BM101: BIOLOGY FOR ENGINEERS

Biomolecules

Instructor: Yashveer Singh, PhD

Slides courtesy: Dr. Durba Pal

11 September 2019 1
Biomolecules
▪ Molecules present in the living
organisms and sustaining the life
processes are known as biomolecules,
particularly the biomacromolecules

▪ The elemental composition of a living

matter is different from a non-living
matter

▪ The major difference is the amount

of carbon present in a living matter

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 Biomolecules
▪ If one looks at the chemical composition of cells
(particularly the carbon compounds), they mostly
have universal set of small molecules: amino
acids, nucleotides, sugars and their
phosphorylated derivatives, and mono-, di-, and
tricarboxylic acids

▪ These small molecules are used to assemble

biomacromolecules: polysaccharides, proteins,
nucleic acids, and lipids (not a true polymer)

Lehninger Principles of Biochemistry 3

Biomolecules
▪ Proteins: are polymers of different amino
acids, linked by peptide bonds (-CONH-)
formed by dehydration (polymerisation)
between -COOH group of one amino acid and
-NH2 group of next amino acid, accompanied
with the removal of H2O. Responsible for
structure and function of cells

▪ Nucleic acids: are polymers of nucleotides,

linked by 3′-5′ phosphodiester bonds (-O-
HPO2-O-). The 3′- C on the sugar of one
nucleotide is linked to the 5’-C on the sugar
of next nucleoside along with the release of a
water molecule. Responsible for storing and
transmitting genetic information
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Biomolecules
▪ Polysaccharides: are polymer of
monosaccharides linked by glycosidic
bonds. Responsible for structure and
energy storage

▪ Lipids: unlike proteins, nucleic acids,

and polysaccharides, lipids are not
polymers. These are biomolecules,
which are either not soluble or sparingly
soluble in water and usually form
aggregated assemblies. Responsible for
structure and energy storage
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 Biomolecules
▪ Cells are not all about the
presence of biomolecules only, one
also needs to look at hierarchical
organization of biomacromolecules
in cells
▪ Biomacromolecules are
assembled employing covalent
bonds (amino acid to protein)
▪ Supramoleculer assemblies
employing noncovalent
interactions leads to the formation
of organelles (plasma membrane is
a complex of lipid and protein)
▪ Supramolecular assemblies
(organelles) are arranged into
anther complex structure, cell
Lehninger Principles of Biochemistry 6
Atomic structure
▪ Atoms are the smallest units of matter-
made up of protons, neutrons and
electrons
▪ Protons and neutrons are heavier than
electrons and reside in the nucleus at the
center of the atom
▪ Adding a proton to an atom makes a new
element, while adding a neutron makes an
isotope, or heavier version, of that atom
▪ Protons and neutrons have
approximately the same mass. Atoms
always have an equal number of protons
and electrons, and the number of protons
and neutrons is usually the same as well.

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Atomic structure
▪ The most abundant atoms in living
matter are carbon, hydrogen, oxygen,
and nitrogen

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How do atoms interact to form molecules?
▪ Covalent bonds (atoms
share electrons): electrons
are shared between outer
orbitals of atoms so as to
make pairs
▪ One shared pair is a single
bond; two shared pairs is a
double bond; three shared
pairs is a triple bond

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 How do atoms interact to form molecules?
Na has only one
e- in its outer
orbital; that e- is
easily donated, or
lost; the result is a
net positive
charge. Cl has a nearly complete
outer orbital; it strongly
accepts another e-; the
result is a net negative
charge

▪ Ionic bonds (strong electrostatic attraction): are the complete transfer of valence
electron(s) between atoms. It is a type of chemical bond that generates two oppositely
charged ions. In ionic bonds, Na loses electrons to become a positively charged cation,
whereas the Cl accepts those electrons to become a negatively charged anion. Ionic bonds
require an electron donor, and an electron acceptor 10
How do atoms interact to form molecules?
▪ Hydrogen bonds: Some
molecules have atoms
covalently bound together, but
one atom may pull the shared
pair of electrons more toward its
nucleus. This creates partial
charges across the molecule
(one side partly negative and
the other side partly positively
charged); this type of molecule
is said to be polar

Partial positives and partial

negatives of two polar
molecules can attract each
other. Water is a good example

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Water as a Strong Solvent
▪ Water’s small size and polarity makes it a
very powerful dissolving agent (solvent) for
many compounds (solute) when they are
added to water, particularly salts and polar
solutes, like sugar
▪ Notice how multiple water molecules
surround the ions by charge – partial
charge attractions

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Hydrophobic Interactions
▪ Nonpolar compounds include the
hydrocarbons like fats and oils, which are
either insoluble or sparingly soluble in
water
▪ It is more energetically favorable for
nonpolar compounds to aggregate
together in water than stay apart
▪ Cell membranes form from lipids due
to hydrophobic interactions

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Van der Waals Interactions
▪ Van der Waals forces are driven by
induced electrical interactions between
two or more atoms or molecules that
are very close to each other.
▪ Van der Waals interaction is the
weakest of all intermolecular
attractions between molecules.
▪ Dipole Dipole forces occur in polar
molecules, that is, molecules that have
an unequal sharing of electrons

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 Bond Distances
▪ Distances between centers of bonded atoms are called bond lengths,
or bond distances
▪ Bond lengths vary depending on many factors, but in general, bond lengths
of the same order for the same pair of atoms in various molecules are very
consistent
▪ Bond lengths are determined by X-ray diffraction of solids, by electron
diffraction, and by spectroscopic methods
▪ Bond lengths range from the shortest of 74 pm for H−H
▪ Bond orders affect bond length

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Bond Distances

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 Bond Energy
▪ The amount of energy required to break a bond is called bond dissociation
energy or simply bond energy.
▪ Bond energy is a measure of the strength of a chemical bond. The larger the
bond energy, the stronger the bond.
▪ Since bond lengths are consistent, bond energies of similar bonds are also
consistent.

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Bond Energy
▪ For covalent bonds, bond
energies and bond lengths depend
on many factors: electron afinities,
sizes of atoms involved in the
bond, differences in their
electronegativity, and the overall
structure of the molecule

▪ There is a general trend in

that the shorter the bond length,
the higher the bond energy

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 Summary
•  Non-covalent bonds determine the shape of many large biomolecules,
which stabilizes complexes composed of two or more different molecules
• There are four main types of non-covalent bonds in biological systems:
hydrogen bonds, ionic bonds, vander Waals interactions,
and hydrophobic bonds. The bond energies for these interactions range from
about 1 to 5 kcal/mol
•  Although any single noncovalent bond is quite weak, several such bonds
between molecules or between the parts of one molecule can stabilize the
three dimensional structures of proteins and nucleic acids and mediate
specific binding interactions
• Examples are phospholipids, which are the main components of
biomembranes, are amphipathic molecules. Noncovalent bonds are
responsible for organizing and stabilizing phospholipids into one of three
structures in aqueous solution
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 Do it yourself
▪ Read Chapter 2 – Chemical Components of Cells from Essential Cell Biology,
B. Alberts, D. Bray, K. Hopkin, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P.
Walter, Garland Science, IV Edition, 2014

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