Chapter 3: Biological Molecules
3.1: Properties of Carbon
 Unique properties of carbon are the foundation for
the diversity of biological molecules and the
chemical processes required for life.
 Related to the great diversity of organisms.
 Carbon-based molecules: organic compounds
 Each C atom is a connecting point from which a
molecule can branch in up to 4 directions
 Shape of molecule determines its function
 Compounds composed of only C-H are hydrocarbons
 Hydrocarbon molecular structure variations
o Carbon Skeletons vary in length
 EX: 2-carbon, 3-carbon, 4-carbon, 6-carbon
o Branched or unbranched
o Double bonds – can vary in location
o Carbon skeletons can form rings
 Compounds with the same formula but different
structures are called isomers.
o Different shapes = unique properties
 EX: Cyclohexane and benzene are liquids not
gases.
 All hydrocarbons are nonpolar due to nonpolar C-H
bonds (nonpolar is the equal sharing of electrons
between two atoms)
3.2: Properties of Organic Molecules
 Unique properties depend on
o Size/shape of Carbon skeleton
 Functional Groups - 5 chemical groups important to
the chemistry of life
o Polar because of N & O atoms
o Participate in chemical reactions in
characteristic ways
o Polarity makes them hydrophilic (water-loving
molecules that are soluble in water)
 Solubility necessary for role in water-based
life.
o 5 Main Functional Groups:
 Hydroxl Group
 (-OH)
 H bonded to O, which is then bonded to
the Carbon skeleton
 Called alcohols
 Ex: Ethanol
 Carbonyl Group
 (C=O)
 C linked by double bond to O
 If carbonyl group is at the end of carbon
chain – called aldehyde
 If the carbonyl group is located within
the carbon chain – called ketone
 Ex: Sugars
 Carboxyl Group
 (C=O + -OH)
 Acts as acid contributing H+ to solution,
becoming ionized
 Called carboxylic acid
o EX: Acetic acid in vinegar gives it the
sour taste
 Amino Group
 (-NH2)
 N bonded to 2 H and C skeleton
 Acts as base picking up H+ from solution
 Called amines
o EX: Amino acids (building blocks of
protein)
 Phosphate group
 (-OPO32-)
 P bonded to 4 O
 Ionized
 Attached to C skeleton by one O
 Abbreviated P
 Organic phosphates
 Involved in energy transfer
o EX: ATP (adenosine triphosphate)
 Methyl Group – also important to chemistry of life
o Nonpolar and not reactive
o Affects molecular structure and function
o C bonded to 3 H
o Methylated compounds
o Affects expression of genes when added to DNA
3.3: Small molecules form larger molecules
 Macromolecules – large biological molecules
o Four main classes: carbohydrates, lipids,
proteins, nucleic acids
o Long chains comprised of smaller, covalentlybonded molecules are called polymers (Greek
poly – many/meros – parts)
o Long molecule consisting of many identical or
similar building blocks strung together –
monomers
 Diversity of polymers
o Cells make vast number of different polymers
 EX: trillion different proteins in nature,
variety potentially endless.
o Made from about 40 to 50 common components
& a few that are rare.
 EX:
 proteins made from only 20 kinds of
amino acids
 DNA built from 4 different monomers
(nucleotides)
o Key to diversity is arrangement
o Monomers are essentially universal
o Our proteins and those of an ant or tree
assembled from same 20 amino acids; different
sequences
o MOLECULAR LOGIC: Small molecules common to
all organisms are ordered into large molecules,
which vary from species to species and even
individual to individual.
 Making Polymers
o Monomers linked together during dehydration
reaction (condensation) to form polymers
 H2O removed
 1 monomer contributes –OH group
 1 monomer contributes H+
 New covalent bond forms linking the 2
monomers
 Reaction same regardless of type of polymer
being formed
 Breaking Polymers
o Polymers broken apart into monomers through
process of hydrolysis
 (Greek: lyse – to break/hydro-water)
o Cell breaks bonds of monomers by adding H2O
 Both Dehydration Reaction and Hydrolysis require
the help of enzymes which are specialized
macromolecules that speed up chemical reactions in
cells: EX: Lactase
3.4: Carbohydrates – Simple Sugars
 Monomer – monosaccharides which are a single unit
of sugar (Greek: monos-single/sacchar-sugar)
o Examples: Glucose and Fructose*
o Function: main fuel source for cellular
respiration
o Chemical Structure:
 3- to 7-carbon skeletons
 5-carbon sugars – pentose
 6-carbon sugars - hexoses
 Molecular formula – (CH2O)n
 Contains a # of –OH (hydroxyl) groups,
which make the monosaccharide an alcohol
 Contains a >C=O (carbonyl) group, which
makes the monosaccharide either an
aldehyde (aldose) or ketone (ketose)
 Monosaccharides combine to form disaccharides (2
monosaccharides) and polysaccharides (more than 2
saccharides)
*Glucose and Fructose are isomers; differ only in
arrangement of carbonyl groups. Minor differences give
isomers different properties. Ex: how they react with
other molecules and makes fructose taste considerably
sweeter than glucose.
3.5: Carbohydrates – Dissaccharides
 Created when two monosaccharides are joined
during a dehydration reaction (condensation)
 During dehydration hydroxyl (-OH) group is removed
from one monomer and H+ is removed from another
monomer. The remaining O forms a bond between
the two monosaccharides (monomers) creating the
disaccharide.
 Examples:
o Maltose – found in germinating seeds; used in
malted milk shakes, Whoppers
o Sucrose – most common, main carbohydrate in
plant sap; extract from sugar cane and sugar
beets – table sugar
3.7 – Polysaccarhides
 Polymers of monosaccharides linked by dehydration
reactions (condensation)
 Function as storage molecules or structural
compounds
 Hydrophilic (reason cotton towels composed of
cellulose absorb water)
 Four Examples
o Starch: found in plants; molecular structure –
coiled into helical shape because of angles of
bonds, can be branched or unbranched; function
– energy storage; major sources in the human
diet – wheat, corn, and rice
o Glycogen: found in animals; molecular structure
– highly branched; function – energy storage;
major storage in liver and muscle cells.
o Cellulose: plants; most abundant organic
compound on Earth; forms cable-like fibrils in
tough walls of plant cells; molecular structure
different from starch and glycogen in that the
glucose monomers are arranged parallel to one
another; cannot be hydrolyzed by most animals;
nutritionally called “insoluble fiber” which can
contribute to digestive health; source – fresh
fruits, vegetables, and grains rich in fiber.
o Chitin – used by insects and crustaceans to build
exoskeleton (why they crunch when crushed);
also found in cell wall of fungi; used by humans
to make strong, flexible, dissolvable thread for
surgical stitches.
3.8 Lipids
 Hydrophobic – mix poorly with water
 Straight chemical chains
 Three categories – oils, fats, steroids
 Main function of oils and fats – energy storage
 Also cushions vital organs and insulates body
 Can be unsaturated or saturated depending on the
number of hydrogen
o Examples:
 Unsaturated Fats: oils – corn oil, olive oil,
vegetable oils. Most plant fats are
unsaturated fats. Because of the shape
caused by the double bond, unable to pack
tightly together and solidify @ room
temperature (liquid at room temperature)
 Saturated Fats: butter, lard. Solid at room
temperature due to the fact the fatty acid
chains pack tightly together. Most animal
fats are saturated.
 TIPS FOR HEALTH: “Hydrogenated vegetable oils”
found in margarine are converted to saturated fats
by adding hydrogens. This creates trans fats, which
have been connected to cardiovascular disease such
as atherosclerosis where lipid containing deposits
called plaques build up within walls of blood vessels,
restricting the blood flow.
 Structure:
o Made from glycerol and fatty acids which are
linked by dehydration reactions (condensation)
o Alcohol with 3 fatty acids = triglyceride
(synonym for fat)
o Glycerol Structure
Fatty Acid Structure
3.9 Phospholipids and Steroids
 Main function of phospholipids steroids –
structure/cellular membranes
o 2 fatty acids attached to glycerol
o 3rd fatty acid is replaced with negatively charged
phosphate group
o Structure fits function
o (Sketch the drawing)
o Assemble to form the bilayer of phospholipids
which forms the cellular membranes
 Fatty acid tails are hydrophobic and cluster
in the center
 Polar heads are hydrophilic and face the
internal and external watery environments
in and out of the cell.
 Steroids: lipids with 4-Carbon skeleton that contains
four fused rings.
o EX: Cholesterol - common component in animal
cell membranes, used as starter material for
other steroids made by animal cells. Other
steroids include hormones such as testosterone
and estrogen.
o Different steroids vary in chemical groups
attached to the rings. (pg. 41 in your book)
o (Sketch Diagram on Board)
3.10 Anabolic Steroids
 Tonight please read the section on Anabolic Steroids
on page 41.
o What are they: synthetic variants of
testosterone
o Use: treat general anemia and diseases that
destroy body muscle.
o Abuse: abused to build muscle mass/strength/
competitive edge
o Consequences: steroid rage, deep depression,
liver damage leading to cancer, alter cholesterol
levels leading to high blood pressure. Serious
side effect for teens: stunt growth by stopping
bone growth
o Sports Organizations have banned use,
implemented drug testing
3.11 Proteins
 Essential to structures and functions of life
 Greek: proteios “first place” – suggest importance of
this macromolecule
 Monomers: amino acids, 20 different amino acids
o Structure of amino acids
Carboxyl makes
the molecule an
acid, hence
amino acid.
 Polymer: proteins
 Function of proteins:
o Structure of cells and organisms>hair,fibers,
tendons, ligaments
o Enzymes (catalyst in reactions) EX: lactase
o Muscles > contractile proteins
o Defensive proteins > antibodies
o Signal proteins > hormones, EX: adrenalin, TSH
o Receptor proteins > built into cell
membranes/transmit signals
o Transport proteins > hemoglobin
o Storage proteins > ovalbumin > egg white/source
of amino acids for developing embryos
3.12 Proteins made from amino acids
 Most elaborate and most diverse in structure and
function of all life’s molecules
 Based on different arrangements of just 20 amino
acids (alpha C, amine/amino group, H, R group,
carboxyl)
 The structure of R group determines specific
properties of each of 20 amino acids.
o Two R groups: polar and nonpolar (DO NOT write
the groups below. These are for discussion only.)
Nonpolar Amino Acids
Ala: Alanine
Gly: Glycine
Ile: Isoleucine
Leu: Leucine
Met: Methionine Trp:Tryptophan
Phe: Phenylalanine Pro: Proline
Val: Valine
Polar Amino Acids
Cys: Cysteine
Tyr: Tyrosine
Ser: Serine
Thr: Threonine
Asn: Asparagine Gln: Glutamine
Polar Basic Amino Acids (Positively Charged)
His: Histidine
Lys: Lysine
Arg: Arginine
Polar Acidic Amino Acids (Negatively Charged)
Asp: Aspartic acid Glu: Glutamic acid
 Cells join amino acids in dehydration reaction.
o Links carboxyl group of one amino acid to amine
group of next amino acid as H2O is removed.
Resulting linkage is a peptide bond.
o Linkage of 2 amino acids = dipeptide
o Continue to link amino acids in long chains results
in polypeptide. Most polypeptides are 100 amino
acids in length; some are 1,000 or more amino
acids.
o NOTE: Long polypeptide chain of specific sequence
is NOT the same as protein
 Functioning protein is 1 or MORE polypeptide
chains precisely coiled, twisted, and folded into
a unique 3D shape.
3.13: Shape determines Function
 Four levels of structure
o 1°(primary) – polypeptide chain (specific sequence
of aa) Ex: Transthyretin, transport protein in blood
made of four polypeptide chains
o 2°(secondary) - -helix formed by coiling the
polypeptide chains; beta-sheets formed by folding
the polypeptide chains into sheets; specific folded
patterns (page 45) Ex: Silk protein of a spider web
created from polypeptide chains folded into
sheets
o 3°(tertiary) – 3D structure(subunit) made from
combination of alpha-helix and beta-sheets linked
together (page 45); described as either globular or
fibrous; results from interactions among R groups
of aa; arrangement of coils and folds give the
specific shape that fits it to its function
o 4°(quaternary) – multiple subunits linked; Ex:
Collagen – fibrous protein with helical subunits
wrapped into larger triple helix.
 Affect of incorrectly folded proteins:
o Accumulation of these proteins can result in
diseases such as Alzheimer’s and Parkinsons
o Prions – infections mishapened proteins
associated with mad cow disease.
o Proteins unique 3D shape determines proper
functioning.
3.15: Linus Pauling
 Physicist and chemist
 Noble prize in Chemistry in 1954
 Studied biological molecules
 First to describe fundamental secondary structures
of proteins, alpha-helix and beta-sheets (pleated
sheets)
 Leading advocate for halting testing of nuclear
weapons
 US Dept. revoked his passport as a result
 1963 won Nobel Peace Prize for producing ban on
nuclear testing. (What is the current news related to
nuclear weapons?)
3.16: Nucleic Acids
 Monomers: nucleotides
o 3 parts of a nucleotide:
 5-carbon sugar: either DNA(sugar –
deoxyribose) or RNA (sugar – ribose)
 Phosphate group
 Nitrogenous base
 DNA: adenine (A); thymine (T); guanine
(G); cytosine (C)
 RNA: adenine (A); uracil (U); guanine
(G); cytosine (C)
 Polymers: nucleic acids (polynucleotide)
o Formed by dehydration when one nucleotide
bonds to sugar of next monomer; results in
repeating sugar-phosphate backbone
o RNA – single polynucleotide strand
o DNA – double helix formed when two
polynucleotides wrap around each other
 Nitrogenous bases protrude from 2 sugarphosphate backbones into center of helix
 Nitrogenous bases always pair up: A-T, C-G
 Held together by hydrogen bonds between
paired bases
o Most DNA molecules have thousands or even
millions of base pairs
 Structure: (page 47)
HOMEWORK: Complete the table on page 48 in the
Chapter Review. Due tomorrow (10-6-15)