29
IMPORTANT
MACROMOLECULES
•  Carbohydrates •  Lipids
•  Proteins
•  Polynucleotides
30
CARBOHYDRATES
•  Principle subtypes:
–  Monosaccharides e.g. glucose
–  Disaccharides e.g. sucrose (glucose + fructose)
–  Polysaccharides e.g. starch, glycogen, cellulose
31
CARBOHYDRATES
•  Glycogen vs. Starch Starch
chemistry
32
A FACT:
•  Approximately 1 trillion tons of
cellulose are synthesized on earth
every year.
33
CHITIN
•  One of the most common
polysaccharides on our planet
34
CHITIN
•  One of the most common
polysaccharides on our planet
35
LIPIDS
•  Principle subtypes:
–  Fats,oils
–  Waxes
–  Phospholipids
–  Steroids
36
HOW SOAP WORKS
•  A SOAP MICELLE
.
37
PROTEINS
•  Some functions: structural, energy
storage, transport, cell movement,
hormones, venom, etc.
38
GENERIC AMINO ACID
39
PROTEIN SYNTHESIS
PEPTIDE
WATER
40
NUCLEOTIDES
41
THE GENETIC CODE
•  DNA - deoxyribonucleic acid
•  RNA - ribonucleic acid
42
3 OTHER NUCLEOTIDES
•  C- AMP
•  ATP
•  Co-enzymes
43
D’ARCY THOMPSON
•  “ we are prisoners of the
perception of our size and rarely
recognize how different the world
must appear to small animals …
Our relative surface area is so
small at our large size, we are
ruled by gravitational forces
acting upon our weight. But
gravity is negligible to very small
animals …” SCALE
•  Length and weight
10-8
10-5
10-1.5
10 0.3
10 1.5
Meters
SCALE
•  Length and weight - volume = L3
10-8
10-13
10-5
10-1.5
10 0.3
10 1.5
Meters
108
Grams
GRAVITY AND COHESION
•  Cohesion ∝ L2
10-8
10-5
Gravity ∝ L3
10-1.5
10 0.3
10 1.5
Meters
108
Grams
10-13
SOMETIMES SIZE
MATTERS
•  e.g. gravity effects on big vs small animals
True
Lies
BODY SIZE AND SUPPORTING
STRUCTURE
•  Proportional skeletal mass increases with body size
BODY SIZE AND SUPPORTING
STRUCTURE
•  Proportional skeletal mass increases with body size
MICROCLIMATES
•  Non-obvious opportunities