Life and its origin: A perspective from Chemistry

Requirements for Life, Chemistry of life, Chemistry of water, Origin of life.

Ganti S. Murthy
Biosciences and Biomedical Engineering
Indian Institute of Technology-Indore
Indore, India
Email: Ganti.Murthy@iiti.ac.in

Notes on how to use these slides

• These slides may be used as a starting point to study the topics. There will be questions from
materials outside the slides. If you want to excel in this course, you need to study the required
reading materials.
•Text Book Unit 2: The Chemistry of Life, Campbell biology 9th edition.
• Please read the required reading materials. They are required reading for a reason and questions
from this material will appear in your final exams. This includes studying the equations, formulae and
other definitions.
•Additional reading materials are just what they are: They are provided to help you explore the topic
in greater detail if you are interested. There will be no questions in final exam from these materials.
 Life on earth
• All life on earth as we know requires energy source, water, and is carbon
based.
• In this unit, we will look into some of the aspects of these three
requirements of life in detail.
• Life as we know on earth is based on carbon. (What is Miller’s
experiment? What is the significance of this experiment to understand
the origin of life on earth? https://byjus.com/biology/miller-urey-
experiment/)
• Silicon although has four valence electrons as Carbon is unlikely to be
basis of life even in alien worlds
(https://www.scientificamerican.com/article/could-silicon-be-the-basi/)
• Scientists have investigated other forms of life based on silicon, sulphur
and ammonia based life forms.
http://plutao.sid.inpe.br/col/dpi.inpe.br/plutao@80/2010/06.29.20.11.2
7/doc/SearchForLife120.html?metadatarepository=&mirror=dpi.inpe.br/
plutao@80/2008/08.19.15.01.21
 Water
• Water is very essence of life. Water makes the life on earth possible.
• Emergent properties of water make it such indispensable for life:
• High specific heat: Water has high specific heat compared to many other
common compounds. This results in moderation of temperature of water bodies,
evaporative cooling (thus enabling organisms to survive in hot conditions).
• Solid water (ice) has lower density than liquid water: This unique property of
water enables formation of an insulating layer of floating ice in water bodies that
facilitates the survival of living organisms in the liquid water below. Water as the
highest density at 4C.
• Solvent for a wide range of chemicals: Water is an excellent solvent for a wide
range of chemicals and all of life is essentially ‘wet chemistry’ i.e. most of the
chemical reactions in cell occur in the presence of water.
 Water Movement in Plants
• Cohesion and adhesion of water molecules:
cohesion and adhesion refer to attractive
forces between similar and dissimilar
molecules respectively. This is ONE of
reasons why water can travel up to 100 m in
trees from the roots to the tip of the leaves.

• Vascular plants which have specialized xylem and phloem system to transport
water and nutrients can grow much taller compared to non-vascular plants such
as algae and mosses.
• The driving force for the upward movement of water is transpiration in leaves,
positive osmotic pressure in the roots, capillary action, cohesion and adhesion of
water. Transpiration accounts for over 99% of the water use by plants.
• There are many unsolved questions in this seemingly simple phenomenon.
• How exactly does the water move? In steps or as a continuous flow?
• How do the plants avoid the cavitation? How do they repair this damage and
make the Xylem functional again?
Reference: Figure 3.3 from Campbells Biology 9th Edition
 Acids and Bases
• Water molecule is polarized due to strongly electronegative oxygen. This
results in formation of a dipole which causes extensive hydrogen bond
formation between water molecules. Due to extensive hydrogen bond
formation, some of the hydrogen ions (protons) are transferred to the
neighboring molecule (Is it really transferred or does it have to do with
the increased probability of being found in the neighboring molecules
orbitals?). Therefore, liquid water has a small concentration of H+ as H3O+
(hydronium ion) and OH-(hydroxide ion).
Ionic product of water (kW)= [H+][OH-]=10 -14 at 25C
pH =-log10[H+]
Since [H+]=10 -7 at 25C in neutral solutions,
pH of a neutral solution at 25C =7
Regardless of the pH of the solution, [H+][OH-]=10 -14 at 25C
• pH <7 indicates acidic conditions (i.e. increased [H+] concentrations)
pH>7 indicates basic conditions (i.e. reduced [H+] concentrations)
 Acids and Bases
• The ionic product of water (kW) is dependent on temperature. The kW
decreases with temperature (minimum at 249C) and increases above 249
C. Therefore, the pH of pure water decreases as it is heated up to 249 C
and increases again thereafter. Note that the total concentrations of [H+]
and [OH-] are equal regardless of the pH for pure water.
• Buffers will maintain the pH of the solution by accepting a proton (H+)
when [H+] are in excess and donating a H+ when the [H+] is reduced. Weak
acids/bases often serve as buffers. Carbonic acid is a common buffer in
oceans and human blood (How can you link the increased CO2 in
atmosphere to ocean acidification? What impact will it have on a mollusk
which has a shell made of CaCO3?).
 Acids and Bases
• Most biological reactions inside the
cell require pH around neutrality.
There are well known exceptions to
this such as the acidic environment
in our stomach or the alkaline
environment of the bile, acidic
fermentations in the production of
acetic acid and lactic acid. (Most
human pathogens cannot survive in
acidic /alkaline environments: What
is the evolutionary significance of
strong acid environments in
scavengers? ).

Reference: Figure 3.10 from Campbells Biology 9th Edition

 Carbon-based life
• Carbon has four valence electrons. Carbon is a versatile element which
forms millions of compounds which form the basis of chemical reactions
that are essential for life.
• Carbon skeletons can vary in : length, branching, double bond position
and presence of rings.
• Due to the versatility of the bonds that a carbon atom can form, organic
molecules containing carbon have the ability to form a multiple types of
isomers. Isomers have the same number of carbon atoms.
• Structural isomers: these are molecules that have differences in the covalent
arrangement of the carbon skeleton. Ex. Isobutanol and n-butanol. Iso-butanol is
produced by many microorganisms while n-butanol is a petrochemical.

Reference (this and next slide): Figure 4.7 from Campbells Biology 9th Edition
 Carbon-based life
• Cis-trans isomers: this arises due to the inflexibility of C=C bonds. They differ in
the arrangement of atoms about a double bond. Many unsaturated fatty acids
have cis and trans isomers. Trans-fats are most often produced during the
hydrogenation of oils (heard of dalda/vanaspati?).

• Enantiomers: these are molecules that are mirror images of each other. They are
represented as Levo and Dextro (basically means left and right) Only one enantiomer of
many pharmaceutical compounds are biologically active (Why? What has that to
do with the protein structure?). Sometime the effectiveness is greatly reduced if
the another enantiomer is used while at other times, the second enantiomer is
completely inactive. Ex. S-ibuprofein (effective) vs. D-Ibuprofein (non-effective).
A side note: Many pharmaceutical companies ‘invent’ new version of old drugs by
changing the percentage of enantiomers. This was not allowed by Indian Law (which
allowed only a process patent not a product patent) and was a major reason for the
affordability of the drugs in India though the rise of the generics industry in India and a
sore point for many international pharmaceutical companies.
 Biologically Important Chemical Groups
Among the millions of compounds that carbon can form, some of the
chemical groups are biologically very important:
• Hydroxyl (-OH): Alcohols; Polar in nature and an dissolve organic
compounds.
• Carbonyl (>C=O): Ketones (if carbonyl group is within the carbon
skeleton) and Aldehyde if the carbonyl group is at the end (-CHO). Very
common in sugars. Fructose (ketose; a common fruit sugar) and Glucose
(Aldose; the monomer of starch and cellulose) are hexose (a sugar
containing six carbon atoms) isomers.
• Carboxyl (-COOH): Act as acids. pKa (what is this?) of common organic
acids lactic, acetic, citric and oxalic acids are between 3.8-4.8. Most
common kidney stones are primarily made of calcium oxalate.
• Amino (-NH2): Amines. Acts a base. Found in ionized forms with a charge
of +1. Carboxyl and Amino groups are essential part of all amino acids.
 Biologically Important Chemical Groups
• Sulfhydryl (-SH): Thiols. Part of many important sulfur proteins. They form
covalent crosslinks and stabilize the tertiary structure of proteins.
• Phosphate (-PO4):Organic phosphates. Very critical part of many cellular
molecules such as ATP/ADP which are the energy currency of the cell.
Cleavage of one phosphate group from Adenosine triphosphate (ATP)
converts it into adenosine diphosphate (ADP) and releases usable energy
to the cell. Enzymes use this released energy to drive the reactions.
• Methyl (-CH3):Methylated compounds. Methylation (addition of Methyl
group) of DNA/ molecules bound to DNA affects expression of genes.
 Radioactive Carbon Dating
•This technique is commonly used to date biological samples was pioneered by Prof.
Willard Libby and his graduate student Ernest Anderson in 1946.
• A radioactive isotope of carbon is produced by the bombardment of C12 with cosmic rays
in the atmosphere. Over long periods, the ratio of C14: C12 is constant in atmosphere due
to establishment of steady state between production of C14 and its radioactive decay.
•All living organisms exchange carbon and therefore their C14:C12 ratio is at equilibrium
with the atmospheric ratio of C14:C12.
•When an organism dies, the exchange of the carbon ceases and therefore there is no new
C14 that can come into the system. However, the C14 already present in the organism
continues its radioactive decay. This therefore skews the C14:C12 ratio. Older samples will
contain less of C14 thus providing a tool to establish the age of biological samples up to
50,000 years. The age of older samples cannot be reliably estimated due to uncertainties.
•Human activities such as fossil fuel burning and atmospheric testing of atomic bobs has
skewed this ratio especially after 1950.
Required Reading Reference:
https://www.acs.org/content/acs/en/education/whatischemistry/landmarks/radiocarbon-dating.html

Additional Reading:
Fascinating application of this technique by FBI to investigate 2001 Anthrax Letters! :
https://www.ncbi.nlm.nih.gov/books/NBK209406/
 Identifying the source of water
•Stable isotopes of hydrogen (H1 and H2: what are their names?) and oxygen
are used extensively to fingerprint the biological samples.
• Stable isotopes of hydrogen and oxygen occur naturally in nature and their
ratios vary among
• Molecules containing mixtures of various stable isotopes have different
masses therefore have slightly different bond energies (What is
isotopologue?). This results in differential fractionation of isotopes in the
reactant and products. selective concentration of heavier isotopes in
biological samples
 Energy
• All life requires energy sources for survival.
• Ultimately the energy sources of most living organisms can be traced to
the solar energy. The distance from the primary energy source
determines the trophic levels of an organism. Trophic level defines the
position of an organism in the food web. In an ecosystems, the trophic
levels range from 1 for primary producers such as plants, 2 for herbivores
to 4-6 for apex predators. The number of trophic levels in a food web
indicates the complexity of the food web. A highly biodiverse and a
healthy food-web has extensive connections between all trophic levels of
the food web.
• In an ecosystems, the trophic levels range from 1 for primary producers
such as plants, 2 for herbivores to 4-5 for apex predators. Decomposers
recycle any unused resources at any trophic level and are the most
important component of the closing the mass flow cycles.
 Energy
• Typically only 10% of the energy is transferred from a lower trophic level
to higher trophic level. This implies that higher trophic levels need much
support from much larger lower trophic levels. This information is used to
model the many aspects of sustainable ecosystems such as the
sustainable fishing catch in oceans, optimal number of deer and tigers in
a national park etc. The low efficiency of energy transfer between the
trophic levels is also the reason why plant based diets
(vegan/vegetarianism) is a more sustainable than a animal based diets
(carnivorous diet).

Reference : Figure 55.4 from Campbells Biology 9th Edition

 Energy
• Some living organisms especially in very niche environments such as the
deep sea ocean vents have developed life forms that are completely
independent of solar energy but still require some form of chemical
energy. Examples of such organisms are chemolithotrophs are some
ocean dwelling iron-oxidizing bacteria which oxidize Fe2+ to Fe3+ to
produce their energy. Note that even these exotic organisms are based on
carbon.

Reference : https://www.smithsonianmag.com/innovation/scientists-
explore-breakthaking-hydrothermal-vents-virtual-reality-180959266/
Explore a 360 view of Hydrothermal vents here:
https://www.youtube.com/watch?v=Ki8ly9gW3dM&feature=youtu.be
 Points to Ponder
• Why is the water so important for life?
• Since Si is similar to C and has four valence electrons, can it form the basis of life
(may be in an alien world as is shown in many science fiction novels and movies)?
• What is the current C14/C12 ratio of atmosphere? What is this ratio for fossil fuels?
Why did this ratio change in 1950s? How is it changing now? What will happen to
this ratio if we move to renewable energy technologies?
• What are the common stable isotopes used in biological studies?
• What are some of the innovative use of the δ2H and δ18O ratios to identify origin of
a food sample?
• Why are the δ13C and δ15N isotopes in tissues of organisms used for constructing
food web? Why does the δ2H value serve as a marker for trophic indicator?
• Why is the plant based diet able to support larger populations? What are the
implications to India’s food security if we all consume meat at the same rate as in
western countries?
 References
• Stable Isotope Facility at Univ. of Wyoming. A great website that talks of application
of stable isotopes to understand ecological processes. Explore this website to learn
more!: http://www.uwyo.edu/sif/stable-isotopes/stable-isotope-measurement-
applications.html
• Although Wikipedia is not an authoritative source, the Wikipedia pages on Isotopic
measurement are quite good. Please read them to understand the basics. But
remember, Wikipedia is not authoritative resource.
https://en.wikipedia.org/wiki/Hydrogen_isotope_biogeochemistry#Naturally_occu
rring_isotope_variation
• Zanden et al. 2016. Expanding the isotopic tool box: Applications of hydrogen and
oxygen stable isotope ratios to food web studies. Front. Ecol. Evol. DOI:
https://doi.org/10.3389/fevo.2016.00020
Life and its origin: A perspective from Chemistry

Ganti S. Murthy
Biosciences and Biomedical Engineering
Indian Institute of Technology-Indore
Indore, India
Email: Ganti.Murthy@iiti.ac.in