Chapter 3 – The Molecules of Cells
How small molecular units are assembled into larger ones
I. Life’s molecular diversity is based on the properties of carbon
(Aim: What makes carbon so special?)
A. Organic compounds – have at least one carbon and
almost always has hydrogen (so CO2 is NOT organic)
B. 4 electons in outer shell, but wants 8
C. To get 8 it can share with other carbons or other atoms
like H, N, O, S, etc...
D. Because it wants 4 electrons, it can make up to 4
covalent bonds with other atoms leading to long,
complicated chains as well as rings, spheres, etc…) –
simply put, it is a great building block!!
E. Hydrocarbons – C and H only
F. Carbon skeleton
G. structural Isomers – same molecular formula, different
structures and thus different properties (a screwdriver and
wrench are both made of metal).
II. Functional Groups help determine the properties of
organic compounds. (AIM: What’s so great about
functional groups?)
A. Functional groups – groups of atoms, acting as a unit,
that give organic molecules their physical properties,
chemical reactivity, & solubility in aqueous solutions.
1. Methane, methanol, acetic acid, methanethiol,
methylamine
B. Hydrophilic as a result
C. Compounds can have far more than one functional
group attached!
D. Go over different functional groups
III. Cells make a huge number of large molecules from a
small set of molecules (AIM: How does the cell make big
from small?)
A. Macromolecules – gigantic molecules (proteins, nucleic
acids (DNA/RNA), carbohydrates, lipids)
B. Cells make macromolecules by linking together small
units
1. Monomers (individual paper clips) – building blocks
(small organic molecules) of polymers
2. Polymers (all the paper clips connected to each other)
– chains of many similar small organic molecules
3. Reactions to build or breakdown polymers (water
involved in both)
a) Dehydration synthesis – combining two monomers
by the removal of a water molecule (dehydrate)
b) Hydrolysis – “breaking apart with water” – used
to break apart two attached monomers through
addition of a water molecule
IV. Carbohydrates – (“carbon and water” class of molecules
ranging from small sugar molecules to large polysaccharides
(polymers of sugar monomers)
A. Monosaccharides – sugar monomers (“single sugar”)
Ex. Glucose, Fructose – show these
1. Have the general formula (CH2O)n
2. Many monosacchrides form ring-shaped molecules in
solution
3. Used mainly for fuel, raw material to form carbon
backbones of other molecules (ie amino acids), as
monomers from which di- and polysaccharides are
synthesized.
4. –ose suffix
5. Sugar = monosaccharide or disaccharide
B. Cells link together monosaccharides to form disaccharides
1. Accomplished by dehydration synthesis
2. Glycosidic linkage links the two monosaccharides
3.
Disaccharide
Maltose
Sucrose
Lactose
Monosaccharide
Glucose + Glucose
Glucose + Fructose
Glucose + Galactose
V. How sweet is sweet (optional)
A. Sweet receptors on our tongue
B. Sugar binds to these receptors, but not the only
compound that can do this
1. Aspartame (Equal or Nutrasweet) made of amino acids
C. All sweetness is relative to sucrose (table sugar)
1. Bitter aftertaste; compounds are also binding to bitter
receptors on tongue
VI. Polysaccharides are long chains of sugar units
(“many sugar units”)
A. Polymers of a few 100 to 1000 monosaccharides
B. Using only glucose, different organisms can build
several different polymers: plant starch, animal starch
(glycogen), and cellulose
C. Dehydration synthesis
D. Plant Starch –
1. Long, relatively unbranched, coiled polymer of glucose
in plants. (one kind of bond)
2. Long term energy storage – plants hydrolyze when
energy is needed.
3. Can be consumed by animals like humans and
hydrolyzed to obtain energy (potatoes, grains, etc…)
E. Glycogen –
1. Storage polysaccharide of animals
2. Very similar to starch (made using glucose, same bond
type) , but with far more branches
F. Cellulose – a polysaccharide used for building
1. Different kind of bond resulting in linear polymers,
which crosslink to other chitin polymers
2. Main structural molecule in the cell walls of plants and
algae
3. Animals cannot hydrolyze cellulose (that’s why you
can’t eat wood) only certain bacteria, protozoans, and
fungi. How come cows can eat grass?
VII. Lipids
A. Include fat (triglyceride), which are mostly energystorage molecules
1. Many carbon and hydrogen, little Oxygen
2. Many different types of lipids with different functions,
all essentially hydrophobic
3. Fat – Three fatty acids and glycerol – formed by
dehydration synthesis
a) Triglyceride = “fat” = 3 fatty acids + 1 glycerol
4. Saturated fats – no double bonds b/w carbons of fatty
acids –carbons are saturated with H. – chains can pack
into tight globules to form things like butter (solid at room
temp)
5. Most plant fats are unsaturated, while animal fats tend
to be richer in saturated
6. Unsaturated fats – double bonds b/w carbons of fatty
acids – chains are bent and can’t pack as well – liquid at
room temp – veg. oil, corn oil, olive oil, etc… (What
happens if we hydrogenate unsaturated fats?)
7. functions: energy storage, cushion vital organs,
insulation
VIII. Phospholipids, waxes, and steroids are lipids with a
variety of functions
A. Phospholipids are the major component of cell
membranes
1. Similar to fat (triglycerides) except only two tails and
has a phosphate containing head
2. Unique in that PO4 has a negative charge and gives it a
hydrophilic head while having hydrophobic tails =
amphipathic (a molecule that is both hydrophobic and
hydrophilic)
3. forms the membranes of cells
B. Waxes – essentially a hydrophobic coating formed by
numerous organisms to ward off water.
1. More hydrophobic than fats
2. One fatty acid linked to alcohol
C. Steroids – lipids whose carbon skeleton forms 4 fused
rings
1. Cholesterol – important steroid formed by animals
(carbon hydrogen emission in structural drawing. Show
3D view and emphasize that we are seeing 2D – not real).
a) Functions in digestion of fats, starting material for
synthesis of female and male sex hormones, and
fluidity of cell membranes
D. Anabolic steroids – big bodies, big problems
1. Synthetic variants of the male hormone testosterone
a) Causes build up of muscle and bone during
puberty in men among other things
b) Downside = liver damage, testicular atrophy,
cholesterol issues, high blood pressure, breast
development in males, masculinization in females, and
antisocial behavior.
IX.
Proteins (“first place” in greek)
A. Proteins are essential to the structures and activities of
life – They are the workers
1. Roles played by proteins:
a) Structural (hair, cell cytoskeleton)
b) Contractile (muscles and motile cells)
c) Storage (ovalbumin (egg white) – source of amino
acids for developing embryo)
d) Defense (antibodies, membrane proteins)
e) Transport (hemoglobin, membrane proteins)
f) Signaling (hormones, membrane proteins,
intracellular signaling proteins)
g) Catalysts (enzymes both free and membrane
bound)
2. Enzymes – protein that serves as a chemical catalyst –
increases the rate of specific reactions without being
used up (hammer and nails analogy) ****does not make a
reaction happen that normally wouldn’t
B. Proteins are made from just 20 kinds of amino acids
1. Amino acids – (monomer) – all have a central alpha
carbon covalently bonded to a -H, amino group -NH2,
carboxyl group –COOH, and one other chemical group –R
(variable group).
2. There are 20 different –R or variable groups, which
give the amino acid its distinct properties.
C. Amino acids can be linked by peptide bonds
1. Amino acids are monomers that are linked together by
peptide bonds via dehydration synthesis to form
polymers.
2. Dipeptide – 2 linked amino acids
3. Polypeptide – many linked amino acids (NOT
necessarily a protein).
X. Overview : A protein’s specific shape determines its
function (hammer, screwdriver, wrench, etc…)
1. Proteins consist of one or more polypeptide chains
folded into a unique shape
2. This 3D shape determines the proteins function
3. The shape the protein takes depends solely on its
amino acid sequence (show this).
4. Proteins can unravel (denature) with changes in heat,
pH, saltiness, etc…
5. The 4 levels of protein structure using transthyretin –
found in blood - important in transport of a thyroid
hormone and Vit. A
a) Primary – aa sequence – aa represented by a three
letter abbreviation or a single letter code.
(1) The amino acids are in a precise order
(2) There are 4 identical polypeptide chains, each
with 127 aa
(3) Changes in the primary structure affect the 3D
structure (show this)
b) Secondary Structure – polypeptide coiling or
folding produced by hydrogen bonding
(1) H-bonds occur b/w –NH (amino) groups and –
C=O group (carbonyl) groups
(2) Depending on amino acid sequence, the
secondary structure takes the form of an alpha helix,
pleated sheet, or omega loop
(3) The R-groups do not play a direct role, but are
important for the type of sec. structure formed
(4) Go over diagramming convention
c) Tertiary structure – is the overall shape of the
polypeptide
(1) Results from the clustering of hydrophobic and
hydrophilic R groups and the bonding (hydrogen,
ionic and covalent) b/w certain R-groups along the
helices, sheets, and loops.
(2) hydrophobic (nonpolar) R groups tend to cluster
within the interior of the protein, away from water –
drives folding
(3) Tertiary shape of transthyretin is globular
d) Quarternary structure - relationship among
multiple polypeptides of a protein
(1) Many, but not all, proteins consist of a
relationship b/w more than one polypeptide chain
(show examples)
(2) Transthyretin – 4 chains, all identical. Some
proteins can consist of different chains or be
additionally complexed with other atoms or
molecules (show examples).
XI. Nucleic Acids – information rich polymers of
nucleotides
A. Nucleotides (monomer) – has 3 functional parts
1. Phosphate group
2. Five-carbon sugar (deoxyribose in DNA, ribose in RNA)
3. Nitrogenous base – (contain nitrogen) five types: A, T,
G, C in DNA. RNA also has A, G, and C, but instead of T it
has U.
a) purines vs. pyrimidines
4. ATP (adenosine triphosphate) is a nucleotide used as
fuel for proteins
B. Nucleic acid polymer form from dehydration synthesis
of nucleotide monomers (just like polysacs and polypeps).
1. Phosphate of one bonds to sugar of next
2. RNA is usually a single polynucleotide strand, but DNA
is a double helix – two polynucleotide strands wrap
around each other
C. DNA double helix
1. Nitrogenous bases point toward the center of the helix
2. A single base hydrogen bonds to the base across from
it on the other strand forming a base pair (A-T, C-G)
(zipper analogy)
3. Most DNA molecules have 1000’s to millions of base
pairs.
4. DNA molecules store the information for building the
primary sequence of proteins in sections called genes.
5. DNA is just a large parts list for the cell (instructions
on how to build every protein)!!!!
D. Two types of nucleic acids
1. DNA – deoxyribonucleic acid
2. RNA – ribonucleic acid