Biology, 12/e

Mader & Windelspecht

Lectures by Tariq Alalwan, Ph.D.

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Learning Objectives
 Describe how protons, neutrons, and electrons relate
to atomic structure.
 Use the periodic table to evaluate relationships
between atomic number and mass number.
 Describe how variations in an atomic nucleus account
for its physical properties.
 Determine how electrons are configured around a
nucleus.
 Describe how elements are combined into compounds
and molecules.
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Learning Objectives (cont.)
 List different types of bonds that occur between
elements.
 Explain the difference between a polar and a nonpolar
covalent bond.
 Describe how water associates with other molecules in
solution.
 Describe why the properties of water are important to
life.
 Analyze how water's solid, liquid, and vapor state allow
life to exist on Earth.
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Learning Objectives (cont.)
 Distinguish between an acid and a base.
 Explain the relationship between H+ or
OH− concentration and pH.
 Analyze how buffers prevent large pH changes in
solutions.

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Chemical Elements
 Matter refers to anything that has mass and occupies
space
 Matter exists in four states: solid, liquid, gas, or plasma

 All matter (both living and non-living) is composed of

basic substances called elements

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Elements
 An element is a substance that cannot be broken
down into substances with different properties (i.e.,
density, solubility, etc.); composed of one type of atom
 Ninety-two elements are naturally occurring
 Six elements make up 95% of the body weight of
organisms
 Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and
Sulfur
 Acronym (CHNOPS)

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Composition of Earth’s Crust and Its
Organisms

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Atoms
 Atoms - smallest part of an element that displays the
properties of the element
 An element and its atom share the same name

 Composed of 3 types of subatomic particles

 Central nucleus
 Protons - positively charged particles, 1 amu
 Neutrons - no charge, 1 amu
 Orbiting clouds around nucleus (electron shells)
 Electrons - negatively charged, very low mass-negligible in
calculations
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Atomic Number and Mass Number
 Each element is represented by one or two letters to
give it a unique atomic symbol
 H = hydrogen, Na = sodium, C = carbon

 The atomic number is equal to the number of

protons in each atom of an element
 The mass number of an atom is equal to the sum of
the number of protons and neutrons in atom’s nucleus
 The atomic mass is approximately equal to the mass
number

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Atomic Number and Mass Number
 The atomic number is written as a subscript to the
lower left of the atomic symbol
 The mass number is written as a superscript to the
upper left of the atomic symbol

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Periodic Table
 Atoms of an element are arranged horizontally by
increasing atomic number in rows called periods
 Atoms of an element arranged in vertical columns are
called groups
 Atoms within the same group share the same chemical
binding characteristics
 Group VIII are the noble gases and are inert
 Atoms shown in the periodic table are electrically neutral
 Therefore, the atomic number tells you the number of
electrons as well as the number of protons
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A Portion of the Periodic Table

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Isotopes
 Isotopes - atoms of the same element that differ in
the number of neutrons (and therefore different
atomic masses)
 Isotopes of an element have the same chemical
properties but different weights
 To determine the number of neutrons from the atomic
mass, subtract the number of protons from the atomic mass
and take the closest whole number
 Example:

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Electrons and Energy
 Electrons are attracted to the positively charged
nucleus; thus, it takes energy to hold electrons in place
 It takes energy to push them away and keep them in
their own shell
 The more distant the shell, the more energy it takes to
hold in place
 Electrons have energy due to their relative position
(potential energy)
 Electrons determine chemical behavior of atoms

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Distribution of Electrons
 The Bohr model is a useful way to visualize electron
location
 Electrons revolve around the nucleus in energy shells
(energy levels)
 For atoms with atomic numbers of 20 or less, the
following rules apply:
 The first energy shell can hold up to 2 electrons
 Each additional shell can hold up to 8 electrons
 Each lower shell is filled first before electrons are placed in the
next shell
 These rules cover most of the biologically significant
elements
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Bohr Models of Atoms

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Valence Electrons
 The outermost energy shell of any atom is called the
valence shell
 The valence shell is important because it determines
many of an atom’s chemical properties
 The octet rule states that the outermost shell is most
stable when it has eight electrons
 Exception: If an atom has only one shell, the outermost
valence shell is complete when it has two electrons

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Valence Electrons (cont.)
 The number of electrons in an atom’s valence shell
determines whether the atom gives up, accepts, or
shares electrons to acquire eight electrons in the outer
shell
 Atoms that have their valence shells filled with electrons
tend to be chemically stable
 Atoms that do not have their valence shells filled with
electrons are chemically reactive

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Molecules and Compounds
 Molecule - two or more atoms react or bond together
 It is the smallest part of a compound that retains its
chemical properties
 NaCl, H2, O2, etc.
 Compound – a molecule containing at least two
different elements bonded together
 CO2, H2O, C6H12O6, etc.
 Formula - tells the number of each kind of atom in a
molecule

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Chemical Bonding
 Bonds that exist between atoms in molecules contain
energy
 Bonds between atoms are caused by the interactions
between electrons in outermost energy shells
 The process of bond formation is called a chemical
reaction

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Types of Bonds: Ionic Bonding
 An ion is an atom that has lost or gained an electron
 An ionic bond forms when electrons are transferred
from one atom to another atom and the oppositely
charged ions are attracted to each other
 Example: formation of sodium chloride
 Chlorine (Cl) has 7 electrons in outer shell
 Sodium (Na) has only 1 electron in outer shell

 Salts are solid substances that usually separate and exist

as individual ions in water

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Formation of Sodium Chloride

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Types of Bonds: Covalent Bonds
 Covalent bonds result when two atoms share electrons
so each atom has an octet of electrons in the outer shell
 Note: In the case of hydrogen, the outer energy shell is
complete when it contains two electrons
 The electrons are not permanently transferred from
one atom to the other like in NaCl
 A pair of (valence) electrons from the outer shell will
“time share” with one atom and then the other
 This also causes the atoms to remain together

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Covalently Bonded Molecules
 A double covalent bond is
formed when two pairs of
electrons are shared
(represented by two parallel
solid lines)
 Example: O2

 A triple covalent bond is

formed when three pairs of
electrons are shared
(represented by three parallel
solid lines)
 Example: N2

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Nonpolar Covalent Bonds
 In a nonpolar covalent bond electrons are shared
equally between atoms
 Examples: hydrogen gas, oxygen gas, methane

 The shape of a molecule may also influence whether it

is polar or nonpolar
 Example: The symmetrical nature of a methane
molecule cancels out any polarities

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Polar Covalent Bonds
 In a polar covalent bond electrons are shared unequally
 Example: water

 Electronegativity is the ability of an atom to attract

electrons towards itself in a chemical bond
 In water, the O atom is more electronegative than the H
atoms and the bonds are therefore polar
 Also, the nonsymmetrical shape, the polar bonds cannot
cancel each other, and water is a polar molecule
 The atom that gets the most time with the electrons
will be slightly negative
 The other will be slightly positive

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Chemistry of Water
 Water is a polar molecule
 The shape of a water molecule and its polarity make
hydrogen bonding possible
 A hydrogen bond is a weak attraction between a slightly
positive hydrogen atom and a slightly negative atom
 When polar molecules are dissolved in water
 It can occur between atoms of different molecules or
within the same molecule
 A single hydrogen bond is easily broken while multiple
hydrogen bonds are collectively quite strong
 It helps to maintain the proper structure and function of
complex molecules (e.g., proteins, DNA, etc.)
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Chemistry of Water

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Properties of Water
 Water molecules cling together because of hydrogen
bonding - gives water many of its unique chemical
properties
 Water has a high heat capacity
 The presence of many hydrogen bonds allow water to
absorb a large amount of thermal energy without a
great change in temperature
 Hydrogen bonds must absorb heat to break, and they release
heat when they form
 The temperature of water rises and falls slowly
 Allows organisms to maintain their normal internal
temperatures, protected from rapid temperature changes
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 Temperature and Water
 A calorie is the amount
of heat energy needed
to raise the temperature
of 1 g of water 1°C
 Converting 1 g of the
coldest liquid water to
ice requires the loss of
80 calories of heat
energy

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Properties of Water (cont.)
 Water has a high heat of evaporization - the energy
required to convert 1g of liquid water to a gas
 To raise water from 99 to 100 °C; ~1 calorie
 To raise water from 100 to 101 °C; ~540 calories!
 Large numbers of hydrogen bonds must be broken to
evaporate water
 This is why sweating cools
 Evaporative cooling is best when humidity is low because
evaporation occurs rapidly
 Great example is when you get out of the shower!
 Reason why temperatures along the coasts are moderate

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Properties of Water (cont.)
 Water is a good solvent because of its polarity
 Polar substances dissolve readily in water

 Hydrophilic “water loving” molecules dissolve in water

(e.g. polar and ionic molecules)
 Hydrophobic “water fearing” molecules do not
dissolve in water (e.g. nonpolar molecules)
 A solution contains dissolved substances, or solutes

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Ionic Compounds Dissociate in Water

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Properties of Water (cont.)
 Water molecules are cohesive and adhesive
 Cohesion – is the ability of water molecules to cling
to each other due to hydrogen bonding
 Water flows freely
 Adhesion – is the ability of water molecules to cling
to other polar surfaces
 Due to water’s polarity
 Capillary action
 Surface Tension
 Allows small nonpolar objects
(e.g. water strider) to sit on top of water
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Water as a Transport
Medium
 Cohesion and adhesion account
for water transport in plants as
well as transport in blood vessels
 Cohesion and adhesion are both
important because combined
together they form an event
called capillary action
 Capillary action defies gravity
and helps move water up the
plant to its leaves
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Properties of Water (cont.)
 Frozen water (ice) is less dense than liquid water
 At temperatures below 4°C, hydrogen bonds between
water molecules become more rigid but also more
open
 Water expands as it reaches 0°C and freezes
 Prevents water from freezing from the bottom up

 Ice forms on the surface first – the freezing of the water

releases heat to the water below creating insulation
 Permits organisms to survive without freezing

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Ice is less dense than water

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Acids and Bases
 pH is a measure of hydrogen ion concentration in a
solution
 When water ionizes or dissociates, it releases an equal
−
number of hydrogen (H+) ions and hydroxide (OH )
ions

 Acids are substances that dissociate in water, releasing

hydrogen ions
 Bases are
+
substances that either take up− hydrogen
ions (H ) or release hydroxide ions (OH )
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The pH Scale
 The pH scale is used to indicate the acidity or basicity
(alkalinity) of a solution
 Values range from 0-14
 0 to <7 = Acidic
 7 = Neutral
 >7 to 14 = Basic (or alkaline)
 Logarithmic scale
 Each unit change in pH represents a 10-fold change in H +
concentration
 pH of 4 is 10X as acidic as pH of 5
 pH of 10 is 100X more basic than pH of
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The pH Scale

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Buffers and pH
 A buffer is a chemical or a combination of chemicals
that keeps pH within normal limits
 Health of organisms requires maintaining the pH of
body fluids within narrow limits
 Human blood is normally pH 7.4 (slightly basic)
 If blood pH drops below 7.0, acidosis results
 If blood pH rises above 7.8, alkalosis results
 Both are life-threatening situations

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Buffers in Nature
 In blood, carbon dioxide reacts with water to form
carbonic acid, a weak acid that dissociates to yield H+
and bicarbonate:

 Addition of excess hydrogen ions shifts the system to

the left, as H+ combine with bicarbonate ions to form
carbonic acid
 Addition of hydroxide ions shifts the system to the
right
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