Some Important Biomolecules

and the Concept of Isomerism

Bernhard H.J. Juurlink

Professor of Anatomy & Cell Biology
College of Medicine, Alfaisal University
 Amino Acids
• The amino acid is comprised of a carboxylate
functional group at one end and an amino
functional group at the other end

Glycine
 Amino Acids
• Amino acids are grouped according to charge, especially in the context of the
peptide bond
– neutral
– basic – have an extra amino group
– acidic – have an extra carboxylate group
• Grouped according to hydrophobicity/hydrophilicity

The Peptide Bond: reaction between

the carboxylate and the amino group
resulting in a Carbon-Nitrogen bond
and the formation of H2O.
 If there are two amino
groups on an amino acid,
then it is hydrophilic and
basic; if there are two
carboxylates, then it is
hydrophilic and acidic. If
there is a ring structure, then
it is hydrophobic
 Simple Carbohydrates typically have the
formula: (CH2O)n
• Ways of classifying:
– Number of carbon atoms
• Trioses (3 carbons)
• pentoses (5 carbons)
• hexoses (6 carbons)
– position of the carbonyl functional group (-C=O)
• aldoses – carbonyl on the first carbon
• ketoses – carbonyl on the second carbon
 Hexoses

D fructose

Aldose Ketose
The aldose glucose and the ketose fructose are in equilibrium between the ring and the
open forms as indicated in the diagrams above with the ring form predominating at pH
7.4. The reason for this equilibrium is that the carbon associated with the carbonyl
oxygen is very electron deficient and will interact with an electron rich oxygen
associated with Carbon 5 of glucose or fructose.

Note that sugars have a carbonyl and many hydroxyls; hence, sugars have many d+ and
d- charges. How do you think that water will interact with sugars?
 Water will become structured around these
delta negative and delta positive charges
• What property does fluids have if they are rich
in sugars?, either simple sugar solutions or
sugars covalently bound to proteins.
 Viscosity increases
What is the consequence if this viscosity
increases?
 The Concepts of: Structural and Stereo Isomers
• Compounds with the same chemical formula but different arrangements of the
atomic elements are said to be structural isomers of each other
– so glucose and fructose are structural isomers.
• Steroisomers have not only the same chemical formula but the sequence of bonds
are the same – what differs is the 3-dimensional orientation in space of the atoms.
Below note that the only differences amongst the aldose hexoses shown is the
direction of the hydroxyls of carbons 2-5. These are all stereoisomers of each
other.

glucose fructose
 The Concept of Epimer as a Subset of Stereoisomers
• Steroisomers that differ from each other in configuration
around only one carbon atom are considered to be epimers –
so glucose and galactose are epimers.

Glucose and Galactose are Epimers

Note the only difference between

glucose and galactose is that the
hydroxyl group associated with
carbon 4 points to the right in
glucose but to the left in galactose:
such small differences are
recognized by the enzymes that
metabolize glucose and galactose
Glucose Galactose
 The Concept of Enantiomer or Optical
Isomers
• Enantiomers are mirror images of each other. That
is they display chirality or handedness in the same
way that the right hand is a mirror image of the
left hand.
– In biology the mirror image are known as the (D) form
and as the (L) form.
– The glucose our body metabolizes is the D-glucose
enantiomer (this is true for most of the sugars our body
metabolizes) while the amino acids our body
metabolizes are the L enantiomers, e.g., L-glutamic acid
 Below are structural formulae of the D and L
enantiomeric (optical isomers) forms of glucose
 Lipids
• Hydrophobic molecules. We will consider the
following:
– fatty acids
– glycerol derivatives
• monoglycerides – glycerol with 1 fatty acid
• diglyceride – glycerol with 2 fatty acids
• triglycerides – gycerol with 3 fatty acids
• phospholipids: glycerol with 2 fatty acids and a phosphate
component
• Sterols such as cholesterol and cholesterol derivatives
 The Fatty Acid

• A carboxylic acid with a long hydrocarbon or aliphatic tail

– may contain only saturated bonds or also unsaturated (i.e.,
double) bonds
Glycerol [Glycerin] and Glycerides
• Glycerol is a 3-carbon atom each of which has
an associated hydroxyl group
• Fatty acids are ligated to glycerol to form
glycerides

Glycerol
 Glycerides: Mono-, Di- and Tri-glycerides

mono-

R = alkyl chain

di-

tri-
 Phospholipids are Glyceride Derivatives

choline may be replaced by other polar compounds such as inositol

 Phospholipids
• Form the lipid bilayer, e.g., phosphatidylcholine
 Cholesterol
• Cholesterol is a sterol. Sterols are
hydrophobic and characterized by ring
structures and alkyl groups
the pink ovoid outlines
the basic structure of a
sterol. The entire
structure depicts
cholesterol

Phytosterol
 Steroid hormones are derivatives of cholesterol, e.g.,
vitamin D, estrogen, testosterone, glucocorticoids

Calcifitriol (active form of vitamin D) Cholesterol

 Pyrimidines
• cyclic compounds similar to benzene except there are two
nitrogens substituting for carbons (and a carbonyl)

Cytosine Thymine Uracil

Pyrimidines are Important in DNA/RNA

Consider the Table of Electrophilicity

 Purines
• Comprised of a pyrimidine ring fused to an imidazole ring –
also important in formation of nucleic acids.
 Purines also give rise to the energy-storing
molecules, e.g., adenosine triphosphate (ATP)
• In this case adenine is covalently linked to a 5 carbon sugar known as ribose to give rise to
adenosine (a base plus a sugar is known as a nucleoside)
• The ribose is then phosphorylated to give rise to ATP (a nucleoside that is phosphorylated is
known as a nucleotide)
 Nucleic Acids
• Comprised of nucleosides linked by a
phosphate

deoxyribose

glucose, a hexose
 Purines and Pyrimidines form the bases for
DNA and RNA
• Purines and pyrimidines hydrogen bond to each
other (A:T, G:C)