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Unit 1 - Introduction
I. Biology - the study of life.
A.Enormous
in scope.
B. Size scale from submicroscopic
molecules to global distribution of
biological communities.
C.
Encompasses life over
huge spans of time from
contemporary organisms to
ancestral life.
• Biology is an ongoing
process.
•During the last few decades
we have had an information
explosion.
II. 10 Major Themes
A.
Emergent Properties properties that emerge as a
result of interactions between
components.
cell – basic unit of
structure and function.
The
C. Heritable Information.

DNA and genes
Correlation between Structure & Function
Interaction with the Environment
Regulation
Unity & Diversity
D.
E.
F.
G.
•
•
1.5 million species
6 kingdoms
8. Evolution.
 Core
theme of biology.
 Life evolves, similar species share common
ancestry, less closely related species share
more ancient common ancestors.
9.
Scientific Inquiry
10. Science,
Technology & Society
III. Water
The cradle of life.
A. Unique properties of water:
1.
2.
3.
4.
5.
Liquid at normal temp.
Provides a medium in which other
molecules can interact.
Composes 2/3 of most organisms.
Forms weak chemical associations.
Simple atomic structure.
B. Water acts like a magnet.
1.
Electronegativity
attracts electrons
of hydrogen and
oxygen in a water
molecule. A
polar molecule.
2. Water clings to polar
molecules.
– Attraction of like molecules.
(Attraction of water to water.)
 Adhesion – Attraction of unlike molecules.
(Attraction of water to another molecule.)
 Cohesion
Water con’t.
3.
Water stores heat, and has a high specific heat,
because of polarity.
Water con’t.
4.
Water is a
powerful
solvent. Water
molecules gather
around charged
molecules.
Water con’t.
5.
Water organizes nonpolar
molecules. Water excludes
nonpolar molecules.
a. Hydrophobic – not soluble in water,
nonpolar.
b. Hydrophilic – soluble in water,
polar.
Water con’t.
6.
Water ionizes.
Water con’t.
7.
Buffers –
minimize
changes in H+
and OH –
concentrations.
III. Carbon
A.
Four bond sites.
III. Carbon, con’t.
B.
Bonds with itself
to form chains or
polymers.
Subunits are joined
by covalent bonds.
-OH is removed
from one subunit
and H+ is removed
from the other
subunit.
Dehydration synthesis
A condensation reaction. A molecule of water
is removed as subunits are linked. Requires
the input of energy to assemble.
Anabolic pathways build macromolecules
from subunits.
This process is carried out by enzymes.
Hydrolysis Reaction
A molecule of water is added as subunits are
broken apart. This process is also carried
out by enzymes.
Catabolic pathways disassemble molecules
into subunits.
C. Can form single,
double, or triple bonds.
D. Can form isomers
(molecules with the
same molecular
formula but a different
structural formula.)
3 types of isomers:
1.
2.
3.
Structural isomers – differ in the covalent
arrangement of their atoms.
Geometric isomers – molecules that have
the same covalent partnerships, but differ
in their spatial arrangements.
Enantiomers – isomers that are mirror
images of each other.
E. Functional Groups:
1.
2.
Hydroxyl Group - -OH polar
molecule, the alcohols, names end in –ol.
Carbonyl Group - -CO or C=O at
the end of a molecule an aldehyde and
their names end in –al. If the C=O is not
at the end the molecule it is a ketone and
their names end in –one.
E. Functional Groups:con’t.
3.
4.
Carboxyl Group - -COOH or
carboxylic acids or organic acids. The
hydrogen on the end tends to dissociate
creating the hydronium ion.
Amino Group - NH2 or
Amines, can act as a base.
E. Functional Groups:con’t.
5.
6.
Sulfhydryl Group - -SH Thiols that
help to stabilize the intricate structure of
proteins.
Phosphate Group -PO4 Transfer
energy between organic molecules.
4 Major Classes of Organic
Molecules
Energy:
 Carbohydrates
and Lipids
• Similar in all organisms
• Unit sequence is not coded by DNA (based on
particular enzymes only.
Information:
 Proteins
and Nucleic Acids.
• Distinctive in each organism.
• Unit sequence is coded by DNA.
Carbohydrates
Sugars and their polymers
1. Monosaccharides –
 Simple
sugars
 CH2O
end in –ose
 Hexoses, trioses,and pentoses.
 Sugars form rings in water solutions.
 Names
2. Disaccharides
 Double
sugars
 In this form the sugar is protected from
being metabolized during transport.
3. Polysaccharides
 Few
hundred to thousands of monomers
long
 General formula (C6H10O5)n
Storage polysaccharides
 Starch
– polymer of glucose.
• Amylose – helical chain (simplest form) found
in plants.
• Amylopectin – helical chain with branches, also
found in plants.
• Glycogen – animal starch, stored in the liver
and muscle (in humans stores about 1 days
worth)
Structural polysaccharides
– composed of chains of the 
form of glucose.
 Cellulose
• Cellulose chains – hydrogen bonds hold the
chain together into units called. Microfibrils.
• Several intertwined microfibrils make a
cellulose fibril.
• Several cellulose fibrils can supercoil making a
very strong cable.
can digest 
glucose but few organisms
can digest  glucose.
Enzymes
Chitin
 Exoskeleton
of insects and some fungi.
Contains the amino group. Sometimes
called an amino sugar.
Lipids
1.
2.
Have little or no affinity for water.
3 main groups:
a. Fats
b. Phospholipids
c. Steroids
3. Fats
 Made
of glycerol and 3 fatty acids
(triglycerides).
 Saturated fats – all single bonds between the
carbons in the fatty acids. Animal fats,
solidify at room temperature.
 Unsaturated fats – have some double and/or
triple bonds between carbons. Plant fats,
liquid at room temp.
3. Fats con’t.
 Hydrogenated
fats are unsaturated fats with
hydrogens added such as peanut butter and
margarine.
 In
animals, fat is used for energy storage
because it takes up less space than
carbohydrates.
4. Phospholipids
 Composed
of 2 fatty acids and 1 phosphate
group attached to the glycerol molecule.
 Major component of the cells membranes.
5. Steroids
 Have
a carbon skeleton of 4 interconnected
rings.
 Cholesterol – part of the animal cell
membrane and is a precursor for many other
steroids.
Proteins
Many structures
Many functions
1. Used for:
a.
b.
c.
d.
e.
f.
g.
Structural support
Storage
Transport of other substances
Signaling from one part of the organism to
another.
Movement
Defense against foreign substances
Enzymes used for chemical reactions
2. Protein facts:
a. Proteins are the most structurally complex
molecules known. Each type of protein has a
complex three-dimensional shape or
conformation.
b. All protein polymers are constructed from the
same set of 20 monomers, called amino acids.
c. Polymers of proteins are called polypeptides.
d. A protein consists of one or more polypeptides
folded and coiled into a specific conformation.
3. A polypeptide is a polymer of amino acids
connected in a specific sequence.
a.
b.
Amino acids consist of four components
attached
to a central carbon atom.
These components include a
hydrogen atom, a carboxyl
group, an amino group, and
a variable R group
(or side chain).
•
Differences in R groups
produce the 20 different
amino acids.
c.
One group of amino acids has
hydrophobic R groups.
d.
Another group of amino acids has polar
R groups, making them hydrophilic.
e.
The last group of amino acids includes
those with functional groups that are
charged (ionized) at cellular pH.
Some R groups are bases, others are
acids.
4. Amino acids are joined together when
a dehydration reaction removes a
hydroxyl group from the carboxyl end of
one amino acid and a hydrogen from the
amino group of another.
The resulting covalent bond is called a
peptide bond.
5. A protein’s function depends
on its specific conformation
a.
b.
A functional protein consists of one or more
polypeptides that have been precisely twisted,
folded, and coiled into a unique shape.
It is the order of amino acids that determines
what the three-dimensional conformation will
be.
c.
d.
A protein’s specific conformation
determines its function.
In almost every case, the function depends
on its ability to recognize and bind to
some other molecule.
1) For example, antibodies bind to particular
foreign substances that fit their binding sites.
2) Enzymes recognize and bind to specific
substrates, facilitating a chemical reaction.
e. Protein Structure
1)
2)
Three levels of structure: primary,
secondary, and tertiary structure, are used
to organize the folding within a single
polypeptide.
Quarternary structure arises when two or
more polypeptides join to form a protein.
3)
The primary
structure of a
protein is its unique
sequence of amino
acids.
•
The precise primary
structure of a protein
is determined by
inherited genetic
information.
Even
a slight change in primary structure can
affect a protein’s conformation and ability to
function.
4)
The secondary structure of a protein results
from hydrogen bonds at regular intervals along
the polypeptide backbone.
Typical shapes
that develop from
secondary structure
are coils (an alpha
helix) or folds
(beta pleated
sheets).
5)
Tertiary structure is determined by a variety of
interactions among R groups and between R
groups and the polypeptide backbone.
These interactions include hydrogen
bonds among polar and/or charged
areas, ionic bonds between charged
R groups, and
hydrophobic interactions and van
der Waals interactions among
hydrophobic R groups.

 While
these three interactions are relatively weak,
disulfide bridges, strong covalent bonds that form
between the sulfhydryl groups (SH) of cysteine
monomers, stabilize the structure.

Quarternary structure results from the aggregation of two
or more polypeptide subunits. Examples:
• Collagen is a fibrous protein of three polypeptides that are
supercoiled like a rope.
– This provides the structural strength for their role in connective tissue.
• Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides.
A protein’s conformation can change in
response to physical and chemical
conditions.
Alterations in pH, salt concentration,
temperature, or other factors can unravel
or denature a protein.
f.

•
These forces disrupt the hydrogen bonds,
ionic bonds, and disulfide bridges that
maintain the protein’s shape.
 Some
proteins can return to their functional
shape after denaturation, but others cannot,
especially in the crowded environment of
the cell.
In
spite of the knowledge of the threedimensional shapes of over 10,000
proteins, it is still difficult to predict
the conformation of a protein from its
primary structure alone.
• Most proteins appear to undergo
several intermediate stages before
reaching their “mature”
configuration.
• The folding of many proteins is protected by
chaperonin proteins that shield out bad
influences.
h. Enzymes
Protein molecules,
Names end in –ase,
These are organic catalysts.
Used by a cell to lower the activation energy
needed to start a chemical reaction.
Induced-fit model is used to describe how an
enzyme works.
Speed – 1,000 or more reactions/second.
Enzyme helpers:
1.
2.
Cofactors – small nonprotein molecules
that are required for proper enzyme
catalysis (ex. Zn, Fe, Cu)
Coenzymes – organic compounds (ex.
Vitamins)
i. Some factors that affect enzyme
action:
1.
2.
3.
Temperature
pH
Salinity
The End of Unit 1