Honors BIOLOGY
Ch. 3 “Biochem”
Class Notes
3.1 Define organic compounds,
hydrocarbons, a carbon skeleton, and an
isomer.
Two categories of compounds:

Organic: made mostly of carbon

Inorganic: mostly without carbon
Hydrocarbons:

molecules that contain hydrogen and
carbon.

all of the examples in the boxes above are
hydrocarbons.
Carbohydrates:

molecules that contain C, H, O in a ratio

(CH2O)n
3.1 Explain why carbon is unparalleled in its
ability to form large, diverse molecules.
Carbon’s versatility:
Family IV makes 4 covalent bonds so it can
bond with other elements but, more importantly,
with other carbons. This creates enormous
variety:

straight carbon chains

branched carbon chains

carbon rings

double and triple bonds

isomers
o structural
o geometric
o optical
Isomers: have the same chemical formula but different
structural formulas.

structural: example: C6H12O6 is the chemical formula
for both glucose and fructose.

geometric: must include a double bond, includes “cis“ and “trans-.”

optical: must have group IV atom at center.
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3.2 Describe the properties of and distinguish between
the six chemical groups important in the chemistry of life.

table 3.2 DO NOT MEMORIZE THIS TABLE!

Be able to recognize the groups.

Know that they have “personalities that they lend to the carbon skeleton to
which they are bound.
Functional Groups: Chemical groups that affect a molecule’s function by
participating in chemical reactions in characteristic ways.









Polar (except methyl)
same as water molecule
hydrophilic “water loving”
“Like dissolves like.”
Polar dissolves polar.
Nonpolar dissolves nonpolar.
Polar and Nonpolar don’t mix. Water and oil.
Cells are mostly water
Functional groups must be able to dissolve in water.
Quiz yourself:
1. Is water polar or nonpolar?
2. If a substance is repelled by water (hydrophobic or “water fearing,” is it
polar or nonpolar?
3.3 Compare the processes of dehydration synthesis and hydrolysis.
Building Macromolecules: monomers  polymers
(anabolic process):
Dehydration Synthesis or
condensation reactions.
H+ and OH- are removed to create bonding sites. This makes
water
Breaking Down Macromolecules: polymers  monomers
(catabolic process):
Hydrolysis
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Ch. 3.3 Molecules of Life: Macromolecules
List the four main classes of macromolecules and
explain the relationship between monomers and
polymers.
Carbohydrates: carbon, hydrogen, and oxygen.



Monomer = monosaccharide (simple sugar)
(CH2O)n where n = 3  8.
A six-carbon monosaccharide would be C6H12O6.
Monosaccharides:
common examples:

glucose: main source of energy in cells

fructose: fruit sugar and the sweetest

galactose: milk
Because all of the simple sugars (say, 6C sugars) have
the same chemical formula but different structural
formulas (built differently) they have slightly different
chemical properties and are called isomers.
Disaccharides: double sugar

two monosaccharides

example: sucrose
Polysaccharides: several to hundreds of
simple sugars put together.

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

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glycogen: animal sugar storage (shortterm) in liver and muscles for quick use.
starch: plant sugar storage
cellulose: plant support
chitin: exoskeleton
Lipids: Triglycerides
Nonpolar therefore they do not mix with water.
Hydrophobic
Monomers for triglyceride: glycerol + fatty acids
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Saturated Fats: solid

carbons are saturated with hydrogen

All C-C bonds are single

single bonds allow F.A. tails to pack
neatly

animal fat is solid at room temperature

cause plaques in blood vessels
(atherosclerosis)
Unsaturated Fats: oil

some carbons have double bonds

forcing hydrogen into it (hydrogenation)

kinks in F.A. tails doesn’t allow for easy packing

liquid at room temperature---oils

Crisco = partially hydrogenated vegetable oil

Hydrogenation caused some double bonds to become
single bonds allowing the oil to be solid at room temp.

Original process caused some double bonds to convert
from cis- bonds to trans-fat bonds.

Trans-fat bonds are not metabolized---cause heart
disease

see supplemental information on Weebly for more info.
Reminder

Lipids: Phospholipids
o
o
Contains both hydrophilic (head)
and hydrophobic parts (tails).
“Like dissolves like.”
Heads with water, tails with tails.
Creates a phospholipid bilayer present in ALL
membranes.
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
Lipids: steroids and cholesterol
Structure of cholesterol
Waxes: see supplemental information on Weebly for more
info.
Examples: Cuticle on leaves, ear wax, bees wax.
Proteins: carbon, hydrogen, oxygen, and nitrogen




Monomer = amino acids (20 different) works like our
alphabet to create variation.
Each A.A. has an amino group and a carboxyl group.
They differ in their side chains “R”.
dipeptides and polypeptides are created by condensation
reactions.
The resulting bond is a peptide bond.
Primary Structure of Protein:
Determined by the kind, sequence and number of amino acids
in a chain.
3.14, 3.15 Secondary, Tertiary, and sometimes Quaternary
Structure:
This chain folds on itself due to the interaction of the different
amino acid side chains (R groups) and the backbone too.
Sometimes, more than one polypeptide must combine to
create a finished protein. (ex] collagen and hemoglobin)
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Functions of Proteins: very diverse
enzymatic: ex] sucrase (digests sucrose)
cell membrane: ex] transmembrane protein
messenger molecules: ex] insulin
immunity: ex] antibodies
structural: ex] muscles, hair, fingernails, hooves, talons, horns
A SPECIAL CASE OF PROTEINS
Enzymes: are biological catalysts

protein

Induced-fit model (fig 3-9; p.57)

substrate

active site

optimal conditions: temp/pH

lose shape/lose function
Coenzymes and Cofactors
Coenzymes: organic molecules that are required by
certain enzymes to carry out catalysis.

They bind to the active site of the enzyme
and participate in catalysis but are not considered
substrates of the reaction.

Coenzymes often function as intermediate carriers of
electrons, specific atoms or functional groups that
are transferred in the overall reaction.

EXAMPLES
o NAD+ (/FAD+ and NADP+) in the transfer of
electrons during glycolysis / cellular respiration
and photosynthesis
o Acetyl Coenzyme A (CoA): the initial step in the
Citric Acid Cycle (aids in transferring an Acyl
group rather than electrons)
o Coenzyme Q (CoQ) which transfers electrons in
the electron transport chain. aka: ubiquinone

Derived from vitamins like niacin (NAD+), riboflavin
(FAD+).
Cofactors: often classified as inorganic substances that are
required for, or increase the rate of, catalysis.
Examples of some ions (minerals) required by different
enzymes:

Fe+2, needed by hemoglobin to carry oxygen and the
cytochromes of the E.T.C.

Zn+2, Zn+3

Cu+1, Cu+2, K+1, Mg+2.

ferrodoxin (Fd): the last acceptor of electrons produced
from sunlight-excited chlorophyll before the electrons are
delivered to the Calvin cycle for incorporation into glucose.
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Nucleic Acids: DNA, RNA, ATP
Monomer: nucleotides (phosphate, sugar, base)
DNA: deoxyribonucleic acid

heredity: material physically passed to next generation

control: genes (DNA) code for protein (enzymes)
Monomer: nucleotide
RNA: ribonucleic acid

messenger (mRNA)

transfer (tRNA)

organization (rRNA).
How are the two types of nucleic acids functionally related?

The hereditary material of DNA contains the instructions for the
primary structure of polypeptides (like enzymes).

RNA is the intermediary that translates those instructions into the
order of amino acids.
Simplified diagram, know this one.
Consider the importance of the nitrogen bases especially adenine:
DNA: the code for proteins
RNA: carries the code to make proteins into the cytoplasm
ATP: energy molecule of the cell
All of these contain the double-ringed nitrogen base: adenine.
Is it just a coincidence that caffeine and chocolate have VERY
similar structures to other ESSENTIAL molecules of life?
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Caffeine
Chocolate
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