2.1 Chemistry and Physiological Reactions

Chapter 2 Part A
Chemistry
Comes Alive
PowerPoint® Lecture Slides

prepared by
Karen Dunbar Kareiva
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© 2016 Pearson Education, Inc. Ivy Tech Community College
Why This Matters:
• Understanding chemistry and biochemistry

helps to determine the most effective solutions
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© 2016 Pearson Education, Inc.

Chemistry and Physiological Reactions
• Body is made up of many chemicals

• Chemistry underlies all physiological reactions:
– Movement, digestion, pumping of heart, nervous
system
• Chemistry can be broken down into:
– Basic chemistry
– Biochemistry

Part 1 – Basic Chemistry
2.1 Matter and Energy
Matter
• Matter is anything that has mass and occupies
space
– Matter can be seen, smelled, and/or felt
– Weight is mass plus the effects of gravity

Matter
• States of matter
– Matter can exist in three possible states:
• Solid: definite shape and volume
• Liquid: changeable shape; definite volume
• Gas: changeable shape and volume

Energy
• Energy is the capacity to do work or put matter

into motion
• Energy does not have mass, nor does it take up
space
• The greater the work done, the more energy it
uses up

Energy (cont.)
• Kinetic versus potential energy

– Energy exists in two possible forms:
• Kinetic – energy in action
• Potential – stored (inactive) energy
– Energy can be transformed from potential to
kinetic energy
• Stored energy can be released, resulting in action

Energy (cont.)
• Forms of energy
– Chemical energy
• Stored in bonds of chemical substances
– Electrical energy
• Results from movement of charged particles
– Mechanical energy
• Directly involved in moving matter
– Radiant or electromagnetic energy
• Travels in waves (example: heat, visible light,
ultraviolet light, and X rays)

Energy (cont.)
• Energy form conversions

– Energy may be converted from one form to
another
• Example: turning on a lamp converts electrical energy
to light energy
– Energy conversion is inefficient
• Some energy is “lost” as heat, which can be partly
unusable energy

2.2 Atoms and Elements
• All matter is composed of elements

– Elements are substances that cannot be broken
down into simpler substances by ordinary
chemical methods
• Four elements make up 96% of body:
– Carbon, oxygen, hydrogen, and nitrogen
– 9 elements make up 3.9% of body
– 11 elements make up <0.01%
• Periodic table lists all known elements

• All elements are made up of atoms, which are:

– Unique building blocks for each element
– Smallest particles of an element with properties
of that element
– What give each element its particular physical &
chemical properties

• Atomic symbol
– One- or two-letter chemical shorthand for each
element
• Example: “O” for oxygen, “C” for carbon
• Some symbols come from Latin names: “Na” (natrium)
is sodium; “K” (kalium) is potassium

Table 2.1-1 Common Elements Composing the Human Body

Table 2.1-2 Common Elements Composing the Human Body (continued)

Table 2.1-3 Common Elements Composing the Human Body (continued)

Structure of Atoms
• Atoms are composed of three subatomic

particles:
– Protons
• Carry a positive charge (+)
• Weigh an arbitrary 1 atomic mass unit (1 amu)
– Neutrons
• Have no electrical charge (0)
• Also weigh 1 amu
– Electrons
• Carry a negative charge ()
• Are so tiny they have virtually no weight (0 amu)

Structure of Atoms (cont.)
• Number of positive protons is balanced by

number of negative electrons, so atoms are
electrically neutral
• Protons and neutrons are found in a centrally
located nucleus; electrons orbit around the
nucleus
• Chemists devise models of how subatomic
particles are put together
– Planetary model
– Orbital model

Structure of Atoms (cont.)
• Planetary model: simplified and outdated

because it incorrectly depicts electrons in orbits,
fixed circular paths
– Still useful for illustrations
• Orbital model: current model used that depicts
orbitals, probable regions where an electron is
most likely to be located (rather than fixed
orbits)
– Shading in regions of greatest electron density
results in an electron cloud around nucleus
– Useful for predicting chemical behavior of atoms
Figure 2.1 Two models of the structure of an atom.
Nucleus Nucleus
Helium atom Helium atom
2 protons (p+) 2 protons (p+)

2 neutrons (n0) 2 neutrons (n0)
2 electrons (e−) 2 electrons (e−)
Planetary model Orbital model
Proton
Neutron
Electron
Electron
cloud
Identifying Elements
• Different elements contain different numbers of

subatomic particles
– Hydrogen has 1 proton, 0 neutrons, and 1
electron
– Helium has 2 protons, 2 neutrons, and 2
electrons
– Lithium has 3 protons, 4 neutrons, and 3
electrons
• Identifying facts about an element include its
atomic number, mass number, isotopes, and
atomic weight
Figure 2.2 Atomic structure of the three smallest atoms.
Proton
Neutron
Electron
Hydrogen (H) Helium (He) Lithium (Li)

(1p+; 0n0; 1e−) (2p+; 2n0; 2e−) (3p+; 4n0; 3e−)

Identifying Elements (cont.)
• Atomic number
– Number of protons in nucleus
– Written as subscript to left of atomic symbol
• Example: 3Li
• Mass number
– Total number of protons and neutrons in nucleus
• Total mass of atom
– Written as superscript to left of atomic symbol
• Example: 7Li

Identifying Elements (cont.)
• Isotopes
– Structural variations of same element
– Atoms contain same number of protons but differ
in the number of neutrons they contain
• Atomic numbers are same, but mass numbers
different
• Atomic weight
– Average of mass numbers of all isotope forms of
an atom

Figure 2.3 Isotopes of hydrogen.
Proton
Neutron
Electron
Hydrogen (1H) Deuterium (2H) Tritium (3H)

(1p+; 0n0; 1e−) (1p+; 1n0; 1e−) (1p+; 2n0; 1e−)

Radioisotopes
• Radioisotopes are isotopes that decompose to

more stable forms
– Atom loses various subatomic particles
• Sometimes loss results in an isotope becoming a
different element
– As isotope decays, subatomic particles that are
being given off release a little energy
• This energy is referred to as radioactivity
• Can be detected and measured with scanners

Radioisotopes (cont.)
• Radioisotopes are a valuable tool for biological

research and medicine
– Share same chemistry as their stable isotopes
so will be taken up by body
• Can then be used for diagnosis of disease
• All radioactivity can damage living tissue
– Some types can be used to destroy localized
cancers
– Some types cause cancer
• Radon from uranium decay causes lung cancer

2.3 Combining Matter
Molecules and Compounds

• Most atoms chemically combine with other
atoms to form molecules and compounds
– Molecule: general term for 2 or more atoms
bonded together
– Compound: specific molecule that has 2 or
more different kinds of atoms bonded together
• Example: C6H12O6
• Molecules with only one type of atom (H2 or O2) are
just called molecules

Mixtures
• Most matter exists as mixtures: two or more

components that are physically intermixed
• Three basic types of mixtures
– Solutions
– Colloids
– Suspensions

Figure 2.4 The three basic types of mixtures.
Solution Colloid Suspension

Solute particles are very Solute particles are larger Solute particles are very
tiny, do not settle out than in a solution and large, settle out, and may
or scatter light. scatter light; do not scatter light.
settle out.
Solute Solute Solute

particles particles particles
Example Example Example

Mineral water Jell-O Blood
Plasma
Settled
red blood
cells
Unsettled Settled

Mixtures (cont.)
• Solutions
– Are homogeneous mixtures, meaning particles
are evenly distributed throughout
– Solvent: substance present in greatest amount
• Usually a liquid, such as water
– Solute(s): substance dissolved in solvent
• Present in smaller amounts
• Example: blood sugar – glucose is solute, and blood
(plasma) is solvent

Mixtures (cont.)
• Solutions (cont.)
– True solutions are usually transparent
• Example: air (gas solution), salt solution, sugar
solution
• Most solutions in body are true solutions of gases,
liquids, or solids dissolved in water

Mixtures (cont.)
• Concentration of true solutions

– Three common ways to express concentrations:
1. Percent of solute in total solution
– How many parts of solute are in 100 total parts of
solution
– Solvent is usually water
– Example: 10 parts salt to 90 parts water is a 10% salt
solution
2. Milligrams per deciliter (mg/dl)
– Deciliter equals 1/100th of a liter
– Example: normal fasting blood glucose levels are
around 80 mg/dl

Mixtures (cont.)
3. Molarity (M) is number of moles of solute per liter of

solvent (water)
– 1 mole of a compound is equal to its molecular weight
(sum of atomic weights) in grams
– Example: glucose (C6H12O6 ) has a molecular wt of
180.12 amu, so 180.12 grams of glucose added to
enough H2O to make 1 liter is a 1 M solution of glucose
– 1 mole of any substance always contains 6.02  1023
molecules of that substance
– This number is called Avogadro’s number
– Molarities in the body are so small (can be 0.0001 M),
they are expressed in millimoles (mM) so
1000 mM  1 M

Mixtures (cont.)
• Colloids
– Also known as emulsions; are heterogeneous
mixtures, meaning that particles are not evenly
distributed throughout mixture
• Can see large solute particles in solution, but these do
not settle out
• Gives solution a cloudy or milky look
– Some undergo sol-gel (solution to gel)
transformations
• Example: Jell-O goes from liquid to gel
• Cytosol of cell is also a sol-gel type solution

Mixtures (cont.)
• Suspensions
– Heterogeneous mixtures that contain large,
visible solutes that do settle out
– Example: mixture of water and sand
– Blood is considered a suspension because if left
in a tube, the blood cells will settle out

Difference Between Mixtures and
Compounds
• Three main differences:
– Unlike compounds, mixtures do not involve
chemical bonding between components
– Mixtures can be separated by physical means,
such as straining or filtering; compounds can be
separated only by breaking their chemical bonds
– Mixtures can be heterogeneous or
homogeneous; compounds are only
homogeneous

2.4 Chemical Bonds
• Chemical bonds are “energy relationships”

between electrons of reacting atoms
– Chemical bonds are not actual physical
structures
• Electrons are the subatomic particles that are
involved in all chemical reactions
– They determine whether a chemical reaction will
take place and if so, what type of chemical bond
is formed

Role of Electrons in Chemical Bonding
• Electrons can occupy areas around nucleus

called electron shells
– Each shell contains electrons that have a certain
amount of kinetic and potential energy, so shells
are also referred to as energy levels
– Depending on its size, an atom can have up to 7
electron shells
– Shells can hold only a specific number of
electrons; the shell closest to nucleus is filled first
• Shell 1 can hold only 2 electrons
• Shell 2 holds a maximum of 8 electrons
• Shell 3 holds a maximum of 18 electrons
Role of Electrons in Chemical Bonding (cont.)
• Outermost electron shell is called valence shell

– Electrons in valence shell have the most
potential energy because they are farthest from
nucleus
– These are electrons that are involved in chemical
reactions

Role of Electrons in Chemical Bonding (cont.)
• Octet rule (rule of eights)

– Atoms desire 8 electrons in their valence shell
• Exceptions: smaller atoms (examples: H and He) want
only 2 electrons in shell 1
– Desire to have 8 electrons is driving force behind
chemical reactions
• Noble gases already have full 8 valence electrons (or
2 for He) so are not chemically reactive
– Most atoms do not have full valence shells
• Atoms will gain, lose, or share electrons (form bonds)
with other atoms to achieve stability of 8 electrons in
valence shell
Figure 2.5a Chemically inert and reactive elements.
Chemically inert elements

Outermost energy level
(valence shell) complete
8e
2e 2e
He Ne
Helium (He) Neon (Ne)

(2p+; 2n0; 2e−) (10p+; 10n0; 10e−)

Figure 2.5b Chemically inert and reactive elements.
Chemically reactive elements

Outermost energy level
(valence shell) incomplete
4e
1e 2e
H C
Hydrogen (H) Carbon (C)

(1p+; 0n0; 1e−) (6p+; 6n0; 6e−)
1e
6e 8e
2e 2e
O Na
Oxygen (O)
(8p+; 8n0; 8e−) Sodium (Na)
(11p+; 12n0; 11e−)
Types of Chemical Bonds
• Three major types of chemical bonds

– Ionic bonds
– Covalent bonds
– Hydrogen bonds

Types of Chemical Bonds (cont.)
• Ionic bonds
– Ions are atoms that have gained or lost
electrons and become charged
• Number of protons does not equal number of
electrons

– Ionic bonds involve the transfer of valence shell

electrons from one atom to another, resulting in
ions
• One becomes an anion (negative charge)
– Atom that gained one or more electrons
• One becomes a cation (positive charge)
– Atom that lost one or more electrons
– Attraction of opposite charges results in an ionic
bond

Figure 2.6ab Formation of an ionic bond.
+ 
Na Cl Na Cl
Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl−)
(11p+; 12n0; 11e−) (17p+; 18n0; 17e−)
Sodium chloride (NaCl)
Sodium gains stability by losing one After electron transfer, the oppositely
electron, and chlorine becomes stable charged ions formed attract each
by gaining one electron. other.

• Most ionic compounds are salts

– When dry, salts form crystals instead of
individual molecules
– Example is NaCl (sodium chloride)

Figure 2.6c Formation of an ionic bond.
Cl−
Na+
Large numbers of Na+ and Cl− ions

associate to form salt (NaCl) crystals.
• Covalent bonds
– Covalent bonds are formed by sharing of two or
more valence shell electrons between two atoms
• Sharing of 2 electrons results in a single bond
• Sharing of 4 electrons is a double bond
• Sharing of 6 electrons is a triple bond
– Allows each atom to fill its valence shell at least
part of the time
– Two types of covalent bonds:
• Polar and nonpolar covalent bonds

Figure 2.7a Formation of covalent bonds.
Reacting atoms Resulting molecules
H
H
C H C H or
H
Structural formula
shows single bonds.
H
H
Hydrogen atoms Carbon atom Molecule of methane gas (CH4)
Formation of four single covalent bonds: Carbon shares four electron pairs with four
hydrogen atoms.

Figure 2.7b Formation of covalent bonds.
O O O O or
Structural formula
shows double bond.
Oxygen atom Oxygen atom Molecule of oxygen gas (O 2)
Formation of a double covalent bond: Two oxygen atoms share two electron pairs.

Figure 2.7c Formation of covalent bonds.
N N N N or
Structural formula
shows triple bond.
Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2)
Formation of a triple covalent bond: Two nitrogen atoms share three electron pairs.

• Covalent bonds (cont.)

– Nonpolar covalent bonds
• Equal sharing of electrons between atoms
• Results in electrically balanced, nonpolar molecules
such as CO2

Figure 2.8a Carbon dioxide and water molecules have different shapes, as illustrated by molecular models.
Carbon dioxide (CO2) molecules are

linear and symmetrical. They are nonpolar.

• Polar covalent bonds

– Unequal sharing of electrons between 2 atoms
– Results in electrically polar molecules
– Atoms have different electron-attracting abilities,
leading to unequal sharing
• Atoms with greater electron-attracting ability are
electronegative, and those with less are
electropositive

• Polar covalent bonds (cont.)

– H2O is a polar molecule
• Oxygen is more electronegative, so it exerts a greater
pull on shared electrons, giving it a partial negative
charge and giving H a partial positive charge
– Having two different charges is referred to as dipole

Figure 2.8b Carbon dioxide and water molecules have different shapes, as illustrated by molecular models.
d−
d+ d+
V-shaped water (H2O) molecules have two

poles of charge—a slightly more negative
oxygen end (d−) and a slightly more positive
hydrogen end (d+).

Figure 2.9 Ionic, polar covalent, and nonpolar covalent bonds compared along a continuum.
Ionic bond Polar covalent Nonpolar

bond covalent bond
Complete Unequal sharing Equal sharing of

transfer of of electrons electrons
electrons
Separate ions Slight negative Charge balanced

(charged charge (d−) at among atoms
particles) one end of
form molecule, slight
positive charge (d+)
at other end
Na+ Cl−
Sodium chloride Water Carbon dioxide

• Hydrogen bonds
– Attractive force between electropositive
hydrogen of one molecule and an
electronegative atom of another molecule
• Not true bond, more of a weak magnetic attraction
– Common between dipoles such as water
• What makes water liquid
– Also act as intramolecular bonds, holding a large
molecule in a three-dimensional shape

Figure 2.10a Hydrogen bonding between polar water molecules.
d+
H H
O
d−
Hydrogen bond
(indicated by
dotted line)
d+
d+
d− d− d−
H H
O O
d+
d +
H H
H
d+
O
H
d −
The slightly positive ends (d+) of the water

molecules become aligned with the slightly
negative ends (d−) of other water molecules.
Figure 2.10b Hydrogen bonding between polar water molecules.
A water strider can walk on a pond because

of the high surface tension of water, a result
of the combined strength of its hydrogen
bonds.
2.5 Chemical Reactions
Chemical Equations
• Chemical reactions occur when chemical
bonds are formed, rearranged, or broken
• These reactions can be written in symbolic
forms called chemical equations
• Chemical equations contain:
– Reactants: substances entering into reaction
together
– Product(s): resulting chemical end products
– Amounts of reactants and products are shown in
balanced equations
Chemical Equations (cont.)
• Compounds are represented as molecular

formulas
– Example: H2O or C6H12O6
– Subscript indicates atoms joined by bonds
– Prefix denotes number of unjoined atoms or
molecules

Chemical Equations (cont.)
• Compounds are represented as molecular

formulas
– Example: H2O or C6H12O6 or H2 or CH4
– In chemical equations, subscripts indicate how
many atoms are joined by bonds, whereas prefix
means number of unjoined atoms (example: 4H)
Reactants Product
H+H  H2 (Hydrogen gas)
4H + 1C  CH4 (Methane)
Types of Chemical Reactions
• Three main types of chemical reactions:

1. Synthesis (combination) reactions involve
atoms or molecules combining to form
larger,
more complex molecule
• Used in anabolic (building) processes
A + B  AB

Figure 2.11a Types of chemical reactions.
Synthesis reactions
Smaller particles are bonded
together to form larger,
more complex molecules.
Example
Amino acids are joined together to
form a protein molecule.
Amino acid
molecules
Protein
molecule

Types of Chemical Reactions (cont.)
2. Decomposition reactions involve breakdown

of a molecule into smaller molecules or
its
constituent atoms (reverse of synthesis
reactions)
• Involve catabolic (bond-breaking) reactions
AB  A + B

Figure 2.11b Types of chemical reactions.
Decomposition reactions
Bonds are broken in larger
molecules, resulting in smaller,
less complex molecules.
Example
Glycogen is broken down to release
glucose molecules.
Glycogen
Glucose
molecules

3. Exchange reactions, also called displacement

reactions, involve both synthesis and
decomposition
• Bonds are both made and broken
AB + C  AC + B
and
AB + CD  AD + CB

Figure 2.11c Types of chemical reactions.
Exchange reactions
Bonds are both made and broken

(also called displacement reactions).
Example
ATP transfers its terminal phosphate
group to glucose to form glucose-
phosphate.
P P P
Adenosine triphosphate Glucose

(ATP)
P P
Adenosine diphosphate Glucose-

(ADP) phosphate
• In living systems, these reactions are also

referred to as reduction-oxidation or redox
reactions
– Atoms are reduced when they gain electrons
and oxidized when they lose electrons
– Example: C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP
• In this example, glucose is oxidized, and oxygen
molecule is reduced

Energy Flow in Chemical Reactions
• All chemical reactions are either exergonic or

endergonic
– Exergonic reactions result in a net release of
energy (give off energy)
• Products have less potential energy than reactants
• Catabolic and oxidative reactions
– Endergonic reactions result in a net absorption
of energy (use up energy)
• Products have more potential energy than reactants
• Anabolic reactions

Reversibility of Chemical Reactions
• All chemical reactions are theoretically

reversible
A + B ←→ AB
• Chemical equilibrium occurs if neither a forward

nor a reverse reaction is dominant
• Many biological reactions are not very reversible
– Energy requirements to go backward are too
high, or products have been removed

Rate of Chemical Reactions
• The speed of chemical reactions can be

affected by:
– Temperature: increased temperatures usually
increase rate of reaction
– Concentration of reactants: increased
concentrations usually increase rate
– Particle size: smaller particles usually increase
rate

Rate of Chemical Reactions
• Catalysts
– Catalysts increase the rate of reaction without
being chemically changed or becoming part of
the product
– Enzymes are biological catalysts

2.1 Chemistry and Physiological Reactions

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2.1 Chemistry and Physiological Reactions

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Chapter 2 Part A

PowerPoint® Lecture Slides

• Understanding chemistry and biochemistry

© 2016 Pearson Education, Inc.

• Body is made up of many chemicals

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

• Energy is the capacity to do work or put matter

© 2016 Pearson Education, Inc.

• Kinetic versus potential energy

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

• Energy form conversions

© 2016 Pearson Education, Inc.

• All matter is composed of elements

© 2016 Pearson Education, Inc.

• All elements are made up of atoms, which are:

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

• Atoms are composed of three subatomic

© 2016 Pearson Education, Inc.

• Number of positive protons is balanced by

© 2016 Pearson Education, Inc.

• Planetary model: simplified and outdated

Helium atom Helium atom

2 protons (p+) 2 protons (p+)

Planetary model Orbital model

• Different elements contain different numbers of

Hydrogen (H) Helium (He) Lithium (Li)

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

Hydrogen (1H) Deuterium (2H) Tritium (3H)

© 2016 Pearson Education, Inc.

• Radioisotopes are isotopes that decompose to

© 2016 Pearson Education, Inc.

• Radioisotopes are a valuable tool for biological

© 2016 Pearson Education, Inc.

Molecules and Compounds

© 2016 Pearson Education, Inc.

• Most matter exists as mixtures: two or more

© 2016 Pearson Education, Inc.

Solution Colloid Suspension

Solute Solute Solute

Example Example Example

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

• Concentration of true solutions

© 2016 Pearson Education, Inc.

3. Molarity (M) is number of moles of solute per liter of

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

• Chemical bonds are “energy relationships”

© 2016 Pearson Education, Inc.

• Electrons can occupy areas around nucleus

• Outermost electron shell is called valence shell

© 2016 Pearson Education, Inc.