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Organic Molecules
Molecules that have carbon atoms are said to be organic. Macromolecules can contain hundreds or
thousands of atoms and most are polymers or molecules that consist of a single unit (monomer)
repeated many times.
Four of carbon’s six electrons are available to form bonds. This is always depicted with four
lines connecting carbon to other atoms. Complex molecules consist of a line or a ring of carbon
atoms. Functional groups are organic molecules that share similar properties because of the types of
atoms clustered together. Often, nitrogen, oxygen, and other atoms add variety to carbon molecules
and identify those clusters.
Draw the bonds that are missing. They can be single or double. Use your knowledge of
valence electrons for carbon, nitrogen and phosphorous.
Functional group
class name
examples
characteristics
Alcohols
Ethanol, glycerol, sugars
Polar, hydrophilic
Carboxylic
acids
Acetic acid, amino
acids, fatty acids, sugars
Polar, hydrophilic, weak
acid
Amines
Amino acids
Polar, hydrophilic, weak
base
Organic
phosphates
DNA, ATP,
phospholipids
Polar, hydrophilic, acid
Ketones
Acetone, sugars
Polar, hydrophilic
Aldehydes
Formaldehyde, sugars
Polar, hydrophilic
----
Fatty acids, oils, waxes
Nonpolar, hydrophobic
-OH
Hydroxyl
O
-C
OH
H
Carboxyl
-N
H
O
-P OOO
Amino
Phosphate
-CO
Carbonyl
-C-H
H
C H
H
Carbonyl
Methyl
Cliffs AP Biology 3rd edition
Chemical reactions
Chemical reactions occur when reacting molecules collide with enough activation energy to trigger the
formation of new bonds. Many reactions occur spontaneously, however a catalyst can accelerate the rate of
reaction because it lowers the activation energy required. A catalyst is any substance that accelerates a
reaction but does not undergo a chemical change itself, thus making the catalyst usable again and again.
Chemical reactions in biological systems are called metabolism, which includes the breakdown of substances
(catabolism), the formation of new substances (synthesis or anabolism), or the transfer of energy.
Metabolic process:
1.result in a net direction that is determined by the concentration of reactiants and the products.
Chemical equilibrium describes the condition where the rat of reaction in the forward direction
equals the rate in the reverse.
2.can utilize enzymes as proteins that act as catalysts. Enzymes act on substrates, like when the
enzyme amylase catalyzes the breakdown of the substrate amylose. Enzymes are substrate
specific. Enzymes perform their function repeatedly, unchanged. Enzymes can work toward
the product or in reverse to the reactants. Enzyme efficiency is affected by temperature and
pH. Beyond their ideal temperature or pH they begin to denature, or break down. Enzymes
are typically easy to identify because they end in the root –ase. Enzymes interact with
substrates to change shape which allows for a new position to allow for substrate reaction.
Once the reaction takes place, the product is released. This is called the induced-fit model.
3.can utilize cofactors that are nonprotein molecules that assist enzymes. A holoenzyme is the
union of the cofactor and the enzyme.
4.can utilize adenosine triphosphate (ATP) as a source of activation energy. ATP is essentially
an RNA adenine nucleotide with two additional phosphate groups. When ATP supplies energy
to a reaction, it is usually the energy in the last bond that is delivered to the reaction. In the
process of giving up this energy, the last phosphate bond is broken and the ATP molecule is
converted to adenosine diphosphate, ADP and a phosphate group. In contrast, new ATP
molecules are assembled by phosphorylation when ADP combines with a phosphate group
using energy obtained from an energy =-rich molecule, like glucose.
Regulation of enzymes equals regulation of chemical reactions
Four common ways to regulate enzymes.
1. Allosteric enzymes have one active binding site for a substrate, one for an allosteric effector.
a. Allosteric activator binds to the enzyme and induces the enzyme’s active shape.
b. Allosteric inhibitor binds to the enzyme and induces the enzyme’s inactive shape.
2. Competitive inhibition is when a substance mimics the substrate and inhibits an enzyme by
occupying the active site. This results in prevention of the enzyme catalyzation.
3. Noncompetitive inhibition is when a substance inhibits the action of an enzyme by binding to
the enzyme at a location other than the active site. The inhibitor changes the shape of the
enzyme which disables it. Many toxins and antibiotics perform this way.
4. Cooperativity is when an enzyme becomes more receptive to additional substrate molecules
after one substrate molecule attaches to an active site. Enzymes can have two or more
subunits, (quaternary structure) with two active sites. Hemoglobin, albeit not an enzyme,
acts in cooperativity.
Four Organic Molecule Classes
Carbohydrates: divided by the number of sugar molecules
1. monosaccharide: 1 sugar molecule
2. disaccharide: 2 sugar molecules linked by glycosidic linkage
3. polysaccharide: serried of connected monosaccharides (it’s a polymer, folks!)
Lipids: three groups
1. triglycerides (or tricylglycerols)
2. phospholipids
3. steroids
Proteins: divided by their function, however it is their structure that identifies them
o
structural proteins
o
storage proteins
o
transport proteins
o
defensive proteins
o
enzymes
1. primary structure
2. secondary structure
3. tertiary structure
4. quaternary structure
Nucleic Acids: two types
1. DNA
2. RNA