Ch2.The chemical context of life concept 2.

1
*Organisms are composed of matter, which is defined as anything that takes up space & has mass.
*Matter is made up of elements. An element is a substance that cannot be broken down to other
substances by chemical reactions.
*A compound is a substance consisting of two or more different elements combined in a fixed ratio. Table
salt, for ex: sodium chloride (NaCl), a compound composed of the elements (Na) & (Cl) in a 1:1 ratio.
Ex: H2O, C6H12O6, Ch4

*Elements of life:
*Of the 92 natural elements, about 20–25% are essential elements that an organism needs to live a
healthy life & reproduce. ex: four most abundant elements oxygen (O), carbon (C), hydrogen (H), &
nitrogen (N)—make up 96% of living matter.
*Trace elements are required by an organism
in only minute quantities, ex: Fe, Cu, Zn, I
Ex: in vertebrates, iodine is required for normal activity
Of thyroid gland. Deficiency of (I) can cause goiter
In human.
Ch2.The chemical context of life concept 2.1
*Evolution of tolerance to toxic elements:
*Some species have become adapted to environments containing elements that are usually toxic, for ex:
Sunflower plants can take up lead, zinc, & other heavy metals in concentrations that would kill most
organisms. Sunflower plants were used to detoxify contaminated soils (after hurricane)

1. Is a trace element an essential element? Explain.

2. WHAT IF? In humans, iron is a trace element required for the proper functioning of hemoglobin, the
molecule that carries oxygen in red blood cells. What might be the effects of an iron deficiency?
Ch2.The chemical context of life concept 2.2
* An element’s properties depend on the structure of its atoms:
*Each element consists of a certain type of atom that is different from the atoms of any other element. An
atom is the smallest unit of matter that still retains the properties of an element.
*Atoms composed of smaller subatomic particles that include, neutrons (no electrical charge), protons
(+ve charge) & electrons (-ve charge).
*Neutrons & protons form nucleus of atom, electrons form a cloud around the nucleus.
Ch2.The chemical context of life concept 2.2
*Atomic number= number of protons in the nucleus
*Mass number= sum of proton + neutron
*ex: Oxygen with atomic no. of 8

*Isotopes: elements have the same number of protons, but different no. of neutrons). , ex: Carbon
*Radioactive isotopes: decay spontaneously, giving off particles & energy.
*researchers use measurements of radioactivity in fossils to date these relics of past life ,Radioactive
isotopes are also useful as tracers to follow atoms through metabolism.
*
Ch2.The chemical context of life concept 2.2
*The energy levels of electrons:
*Energy/ is defined as the capacity to cause change, ex: by doing work.
*Potential energy/ is the energy that matter possesses because of its location or structure. For ex, water in
a reservoir on a hill has potential energy because of its altitude.
*an electron’s state of potential energy is called its energy level or electron shell.
*Electrons can move to higher or lower shells by releasing energy respectively.
*Chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, or
valence shell, valence electrons occupy valence shell.
*Atoms with completed valence shells are unreactive, while atoms with incomplete valence shells are
reactive.
Ch2.The chemical context of life concept 2.3
*Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms.
*This usually results in atoms staying close together, held by attractions called chemical bonds.
*covalent bond/is when two atoms share electrons.
*Molecule/ two or more atoms held together by covalent bonds constitute a molecule.
*In a structural formula, a single bond is sharing one pair of electrons, ex: H-H
*A double bond, is sharing of two pairs of electrons, indicated by double line between atoms, ex: O=O
*Pure elements are composed of molecules of one type of atom, such as H2 & O2.
*Molecules composed of a combination of two or more types of atoms are called compounds, ex: H2O,
CO2, CH4….etc.
Q/What is the atomic number of magnesium? How many protons and electrons does it have? How many
electron shells? How many valence electrons?
Ch2.The chemical context of life concept 2.3
*Electronegativity/is the attraction of a particular atom for the electrons in a covalent bond.
*The more electronegative an atom, the more strongly it pulls shared electrons toward itself. Ex: in water
molecule, oxygen atom has high electronegativity thus high affinity to pull H atom.

*Unequal sharing of electrons causes a partial +ve or –ve charge for each atom or molecule.
*Ionic bond/attraction between oppositely charged atoms (anion & cation), ex: NaCl
*anion is negatively charged ion, cation is positively charged ion.
Ch2.The chemical context of life concept 2.3
*Most strongest bonds in organisms are covalent bonds that form a cell’s molecules. Weak chemical
bonds like ionic bonds & hydrogen bonds are important as well.
*many large biological molecules are held in their functional form by weak bonds. Give example.
*Hydrogen bond/ forms when a H atom covalently bonded to one electronegative atom, is also attracted
to another electronegative atom, ex: electronegative partners in living cells are usually O or N atoms.
*Biological molecules recognize & interact with each other based on molecular shape, molecules with
similar shape can have similar biological effects.
Q/WHAT IF? If you were a pharmaceutical researcher, why would you want to learn the three-dimensional
shapes of naturally occurring signaling molecules?
Ch2.The chemical context of life concept 2.4
*Chemical reactions make & break chemical bonds:
*Chemical reactions/ are the making & breaking of chemical bonds.
*Reactants/ are starting molecules in a chemical reaction.
*Products/ are the final molecules in a chemical reaction.
*All chemical reactions are reversible. Chemical equilibrium is reached when the forward & the reverse
reaction rates equal.

Q/Which type of chemical reaction occurs faster at equilibrium, the formation of products from reactants
or reactants from products?
Ch2.The chemical context of life concept 2.5
*Hydrogen bonding gives water properties that help life possible on earth:
*All organism are made mostly of water & live in an environment dominated by water.
*water molecules are polar, with the oxygen region having a partial –ve charge (δ−) & the hydrogen region
a slight +ve charge (δ+). Two water molecules are held together by a hydrogen bond.
*Water is polar due to uneven distribution of the charges, (partial +ve & -ve)

*Four emergent properties of water contribute to earth’s suitability for life:

Cohesive behavior, ability to moderate temperature, expansion upon freezing, versatility as a solvent.
1-Cohesion of water molecules/ water molecules are linked together by multiple H-bonds. The molecules
stay together because of cohesion.
Ch2.The chemical context of life concept 2.5
*Cohesion due to hydrogen bonding contributes to the transport of water & nutrients against gravity in
plants.
*Adhesion, is the clinging of one substance to another, Adhesion of water to cell walls by hydrogen bonds
helps counter the downward pull of gravity.
*Surface tension, is a measure of how hard it is to break the surface of a liquid. Surface tension is related
to cohesion.
*Hydrogen bonds in water give it unusually high surface tension.
Ch2.The chemical context of life concept 2.5
2-Moderation of temperature by water/ water absorbs heat from warmer air & releases stored heat to
cooler air.
*water can absorb or release a large amount of heat with only a slight change in its own temperature.

*Temperature & heat:

*Kinetic energy is the energy of motion
*Thermal energy is the measure of the total amount of kinetic energy due to molecular motion
*Temperature represents the average kinetic energy of molecules
*Thermal energy is the transfer from one body of matter to another is defined as heat.

*ex: an ice cube cools a drink down not by adding

Coldness, but by absorbing thermal energy from
The liquid as the ice itself melt.
Ch2.The chemical context of life concept 2.5

*Water’s high specific heat:

*The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that
substance to change its temperature by 1°C.
*Water resists changing its temperature, why? because of its high specific heat.
*The specific heat of water is 1cal/g/°C.
*Water will change its temperature less than other liquids when it absorbs or looses a given amount of
heat.
Ch2.The chemical context of life concept 2.5
*Heat is absorbed when hydrogen bonds break, heat is released when hydrogen bonds form. The high
specific heat of water keeps temperature fluctuations within limits that permit life.

*Evaporative cooling (liquid transform to gas), as liquid evaporates, its remaining surface cools, a process
called evaporative cooling. This property in water helps stabilize temperatures in organisms & bodies of
water.
*Floating of ice in liquid water, this happens because H-bonds in ice are more ‘ordered’ making ice less
dense. What will happen if ice sank to the bottom of water bodies?
Ch2.The chemical context of life concept 2.5
*Water: The solvent of life
*A liquid that is a completely homogeneous mixture of two or more substances is called a solution.
*The dissolving agent of a solution is the solvent, & the substance that is dissolved is the solute. In this
case, water is the solvent and sugar is the solute. An aqueous solution is one in which water is the solvent.
*Water is a versatile solvent due to its polarity, which allows it to form H-bonds easily.

*Hydrophilic & hydrophobic substances:

*Any substance that has an affinity for water is said to be hydrophilic
*substance that has no affinity for water is said to be hydrophobic
*Colloid is a stable suspension of fine particles in a liquid.
Ch2.The chemical context of life concept 2.5
*Most biochemical reactions occur in water. Chemical reactions depend on collisions of molecules & thus
on the concentration of solutes in aqueous solution.

*Acids & Bases:

*Sometimes a hydrogen (H+) ion is transferred from one water molecule to another, leaving behind a
hydroxide ion (OH−). The proton binds to the other water molecule, making that molecule a hydronium
ion (H3O+).

*H+ & OH− are very reactive.

*Acids increase the H+ concentration in water, while bases reduce the concentration of H+ & increase
OH−.
*Acid, is any substance that increases the H+ concentration of a solution, ex: HCl, Lemon juice
*Base, is any substance that reduces the H+ concentration of a solution & increase OH-, ex: NaOH
Ch2.The chemical context of life concept 2.5
*Acidic solutions have pH values less than 7, Basic solutions have pH values greater than 7. most biological
fluids have pH values in the range of 6 to 8. Neutral is 7, ex: pure water.

*Buffers/ The internal pH of most living cells is close to 7. Even a slight change in pH can be harmful
because the chemical processes of the cell are very sensitive to the concentrations of H+ & OH- ions. The
pH of human blood is very close to 7.4, which is slightly basic. A person cannot survive for more than a
few minutes if the blood pH drops to 7 or rises to 7.8.
*A buffer, is a substance that minimizes changes in the concentrations of H+ & OH− in a solution. Most
buffers consist of an acid-base pair that reversibly combine with H+.
Ch2.The chemical context of life concept 2.5
*Carbonic acid is a buffer that contributes to
pH stability in human blood.

*Acidification of water:
*Human activities such as burning fossil fuels threaten water quality.
CO2 is the main product of fossil fuel combustion.
*CO2 dissolved in sea water forms carbonic acid, this causes ocean acidification.
which lowers ocean pH. Based on measurements of CO2 levels in air bubbles
trapped in ice over thousands of years, scientists calculate that the pH of the
oceans is 0.1 pH unit lower now than at any time in the past.

Q/WHAT IF? Would lowering the ocean’s carbonate concentration

have any effect, even indirectly, on organisms that don’t form CaCO3?
Explain.