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BIOCHEMISTRY
The chemical
basis of life
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ATOMS


Basic unit of matter
Two regions


Nucleus
Electron cloud
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Subatomic Particles
• Protons 
• Positively charged particles
• Located in the nucleus
• Neutrons 
• Neutral particles
• Located in the nucleus
• Electrons 
• Negatively charged particles
• Located in the electron cloud
• These are the particles involved when
atoms bond with other atoms
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 Electrons
orbit the nucleus.
 An atom is only about
0.0000000001 meters big. It
would take 10 BILLIONS atoms
lying side by side to equal 1
meter!
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Atomic Number
 The
number of protons distinguishes
an atom of one type from another.
 All atoms of the same element have
the same number of protons.
 This unique number is
called the atomic number.
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Atomic Mass
 The
atomic mass is equal to
the total number of protons
plus neutrons in an atom.
Atomic Mass = P + N
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Mass Number
 The
mass number can be written
as a superscript above the symbol
and the atomic number as a
subscript below the symbol.
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Elements & Isotopes

Elements: Simplest Pure Substance

Elements of Life
• 96%  Carbon (C), Hydrogen (H), Oxygen (O), and
Nitrogen (N)
• 3%  P, S, Ca, K, Na, Mg, Fe, Cl
• 1%  other trace elements

Isotopes
• Atoms of the same element that contain a
different number of neutrons
• Radioactive isotopes will breakdown at a specific
rate and are used in determining the age of
various things (i.e. fossils & rocks)
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Isotopes
Atoms of the same element can have
different numbers of neutrons.
 These different forms of the same
element are called isotopes.


The atomic mass is the average mass
of all the known isotopes of the
element.
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Atoms

All atoms are neutral; they have the
same number of electrons as protons.
Example: An atom of 42He has an atomic
number of 2 and a mass of 4.
Therefore, it has 2 protons and 2
neutrons in its nucleus.
Since it has 2 positive protons (neutrons
are neutral) it must have 2 negative
electrons to make the total charge
neutral.
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How are electrons arranged?
Electrons are located in different energy
levels.
 The farther away from the nucleus the
electron is found, the higher the energy.
 As electrons move from a lower level to
a higher level energy is absorbed.
 As electrons move from a higher level to
a lower level energy is release in the
form of light.

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Periodic Table
Group
Period



The elements are listed in order of increasing
atomic number.
By looking at the row (period) number you can
determined how many energy levels an atom
has.
By looking at the column (group) number you
can determine how many electrons are in the
outermost level.
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Comparing Atoms
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How does one kind of atom
differ from another?
Number
of protons
determines an element.
Even if atoms bond or
break apart, the
number of protons will
always be the same.
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Chemical Compound
 Pure
substance formed by two
or more elements chemically
combined.
 Ex: water: H2O, sodium chloride NaCl
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Types of Bonds
 Ionic:
The TRANSFER of electrons
between a metal and a nonmetal
 Covalent: The SHARRING of electrons
between two or more nonmetals
 Two
Types: Polar and Nonpolar
 Metallic:
A “sea of electrons” around
two or more metals
 Animations:
http://ithacasciencezone.com/chemzone/lessons/03bonding/mleebon
ding/covalent_bonds.htm
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Bonding by Analogy

Sometimes it helps to think
of bonds (which you can't
see) in terms of familiar
things you can see. This is
called an analogy. Let's
use the natural attraction
between dogs and bones as
an analogy to the
attraction between
opposite charges and
atomic or intramolecular
bonds.
http://ithacasciencezone.com/chemzone/lessons/03bondi
ng/dogbonds.htm#Ionic%20Bonding
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A neutral atom contains an equal number
of positive and negative charges.
 In a sense, the atoms fight over the
available electrons in much the same way
two or more dogs will fight over bones.




The bone and the electron are very similar.
The Dog - Bone analogy works quite well
for three of the four types of atomic
bonds. (van der Waal's forces are the
only one which cannot be represented
with this analogy)
http://ithacasciencezone.com/chemzone/lessons/03bonding/dogbo
nds.htm#Ionic%20Bonding
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 Ionic
bonds: One big greedy thief dog!
 Covalent bonds: Dogs of equal
strength.
 Polar Covalent bonds: Unevenly
matched but willing to share.
 Metallic bonds: Mellow dogs with
plenty of bones to go around.
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Ionic Bonds
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Covalent Bonds



Sharing of electrons
These are stronger bonds
than either of the other two
types because the electrons
are shared.
Your body is based upon
carbon bonding.


So the covalent bond is
considered the most important
bond with regards to life.
Interestingly, Si, just above C
in the periodic table, with its
covalent bonding, is the
basis for the computer
industry.
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Metallic Bonds
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Van der Waals Bonds
 When
molecules
are close together
an attraction can
develop between
oppositely
charged regions of
nearby molecules
 Example:
water
molecules
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Geckos and Van der Waals
Geckos can stick to so many surfaces
in a seemingly impossible manner.
 Specifically, the tiny hairs on the
gecko's feet (called setae) are split
at the microscopic level into as
many as 1,000 branches.

As a result, even though the Van der Waals
forces acting on an individual tip is small, the
adhesion of a billion or so tips
adds up to enough force to let
the gecko stick to basically
anything.
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Water (H2O)
 Most
abundant compound
in organisms
 Water is polar
 Unequally
shares electrons between
hydrogen & oxygen atoms
• Makes it possible for
other compounds to
dissolve in water
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Water has Hydrogen Bonds
 Adhesion
– the attraction of unlike
molecules to one another
 Cohesion – the attraction of
like molecules to one another
Cohesion causes water to
form drops, surface tension
causes them to be nearly
spherical, and adhesion keeps
the drops in place.
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Property Meaning
Importance
1. Transparency
Light passes through water
Light reaches chloroplast in cells and
aquatic plants
2. Universal
Solvent
Many compounds dissolve in
water
Dissolved compounds can be brought
to cells (via sap or blood) or move
about cell cytoplasm.
3. Cohesion
4. Adhesion
Water molecules stick
together due to H bonds.
Water molecules stick to
other molecules
Small animals may walk on water.
5. Heat Capacity
Large amounts of energy are
needed to raise temp of
water
Water bodies have stable
temperatures. Body temps can be
maintained. Transfer of heat from
warm to cool body parts
6. Heat Point
Capacity
7. Density of Ice
Much energy needed to pull
water molecules apart.
Ice is less dense than water
so it floats
In nature, water rarely boils so life is
spared.
Ice insulates organisms living
beneath
8.Evaporation
Evaporation (boiling)
requires much energy.
Evaporation can cool warm cells
Capillary action. Water pulled to top
of trees
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Properties of Water
 Solutions
and suspensions
 Mixtures
are composed of 2 or more
elements or compounds that are
physically mixed, but not chemically
combined
 There are two types of mixtures that
can be made with water
• Solutions
• suspensions
 Solutions
solvent
– made of a solute and a
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Properties of Water
 Solutions
 Made
of a solute and a solvent
 Usually water acts as a solvent
• Polar water molecules are able to pull apart
the solute to form a solution
• Water is known as the “universal solvent”
 Many
biological fluids are solutions
 Solutions are also known as
homogeneous mixtures
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Properties of Water
 Suspensions
 Particles
do not dissolve in H2O and
remain suspended
 Colloids are a type of suspension
 Examples of suspensions: smoke, fog,
jello, blood
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pH scale and buffers

The pH of substances ranges from 0-14
7 = neutral
 0 - 6.9 = acid
 7.1 - 14 = base


Buffers
Prevent sharp, sudden changes in pH so
that the body can maintain homeostasis
 pH of most fluids in the body = 6.5 - 7.5

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Acidic (acid)
0-7
Neutral
Basic (base)
7 - 14
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Acids, Bases and the pH scale
[H+] = concentration of hydrogen ions
[OH-] = concentration of hydroxide ions
 The pH scale measures the concentration of H+
ions (how acidic something is)
Ranges from 0-14
At 7: H+ ions and OH- ions are equal so it is neutral
 0-7: acidic, has more H+ ions
 7-14: basic, has more OH- ions
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 ACIDS: release H+ when
mixed with water
Sour, corrosive
Ex: HCl, H2SO4
Always have H at front of formula
BASES: release OH- when
mixed with water
Bitter, slippery, usually in cleaners
NaOH, CaOH
Always have OH at end of
formula
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What is a buffer?
 Buffers are weak acids or bases that react
with strong acids and bases to prevent
sharp changes in pH
Helps to neutralize
Help to control pH in blood, digestive tract,
etc. to maintain homeostasis
Ex: Antacids buffer the stomach from the
Hydrochloric Acid (HCl)
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Organic vs. Inorganic

All compounds can be separated into two
groups:

Inorganic
• Does not contain carbon
• Non-living (never alive)
• Examples: Oxygen gas, metals, rocks, water

Organic
• Contains carbon
• Living (or dead – once was alive)
• Examples: wood, grass, diamonds, petroleum
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Inorganic Compounds
 Usually
do not contain CARBON
(except good old CO2)
 WATER-- a very curious material
 salts, compounds in our bones,
etc. but none as numerous as the
ORGANIC compounds in living
things
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Why Carbon Compounds?
Carbon (C) forms strong, stable
COVALENT bonds
 Carbon forms almost infinite chains
when bonded to other C atoms
 Chains may form as ring structures
with single or double bonds


Ex: Polymerization
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We eat polymers!
 Hey,
come on over here and have a
big slice of POLYMER pizza. It's not as
strange as it sounds. French fries are
loaded with a polymer called
starch, which your body
digests into sugar to use
as fuel.
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Polymerization
 Monomers
 One
(small)
unit of a compound
 Polymers
 Many
monomers combine to
make a polymer
 Macromolecules
 Many

(huge)
large molecules combined
Polymers are everywhere:
http://pslc.ws/macrog/paul/
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Containers

Fast food often comes in
boxes made of polystyrene foam.



Cup lids are made of polystyrene, but in plastic form
instead of foam.
Napkins are made of paper, which is made from
wood pulp, and that wood pulp has an awful lot
of the polymer cellulose.
The trays are made of polyethylene. Most of the
prizes in the kids' meals are made from
polystyrene and polyethylene or polyvinyl
chloride.
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Clothing



The polymers in clothes can be everything from
plant materials, to synthetics, to proteins like
silk and wool.
Sweaters are also made out of acrylics, like
polyacrylonitrile.
Spandex is a special kind of polyurethane that's
very stretchy. Spandex is also used in bicycle
pants, swim suits, and other items of
stretchwear.
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Carbohydrates


Made of C, H, & O
Functions



Main energy source in organisms
Structural component in plants
Types

Sugars
• gives off energy when broken down
• Cellulose  twisted chain of sugars, not digestible by
humans
• Chitin  hard cellulose found in the exoskeletons of
invertebrates
• Ex. Sucrose, fructose, glucose

Starches
• used as a storage molecule for sugars
• Many athletes eat these before events
• Ex. Bread, rice, pasta, corn
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Lipids

Made of C, H, O



Commonly called fats, oils, & waxes
Functions






in the form of glycerol and fatty acid chains
Storage of energy
Parts of biological membranes
Water proof coverings
Chemical messengers (steroids)
Insoluble in water
Ex. Lard, butter, oil, hormones, steroids
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Steriods

Steroids occur in animals in something called
hormones. The basis of a steroid molecule is a
four-ring structure, one with five carbons and
three with six carbons in the rings.

Many body builders and athletes use anabolic steroids
to build muscle mass. The steroids make their body
want to add more muscle than they normally would be
able to.
• The body builders wind up stronger and bulkier (but not
faster).
Never take drugs to enhance your body. Those body builders
are actually hurting their bodies. They can't see it because it
is slowly destroying their internal organs and not the muscles.
When they get older, they can have kidney and liver problems.
Some even die!
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Lipids...
 Saturated
fats
 all
Carbons attached by single bonds
with the maximum H atoms
 meats, dairy
 Unsaturated
C
fats
atoms joined by double bond, not
with the maximum H atoms
(more
double bonds=polyunsaturated)
 liquid fats at room temp.--sesame,
peanut, canola oils
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Fats


There are two kinds of fats, saturated and unsaturated.
Unsaturated fats have at least one double bond in one of
the fatty acids.


A double bond happens when two electrons are shared or
exchanged in a bond. They are much stronger than single bonds.
Saturated fats have no double bonds.
Fats have a lot of energy stored up in their molecular
bonds. That's why the human body stores fat as an energy
source. When it needs extra fuel, your body breaks down
the fat and uses the energy.
One molecule of sugar only gives a small amount of
energy, a fat molecule gives off many times more.
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Trans Fats
 Trans
fats are unsaturated fats
 Found in partially hydrogenated oils
 Have recently been removed from
many foods due to health concerns






N.Y restaurants
Frito Lay
Krispy Kreme
Girl Scout Cookies
Wendy’s
etc…
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and more fats…
 Sterols
 cholesterol
(HDL, LDL)
 build cells, chemical messengers
 Phospholipids
 molecules
that have parts that
dissolve in water and parts that do
not
 cell membrane structure--bilayers
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Nucleic acids
Made of C, H, O, N, & P
 Monomers are called nucleotides



Nucleotides are made up of a 5-carbon
sugar, phosphate group and a nitrogen
base
Functions
Store hereditary information
 Transmit hereditary information


Two types
RNA (ribonucleic acid)
 DNA (deoxyribonucleic acid)

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Proteins


Made of C, H, O, & N
Monomers of proteins are amino acids



There are 20 different amino acids that combine in
different ways to make millions of proteins
The most diverse macromolecules
Functions





Control the rates of chemical reactions (enzymes)
Regulate cell processes
Used to form bone & muscles
Transport substances into or out of cells
Help fight disease
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Protein
Burgers are full of proteins,
which your body uses to
build and repair itself.
 The pepperoni and the cheese on this
pizza are also loaded with proteins.


And popcorn is formed from starch, while a hot
dog is yet another source of protein. (Of course,
buttery popcorn and hot dogs also contain a lot
of fat. Fat molecules are big, but they're not
polymers.)
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Proteins & Digestion
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Polymer OR Protein
 As
we discussed
earlier, sweaters can
be made from
polymers.
 Sweaters can also be
made from wool,
which is a protein
called keratin.
 So
is your hair and
fingernails, by the
way.
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Those fabulous proteins...
of C-H-O-N
 Build structures, carry out metabolism
 made up of AMINO ACIDS
 Organics

20 common amino acids
• an amino group (NH2) on one end
• an acid or carboxyl group (-COOH) on the other
• a Hydrogen (H) atom
• a fourth compound - which determines the nature
of the amino-acid
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Amino Acid
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 Amino
Acids form
covalent
bonds
(PEPTIDE
BONDS) and
may form
EXTREMELY
long chains
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Protein structure
 One
or more polypeptide chains
 enzymes
Catalysts: decrease start up energy of RXN
 may accelerate RXN by 1010 times
 regulate chemical pathways,
release energy, transfer info
 involved in all life processes,
even in enzyme production!

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Enzymes
They usually speed up the rate of a
reaction by lowering the
amount of activation
energy needed to
start the reaction.
 end with -ase.
 Ex. lactase

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Chemical reactions
Chemical
reactions involve
the making and
breaking of
chemical bonds.
 Chemical bonds
“store” energy.
 When a bond is
broken, energy is
released (heat,
light, sound)

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Exothermic Reaction

Energy is
Released

Ex. Fireworks,
cellular
respiration,
digestion
These reactions
involve the
breaking of
polymers into
monomers

http://www2.unisiegen.de/~pci/versuc
he/english/v41-1.html
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Endothermic Reaction is one in which
energy is absorbed (stored in bonds)
 The joining of monomers into polymers.
 Ex. Photosynthesis, making proteins,
etc.

http://www.chemistryvideos.org.uk/chem%20clips/KS3%20Endothermic/enothermic.html
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Exothermic = Exergonic
Endothermic = Endergonic
http://www2.uni-siegen.de/~pci/versuche/english/kapitel4.html
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Summary
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