1.

The
Chemical
Basis of Life
1.1 Introduction
 •By the end of this topic, you will be able to understand the chemical
basis of life, and many more:

• Define biochemistry.
• Describe the elements of biological systems.

Objectives
• Differentiate between monomers and polymers.
• Understand the evolution of metabolic pathways.
• Define Gibb’s free energy and change of free energy.
• Describe system and process.
• Differentiate between exergonic and endergonic reactions.
• Explain the two laws of thermodynamics.
• Answer whether life obeys the laws of thermodynamics or not.
• Describe the prebiotic world along with the Miller-Urey
experiment.
• Illustrate the RNA theory.
• Distinguish between the present life-forms.
• Define the endosymbiotic theory.
 What is Biochemistry?
❑ Biochemistry is the scientific discipline that seeks to explain life at the
molecular level. It offers answers to such fundamental questions as:

✔ “What are we made of ?” and

✔ “How do we work?”

❑ Biochemistry is also a practical science:

✔ It generates powerful techniques that underlie advances in other fields,

such as genetics, cell biology, and immunology;

✔ It offers insights into the treatment of diseases such as cancer and

diabetes; and

✔ It improves the efficiency of industries such as wastewater treatment,

food production, and drug manufacturing.

❑ Biochemistry has traditionally been a science of reductionism: it

attempts to explain the whole by breaking it into smaller parts and
examining each part separately.
 Elements found in biological
systems

❑ An element is a pure substance which cannot be broken down by

chemical means, consisting of atoms (the basic chemical units).

❑ Only a small subset of the known elements are found in living

systems.

❑ The most abundant of these elements are: C, N, O, and H, followed by

Ca, P, K, S, Cl, Na, and Mg.

❑ Certain trace elements are also present in very small quantities.

❑ Virtually all the molecules in a living organism contain carbon, in

addition they are also constructed from H, N, O, P, and S. Most of
these molecules belong to one of a few structural classes, known as
functional groups.
 The most abundant elements are most darkly shaded; trace
elements are most lightly shaded.

Figure Courtesy: Essential Biochemistry

 Biological Molecules
❑ Biological molecules are composed of a subset of all possible elements
and functional groups.

❑ Cells contain four major types of biological molecules:

1. Amino Acids
The simplest compounds are the amino acids, so named because
they contain an amino group (-NH2) and a carboxylic acid group (-
COOH).

2. Carbohydrates
Simple carbohydrates (also called monosaccharides or just sugars)
have the formula (CH2O)n.

3. Nucleotides
A five-carbon sugar, a nitrogen-containing ring (bases), and one or
more phosphate groups are the components of nucleotides. For
example, adenosine triphosphate (ATP) contains the nitrogenous
group adenine linked to the monosaccharide ribose, to which a
triphosphate group is also attached:
 Figure courtesy: Essential Biochemistry

❑ The most common nucleotides are mono-, di-, and triphosphates containing
the
nitrogenous ring compounds (or “bases”) adenine, cytosine, guanine,
thymine, or uracil (abbreviated A, C, G, T, and U).

4. Lipids
The fourth major group of biomolecules consists of the lipids. These
compounds cannot be described by a single structural formula since
they are a diverse collection of molecules. However, they all have in common a
tendency to be poorly soluble in water because the bulk of their
structure is hydrocarbon-like.
 Biological Polymers
❑ The universal feature of nature: A few kinds of building blocks can be
combined in different ways to produce a wide variety of larger
structures. These larger structures are known as “Macromolecules”.

❑ Generally, macromolecules are “polymers”-made up of “monomers”-

the building block, or subunit of a large molecule.

❑ Amino acids, monosaccharides, and nucleotides each form polymeric

structures with widely varying properties. In most cases, the individual
monomers become covalently linked in head-to-tail fashion.

❑ The linkage between monomeric units is characteristic of each type of

polymer. The monomers are called residues after they have been
incorporated into the polymer.

❑ Lipids do not form polymers, although they do tend to aggregate to

form larger structures.
Figure courtesy: Essential Biochemistry
 There are three major kinds of biological
polymers
1. Proteins

Polymers of amino acids are called polypeptides or proteins. The

amino acid residues are linked to each other by amide bonds called
peptide bonds.

Proteins are the most structurally variable and therefore, the most
functionally versatile of all the biopolymers.
 There are three major kinds of biological polymers
2. Nucleic Acids
❑ Polymers of nucleotides are termed
polynucleotides or nucleic acids, better known as
DNA and RNA.

❑ Each nucleic acid is made from just four

different nucleotides: the residues in RNA contain
the bases adenine, cytosine, guanine,
and uracil, whereas the residues in DNA
contain adenine, cytosine, guanine, and
thymine.

❑ Polymerization involves the phosphate

and sugar groups of the nucleotides,
which become linked by phosphodiester
bonds.

❑ Nucleic acids tend to have more regular

structures than proteins. This is in
keeping with their primary role as carriers of
genetic information, which is contained in their
 There are three major kinds of biological polymers

3. Polysaccharides

❑ Polysaccharides usually contain only one

or a few different types of monosaccharide
residues.

❑ As polysaccharides are homogeneous in

nature, tends to limit their potential for carrying
genetic information in the sequence of their
residues (as nucleic acids do) or for adopting
a large variety of shapes and mediating chemical
reactions (as proteins do).

Polysaccharides perform essential cell

functions by serving as fuel-storage
molecules and by providing structural support.
1.The Chemical Basis of Life

1.2 Energy and Metabolism

Part 1
 Purpose of Energy
❑ In order to stay alive and to reproduce themselves--living
organisms and cells must need to perform work. In fact, cells
require energy for all the functions of living, growing, and
reproducing.

❑ They require energy to assemble small molecules into polymeric

macromolecules.

❑ And unless the monomeric units are readily available, a cell must
synthesize the monomers, which also requires energy.

❑ Cellular processes such as the building and breaking down of

complex molecules occur through stepwise chemical reactions.
Some of these chemical reactions are spontaneous and release
energy, whereas others require energy to proceed.

❑ All of the chemical reactions that take place inside cells, including
those that use energy and those that release energy, are
collectively known as the cell’s metabolism.
 Most life forms on earth get their
energy from the sun. Plants use
photosynthesis to capture
sunlight, and herbivores eat
those plants to obtain energy.
Carnivores eat the herbivores,
and decomposers digest plant
and animal matter.

Figure courtesy: Openstax College: Biology

Figure Courtesy: www.edx.org
 Evolution of Metabolic Pathways

❑ Metabolism is a complex process, and the complexity

varies from organism to organism.

❑ The origin and evolution of metabolic pathways allowed

primitive cells to become more chemically independent
from the prebiotic sources of essential molecules.

❑ The mechanism of emergence of new metabolic

processes would imply recycling and modifying of old
molecular devices, e.g., oxygenic from anoxygenic
photosyntheses or aerobic from anaerobic respirations.
 Metabolic Pathways: Anabolic & Catabolic

There are two types of metabolic pathways that are characterized by their ability to
either synthesize molecules with the utilization of energy (anabolic pathway) or break
down of complex molecules by releasing energy in the process (catabolic pathway).
 Anabolic Pathway

❑ Requires an input of energy to synthesize complex molecules from

simpler ones.

❑ Examples:
✔ Synthesizing sugar from CO2
✔ Synthesis of large proteins from amino acid building blocks, and
✔ The synthesis of new DNA strands from nucleic acid building blocks.

❑ All these biosynthetic processes are critical to the life of the cell, take
place constantly, and demand energy provided by ATP and other high-
energy molecules like NADH (nicotinamide adenine dinucleotide) and
NADPH
 Catabolic Pathway

❑ Catabolic pathways involve the

degradation (or breakdown) of
complex molecules into simpler
ones.

❑ Molecular energy stored in the

bonds of complex molecules is
released in catabolic pathways
and harvested in such a way that
it can be used to produce ATP
(adenosine triphosphate, or ATP).

❑ Other energy-storing molecules, ❖ ATP is the primary energy currency of the

such as fats, are also broken down cell. It has an adenosine backbone with
through similar catabolic three phosphate groups attached.
reactions to release energy and
make ATP.
Figure Courtesy: www.edx.org
 Evolution of Organism

Despite the differences between organisms and the complexity of

metabolism, researchers have found that all branches of life share
some of the same metabolic pathways, suggesting that all
organisms evolved from the same ancient common ancestor.

Evidence indicates that over time, the pathways diverged, adding

specialized enzymes to allow organisms to better adapt to their
environment, thus increasing their chance to survive. However, the
underlying principle remains that all organisms must harvest
energy from their environment and convert it to ATP to carry out
cellular functions.
 Free Energy

❑ Free energy is called Gibbs free energy (abbreviated with the

letter G) after Josiah Willard Gibbs, the scientist who developed
the measurement and has units of joules per mol (J . Mol -1).

❑ Free energy has two components: enthalpy and entropy.

❑ Enthalpy (abbreviated H, with units of J . Mol-1) is taken to be

equivalent to the heat content of the system.

❑ Entropy (abbreviated S, with units of J . K-1 . Mol-1) is a measure

of how the energy is dispersed within that system. Entropy can
therefore be considered to be a measure of the system’s
disorder or randomness, because the more ways a system’s
components can be arranged, the more dispersed its energy.
 Free Energy Change
❑ Every chemical reaction involves a change in free energy, called delta G
(ΔG). The change in free energy can be calculated for any system that
undergoes such a change, such as a chemical reaction.

❑ To calculate ΔG, subtract the amount of energy lost to entropy (denoted

as ΔS) from the total energy change of the system (denoted as ΔH) . The
formula for calculating ΔG is as follows, where the symbol T refers to
absolute temperature in Kelvin (degrees Celsius + 273):

ΔG = ΔH − T ΔS

❑ The standard free energy change of a chemical reaction is expressed as

an amount of energy per mole of the reaction product (either in
kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal) under
standard pH, temperature, and pressure conditions are generally
calculated at pH 7.0 in biological systems, 25 degrees Celsius, and 100
kilopascals (1 atm pressure), respectively.
1.The Chemical Basis of Life

1.2 Energy and Metabolism

Part 2
 What is a System?
❑ A system is defined as the matter within
a defined region of space.

❑ The matter in the rest of the universe is

called the surroundings.

❑ A system can be:

Isolated, if it exchanges neither
matter nor energy with its
surroundings.
Closed, which exchanges energy
but not matter with its surroundings.
OR,
Open, if exchanges both energy
and matter with its surroundings. A
living organism is an open system.
Energy is exchanged between them and
their surroundings, as they consume
energy-storing molecules and
release energy to the environment by
❑ Organisms obtain energy from
their surroundings in two ways:

1. They take up chemical

fuels (i.e., glucose) from
the environment and
extract energy by oxidizing
them.
OR,

2. They absorb energy from

the sunlight.

Figure courtesy: Free course material from edX.org

 Laws of Thermodynamics

❑ Thermodynamics refers to the study of energy and energy

transfer involving physical matter.

❑ The laws of thermodynamics govern the transfer of energy in

and among all systems in the universe.

❑ Does living system obey the laws of thermodynamics?

❑ Like any system in the universe living organisms obey the laws
of thermodynamics. Actually two laws dictate the ways living
organisms use their energy.
The First Law of Thermodynamics

❑ The First Law of

Thermodynamics states that
the total energy of a system
and its surroundings is
constant. In other words,
the energy content of the
universe is constant; energy
can be neither created nor
destroyed. Energy can take
different forms, however.
 The Second Law of Thermodynamics

❑ The Second Law of

Thermodynamics states that the
total entropy of a system and its
surroundings always increases
for a spontaneous process.

❑ The more energy that is lost by

a system to its surroundings, the
less ordered and more random
the system is. Scientists refer to
the measure of randomness or
disorder within a system as
entropy. High entropy means
high disorder and low energy
 FIGURE :Some energy interconversion in living
organisms. During metabolic energy
transductions, the randomness of the system
plus surroundings (expressed quantitatively as
entropy) increases as the potential
energy of complex nutrient molecules
decreases.
(a) Living organisms extract energy from their
surroundings;
(b) convert some of it into useful forms of
energy to produce work;
(c) return some energy to the surroundings as
heat; and
(d) release end-product molecules that are
less well organized than the starting fuel,
increasing the entropy of the universe. One
effect of all these transformations is (e)
increased order (decreased randomness) in
the system in the form of complex
macromolecules.

Figure courtesy: Principles of Biochemistry

 Spontaneous (Exergonic) Reaction

❑ If energy is released during a chemical reaction, the ΔG

becomes negative (ΔG < 0).

❑ Negative ΔG also means that the products of the reaction have

less free energy than the reactants, because they gave off some
free energy during the reaction. Reactions that have a negative
ΔG and consequently release free energy are called exergonic
reactions. Exergonic means energy is exiting the system.

❑ These reactions are also referred to as spontaneous reactions,

because they can occur without the addition of energy into the
system. These reactions are thermodynamically favorable (don’t
require any energy input).
 Non-spontaneous (Endergonic) Reaction

❑ If a chemical reaction requires an input of energy rather

than releasing energy, then the ΔG for that reaction will be
a positive value.

❑ In this case, the products have more free energy than the
reactants. Thus, the products of these reactions can be
thought of as energy-storing molecules. These chemical
reactions are called endergonic reactions, and they are
non-spontaneous.

❑ An endergonic reaction will not take place on its own

without the addition of free energy.
Exergonic and endergonic reactions result in changes in Gibbs free
energy. Exergonic reactions release energy; endergonic reactions
require energy to proceed.
1.The Chemical Basis of Life

1.4 The origin and Evolution of Life

 The Prebiotic World

❑ A combination of theory and experimental data leads

to several plausible scenarios for the emergence of life
from non biological (prebiotic) materials on the early
earth.

❑ One theory holds that Earth's early atmosphere was

highly reduced, rich in methane (CH4), ammonia (NH3),
water (H2O), and hydrogen (H2), and that this
atmosphere was subjected to large amounts of solar
radiation and lightning.
 The Miller-Urey Experiment

❑ In the 1930s, Oparin and Haldane independently

suggested that ultraviolet radiation from the sun or
lightning discharges caused the molecules of the
primordial atmosphere to react to form simple
organic (carbon-containing) compounds.

❑ This process was replicated in 1953 by Stanley

Miller and Harold Urey, who subjected a mixture of
H2O, CH4, NH3, and H2 to an electric discharge for
about a week. The resulting solution contained
water-soluble organic compounds, including
several amino acids (which are components of
proteins) and other biochemically significant
compounds.

Courtesy: http://www.as.utexas.edu
 Problem Associated With Miller-Urey
Experiment
❑ The gases they used (a reactive mixture of methane and ammonia) did
not exist in large amounts on early Earth. On the other hand, modern
scientists believe the primeval atmosphere contained an inert mix of
carbon dioxide and nitrogen.

❑ In 1983, Miller repeated the experiment with correct combo and the
resulted mixture created a colorless brew containing few amino acids.

❑ Miller’s student, Jeffry Bada noticed that the reaction actually produced
chemicals like nitrites which,
✔ destroy amino acids as quickly as they form.
✔ water acidic—which prevents amino acids from forming.

❑ Bada reran the experiment adding iron and carbonate minerals, thought
to neutralize nitrites and acids in primitive earth. He still got the same
watery liquid as Miller did in 1983, but this time it was chock-full of amino
acids.

❑ So, this result moves toward more realism in terms of what the
conditions were on early Earth."
 The RNA World Theory

❑ The most prominent hypothesis for

the origin of the first life is called the
“RNA world.”

❑ According to the RNA world

hypothesis, life began with RNA,
before a genetic takeover occurred
implicating primitive biosynthetic
machinery and natural selection to
result in DNA.

Figure courtesy: Principle of Biochemistry

Courtesy: http://www.as.utexas.edu
 Problems With The “RNA World”
Hypothesis
First, RNA molecules would have to arise by unguided, non-biological
chemical processes. But RNA is not known to assemble without the help of
a skilled laboratory chemist intelligently guiding the process.

Second, while RNA has been shown to perform many roles in the cell, there
is no evidence that it could perform all the necessary cellular functions
currently carried out by proteins.

Third, the RNA world hypothesis can’t explain the origin of genetic
information.

Fourth, and most fundamentally — the RNA world hypothesis can’t explain
the origin of the genetic code itself. In order to evolve into the
DNA/protein-based life that exists today, the RNA world would need to
evolve the ability to convert genetic information into proteins.

Courtesy: https://evolutionnews.org
❑ A new study, titled “Selective prebiotic formation of RNA
pyrimidine and DNA purine nucleosides,” appeared June 3 in
Nature.

❑ According to the new finding, “The nucleic acids, RNA and

DNA, are clearly related,” and they both derive from a hybrid
ancestor, rather than one preceding the other.
The Earth’s Present Life-Forms
The earth’s present-day life-forms are of two types, which are
distinguished by their cellular architecture:

1. Prokaryotes are small unicellular organisms that lack a

discrete nucleus and usually contain no internal membrane
systems. This group comprises two subgroups :
the eubacteria (usually just called bacteria),
exemplified by E. coli, and the archaea (or archaebacteria),
best known as organisms that inhabit extreme environments.

2. Eukaryotic cells are usually larger than prokaryotic cells

and contain a nucleus and other membrane-
bounded cellular compartments (such as mitochondria,
chloroplasts, and endoplasmic reticulum). Eukaryotes may
be unicellular or multicellular. This group (also called the
eukarya) includes microscopic organisms as well as familiar
macroscopic plants and animals
Courtesy: http://courses.washington.edu
 Endosymbiotic Theory
❑ Eukaryotic cells may have evolved when multiple cells joined into one.
They began to live in what we call symbiotic relationships. The theory that
explains how this could have happened is called endosymbiotic theory.

❑ The mitochondrion and the chloroplast are both organelles that were
once free-living cells. They were prokaryotes that ended up inside of other
cells (host cells). They may have joined the other cell by being eaten (a
process called phagocytosis), or perhaps they were parasites of that host
cell.

❑ During the 1950s and 60s, scientists found that both mitochondria and
plastids inside plant cells had their own DNA. It was different from the rest
of the plant cell DNA.

❑ A scientist named Lynn Margulis put all of this information together and
published it in 1967. Her paper is called “On the origin of mitosing cells”.
Two main tenets of Margulis’s theory, that mitochondria are the
descendants of oxygen-respiring bacteria and that chloroplasts were
originally photosynthetic bacteria, are now almost universally accepted.
 Evolution of eukaryotes through endosymbiosis.

Figure courtesy: Principle of Biochemistry

 Summary
1. The unique properties of carbon make it a central part of biological molecules.
2. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many
molecules important for cellular function.
3. Cells perform the functions of life through various chemical reactions.
4. A cell’s metabolism refers to the chemical reactions that take place within it.
5. There are two metabolic pathways: catabolism and anabolism.
6. Catabolism is associated with release of energy. On the other hand, anabolic
processes require energy.
7. Energy comes in many different forms.
8. System refers to the matter and its environment involved in energy transfers.
Everything outside of the system is called the surroundings. Single cells are
biological systems.
9. The first law of thermodynamics states that the total amount of energy in the
universe is constant.
10. The second law of thermodynamics states that every energy transfer involves
some loss of energy in an unusable form, resulting in a more disordered system.
11. The free energy of a system is determined by its enthalpy and entropy.
12. Living organisms obey the laws of thermodynamics.
13. Modern prokaryotic and eukaryotic cells apparently evolved from simpler
nonliving systems.
14. The three domains of life are bacteria, archaea, and eukarya.