a presentation of how life originated on earth due to chemicals and how these chemicals represent the building blocks of life all around us. by Dr. tithi parija (asst. professor) from KIIT school of biotechnology

1. Chemical essence of life
Chemical Essence of Life

2. Atoms are nature’s building material
• Any substance in the
universe that has mass,
occupies space is defined
as matter.
• All matter is composed
of extremely small
particles called atoms.
• 92 naturally occurring
elements
Basic structure of atoms. All atoms have a nucleus
consisting of protons and neutrons, except hydrogen,
the smallest atom, which has only one proton and no
neutrons in its nucleus. Oxygen, for example, has
eight protons and eight neutrons in its nucleus.
Electrons spin around the nucleus a far distance away
from the nucleus.

4. Essential elements of Life
• 25 out of 92 natural
elements essential to
life
• C, O, N, H- make up
96.3 % of living matter
• P, S, Ca, K- remaining
4% of an organism’s
weight

6. Water: A Molecule
Essential for Life
• Water is the most abundant liquid on Earth.
• It covers 70% of our planet.
• It moderates our weather, shapes our land
and is essential to the existence of life.
• The Earth’s position in the solar system means
that it is not close enough for the water to
boil, nor is it too far away for it to freeze.

7. Overview: The Molecule That Supports All of Life
– Water is the biological medium here on Earth
– All living organisms require water more than any
other substance
– The abundance of water is the main reason the
Earth is habitable
– Water is involved in the reactions of life:
photosynthesis and respiration

8. The Water Cycle

9. Water

10.  Most cells are surrounded by
water.
 Cells are about 70–95%
water.
 Water is the only common
substance that exists in the
natural world in all three
physical states of matter:
solid ice
liquid water
water vapor

11. POLARITY
• In a water molecule, two hydrogen
atoms form single polar covalent
bonds with an oxygen atom.
– Because oxygen is more
electronegative than hydrogen,
the region around the oxygen
atom has a partial negative
charge.
– The regions near the two
hydrogen atoms have a partial
positive charge.
– The slightly negative regions of
one water molecule are
attracted to the slightly positive
regions of nearby water
molecules, forming hydrogen
bonds.
• Each water molecule can form
hydrogen bonds with up to four
neighbors.
• The water molecule is a polar
molecule (opposite ends have
opposite charges)
• The polarity of water molecules
results in hydrogen bonding
Hydrogen
bonds
+
+
H
H+
+
 –
 –
 –
 –

13. Four emergent properties of water contribute to
Earth’s fitness for life
• Four of water’s properties that facilitate an
environment for life:
Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent

14. Cohesion
• The hydrogen bonds joining water molecules are weak
• Collectively, hydrogen bonds hold water together, a
phenomenon called cohesion.
• Adhesion of water to plant cell walls also helps to
counter gravity
– Water molecules move from the roots to the leaves of a plant
through water-conducting vessels.
– As water molecules evaporate from a leaf, other water
molecules from vessels in the leaf replace them.
– This upward pull is transmitted down to the roots.

15. Helps pull water up through the microscopic vessels of plants
 Adhesion, clinging of
one substance to
another, contributes
too, as water adheres
to the wall of the
vessels.
 Surface tension, a
measure of the force
necessary to stretch or
break the surface of a
liquid, is related to
cohesion.

17. Water moderates air temperature
• Water stabilizes air temperatures by absorbing heat
from warmer air and releasing heat to cooler air.
• Water can absorb or release relatively large amounts
of heat with only a slight change in its own
temperature.
• Atoms and molecules of water have kinetic energy,
the energy of motion, because they are always
moving.
• Heat is a measure of the total quantity of kinetic
energy due to molecular motion in a body of matter.
• At sea level, water freezes at 0°C and boils at 100°C.

18. • Water has a high specific heat, which allows it
to minimize temperature fluctuations to
within limits that permit life
– Heat is absorbed when hydrogen bonds break
– Heat is released when hydrogen bonds form
• Evaporation
– Is the transformation of a substance from a liquid
to a gas
• Evaporative cooling
– Is due to water’s high heat of vaporization
– Allows water to cool a surface

19. Expansion upon Freezing
• Most materials contract as they solidify, but water expands.
• The hydrogen bonds in ice are more “ordered” than in liquid
water, making ice less dense
Liquid water
Hydrogen bonds
constantly break and re-form
Ice
Hydrogen bonds are stable
Hydrogen
bond

21. Insulation of Bodies of Water by
Floating Ice
• Ice floats in liquid water because hydrogen bonds in ice
are more “ordered,” making ice less dense
• If ice sank, all bodies of water would eventually freeze
solid, making life impossible on Earth
• The surface layer of ice insulates liquid water below,
preventing it from freezing and allowing life to exist
under the frozen surface

22. The Solvent of Life
• Water is a versatile solvent due to its polarity
• It can form aqueous solutions
• Water is an effective solvent because it readily forms
hydrogen bonds with charged and polar covalent
molecules.
• Even large molecules, like proteins, can dissolve in water if
they have ionic and polar regions.
• Any substance that has an affinity for water is hydrophilic
• Hydrophobic molecules are major ingredients of cell
membranes

23. • The different regions of the polar water molecule can interact
with ionic compounds called solutes and dissolve them
• When an ionic compound is dissolved in water, each ion is
surrounded by a sphere of water molecules, a hydration shell
Negative
oxygen regions
of polar water molecules are
attracted to sodium cations
(Na+).
+
+
+
+
Cl –
–
–
–
–
Na+Positive
hydrogen regions
of water molecules
cling to chloride anions (Cl–).
+
+
+
+
–
–
–
–
–
–
Na+
Cl–

24. The emergent properties of water support life
on earth and may contribute to the potential
for life to have evolved on other planets.

25. Carbon and Molecular Diversity of
Life
• Carbon- The backbone of Biological Molecules
(Living organisms are made up of chemicals mostly based on Carbon)
• Organic Chemistry - study of Carbon compounds
• Carbon atoms can form diverge molecules by bonding
to four other atoms
• Carbon chains form the skeletons
of most organic molecules
• Functional groups most important
in chemistry of life
(number and arrangement of functional group give
each molecule an unique property)

26. What about Carbon?
• Almost all molecules
associated with life contain
Carbon
• The structure of a Carbon
atom allows it to form up to
four atomic bonds
• The electro negativity of
Carbon is such that carbon
can form either polar or
nonpolar atomic bonds
• Reduced forms of Carbon-
based molecules are
believed to have utilized
energy to structurally
undergo change to form the
four types of organic
molecules that living things
make: proteins, nucleic
acids, carbohydrates and
lipids

27. Carbon
Importance of Carbon
• Photosynthesis
• Respiration
• Decomposition
Carbon is the basic building
block for all forms of life on
Earth. Fortunately, carbon is
also one of the most abundant
elements on our planet. Like all
matter, carbon can neither be
created nor destroyed, and so
all living organisms find a way
to continually reuse the carbon
supply that is available.

28. • Carbon is a central
element to life because
most biological
molecules are built
on a carbon framework.
• Groups of atoms known
as functional groups can
confer special
properties on carbon-
based molecules.

29. Isotopes of Carbon
• Over 99% of the carbon
found in nature exists as
an isotope with six
neutrons(carbon-12)
• Most of the rest of the
naturally occurring
carbon is carbon-13
• Rarest carbon isotope is
carbon-14 (radioactive
isotopes)

30. Structural Isomers
Srtuctural Isomers
1-butane and isobutane
Geometric isomers
Cis-2-Butane
and Trans-2-butane
• Enantiomers
– Chiral molecule
– D-glyceraldehyde and L-
glyceraldehyde

31. Biomolecules of Life

32. Molecules of life
Organic molecules(Type of
molecule that consists
primarily of carbon and
hydrogen atoms)
• Carbohydrates
• Proteins
• Lipids
• Nucleic Acids
• These molecules are huge
in size – macromolecules
• Most macromolecules are
polymers build from
monomers

33. Synthesis and breakdown of polymers
• Condensation reaction-
monomers connected by a
reaction in which two
molecules covalently linked to
each other by loss of a water
molecule (dehydration)
• Hydrolysis – polymers
disassemble to monomers by
hydrolysis(break with water).
Bonds between the monomers
are broken by addition of water
molecule

34. Carbohydrates
• Formed from the building blocks or
monomers of simple sugars(glucose)
• Make up 1-20% of cell mass, so they
are the most abundant class of
biomolecules.
• Contain C, H, O (ratio 1:2:1)
• Important source of energy for cells
• Provide a means of transporting and
storing that energy.
• Also good for providing structural
support.

35. • All sugars are carbohydrates. Another word for sugar is saccharide.
• Monosaccharides (mono = one, saccharide = sugar, aka "one sugar")
are monomers of carbohydrates; they are small sugars, and
Monosaccharides vary in how many carbons they contain, but most
commonly, they have three, five, or six, and as many as seven carbons.
• 1 sugar
• Building blocks of other carbohydrates
• Most water-soluble sugars
• Most have a 5-C or 6-C ring ( when they dissolve in water, they form little
rings)
• All monosaccharides have two things:
– A carbonyl group, or a carbon that forms a double bond with an oxygen,
written as C=O, and two other atom friends that we call A and B (4 bonds total
for carbon)
– Some hydroxyl groups (–OH)
• These monomers can be linked to form disachharides and larger
carbohydrate polymers, polysaccharides or complex carbohydrates.

36. Monosaccharide Structure
glucose Fructose (structural
isomers)
Galactose
(stereoisomer)
deoxyriboseribose
Glucose = blood sugar; instant E for cell; building block
Galactose & fructose = isomers of glucose: have same molecular formula but atoms
are arranged differently so have different chemical properties

37. Disaccharides
• Double sugar
• Consist of 2 monosaccharides
• Must be broken down to be
absorbed
• Serves transport molecules in
plants, provide nutrition in
animals
• Effective reservoirs of
glucose
• Sugarcane, sugar beets rich
in sucrose
• Lactose preserved for
offspring

38. Polysaccharides
• “Many sugars”
• Chains of glucose
• Least water-soluble of
carbohydrates
– More complex = less
soluble
• Good energy storage
product
• Must be broken down
to be absorbed

39. Polysaccharide Structure: Starch
Spiral structure, insoluble
OH groups stick out from coils
Storage carbohydrate of plants

40. • Potato starch:
20% Amylose
80% Amylopectin

41. Filamentous (branched) chains, insoluble
Storage carbohydrate of animal tissues
Equivalent to starch in plants
Much longer and more branched than starch
Stored in muscle & liver cells
Polysaccharide Structure: Glycogen

42. Polysaccharide Structure: Cellulose
Every other sugar is “upside-down”
Sheets form by H-bonding between chains
Structural carbohydrate of plants
Makes up cell walls
Polymer of beta glucose, β- (1to 4) linkage
Unbranched tough fibers

43. Modified polysaccharide
Nitrogen groups attached to glucoses
N-acetylglucosamine (substituted version of glucose)
Strengthens cuticle of arthropods & cell walls of fungi
structural carbohydrate of animals & fungi
Polysaccharide Structure: Chitin

44. Complex Carbohydrates
• Four polysaccharides are critical in
the living world:
– starch
– glycogen
– cellulose
– chitin
Starch -polysaccharide of glucose
with α-glycosidic linkages.
Glycogen -highly branched
polysaccharide of glucose.
Cellulose -polysaccharide of glucose,
but its individual
monosaccharides are connected
by β-glycosidic linkages.
Chitin is similar to cellulose except
the glucose monomer of chitin
has a nitrogen-containing
appendage
Potato Liver Algae Tick
starch
glycogen cellulose chitin

46. Lipids
Fats & oils
Contain C, H, O
Less O than carbohydrates
Some also have P
Non-polar
Insoluble in water(hydrophobic)
C-H bonds stores more energy
than carbohydrates
There are three kinds of lipids, and
each one has a different function
Fats/oils/waxes
Vitamins, Terpenes,
Postaglandins
Steroids

47. Fats/Oils
• Fats are non-polymer large molecules
• Constructed from - fatty acids (14-20 carbons and
carboxyl group present) and glycerol (3 carbon and 3
OH group)
• C-H bond-long term energy storage
• Triglyceride or triacylglycerol

48. Saturated fats pack more
tightly than unsaturated
fats, and tend to be more
solid
• Saturated fat
– Internal C atoms bonded to at
least 2 H atoms
– Fatty acid with no double
bonds in its carbon tail
• Unsaturated fat
– Lipid with one or more double
bonds in a fatty acid tail
– Monounsaturated (one double
bond), Polyunsaturated (more
than one double bond)
– Cis and trans forms
– Trans fats linked to ↑ LDL and
↓HDL (increased risk of
coronary heart disease)

50. • Saturated fats - solid at
room temperature
• Most animal fats are
saturated
– exemption : some fish oils
• Most plant fats are
unsaturated
– Exemption: tropical plant
oils like palm and coconut
oils (saturated and still
liquid at room
temperature)
• Oil + hydrogen = Solid fat
Eg : peanut butter
• Increase in carbohydrates
– converted to fats

51. Some lipids are vitamins

52. Waxes
Long-chained fatty acids bonded to
long-chain alcohols
Repel water
solid at room temperature due to the
high degree of saturation
Protects and Lubricates, add pliability
to hair and skin, sealing
Beewax ( mixture of wax,
hydrocarbons, alcohols) used to make
honeycombs

53. Waxes
• Plant surfaces exposed to air,
for example, have a protective
covering made largely of wax
• Waxes are part of water-
repellent and lubricating
secretions in plants and
animals
• Waxes tend to be used for
functions other than energy
storage, like waterproofing
leaves and fur

54. Phospholipids • Glycerol backbone with phosphate
group & 2 fatty acid tails
• Charged phosphate gr linked to charged
organic molecule (choline,
ethanolamine, amino acid serine)
• Tails are non-polar, Head is polar
• Ambivalent behavior towards water
• Make up double-layered cell
membranes
• Help regulate what crosses boundary of
cell

55. Glycerol- Forms backbone
Fattyacids attached to glycerol
Phosphate group attached to one end
of glycerol
Charged phosphate group has a
charged organic molecule like, choline,
ethanolamine,or serine

56. Terpenes
• Long chain lipids
• Components of
biologically imp
pigments (Cholrophyll,
retinal pigments)
• Rubber

57. Steroids
Backbone of 4 C-rings no fatty acid tails
Differ in functional groups
In all eukaryotic cell membranes
Steroids are essential for human life
(homeostasis, vitamin D, sex & metabolic hormones)

58. Steroids
• Examples
– Cholesterol is an important constituent of membranes
– Testosterone and the estrogens are steroid hormones regulate
sexual development in vertebrates
– Cortisol and related hormones play many regulatory roles in
the digestion of carbohydrates and proteins, in the
maintenance of salt balance and water balance, and in sexual
development.

59. Nucleotides
Contain C, H, O, N, P:
N base, pentose sugar &
phosphate gr
5 N bases
adenine, thymine, guanine,
cytosine, uracil
Important in energy
production,
metabolism, cell
signalling

60. Nitrogen-Containing Bases
Purines (double-ringed)
Pyrimidines (single-ringed)
Adenine Guanine
UracilThymine Cytosine

61. Genes are made of DNA
Still …
How does DNA store genetic info?
The answer lies in the structure of DNA

62.  Polymer of nucleotides:
– Phosphate
– Deoxyribose sugar
– Nitrogen-containing base (A, C,
G, T)
 All nucleotides are identical
except for base
DNA Structure

63. Structure of DNA

64. RNA
Carries out protein synthesis
Similar to DNA except:
– Single strand of nucleotides
– Ribose instead of deoxyribose, OH
instead of H at C-2
– Uracil replaces thymine

65. DNA vs RNA

67. Proteins
Proteins are an
extremely
diverse group of
biological
molecules
composed of
the monomers
called amino
acids

68. Types of Protein
Table 3.3

69. Amino Acid
• Amino acid
– Small organic compound with a carboxyl group,
amine group, and a characteristic side group (R)
D and L amino acids

70. glycine (G)
alanine (A)
valine (V) leucine (L)
Amino acid structures
serine (S) threonine (T)
cysteine
methionine (M)
phenylalanine (F) tyrosine (Y)
proline
isoleucine (I)
lysine (K)
tryptophan (W)
histidine (H)
aspartic
acid (D)
glutamic
acid (E)
aspargine (N) glutamine (Q)
arginine (R)
3
+
+
2
2-2

71. Chemical classes of 20 amino acids

74. Beginnings of a Protein
Figure 3.18
ala
ala
gln
gln
ile
ile
. . . produces a polypeptide chain like this:
A typical protein would
consist of hundreds of
amino acids
The linkage of several amino acids . . .

83. Levels of Protein Structure
Primary structure
Secondary structure
Tertiary structure
(a)
(b)
(c)
(d) Quaternary structure
amino acid sequence
beta pleated sheet
alpha helix
random coil
folded polypeptide
chain
two or more
polypeptide chains
Four Levels of Structure In Proteins
The primary structure of any
protein is simply its sequence
of amino acids. This sequence
determines everything else
about the protein’s final shape.
Structural motifs, such as
the corkscrew-like alpha
helix, beta pleated sheets,
and the less organized
“random coils” are parts
of many polypeptide
chains, forming their
secondary structure.
These motifs may persist
through a set of larger-scale
turns that make up the
tertiary structure of the
molecule
Several polypeptide chains
may be linked together in a
given protein, in this case
hemoglobin, with their
configuration forming its
quaternary structure.

85. Biology/Chemistry of Protein Structure
Primary
Secondary
Tertiary
Quaternary
Assembly
Folding
Packing
Interaction
STRUCTURE
PROCESS

86. Super Secondary Structures
• Motifs
– similar structures can
combine, fold or crease to
form motif
– Many protein use it bind to
DNA
– Useful in determining
function of unknown protein
• Domains
– Functional units within large
structures, bind to DNA
– Multiple domain perform
different parts of protein
function
Domains

87. Lipoproteins
• Lipoproteins are biological
molecules that are
combinations of lipids and
proteins.
• High-density and low-
density lipoproteins (HDLs
and LDLs, respectively),
which transport cholesterol
in human beings, are
important determinants of
human heart disease.
Glycoproteins
• Glycoproteins are
combinations of
carbohydrates and proteins.
• The signal-receiving
receptors found on cell
surfaces often are
glycoproteins.

88. Protein Folding
• Compact, globular
folding arrangement of
the polypeptide chain
• Chains fold to optimise
packing of the
hydrophobic residues in
the interior core of the
protein
• Chaperon protein

91. Protein Denaturation
Ionic strength, ph, temperature

93. Biological Molecules

94. • Starch is the nutrient storage form of carbohydrates in
plants.
• Glycogen is the nutrient storage form of carbohydrates
in animals.
• Cellulose is a rigid, structural carbohydrate found in the
cells walls of many organisms.
The most abundant carbohydrate on the planet is
cellulose—the hard stuff plants are made of—but few
organisms can actually break it down to eat it.
• Chitin is a tough carbohydrate that forms the external
skeleton of arthropods.