Chapter 3
 The
molecules of life
• Made by living cells
 Cells consist of a very high proportion of the
molecules of life




Carbohydrates
Lipids
Proteins
Nucleic acids
• They are organic compounds
 Molecules consisting of carbon and at least one
hydrogen atom
 Why
carbon?
• Versatile bonding behavior
• Forms four covalent bonds
 With other atoms including other carbon atoms
 Why
carbon?
• Carbon atoms bond
together to form the
backbones of these
molecules
 Chains and rings
• Other atoms are attached
 Nitrogen, phosphorous,
sulfur
• Functional groups are
attached
 Why
carbon?
• Functional groups
 Certain atoms or clusters of atoms covalently bonded
to a carbon in the backbone
 The number, kind, and arrangement give rise to
specific chemical properties
 Polarity, acidity, hydrophobicity, etc.
 Why carbon?
• Functional groups
 Hydroxyl: polar
 Sugars and alcohols
 Methyl: non-polar
 Fatty acids
 Carboxyl: very acidic
 Amino acids
 Amine: very basic
 Amino acids
 Phosphate: polar, reactive
 Nucleotides, DNA, RNA, ATP, phospholipids
 Why
carbon?
• Functional groups
 Minor differences in functional groups can make a
difference in the function of the entire molecule
 Chemical/metabolic
reactions
• Cells build large molecules of life from pools of
smaller molecules in chemical reactions
 Monomers are simple organic building blocks
 Polymers consist of multiple monomers
 Cells build polymers from monomers and break down
polymers to release monomers
 Chemical/metabolic
reactions
• Condensation
 Two molecules are covalently
bonded into a larger molecule
 Water forms as a product of
condensation
 Chemical/metabolic
reactions
• Hydrolysis (also called
cleavage)
 Larger organic molecules are
broken down to smaller
molecules
 Water is used as part of the
reaction
 Chemical/Metabolic
reactions
• Functional group transfer
 A functional group is transferred from one to another
molecule
• Electron transfer
 One or more electrons are taken from one molecule
and donated to another
• Rearrangement
 Internal bonds are juggled to convert an organic
compound to another (no atoms added or removed)
 Sources
of carbohydrates?
• Sugars
• Grains and breads
• Fruits and vegetables
• Cheese (dairy)
• Nuts and seeds
 Made
of carbon, hydrogen, and oxygen
• Monomers have a 1:2:1 ratio (C6H12O6)
 Used
for energy, energy storage, and
structure
 The monomer is monosaccharides
 Monosaccharides
• Simple sugars or reducing sugars
• Consist of a 5 or 6 carbon backbone
 Chain or ring
 Monosacharides
• Laboratory test
 Monosaccharides can be detected because they
reduce Benedict’s solution (blue  orange)
 Thus the name “reducing sugar”
 Monosaccharides
• Examples
 Glucose (C6H12O6)
 Product of photosynthesis
 Used as the monomer for many polysaccharides
 Fructose
 Found in fruit
 Deoxyribose and ribose
 Important for DNA and RNA
 Disaccharides
• Two monomers covalently bonded
• Included with other short-chain carbohydrates
• Laboratory test
 No specific test
 Disaccharides
• Examples
 Sucrose: glucose + fructose
 Table sugar from sugar cane or sugar beets
 Lactose: glucose + galactose
 Sugar found in milk
 Lactose intolerance: no enzymes to break lactose down
 Polysaccharides
• Also called complex carbohydrates
• Consist of very long chains of glucose
monomers
 100s to 1000s long
 Polysaccharides
• Laboratory test
 Iodine interacts with the coils of long polymers
(yellow  blue to black)
 Polysaccharides
• Example: Starch
 Bonding patterns of the glucose monomers may produce
coils or branching
 Starches are used to store energy
 Polysaccharides
• Example: Starch
 Animal starch is called glycogen
 Stored in liver and muscle cells
 Plant starches include amylose and amylopectin
 Stored temporarily in leaves following photosynthesis
 Stored for long-term use in other plant parts (potato)
 Polysaccharides
• Example: Cellulose
 Glucose chains stretch side by side and are held
together by hydrogen-bonds
 Stabilized in a bundled pattern creating fibers used for
structural support of plant cell walls, stems, wood, etc.
 Cotton is almost pure cellulose
 We lack enzymes to digest cellulose
 Dietary fiber
 Polysaccharides
• Example: Chitin
 Similar to cellulose except that it is modified with a
nitrogen-containing group on each monomer
 Found in exoskeletons and fungi cell walls
 Sources
of lipids
• Butter
• Oils
• Deserts and some candies
• Nuts
• Meats
• Egg yolks
 Consist
of carbon and hydrogen with
very little oxygen
• No specific ratio
 Used
for energy storage, cell
membranes, insulation, water barriers,
cell to cell signals
 No specific monomers
• Many lipids use fatty acids, but not all of them
 Laboratory
tests
• Fatty, oily or waxy feeling
• Insoluble in water
• Brown paper test
• Sudan IV dye
 Fats
and oils (triglycerides)
• Consists of a glycerol molecule and three fatty
acid molecules
 Fats
and oils
• Fatty acids: long carbon
chains (4-36 carbons long)
 Saturated fatty acids
 Each carbon atom is saturated
with hydrogen atoms
 No double bonds between
carbons
 Solid at room temperature
 “fats”
 Fats
and oils
• Fatty acids: long carbon
chains (4-36 carbons long)
 Unsaturated fatty acids
 Some carbons are not saturated
with hydrogen
 One or more double bonds
between carbon atoms
 Liquid at room temperature
 Double bonds make kinks which
prevent them from packing
tightly
 “Oils”
 Fats
and oils
• Fatty acids: long carbon
chains (4-36 carbons long)
 Trans-fatty acids
 Hydrogenated unsaturated fats
 Breaks double bonds and forces
hydrogen atoms to bond
 Diet high in trans fatty acids
increases risk of heart attack
 Phospholipids
• Two fatty acids and one phosphate
group attached to glycerol
 Similar to triglycerides except that one
fatty acid is replaced by a phosphate group
 Fatty acids are hydrophobic (tails)
 Phosphate group is hydrophilic (head)
 Phospholipids
• Cell membranes are composed of
two layers of phopholipids
 The heads of one layer are exposed
to the cell’s water based fluid interior
 The heads of the other layer are
exposed the water based fluid
surroundings of the cell
 Sandwiched between the two are all
of the hydrophobic tails
 Nicely protected from any water based
fluids
 Waxes
• Composed of tightly packed fatty acids bonded
to long-chain alcohols or carbon rings
• Firm and water repellent
• Examples
 Beeswax
 Water fowl’s feathers
 Plant cuticles
 Sterols
• Consist of a rigid backbone of four carbon rings
and no fatty acids
• The properties and functions are determined by
the number and type of functional groups
• Examples
 Cholesterol
 Bile salts
 Vitamin D
 Steroid hormones
 Sources
of protein
• Beef and pork
• Poultry
• Eggs
• Milk
• Nuts
• Beans
• Fish
 Complex, large, and
diverse molecules
consisting of carbon, hydrogen, oxygen,
nitrogen, and sometimes sulfur
• Two main types: fibrous and globular
 Used for
• Structure
• Enzymes
• Defense
• Transport
• Movement
• Regulatory
hair, nails, feathers
cellular reactions
antibodies
hemoglobin
muscle
hormones
 Monomers
are amino acids
 Laboratory test
• Biruret’s reagent turns violet/purple in the
presence of protein
 Amino
acids
• Have a central carbon bonded to
 An amino group
 A carboxyl group (the acid)
 A hydrogen atom
 One of 20 possible R groups
 Each group confers different
properties to the amino acid
 Polar, charged, acid, etc
tyrosine (tyr)
lysine (lys)
glutamate (glu)
UNCHARGED,
POLAR AMINO ACID
POSITIVELY CHARGED,
POLAR AMINO ACID
NEGATIVELY CHARGED,
POLAR AMINO ACID
valine (val)
phenylalanine (phe)
methionine (met)
glycine (gly)
proline (pro)
 Amino
acids
• Are linked together into polymers by a
specialized type of condensation reaction called
a peptide bond
 The carbon of one amino acid’s carboxyl group is linked to
the nitrogen of another amino acid’s amino group
 Amino
acids
• The sequence of amino acids is determined by
instructions in the DNA (genes)
• The sequence determines what type of protein is
synthesized
• Cells can make all of the many different types of
proteins from only 20 kinds of amino acids
 Terminology
• Amino acid
 Monomer of proteins
• Peptide bond
 Covalent bond joining amino acids
• Peptide
 A chain of 2 or more amino acids
• Polypeptide
 A chain of many amino acids
• Protein
 Finished and modified polypeptide
 Protein
structure
• Protein structure is related to protein function
 Just like tools have to be the right shape for a job
 Screw driver + screw Hammer + nail
 If the protein isn’t shaped correctly, then it will not
function correctly
 Protein
structure
• Primary structure
 The unique sequence of amino acids for each protein
 Protein
structure
• Secondary structure
 As a polypeptide is synthesized regions or stretches
of the amino acid chain will twist, bend, loop, or fold
 Hydrogen bonds can hold the twists in place to make
 Helixes
 Coils like a spiral staircase
 Sheets or loops
 Flat sheet-like regions
 Protein
structure
• Tertiary structure
 Final three dimensional folding of the polypeptide
 Held together by hydrogen bonds, disulfide bonds,
and other weak interactions
 Becomes a working molecule
 Protein
structure
• Quaternary structure
 Two or more polypeptide chains are bound or
associate together
 Not all proteins have a fourth level of structure
 Protein
structure
• Denaturation
 When a protein unfolds and becomes unusable
 Caused by




Temperature change
pH change
Salt concentration change
Detergents
 Homeostasis keeps cellular environment within the
ranges that will prevent denaturation
 Protein
structure
• Mutations in the genes coding for a protein can
lead to misshaped proteins
 If the wrong amino acid is placed in a protein sequence, it
can change the chemical interactions
 Example
 The protein hemoglobin and sickle-cell anemia

Hemoglobin and sickle-cell anemia
• A globular protein which carries
oxygen through the blood
 Hemoglobin’s ability to bind oxygen
depends on its structure
 Primary structure: amino acid sequence
(glutamate is the 6th amino acid)
 Secondary structure: multiple helixes
 Tertiary structure: folds up as globin to
form a pocket that cradles heme
 Heme is a functional group with an iron
atom at its center
 Quaternary structure: Four globulin
molecules (two alpha and two beta) held
together by hydrogen bonds
 Hemoglobin
and sickle-cell anemia
• Sickle-cell anemia is a genetic disease where the
hemoglobin is mis-shapen because of a mutation
resulting in a different amino acid at the 6th
position
 Glutamate is replaced with valine
 Hemoglobin
and sickle-cell
anemia
• Because of the mutation (glutamate 
valine), the shape and thus the function of
hemoglobin changes
 When available oxygen is low, the protein
forms large clumps
 The red blood cells distort into sickled shape
 The sickle cells clog blood vessels and
disrupt blood circulation
• A protein’s structure dictates its function!
 Sources
of nucleotides
• We synthesize our own
• Beef
• Fish, sardines
• Seafood
• Mushrooms
• Beans
• Vegetables
• Eggs
 Consist
of
• Carbon, hydrogen, oxygen, nitrogen, and
phosphorous
 Used
for energy (ATP), co-enzymes, cell
messengers, and genetic material (DNA,
RNA)
 Nucleotides are the monomer
• They form long polymers called nucleic acids
 Nucleotides
• A simple 5-carbon sugar (deoxyribose or
ribose)
• 1-3 phosphate groups
• A nitrogenous base
 Nucleotides
• ATP
 Used as the energy currency of the cell
 Has three phosphate groups
 Transfers its 3rd phosphate group to prime other molecules
for action
 Nucleotides
• NAD+, NADP+ and FAD
 Used as co-enzymes to move high energy electrons
and hydrogen
 Nucleic
acids: DNA and RNA
• Chains of four types of nucleotides
 Adenine, guanine, thymine (or uracil), and cytosine
 Nucleic
acids: DNA and RNA
• DNA encodes genetic
instructions
 Double stranded
 Located in the nucleus
 Makes up chromosomes
 Nucleic
acids: DNA and RNA
• RNA carries genetic instructions
 Single stranded
 Made in the nucleus, but functions in the
cytoplasm






Organic molecules
Carbon
Carbohydrates
• Monosaccharides, disaccharides, polysaccharides
Lipids
• Fatty acids
Proteins
• Amino acids, structure
Nucleotides
• ATP, DNA, RNA