Biological
Molecules
Organic Chemistry &
Functional Groups
Organic Compounds

Carbon-based molecules

Second most abundant type of compound
found in organisms

Over 2 million known organic compounds

Properties of organic compounds depend on
its size, shape, and type of functional
group attached to it
What is a Functional Group?
Atoms, such as nitrogen, oxygen, phosphate
and sulfur covalently bonded to a carbon
backbone
 They are groups that change both the
structure and behavior of a molecule, i.e.,
solubility, reactivity with other molecules
 They help chemists and biochemists
classify different molecules found in living
organisms
 Functional groups containing nitrogen or
oxygen are polar and therefore hydrophylic
and thus water-soluble

Functional Groups in Biological
Molecules
GROUP
Methyl
Hydroxyl
STRUCTURAL FORMULA
H
-C-H
H
- OH
COMMON LOCATION
fats, oils, waxes
sugars, other alcohols
H
Aldehyde
-C
sugars
OH
Ketone
-C=O
sugars, hormones
O
Carboxyl
-C
sugars, fats, amino acids
OH
Functional Groups in Biological
Molecules
GROUP
Amino
STRUCTURAL FORMULA
H
H
-N
or - N - H
H
H
COMMON LOCATION
amino acids, proteins
Phosphate
O- O - P - OO
DNA, RNA, ATP, lipids
Sulfhydryl
-S-H
proteins
Five Classes of Chemical
Reactions in Biological Systems
Five Classes of Reactions
1.
2.
3.
4.
5.
Functional-group transfer
Electron transfer
Rearrangement
Condensation (dehydration)
Cleavage (hydrolysis)
1. Functional-Group Transfer
one molecule gives up a functional
group, which another molecule
accepts
 seen in metabolic reactions, ex.,
glycolysis

2. Electron Transfer
one or more electrons stripped from
one molecule are donated to another
molecule
 seen in metabolic reactions, ex.,
Kreb’s cycle, glycolysis

3. Rearrangement
a juggling of internal bonds converts
one type of organic compound into
another
 seen in many metabolic pathways ex.,
glycolysis, Kreb’s cycle, etc.

4. Condensation (Dehydration)
through covalent bonding, two
molecules combine to form a larger
molecule
 many successive condensation
reactions leads to polymerization
 cells undergo condensation reactions
to produce complex carbohydrates,
lipids and proteins

Polymerization &
Condensation/Dehydration
Reactions
5. Cleavage (Hydrolysis)
a molecule splits into two smaller ones
 hydrolysis, is a very common biological
cleavage. It is like condensation in
reverse
 cells hydrolyze large polymers like
starch and proteins, then use the
released subunits as building blocks
or energy sources

Hydrolysis/Cleavage
Reactions
Carbohydrates
Carbohydrates
a simple sugar or a molecule composed
of two or more sugar units
 can be used as either an immediate
energy source, stored energy source
or structural material
 3 classes are: 1) monosaccharides, 2)
oligosaccharides, 3) polysaccharides

Monosaccharides








Simplest carbohydrates
Also called simple sugars
Suffix - ose
Glucose, Fructose, Galactose (hexoses)
Ribose (pentose)
Empirical formula is generally CH2O
Usually form ring structures in aqueous
solution
functional groups include: hydroxyl and
aldehyde or ketone
Aldehyde vs.
Keytone
ISOMERS
both have
chemical
formula of
C6H12O6
Glucose Ring Structures
Oligosaccharide
Is a short chain of two or more
covalently bonded sugar units
 Two or more monosaccharides join by
dehydration reactions
 Disaccharide = two sugars

– lactose - milk sugar (glucose + galactose)
– sucrose - fruit sugar (glucose + fructose)
– maltose - beer, seeds (glucose + glucose)
Sucrose
Dehydration
Reaction in
Maltose
Formation
Complex Carbohydrates
Polysaccharides
straight or branched chain of hundreds
or thousands of the same or different
sugar units (monomers)
 glucose-based polysaccharides:

– starch - plant energy storage
– cellulose - plant structural form
– glycogen - animal energy storage
Polymers of Glucose
Fats & Lipids
Five Classes of Lipids
Fatty Acids
 Triglycerides
 Phospholipids
 Waxes
 Sterols

Fatty Acids
Contains a carbon backbone of up to
36 carbon atoms
 Contains a carboxyl group at one end
 Can be saturated (only single bonds)
 Can be unsaturated (may have one or
more double or triple bonds)
 Saturated are solid at room
temperature
 Unsaturated are liquid

Saturated vs. Unsaturated Fatty
Acids
Saturated & Unsaturated Fatty
Acids
Trans Fatty Acids

Increases the « bad » LDL
cholesterol (low-density lipoprotein)
and decreases the good HDL (highdensity lipoprotein)

Suggested that you should not
consume more than 2 g of trans
fat/day in a 2000 kcal/day diet
Myristic Acid – a
Saturated fatty-acid
Elaidic Acid - a
Trans- fatty acid
Oleic Acid in olive
oil – cis-fatty acid
O
OH
O
O
OH
OH
Other Effects of Trans Fats
Cancer
 Type 2 diabetes
 Obesity
 Liver Dysfunction
 Ovulatory Infertility

What if Trans fats are not
labelled?

add up the values for saturated,
polyunsaturated and
monounsaturated fats. If the
number is less than the "Total
fats" shown on the label, the
unaccounted is trans fat.
Triglycerides
Composed of a glycerol molecule and
three fatty acids
 Body’s most abundant lipid & best
source of energy
 FAT!!!
 Adipose tissue contains high
concentrations of triglycerides

Condensation
Reaction in
Triglycerides
Phospholipids
Main component of cell membrane
 Hydrophilic head - glycerol +
phosphate
 Hydrophobic tail - 2 fatty acids

Phospholipid
WAXES
Waxes
Long-chain fatty acids linked to an
alcohol or carbon rings
 Very water repellent

Paraffin Wax

Breathing in paraffin candle wax may
be carcinogenic
Bee’s Wax
Sterols/Steroids
No fatty acid tails!
 Backbone of 4 fused carbon rings
 Sterols differ functional group types
and positions
 Examples: cholesterol and hormones

Cholesterol
Anabolic Steroids
Synthetic variants of testosterone
 Overdosing causes:

•
•
•
•
Mood swings
Liver damage leading to cancer
High blood pressure
Shrinks testicles, reduces sex drive & causes
infertility & breast enlargement in men
• Disrupts menstral cycle & leads to male
characteristics in females
• Stunts growth & stops bone growth in teens
Proteins
Silk Proteins
Protein

Biological polymer constructed from amino
acid monomers

Tens of thousands of proteins found in the
human body

Each protein has its unique threedimensional structure that corresponds to
a specific function

Seven classes of proteins
Classes of Proteins Protein

Structural – silk, hair, fibers, ligaments

Contractile – muscle

Storage – ovalbumin

Defensive – antibodies

Transport – hemoglobin, membrane

Signal – certain hormones

Enzymes - catalyst
Protein Shape

Consists of one or more polypeptide
chains

Either globular or fibrous in shape

Can be denatured (unraveled) by
heat, changes in salt concentration
and pH
Basic Structure of an Amino
Acid
Water vs. Fat-Soluble Amino Acids
Peptide-Bond Formation
Structural Levels

Primary 1°

Secondary 2°

Tertiary 3°

Quaternary 4°
Primary Structure

Amino acid sequence
Secondary Structure

Either alpha helix or pleated sheet

Patterns maintained by hydrogen bonding
between the –N-H groups and – C=O groups
Tertiary Structure

Globular – contain mixture of  -helix and pleated
sheets

Fibrous – almost entirely helical

Maintained by hydrogen bonding and ionic bonding
between R groups of the amino acids.
Quaternary Structure

Results from bonding interactions
between different polypeptides or
subunits
Quaternary Structure
of Collagen
Ribbon vs. Space-filling
Models of Proteins
Enzymes
Enzymes in General
speed up metabolic reactions that
would normally take years to undergo
by lowering the “activation energy”
needed for a reaction to occur
 are named by adding the suffix “ase”
to part of the name of the substrate
(ex. sucrase)

Enzymes Decrease the
Activation Energy
Mexican Jumping Bean analogy for energy of
activation (EA) and the role of enzymes
Characteristics of Enzymes
Do not make any reaction occur that
would not normally occur naturally
 Do not get used up during the
reaction
 Can work both in the forward and
reverse directions of a reaction
 Are highly selective to specific
substrates

Induced-Fit Model
Enzymes have specifically shaped “active
sites” on their surfaces that interact with
the substrate(s)
 As the substrate enters this active site it
induces the enzyme to change shape so
that the active site fits even more snugly
around the substrate (clasping handshake)
 This “induced-fit” strains the pre-existing
bonds within the substrate(s) and
promotes the formation of new bonds (in
products)

The role of sucrase in sucrose
cleavage
Hexokinase is an enzyme that catalyzes the ATPdependent phosphorylation of glucose to glucose-6phosphate. This is the first step and the first
rate-limiting step the glycolytic pathway
Induced-Fit
Model of
Hexokinase
Factors Affecting Enzyme
Activity
Temperature - causes denaturation of
the secondary & tertiary structures
of the enzyme, hence changing the
shape of the active site, therefore
destroying enzymatic action
 pH - same as above
 Salinity - same as above

Effect of Temperature on
Different Enzymes
Allosteric Control
allo - different
 steric - structure
 enzymes can be activated or inhibited
when a specific substance combines
with them at a site other than the
active site or within the active site

Enzyme Inhibitors
Feedback Inhibition

When an end product accumulates,
some of the excess product binds to
an enzyme molecule, hence acting as
an allosteric inhibitor and therefore
blocking the production of more
product
Coenzymes
A coenzyme can alter the shape of
the enzyme’s active site allowing a
better fit with its substrate
 they can also serve as transfer
agents of atoms, electrons, H+ ions or
functional groups.

Nucleic Acids
What is the problem
with the figure of the
double helix?