Download Chapter 3 -- Biochemistry

Honors Biology
“The Chemistry of Life”
Chapter 2
This material is a quick review from
your middle school science curriculum.
ROOT WORD
MEANING
Ad-
To, near
Co-
Hydro-
together
related to water
-lysis
Split, loosen
Mono-
one
Di-
two
Poly-mer
Tri-saccharide
IsoIn-
consisting of many units
segment
consisting of three
sugar
Same, equal
Not, without
Important Root Words
Proton 
Neutron
Electron
Proton
+ (nucleus)
 0 (nucleus)
 - (orbital)
Electron
Neutron
General Atomic Structure

An atom is the smallest part of all matter.

Matter that contains only one kind of an
atom is known as an element.

Examples of Elements:

Each element is unique in the number of
protons its atoms contain
◦ C, H, O, P, N, Na, Cl
◦ An atom containing 6 protons is a carbon atom
◦ An atom containing 8 protons is an oxygen
atom
ATOM
vs.
ELEMENT

When an atom loses or gains an electron
it becomes an ion.
POSITIVE IONS vs. NEGATIVE IONS
-2 or more atoms
bonded together
EXAMPLES:
-2 or more different
atoms bonded together
MOLECULES
NaCl
H2O
O2
COMPOUNDS
NaCl
H2O
----
DO YOU SEE A PATTERN BETWEEN A MOLECULE AND A COMPOUND??
MOLECULE
vs.
COMPOUND
Comprehension Check
• What is the difference between a
molecule and a compound?
• Would 2Fe be a molecule, a compound
or neither?
• What about O2?
# of atoms = subscript # (if there is no # “assume”
1)
 Ex: H2O
# Hydrogen atoms = 2 atoms
# Oxygen atoms = 1 atoms
TOTAL
= 3 atoms



If there is a BIG number (coefficient) in FRONT of
the element or formula, then distribute through all
subscripts
Ex: 2H2O
# H atoms 2 x 2 = 4 atoms
# O atoms 2 x 1 = 2 atoms
TOTAL
= 6 atoms
Counting # of Atoms in a Compound

Write down everything you know about
the following equation (for example: name
the compounds involved, # of molecules,
# of atoms in each molecule and the
products/reactants):
C6H12O6 + O2  CO2 + H20
Understanding Formulas and Equations
1. Compounds Involved
2. # of molecules
3. # of atoms in each
molecule
1.
Sugar, Carbon Dioxide,
Water
2.
1 Sugar, 1 Oxygen, 1
Carbon Dioxide, 1 Water
3.
24 in Sugar, 2 in Oxygen,
3 in Carbon Dioxide, 3 in
Water
4.
Carbon Dioxide, Water
5.
Sugar, Oxygen
4. Products
5. Reactants
C6H12O6 + O2  CO2 + H20
N2 + H2  NH3
Na + O2  Na2O
C6H12O6  C2H5OH + 2CO2
Identify the products and reactants in the
chemical equations and then balance each.
ANSWERS:
REACTANTS  PRODUCTS
N2 + 3H2  2NH3
4Na + O2  2Na2O
C6H12O6  2C2H5OH + 2CO2
Comprehension Check
Can you balance the equation below?
C6H12O6 + O2  CO2 + H20
C6H12O6 + O2  6CO2 + H20
C6H12O6 + O2  6CO2 + 6H2O
C6H12O6 + 6O2  6CO2 + 6H2O
A simple solution is
basically two substances
that are going to be
combined.
 A solute is the substance
to be dissolved (sugar).
 The solvent is the one
doing the dissolving
(water).
 As a rule of thumb, there is
usually more solvent than
solute.

SOLUTIONS (Solvent vs. Solute)
Hydrogen bond
Water is a polar molecule
This electric charge allows the water molecule to "wiggle" its
way between certain atoms in some molecules (salts).
WATER: The Universal Solvent
Ion in
solution
Salt
crystal
Comprehension Check
• Why is water the universal
solvent?
pH scale
Oven cleaner
Bleach
Ammonia solution
What type of
scale is this????
Soap
Sea water
Neutral
Increasingly Acidic
Each step up the
scale means that
there is 10x more
H+ or OH- than
the next step.
Acid:
more H+
Human blood
Pure water
Milk
Normal
rainfall
Acid rain
Tomato
juice
Lemon juice
Stomach acid
Neutral : equal
amounts of
OH- and H+
Base: more
OH-
Compounds that break apart
in water to form a hydrogen
ions (H+).
Compounds that break
apart to form a negatively
charged hydroxide ions
(OH-) in water.
The more H+ ions, the
stronger the acid.
The more OH- ions,
the stronger the base.
ACIDS
BASES

The blood of humans is so sensitive to H+
concentration that a small change from
your normal pH of 7.4 can result in your
death. Buffer systems regulate this using
weak acids and weak bases.
Why is pH important?
Comprehension Check
• How can we test to find if a
solution is an acidic or basic?
• What can pH tell us about a
solution?
Activation Energy is the minimum
amount of energy needed to start a
reaction
 A substance known as a catalyst can
help lower activation energy
 An enzyme is a special kind of catalyst

Starting a Reaction

Chemical Change: a reaction where the
products can NOT return to their form as
reactants
Example: Log + Fire  Ashes

Physical Change: a reaction where the
products can return to their form as
reactants
Example: Ice + Heat  Water
ALWAYS ASK YOURSELF “Can I go back to the original?”
CHEMICAL CHANGE vs. PHYSICAL CHANGE

Frying an Egg

(chemical)

Vaporization of Dry
ice
(physical)

Breaking Glass
(physical)

Souring Milk
(chemical)
Boiling water
(physical)

Burning Gasoline
(chemical)

Compression of a
spring
(physical)
Determine whether these are physical or chemical changes:
Comprehension Check
• What is the difference between a
physical and a chemical change?
• Which reaction has a lower activation
energy, the melting of an ice cube or
the frying of an egg?
Chapter 3 -- Biochemistry
Honors Biology
This is new content that you did not
learn in middle school!
Compounds Important to Life
1.
Organic Compounds


Compounds derived from living things and containing carbon
Most common organic compounds in living things classified in
four groups




2.
Carbohydrates
Fats (Lipids)
Proteins
Nucleic Acids
Inorganic Compounds


Compounds derived from non-living things
Some inorganic compounds are essential for life:





Water
Carbon dioxide
Nitrogen compounds
Minerals
Vitamins
Carbon (Organic) Compounds

Carbon links readily with other atoms (it has 4
bonding sites to form covalent bonds), it forms the
backbone upon which other atoms can build.

Carbon also bonds to other carbon atoms forming
chains, rings or branched chains.
**All of these compounds
are isomers because they
have the same number of
atoms, but different
structures!**
Comprehension Check
• Which set of molecules below would
be isomers?



Hydrogen Bonds
 Hydrogen bond: forms
when a hydrogen atom
covalently bonded to one
electronegative atom is
attracted to another
electronegative atom
 This is a bond BETWEEN
molecules (different from
polar covalent bond)
 Intermolecular forces
 FON, DNA, folding in
protein
O
H
H
N
H
Hydrogen Bonds Video
Are inorganic compounds important?
 Life first evolved in water and most life on this planet lives
in water.
 Plants and animals are 70%-90% water.
 Pure water is rare
 Because of all these facts, water is the most
important inorganic compound






Water is polar
Water is the universal solvent
Most cellular activities take place in water
Adhesion/Cohesion
Stabilizing role within living organisms (high specific heat)
Expansion on freezing
Comprehension Check
Assume the arrows in the models below
indicate the “pull” of electrons in a
particular direction. Using this
information, determine which molecules
are polar or nonpolar. Using this
information, determine which would
dissolve in water.



Comprehension Check
• Is C02 an organic compound? Why or why not?
• Are the hydrogen bonds between water molecules
strong enough to make water a substance that is
hard to heat?
• Name 3 important chemical or molecular
characteristics about water.
• Which of the picture below is showing adhesion
and which is showing cohesion?
Carbon Compounds
 Monomers
 Basic organic units which make up
polymers
 Polymers
 Compounds consisting of repeated
linked units/monomers
 Macromolecules are large polymer
units
Example: Carbohydrates include both
sugar (simple carbs or monomers) and
starch (complex carbs or polymers)
Monomers  Polymers
 Reactions between organic compounds either build
monomers into polymers or break polymers into monomers.
 Condensation Reaction (Dehydration Synthesis)
 Occurs when two monomers are chemically combined
and water is released
Example: 2 Amino Acids  1 Protein + H2O
 Hydrolysis Reaction
 Occurs when a polymer is broken down with the addition
of water
 A reversal of condenstaion
Example: 1 Disaccharide + H2O  2 Monosaccharides
Hydrolysis Animation
Glucose
Glucose
Maltose
Comprehension Check
1. Match the definition with the correct term.
A. Condensation
B. Hydrolysis
C. Monomer
D. Polymer
______
Large molecule that consists of many subunits called
D.
monomers
______
Identical or similar subunits of a polymer
C.
A.
______
Process of linking monomers to form a polymer
______
Loss of a water molecule between two monomers to
A.
form a covalent bond between the monomers
______
Breaking the covalent bond between monomers by
B.
adding a water molecule
Carbohydrates
 Organic compounds that contain carbon,
hydrogen and oxygen in a set ratio
(CH2O: Hydrogen and oxygen are in the same
ratio as water)
 Monomers = Monosaccharide
 Dimer = Disaccharides
 Polymers= Polysaccharides
 There are two main functions of carbohydrates:
 Structure (arthropods-- glycogen and plants-cellulose)
 Energy
Carbohydrates
Three groups of carbohydrates exist
1.
Monosaccharide (monomers)

Examples: Glucose, Fructose, and
Galactose

General Form: C6H12O6

All three are isomers of one another
2.
Disaccharides (dimer)

Two monosaccharides form in a
condensation reaction forming a
double sugar (12 Carbon Sugars)

General Form: C12H22O11 (why not
exactly CH2O?)

Examples: Sucrose, Maltose,
Lactose
3.
Polysaccharides (polymer)

Complex molecule composed of
three or more monosaccharides

Examples: Glycogen (Animal),
Cellulose (Plant)
Comprehension Check
Imagine there were three different solutions on
your desk. If you were to taste each solution, how
could you decide if you were tasting a
monosaccharide, disaccharide, or polysaccharide.
• Which would be sweetest, a mono-, di-, or
polysaccharide?
• Using the concept of molecular structure, explain
why polysaccharides taste different than
monosaccharides?
Testing for Carbohydrates
 Monosaccharide (Sugar) 
Benedict’s Test
 Add equal parts of the solution
and benedicts
 Heat for a few minutes
 Bright Colors = Sugar Present
 Polysaccharide (Starch) 
Iodine Test
 Add equal parts of the solution
and iodine
 If it turns black/dark purple
there is starch present
Lipids
 Fatty Compounds made up of carbon, hydrogen and
oxygen (Fats, Oils and Waxes)
 The monomers that make-up most lipids is called a fatty
acid
 Lipid polymers are a little different than the others, they
are Made up of long straight hydrocarbon chain with a
carboxyl group attached to one end
 Important characteristics of lipids:
 Do not dissolve in water
 Store energy efficiently
 Important functions of lipids:
 Cell Membrane (Lipid Bi-layer)
 Long term energy storage
 Prevent Desiccation
Lipids
 Four kinds of lipid polymers exist:
 Triglyceride
 Macromolecules which are
composed of three fatty acid
molecules attached to one
glycerol molecule
 Examples: Oils from plants
(peanut, olive, corn), Fats
from animals (butter, lard)
 Phospholipids
 two fatty acids and a
phosphate group are
attached to glycerol
 Waxes
 Long fatty acid chain joined
to a long alcohol chain
 Steroids/Blood Lipids
(Cholesterol)
 Lipids which are composed
of four carbon rings
 Considered lipids because
they do not dissolve in water
Testing for Lipids
 Lipid (Fat) Test  Brown Paper Towel Test
 Add and few drops of the solution to a BROWN paper towel
 Wait for the solution to DRY
 If it is transparent there is lipid present


Proteins
Organic compounds composed of hydrogen, oxygen, carbon and nitrogen
Monomers: Amino Acids
 When amino acids link, they share a peptide bond and
form a long chain called a protein
 Basic Structure of a Protein:



There are two types of proteins
 Dipeptide (Two amino acids bonded together)
 Polypeptides (Long chain of amino acids)
Proteins can be both fibrous and globular
 Examples:Hair, Spider Webs, Hemoglobin
TWO main functions of proteins:
 Build body tissues
 Form enzymes
Functional Groups
A cluster of atoms in a compound that
influences the properties of that
compound.
Example: hydroxyl group, phosphate
group, carboxyl group, R group
More on functional groups
 The functional groups are
– Hydroxyl group—consists of a hydrogen
bonded to an oxygen
– Carbonyl group—a carbon linked by a double
bond to an oxygen atom
– Carboxyl group—consists of a carbon doublebonded to both an oxygen and a hydroxyl group
– Amino group—composed of a nitrogen bonded
to two hydrogen atoms and the carbon skeleton
– Phosphate group—consists of a phosphorus
atom bonded to four oxygen atoms
Copyright © 2009 Pearson Education, Inc.
Test for Protein
 Protein Test  Biuret’s
Test
 Add equal parts solution
and biuret
 If the solution turns
lavender then there is
protein present
Comprehension Check
• What type of
organic compounds
are these?
ENZYMES
 Enzymes speed up chemical reactions and lower
activation energy
 3-Dimensional structure (what type of protein is this?)
 Names usually end in –ase
 Examples: Maltase, Amylase, Carbonic Anhydrase
 Enzyme function can be regulated by temperature and pH
 Enzymes can be reused over and over again!
Enzyme Activity
-Enzymes are very specific. The substrate must fit into the
active site on the enzyme. (Enzyme-Substrate Complex)
-“Lock and Key Model” is often used to describe enzyme
function:
Coenzymes
 Help substrates fit into the active site
on the enzyme
 REMEMBER: Vitamins are NOT
proteins!
Comprehension Check
• What do enzymes have to do with
activation energy?
• Are vitamins an organic compound?
Nucleic Acids
 Nucleotides
 Monomer unit of nucleic acids
 Made up of phosphate group, five carbon
sugar and a ring shaped nitrogen base
Three main types of nucleic acids:
 DNA
 Polymer that records instructions for the cell
and transmits them from generation to
generation
 RNA
 Polymer that reads instructions from DNA and
carries them out
 ATP
 Molecule used to store/release energy in
cellular reactions
Comprehension Check
• What is the major function of:
»Carbohydrates
»Lipids
»Proteins
»Nucleic Acids
• What is the advantage for organic
compounds to consist of polymers
built from smaller monomers?