Lecture 2

Chemical basis Water and Life Carbon and

of life Molecular
Diversity
Phorutai Pearngam (Pear)
phorutai.pea@mahidol.edu
Academic year 2023-2024
Overview of today’s lecture
❑ The chemical context of life

❑ Water and life

❑ Carbon and the molecular diversity of life

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 Elements and compounds

The structure of
atoms and properties
The chemical
context of life
Chemical bounding
and interaction

Chemical reactions
3
Elements and compounds
▪ Organisms are composed of matter, anything that takes up
space and has mass
▪ Matter is made up of elements
▪ An element is a substance that cannot be broken down to
other substances by chemical reactions
▪ Today, chemists recognize 92 elements occurring in nature This Photo by Unknown Author is licensed under CC BY-SA-NC

▪ A compound is a substance consisting of two or more

elements in a fixed ratio
▪ A compound has characteristics different from
those of its elements

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The elements of Life
▪ Of the 92 natural elements, about 20–25% are
essential elements
▪ The essential elements are similar among
organisms, but there is some variation
• Humans need 25 elements, but plants need only 17
▪ Carbon (C), hydrogen (H), oxygen (O), and nitrogen
(N) make up ~96% of living matter
▪ Most of the remaining ~4% consists of calcium (Ca),
phosphorus (P), potassium (K), and sulfur (S)
▪ Trace elements are those required by an organism
in minute quantities
▪ Some elements can be toxic, for example, arsenic

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The structure of atoms and properties
▪ Atom is the smallest unit having the properties of an elements
▪ Atoms are composed of subatomic particles including three major kinds which are
neutrons, protons, and electrons
▪ Protons and neutrons are packed together tightly at
the center, atomic nucleus
▪ Moving electrons form a “cloud” of negative charge
around the nucleus using the attraction between
opposite charges
▪ Neutron mass and proton mass are almost identical
(~1.7 x 10-24 g) and are measured in the unit called
Dalton (Da)
▪ Neutrons and protons have masses close to 1 Dalton
▪ The mass of an electron is only about 1/2,000 that of
a neutron or proton
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Atomic Number and Atomic Mass
The actual atomic mass is
▪ Atoms of the various elements differ in their number of 22.9898 daltons
subatomic particles
▪ Atomic number is the number of protons Mass number

▪ All atoms of a particular element have the same number of 23

protons
▪ An atom is neutral in electrical charge, which means that its
11 Na
protons must be equal to number of electrons
Atomic number
▪ Mass number is the total number of protons and neutrons
▪ The number of neutrons can be determined by subtracting Number of protons = 11
the atomic number from the mass number Number of electrons = 11
▪ Atomic mass is the atom’s total mass (proton + neutron + Number of neutrons = 12
electron), can be approximated by the mass number

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Isotopes
▪ All atoms of an element have the same number of protons but may differ in number of
neutrons therefore have different mass
▪ Isotopes is atoms of the same element which their number of neutrons are different

▪ Radioactive isotope is the isotope of the element

that the nucleus decays spontaneously, giving off
particles and energy.
▪ When the radioactive decay leads to a change in the
number of protons, it transforms the atom to an atom
of a different element

https://experiment.com/u/iA41fA

This Photo by Unknown Author is licensed under CC BY-ND

Radioactive Tracers
▪ Some applications of radioactive isotopes in biological research are….
▪ The radioactive isotopes are incorporated into biologically active molecules, and be used as a
tracer to track atoms during metabolism
▪ Determining the age of fossil

Yellow in PET scan shows elevated level of

Radiometric dating is a process that measures radioactively labeled glucose, indicating high
the radioactive decay of certain elements metabolic activity, typical of cancerous tissue.
The energy level of electrons
▪ Energy is defined as the capacity to cause change
▪ Potential energy is the energy that matter possesses
because of its location or structure
▪ The electrons of an atom have potential energy due to
their distance from the nucleus that exist as fixed level of
potential energy called electron shells

▪ When electron absorbs energy, it moves to a

shell further out from the nucleus
▪ When an electrons lose energy, it falls back to a
shell closer to the nucleus

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 Electron Distribution and Chemical Properties
▪ The chemical behavior of an atom is determined by the distribution of electrons in the
atom’s electron shells

▪ Each electron shell contains electrons at a particular

energy level
▪ s,p,d,f are orbital types that contain different
number of electrons
▪ The distribution of electrons follows the arrow
direction
https://sciencenotes.org/list-of-electron-configurations-of-elements/
Electron Distribution and Chemical Properties
▪ The periodic table of the elements, shows this distribution of electrons for the first 18 elements

Potassium
19K

▪ The first shell can hold no more than 2 electrons

▪ The chemical behavior of an atom depends mostly on the number valence electrons
those are found in the outermost shell, so called valence shell
Electron Orbitals
▪ We can never know the exact location of an electron instead we describe the space in which an
electron spends most of its time
▪ An orbital is the three-dimensional space where an electron is found 90% of the time
▪ Each electron shell contains a specific number of orbitals of distinctive shapes and orientations
a. Electron distribution diagram c. Superimposed electron orbitals
s

s, p
b. Separate electron orbitals

How many electrons in 1s, 2s, and 2p orbitals for Ne?

1s = 2, 2s = 2, 2p = 6
Atom animated--nucleus & electron orbitals (electron cloud)

https://youtu.be/Rz1turGsGow
Chemical bounding and interaction
▪ Atoms with incomplete valence shells can interact with other atoms in such a
way that each partner atom completes its valence shell
▪ The atoms either share or transfer valence electrons
▪ These interactions usually result in atoms staying close together, held by
attractions called chemical bonds

In this biology class, we will study the basic of…

1. Covalent bonds
2. Ionic bonds
3. Weak chemical interaction
3.1 Hydrogen bonds
3.2 Van der Waals interaction

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1. Covalent bonds
▪ A covalent bond is the sharing of a pair of valence electrons by two atoms
▪ In a covalent bond, the shared electrons count as part of each atom’s valence shell
▪ A molecule consists of two or more atoms held
together by covalent bonds
▪ A single covalent bond, or single bond, is the sharing
of one pair of valence electrons
▪ A double covalent bond, or double bond, is the
sharing of two pairs of valence electrons

H2 O2

▪ When the bonds form, they give the atom a

full complement of electrons in the valence shell
1. Covalent bonds
Lewis dot structure:
Molecular name: Dots represent the
Name and numbers of valence electrons
atoms
structural formula:
▪ The valance of atom is the bounding Bonding (line) and
atoms
capacity, which equals the number of
electrons required to complete the
atom’s valence shell
▪ A compound is a combination of two or
more different elements
1. Covalent bonds
▪ Atoms in a molecule attract shared bonding electrons to varying degrees, depending on
the element
▪ Electronegativity (EN) is the attraction of a particular atom for the electrons of a
covalent bond ; very high EN elements are F, O, N, Cl
▪ The more electronegative an atom, the more strongly it pulls shared electrons toward
itself
Polar covalent bond:
Nonpolar covalent bond:
one atom is more electronegative, and
the atoms share the electron equally
the atoms do not share the electron
equally
δ–

δ+

δ+
2. Ionic bonds
▪ Two atoms are so unequal in their attraction for valence electrons that the more
electronegative atom strips an electron completely away from its partner NOT SHARE!!
▪ The two resulting oppositely charged atoms (or molecules) are called ions
▪ A cation is a positively charged ion (The one who lose an electron)
▪ An anion is a negatively charged ion (The other who take an electron)
▪ The opposite charges attract each other, this attraction forms an ionic bond
Sodium chloride (NaCl)

+
11Na
-
11Na 17Cl 17Cl

Proton : 11 17 11 17
Electron: 11 17 10 18
2. Ionic bonds
▪ Compounds formed by ionic bonds are called ionic compounds, or salts
▪ Salts, such as sodium chloride (NaCl) or table salt, are often found in nature as crystals
▪ Each salt crystal is an aggregate of vast numbers of cations and anions bonded by their
electrical attraction and arranged in a three-dimensional lattice

▪ The formula for an ionic compound indicates only the ratio of elements but not define
number of atoms like a covalent compound
▪ For example, MgCl2 is the compose of two Cl- for each Mg2+
▪ The ionic bonds are much weaker in water because each ion is partially shielded by its
interactions with water molecules
3. Weak chemical interaction
▪ Most of the strongest bonds in organisms are covalent bonds that form a cell’s
molecules
▪ Weak chemical bonds, such as ionic bonds, hydrogen bonds and van der Waals
interaction are also important to life
▪ Weak chemical bonds reinforce shapes of large molecules and help molecules adhere
to each other
3.1 Hydrogen bonds
▪ A hydrogen bond forms when a hydrogen atom covalently bonded to one
electronegative atom is also attracted to another electronegative atom
▪ In living cells, the electronegative partners are usually oxygen or nitrogen atoms
3.2 Van der Waals Interactions
▪ If electrons are distributed asymmetrically in molecules or atoms, they can result in
“hot spots” of positive or negative charge
▪ Van der Waals interactions are attractions between molecules that are close together
as a result of these charges
Van der Waals forces help geckos stick to surfaces

https://www.zmescience.com/science/physics/direct-measurement-of-van-
der-waals-force-made-for-the-first-time/ https://www.expii.com/t/van-der-waals-forces-overview-role-in-biology-10246
Molecular shape and function
▪ Molecules with more than two atoms have more
complicated shapes that are determined by the
positions of the atoms’ orbitals
▪ In a covalent bond, the s and p orbitals may hybridize,
creating specific molecular shapes
▪ Molecular shape is crucial to determines how
biological molecules recognize and respond to
one another with specificity
▪ If the shapes of biological molecules are
complementary, they can possibly bind
temporarily to each other by forming weak
interactions
▪ Molecules with similar shapes can have similar
biological effects
Chemical reactions
▪ Chemical reactions are the making and breaking of chemical bonds
▪ The starting molecules of a chemical reaction are called reactants
▪ The final molecules of a chemical reaction are called products
▪ Matter is conserved in a chemical reaction: Reactions cannot create or destroy atoms
but can only rearrange or redistribute the electrons among them
▪ Thus, all atoms of the reactants must be accounted for in the products
The summarizes photosynthesis:

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Chemical reactions
▪ All chemical reactions are reversible: products of the forward reaction become
reactants for the reverse reaction
▪ Chemical equilibrium is reached when the forward and reverse reaction rates are
equal which means that the concentrations of reactants and products have stabilized
at a particular ratio, but does NOT mean that they are equal in concentration

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https://www.chemistrylearner.com/chemical-reactions/reversible-reaction
 Hydrogen bound in water

Water Four emergent properties of

water to suitability of life
and Life 1. Cohesion of water molecules
2. Ability to moderate temperature
3. Floating of ice on liquid water
4. The solvent of life

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Hydrogen bound in water
▪ The covalent bonds in a water molecule are polar covalent bonds because oxygen is
high electronegativity, so, the electrons of the covalent bonds spend more time
closer to oxygen than to hydrogen
polar covalent
▪ The water molecule is a polar molecule, meaning that its
bonds overall charge is unevenly distributed; oxygen has partial
positive, hydrogen has partial negative
▪ Polarity allows water molecules to form hydrogen bonds
with each other

The extraordinary properties of

Oxygen can form water emerge from this hydrogen
two hydrogen
bonds bonding

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Cohesion of water molecules Cohesion
▪ Cohesion is a phenomenon that hydrogen bonds
collectively hold the substance together water-conducting
cells
▪ It results high surface tension, a measure of how
difficult it is to stretch or break the surface of a
liquid
▪ Cohesion contributes to the transport of water and Direction
of water
Adhesion
dissolved nutrients in vascular plants movement

▪ Adhesion of water by hydrogen bonds to

For example, the surface tension of
the molecules of cell walls helps counter
water allows a spider to walk across a the downward pull of gravity
pond without breaking 29
Water can moderate temperature

▪ Water moderates air temperature by absorbing heat from air that is warmer and releasing
stored heat to air that is cooler with only a slight change in its own temperature
▪ To understand how does water moderate temperature, we need to understand the
concept of temperature and heat 30
Temperature and Heat
▪ Kinetic energy is the energy of motion
▪ Temperature is a measure of the average kinetic of molecules in a body matter
▪ Thermal energy is a total kinetic energy of a body matter, depend on body matter’s volume
▪ Heat is a measure of thermal energy in transfer from one body of matter to another

Temperature measures the

intensity of heat due to the
average kinetic energy

Thermal energy from

total kinetic energy
Kinetic energy from
atom’s movement
At the boiling point…
- Both have temperature at 100 °C
- Which has more amount of thermal
energy?

https://www.tec-science.com/thermodynamics/temperature/temperature-
and-particle-motion/
32
Temperature and Heat
▪ Whenever two objects of different temperature are brought together, thermal
energy passes from the warmer to the cooler object until the two are the same
temperature
▪ Unit of heat
▪ Calorie (cal): The amount of heat it takes to raise the temperature of 1 g of
water by 1°C
▪ Kilocalorie (kcal), 1,000 cal: The amount of heat it takes to raise the temperature
of 1 kilogram (kg) of water by 1°C
▪ The joule (J) is another unit of energy
1 J = 0.239 cal, or 1 cal = 4.184 J
Water’s High Specific Heat
▪ The specific heat of a substance is the amount of heat that Specific Heat
must be absorbed or lost for 1 g of that substance to change (1 cal/g /°C)

its temperature by 1°C

▪ Specific heat can infer how well a substance resists changing
its temperature when it absorbs or releases heat
▪ The specific heat of water is 1 calorie per gram and per https://serc.carleton.edu/details/images/87588.html

degree Celsius, 1 cal/g /°C)

▪ Water has a high specific heat due to hydrogen bounding, so, water resists changing its
temperature
• Heat is absorbed when hydrogen bonds break
• Heat is released when hydrogen bonds form
▪ The water that covers most of Earth keeps temperature fluctuations on land and in water
within limits that permit life
Evaporative Cooling
▪ Evaporation is transformation of a substance from liquid to gas
▪ Heat of vaporization is the quantity of heat a liquid must absorb for 1 g to be converted
from the liquid to gas
▪ As a liquid evaporates, its remaining surface cools, a process called evaporative cooling
▪ Evaporative cooling of water helps stabilise
temperatures in organisms and bodies of water
▪ Contribute to the stability of temperature in
lakes and ponds
▪ Provides a mechanism that prevents
terrestrial organisms from overheating
Floating of Ice on Liquid Water
▪ Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice
less dense
▪ Above 4°C: water behaves like other liquids
▪ 4°C to 0°C: water begins to freeze because more and
more of its molecules are moving too slowly to break
hydrogen bonds
▪ 0°C: the molecules become locked into a crystalline
lattice, each water molecule hydrogen bonded to four
partners
▪ If ice sank, then eventually ponds, lakes, and even oceans could freeze solid, making life
impossible on Earth
▪ When a deep body of water cools, floating ice insulates the water below enabling
survival of aquatic life under the frozen surface

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Water is the solvent of life
▪ Solution is a liquid that is a completely
homogeneous mixture of two or more
substances
▪ The dissolving agent of a solution is the
solvent, and the substance that is dissolved
is the solute
▪ An aqueous solution is one in which the
solute is dissolved in water, and water is
the solvent
▪ Water is a versatile solvent due to its
polarity, which allows it to form hydrogen
bonds easily
▪ When an ionic compound is dissolved in water,
each ion is surrounded by a sphere of water
molecules called a hydration shell 37
Water is the solvent of life
▪ A compound does not need to be ionic to dissolve in water
▪ Many compounds made up of nonionic polar molecules such as the sugar
▪ Such compounds dissolve when water molecules surround each of the solute molecules,
forming hydrogen bonds with them
▪ Large proteins can dissolve in water if they have ionic and polar regions on their surface

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Hydrophilic and Hydrophobic Substances
▪ Hydrophilic substances: Have an affinity for water
▪ a compound with numerous regions of partial positive and partial negative charges
that can form hydrogen bonds
▪ Hydrophobic substances: Do not has an affinity for water
▪ nonionic and nonpolar, or otherwise cannot form hydrogen bonds
▪ Hydrophobic molecules related to oils are major ingredients of cell membranes

https://rsscience.com/cell-membrane/
 Organic chemistry

Carbon and
the molecular Molecular diversity from the
diversity of life bounding of carbon atoms

Chemical groups to
molecular function

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Organic chemistry: Carbon is the backbone of life
▪ Living organisms consist mostly of carbon-based compounds
▪ Carbon is unparalleled in its ability to form large, complex, and diverse molecules
▪ Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all
composed of carbon compounds
▪ Organic chemistry is the study of compounds that contain carbon
▪ Most organic compounds contain hydrogen atoms in addition to carbon atoms
▪ The major elements of life—C, H, O, N, S, and P—are quite uniform from one organism to
another, reflecting the common evolutionary origin of all life

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Carbon atoms can form diverse molecules
▪ Electron configuration is the key to an atom’s characteristics, which determines the kinds
and number of bonds an atom will form with other atoms

▪ Four valence electrons can form four covalent bonds enabling carbon
to form large, complex molecules
▪ In molecules with multiple carbons, each carbon bonded to four
other atoms has a tetrahedral shape such as CH4

▪ However, when two carbon atoms are joined by a double

bond, the atoms joined to the carbons are in the same
plane as the carbons such as C2H4

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 Carbon atoms can form diverse molecules
▪ The number of electrons required to fill the valence shell of an atom is generally equal to
the atom’s valence, the number of covalent bonds it can form
▪ The electron configuration of carbon gives it covalent compatibility with many different
elements
▪ The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen)
are the “building code” that governs the architecture of living molecules

Number of electrons needed to fill the valence shell 1 2 3 4

Valence: Number of bonds the element can form 1 2 3 4

▪ Carbon atoms can partner with atoms other than hydrogen such as CO2, Urea; CO(NH2)2
Molecular Diversity Arising from Carbon Skeleton Variation
▪ Carbon chains form the basis of most organic molecules.
▪ Carbon skeletons vary in length and may be straight, branched, or arranged in
closed rings
Hydrocarbons
▪ Hydrocarbons are organic molecules consisting of only carbon and hydrogen
▪ Many organic molecules, such as fats have long hydrocarbon tails attached to a
nonhydrocarbon component
▪ Hydrocarbons can undergo reactions that release a large amount of energy

A fat molecule consists of nonhydrocarbon

Mammalian adipose cells component joined to three hydrocarbon tails
stockpile fat molecules as a that can be broken down to provide energy
fuel reserve (Black = carbon; gray = hydrogen; red = oxygen)
Isomers
▪ Isomers are compounds with same molecular formula (same elements and
quantities) but different structures and properties
▪ Structural isomers have different covalent arrangements of their atoms
▪ Cis-trans isomers have the same covalent bonds
but differ in spatial arrangements

▪ Enantiomers are isomers that are mirror images of each other

▪ The concept of enantiomers is important in the

pharmaceutical industry because the two
enantiomers of a drug may not be equally effective
A few chemical groups are key to molecular function
▪ Distinctive properties of organic molecules depend on the carbon skeleton and on the
molecular components attached to it
▪ A number of characteristic groups can replace the hydrogens attached to skeletons of
organic molecules
• The differences between estradiol (a type of estrogen) and
testosterone
• They differ only in the chemical groups attached to the rings
• The different actions of these two molecules on many targets
throughout the body are the basis of sexual characteristics

▪ Functional groups are the components of organic molecules that are most commonly
involved in chemical reactions
▪ The number and arrangement of functional groups give each molecule its unique
properties
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49
ATP: An Important Source of Energy for Cellular Processes
▪ Adenosine triphosphate (ATP), is the primary energy-
transferring molecule in the cell
▪ ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups
▪ Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP, and
release energy that can be used by the cell