Chapter2:

TheChemicalContextofLife

ReminderfromChapter1:
Organisms are natural systems to which basic
concepts of chemistry and physics apply. One of
the main themes of biology is the organization
of life on a hierarchy of structural levels, with
additional properties emerging at each
successive level. In this chapter, we will see how
the theme of emergent properties applies to the
lowest level of biological organization.

Matter consists of chemical elements in pure

form and in combinations called compounds
All life is composed of matter.
Matter = anything that takes up space and has mass.
Matter exists in diverse forms, each with its own
characteristics.
All matter is made up of chemical elements.
Element = a substance that cannot be broken down
to other substances by chemical reactions.
Compound = combination of two or more elements in
a fixed ratio. Compounds have emergent properties i.e. characteristics different from those of its elements.

Life requires about 25 elements

Of the 25, 6 elements make up 97.6% of living
matter (carbon, oxygen, hydrogen, nitrogen,
phosphorous, sulfur)( Table 2.1). These
elements form stable covalent bonds.
Trace elements = those required by an
organism in minute quantities (less than 0.01%)
- Ex: Iron (Fe), Iodine (I), Copper (Cu), Zinc
(Zn), etc.
Deficiencies in trace elements can cause illness.
e.g. lack of iron and iodine cause anemia and
goiter, respectively.

Atomic structure determines the

behavior of an element
Atoms = fundamental unit of matter. Smallest possible
amount of an element that retains that elements
properties.
Each element consists of a certain kind of atom, which
is different from the atoms of other elements.
Atoms are composed of even smaller parts. Only three
kinds of subatomic particles are relevant from a
biological perspective: protons, neutrons, and electrons.

Neutrons and protons are packed together tightly at the

center of an atom to form a nucleus. The electrons move
about this nucleus at almost the speed of light.
Electrons (-) and protons (+) are electrically charged,
whereas the neutron is neutral. Protons give the nucleus a
positive charge, and it is the attraction between opposite
charges that keeps the rapidly moving electrons orbiting
around the nucleus.
The unit of measurement for atomic particles is the dalton.
Neutrons and protons have a mass of 1 dalton each. Electron

mass is negligible.

Atoms of the various elements vary in their number of subatomic

particles. All atoms of a particular element have the same number of
protons in their nuclei. This is their atomic number.
Mass number = sum of protons and neutrons in the nucleus of an
atom.
Atomic mass (weight) = since neutrons and protons have a mass
close to 1 dalton, the mass number tells us the approximate mass of
the whole atom.
Isotopes = variant forms of elements. Have same number of
protons and electrons, but different number of neutrons. The
nucleus of 14C is unstable and therefore radioactive.
Radioactive isotopes = nucleus decays spontaneously giving off
particles and energy. Dangerous to life because it causes mutations
in DNA. However, radioactive isotopes can also be useful in biological
research and medicine as tracers. Living cells cannot distinguish
radioactive isotopes from nonradioactive atoms of the same
elements.

Energy levels
Atoms are mostly empty space. When two atoms approach each
other during a chemical reaction, their nuclei do not come close
enough together to interact. Only electrons are directly involved in
the chemical reactions between atoms.
An atoms electrons vary in the amount of energy they possess
(Fig 2.7).
Energy = ability to do work.
Potential energy = energy that matter stores because of its
position or location.
Matter has a natural tendency to move to the lowest possible state
of potential energy. Electrons of an atom also have potential energy
because of their position in relation to the nucleus. The negatively
charged electrons are attracted to the positively charged nucleus.
The more distant the electrons are from the nucleus, the greater
their potential energy.

Energy levels (continued)

Changes in the potential energy of electrons can only occur in

steps of fixed amounts. The different states of potential energy for
electrons in an atom are called energy levels or electron shells.
Electrons in first shell closest to nucleus have the lowest energy.
Electrons in the second shell have more energy, electrons in third
shell have more energy still, and so on.
An electron can change its shell, but only by absorbing or losing an
amount of energy equal to the difference in potential energy
between the old shell and the new shell.

Electron orbitals
We can never know the exact trajectory of an electron.
Instead, we describe the volume of space in which an
electron spends most of its time (Fig 2.9).
Orbital = three-dimensional space where an electron is
found 90% of the time.
No more than two electrons can occupy the same
orbital.
First shell has a single spherical orbital and can hold only
2 electrons. An atom with more electrons must use higher
shells.
The second electron shell can hold 8 electrons, two in
each of four orbitals (1 spherical and 3 dumbbell-shaped).

Electron configuration and chemical

properties
The chemical properties of an atom depend mostly on
the number of electrons in its outermost shell (Fig 2.8).
valence electrons = electrons in outer most shell
valence shell = outermost energy shell.
Valence = an atoms bonding capacity (# of electrons
needed to fill outer shell).
Atoms with a complete valence shell are not reactive. All
other atoms are chemically reactive because they have
incomplete valence shells with unpaired electrons.

Atoms combine by chemical bonding to form

molecules
When atoms with incomplete outer shells react, each
atom gives up or acquires electrons so that partners end
up with completed outer shells.
Atoms do this by either sharing (covalent bonds) or
transferring outer electrons (ionic bonds) resulting in
chemical bonds.
The strongest chemical bonds are covalent bonds and
ionic bonds.

Covalent bonds
Covalent bond = two atoms sharing one or more pairs of outer
shell electrons ( Fig 2.10 and 11).
Molecule = two or more atoms held together by covalent
bonds.
The number of single covalent bonds an atom can form is equal
to the number of additional electrons needed to fill its outer shell
(i.e. it's valence).
Double bond = sharing of 2 pairs of electrons. Stronger than
single bonds. Atoms in a covalently bonded molecule are
constantly in a tug-of-war for the electrons of their covalent
bonds.
Electronegativity = an atoms attraction for the shared electrons of the bond. The
more electronegative an atom, the more strongly it pulls electrons towards itself.
Nonpolar covalent bonds = electrons shared equally between the atoms of equal
electronegativity (H2, O2, CH4 ). Water is made up of 2 kinds of atoms with differing
electronegativity (O>H). Oxygen attracts electrons more strongly than hydrogen.
Polar covalent bond = chemical bond in which shared electrons are pulled closer to
the more electronegative atom, making it partially negative and the other atom
partially positive (Refer to Fig 2.12). H2O, even though is neutral overall, has a slightly
negative pole and two slightly positive poles, making it a polar molecule.

Ionic bonds
Refer to Fig 2.13
Ionic bonds = attractions between ions of opposite charge
(e.g. table salt, NaCl). Much weaker than covalent bonds.
When atoms of chlorine and sodium collide, chlorine atom
strips sodiums outer electron away. This results in sodium
having a positive charge and chlorine having a negative
charge. Two ions of opposite charge attract each other;
when the attraction holds them together, it is called an ionic
bond.
Ion = atom or molecule with an electrical charge resulting
from a gain or loss of one or more electrons.
anion = ion with negative charge; cation = ion with a
positive charge
NaCl is a type of salt. Salts are ionic compounds that often

exist as crystals in nature.

Weak chemical bonds play important roles

in the chemistry of life
Weak bonds, unlike covalent bonds, allow interactions
between molecules to be brief; molecules may come
together, change in some way and then separate.
The most important weak bond in living matter is the
hydrogen bond.
Hydrogen bond = occurs when a hydrogen atom
covalently bonded to one electronegative atom is also
attracted by another electronegative atom. In living cells,
the electronegative partner involved are usually oxygen
and nitrogen atoms. (refer to Fig 2.15)
Hydrogen bonds, ionic bonds, and other weak bonds,
form between and within molecules. Although these
bonds are individually weak, their cumulative effect can

re-enforce the 3-D

shape of a large molecule.

A molecules biological function is

related to its shape
Molecular shape is important in biology because it is the
basis for how most molecules of life recognize and
respond to one another.
Recognition and binding of neurotransmitters to cell
surface receptors in synapses of brain cells is basis on
intercellular communication in the nervous system (Fig
2.16 and 17).

Chemical reactions make and break

chemical bonds
Living matter is not static. There is constant flux, as new molecules
are being built and others are being broken down. The goal of
biochemistry is not simply to catalogue the molecules that make up
the living world, but to understand how these molecules are
transformed into others in biochemical pathways. These
transformations always involve chemical reactions.
In a chemical reaction, reactants (start materials) interact, atoms
rearrange with the breaking and reformation of bonds, and products
(end materials) result.
Matter is conserved in a chemical reaction. Reactions cannot create
nor destroy matter but can only rearrange it.
Living cells carry out thousands of chemical reactions that rearrange
matter in significant ways.
Some chemical reactions go to completion, others are reversible.

of forward reaction

Chemical equilibrium
= point at which rate

Chapter3:
WaterandtheFitnessoftheEnvironment

The polarity of water molecules results in hydrogen

bonding
Oxygen is more electronegative than hydrogen.
Consequently, the electrons of the polar bonds spend more
time near the oxygen atom. This makes water a polar
molecule.

The unique (emergent) properties of water arises from

attractions among these polar molecules.
Each water molecule can hydrogen bond (H-bond) to a max of
four neighbors. H-bond = electrostatic attraction between a
hydrogen in a polar bond to an electronegative atom of another
molecule.
The charged regions of a polar molecule are attracted to
opposite charges of neighboring polar or ionic molecules.

Organisms depend on the cohesion of water

molecules
Water molecules stick together as a result of H-bonding.
H-bonds form, break, and reform very frequently. At any
given time, a substantial portion of all molecules are
bonded to their neighbors, giving water more structure
than most liquids.
Cohesion = tendency of molecules to stick together.
Much stronger for water than for other liquids. Important
in water transport in plants.
Adhesion = the clinging of one substance to another.
Also important in water transport in plants.
Surface tension = a measure of how difficult it is to
stretch or break the surface of a liquid. Higher for water

than for most liquids.

Water contributes to earth's habitability by

moderating temperatures
Water stabilizes air temperature by absorbing heat from
air that is warmer and releasing the stored heat to the air
that is cooler.
Water can store a lot of energy (heat) with only a slight
increase in its own temperature.
Heat = measure of the total quantity of kinetic energy
(energy of motion) due to molecular motion in a body of
matter.
Temperature = measures intensity of heat due to the
average kinetic energy of the molecules.
Calorie = amount of heat energy it takes to raise the
temp of 1 gram of water by 1C (Food calorie = 1000

calories)

Water's high specific heat

Specific heat = amount of heat that must be absorbed
or lost for 1 gram of that substance to change
temperature by 1 C.
Compared to most substances, water has an unusually
high specific heat (10x that of Fe) This is due to Hbonding. A calorie of heat causes a relatively small
change in temperature of water because much of that
heat energy is used to disrupt H-bonds before water
molecules can begin to move faster.
Conversely, when the temperature of water drops
slightly, many additional H-bonds form, releasing a lot of
heat energy.
Water buffers against extreme changes in temperature.

Evaporative cooling
Molecules in a liquid stay close together because they
are attracted to one another. Molecules moving fast
enough to overcome these attractions can depart from
the liquid and enter into gas state.
Heat of Vaporization = quantity of heat a liquid must
absorb for 1 gram of it to be converted from liquid to
gaseous state.
Water's high heat of vaporization helps moderate earth's
climate. A considerable amount of solar heat absorbed by
tropical seas is consumed during evaporation of surface
water. Thus, as moist tropical air circulates poleward, it
releases heat as it condenses to form rain.
Evaporative cooling also helps moderate temperature in
lakes and ponds, and prevents terrestrial organisms from

overheating.

Ice floats
Water is one of the few substances that is less dense as
a solid than as a liquid. (Fig 3.5)
If ice sank, eventually all bodies of water would freeze
solid since floating ice insulates liquid water below.
Ice floats because as temperature decreases, there is
less energy to break H-bonds, so eventually all water
molecules are H-bonded to one another resulting in a
crystal lattice structure in which water molecules are less
densely packed.

Water as the solvent of life

Water dissolves more solutes than any other liquid called Universal Solvent.
Solution = liquid that is a homogenous mix of 2 or
more substances
Solvent = dissolving agent
Solute = substance that is dissolved
Aqueous solution = one in which water is solventThe
versatility of water as a solvent is based on its polarity.
Ions and polar water molecules have a mutual affinity
through electrical attractions. E.g. Cl- attracted and
surrounded by positive part of water and Na+ attracted
and surrounded by negative part of water molecules - the
resulting sphere of water molecules around each ion is

called the hydration

shell.

A compound does not have to be an ion to be dissolved

by water. Polar compounds are also water-soluble ( E.g.
proteins, carbohydrates, nucleic acids).(refer to Fig 3.8:
hydration of soluble protein) and become surrounded by a
hydration shell as well.
Hydrophilic = any substance with an affinity for water
(ions, polar molecules), even if that substance does not
dissolve (E.g. cellulose)
Hydrophobic = any substance that neither dissolves
nor has an affinity for water (nonpolar). E.g fats, waxes,
etc...

Solute concentrations in Aqueous solutions

Knowing concentrations is important in biology. This
allows the combinations of substances in fixed ratios to
make chemical solutions.
Molarity = Number of moles/Liter
A mole (mol) is a quantity = 6.02 x 1023 (Avogadros
Number) molecules
Molecular weight(mass) = sum of the weight of all
the atoms in a molecule.
Molar Mass = molecular weight(mass) (in grams)
of a particular substance per 1 mole of that
substance
e.g. 1 mole of sucrose has 6.02 x 1023 molecules and
weighs 342 g. 1 mole of ethanol also has 6.02 x 10-23

Acids and Bases

In pure water, [H+] = [OH-] = 10-7
Acid = substance that increases the [H+] of a solution. A
strong acid, such hydrochloric acid, dissociates completely
when mixed with water.
Base = A substance that reduces the [H+] in a solution. A
strong base, such as sodium hydroxide, dissociates
completely when mixed with water.
Some bases, such as ammonia, reduce [H+] directly by
accepting hydrogen ions
Weak acids and bases do not dissociate completely.
Ex: Carbonic Acid

The pH scale
pH = -log [H+]
For a neutral solution [H+] is 10-7 M, therefore -log 10-7 =
-(-7) = 7
Each pH unit represents a 10 fold change in
concentration.

Buffers
Because biological systems are very sensitive to pH,
they need to minimize changes in pH. They do this with
buffers.
Buffers = compounds that resist changes to their own
pH when acids or bases are introduced.
A buffer works by accepting hydrogen ions from the
solution when they are in excess and donating hydrogen
ions to the solution when they have been depleted. Most
buffers are weak acids or bases. (acid-base pairs)
Examples of physiological buffers: carbonate and
phosphate buffers

Chapter 4: Carbon and the molecular diversity of life

Biological diversity reflects molecular diversity.

Of all chemical elements, carbon is unparalleled
in its ability to form molecules that are large,
complex, and diverse. This chapter focuses on
the concepts of molecular architecture that
highlight carbon's importance to life.

Carbon atoms are the most versatile building

blocks of molecules
Valence of the major elements (Fig 4.4).
The chemical characteristics of an atom depend on its
valence electrons, by determining the number of bonds
an atom will form with other atoms.
The tetravalence of carbon explains its versatility at
making large, diverse, complex molecules possible

Variation in carbon skeletons contributes to

diversity of organic molecules
Variation in carbon skeletons is important source of
molecular complexity and diversity.
Hydrocarbons = organic molecules consisting of only
carbon and hydrogen(Fig 4.5).
Major component of petroleum, a fossil fuel.
Nonpolar, therefore hydrophobic (Fig 4.6)
can vary in lengthPosition of double bonds can vary
may be branched or unbranched
can be arranged in rings

Isomers = compounds with same molecular formula but

different structures and hence properties.
Types of isomers (Fig 4.7):
1. Structural isomers - differ in covalent arrangement of
their atomscontributes significantly to their variation e.g.
18 types for C8H18, and 366,319 types for C20H42
2. Geometric isomers - have same covalent
relationships, but differ in spatial arrangements (cis- and
trans-) arise from inflexibility of double bonds have
distinct biological activities (ex: retinal)
3. Enantiomers - molecules that are mirror images of
each other asymmetric carbon attached to 4 different
atoms or groups of atoms. thalidomide was a mix of 2
enantiomers: one with sedative properties, the other
caused birth defects L-Dopa vs D-Dopa is another

example (fig 4.8).

Functional groups
The distinctive properties of organic molecules depend
not only on arrangement of carbon skeleton, but also on
other molecular components attached to that skeleton.
Functional groups = groups of atoms attached to
carbon skeleton which are commonly involved in chemical
reactions.
All functional groups studied here are hydrophilic.

Hydroxyl group (-OH) compounds containing -OH are

alcohols. Eg. ethanol, sugars, phenol -OH group is polar.
Therefore such compounds dissolve in water (sugars)
Carbonyl group (C=O) aldehyde = carbonyl group on end
carbon of chain ketone =- carbonyl group attached to internal
carbon Variation in locations of functional groups along carbon
chain is a source of variation.
Carboxyl group (-COOH) compounds containing carboxyl
group are called carboxylic acids. Eg. formic acid, acetic acid,
amino acids they are weak acids because they are a source of H +
ions
Amino group (-NH2) compounds containing amino group are
called amines. Eg. amino acids Note: amino acids are both amines
and carboxylic acids. Amino group can act as a base.
Sulfhydryl group (-SH) organic compounds containing
sulfhydryls are called thiols important in stabilizing protein
structure.
Phosphate group
formed by
Phosphate is an anion