The Chemistry of Life

By Maria Katrina L.
Costiniano, RN, MAN
The Chemistry of Life

Basic Chemistry; Chemical Reactions; Acids and Bases; Water; Organic Molecules
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
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Part 1 – Basic Chemistry
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

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

Atoms and 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

Atoms and Elements
• 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

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
Two models of the structure of an atom

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
Atomic structure of the three smallest atoms

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

Isotopes of Hydrogen

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

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

Mixture
• Most matter exists as mixtures: two or more

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

Types of Mixture

Solutions
• 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

Colloids
• Colloids
– Also known as emulsions; are heterogeneous
mixtures, meaning that particles are not evenly
distributed throughout mixture
– Some undergo sol-gel (solution to gel)
transformations

Suspensions
• Suspensions
– Heterogeneous mixtures that contain large,
visible solutes that do settle out
– Example: mixture of water and sand

Chemical Bonds
• Chemical bonds are “energy relationships”

between electrons of reacting atoms
• Electrons are the subatomic particles that are
involved in all chemical reactions

Roles 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

Roles of Electrons in Chemical Bonding cont.
• Outermost electron shell is called valence shell

• Octet rule (rule of eights)
– Atoms desire 8 electrons in their valence shell
– Desire to have 8 electrons is driving force behind
chemical reactions
– Most atoms do not have full valence shells

Chemically inert and reactive elements

Chemically inert and reactive elements

Types of Chemical Bonds
• Three major types of chemical bonds

– Ionic bonds
– Covalent bonds
– Hydrogen bonds

Ionic Bonds
• Ionic bonds
– Ions are atoms that have gained or lost
electrons and become charged
– 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
Formation of ionic bond

Covalent Bonds
• Covalent bonds
– Covalent bonds are formed by sharing of two or
more valence shell electrons between two atoms
– Allows each atom to fill its valence shell at least
part of the time
– Two types of covalent bonds:
• Polar and nonpolar covalent bonds

Formation of covalent bonds

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

• 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

Hydrogen bonds
• Hydrogen bonds
– Attractive force between electropositive
hydrogen of one molecule and an
electronegative atom of another molecule
– Common between dipoles such as water
– Also act as intramolecular bonds, holding a large
molecule in a three-dimensional shape

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 Free PowerPoint Templates
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

Synthesis

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

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

4. Reversible Reactions
• All chemical reactions are theoretically
reversible
A + B ←→ AB
• Chemical equilibrium occurs when the rate of

product formation is equal to the rate of reactant
formation.

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
– Catalysts increase the rate of reaction without being
chemically changed or becoming part of the product
• Enzymes are biological catalysts
Biochemistry
• All chemicals either organic or inorganic

– Inorganic compounds
• Water, salts, and many acids and bases
• Do not contain carbon
– Organic compounds
• Carbohydrates, fats, proteins, and nucleic acids
• Contain carbon, are usually large, and are covalently
bonded
• Both equally essential for life

Water
Water
• Most abundant inorganic compound
– Accounts for 60%–80% of the volume of living
cells
• Most important inorganic compound because of
its properties
– High heat capacity
– High heat of vaporization
– Polar solvent properties
– Reactivity
– Cushioning
Water Properties
• High heat capacity

– Ability to absorb and release heat with little
temperature change
– Prevents sudden changes in temperature
• High heat of vaporization
– Evaporation requires large amounts of heat
– Useful cooling mechanism

Water Properties
• Polar solvent properties

– Dissolves and dissociates ionic substances
– Forms hydration (water) layers around large
charged molecules
• Example: proteins
– Body’s major transport medium

Water Properties
• Reactivity
– Necessary part of hydrolysis and dehydration
synthesis reactions
• Cushioning
– Protects certain organs from physical trauma

Salts
• Salts are ionic compounds that dissociate into

separate ions in water
– Separate into cations (positively charged
molecules) and anions (negatively charged)
• Not including H+ and OH– ions

Acid- Base Balance
• Acids and bases are both electrolytes

– Ionize and dissociate in water
• Acids
– Are proton donors: they release hydrogen
ions (H+), bare protons (have no electrons) in
solution
– Important acids
• HCl (hydrochloric acid), HC2H3O2 (acetic acid,
abbreviated HAc), and H2CO3 (carbonic acid)

Bases
• Bases
– Are proton acceptors: they pick up H+ ions in
solution
• Example: NaOH → Na+ + OH–
– When a base dissolves in solution, it releases a
hydroxyl ion (OH –)
– Important bases
• Bicarbonate ion (HCO3–) and ammonia (NH3)

pH
• pH: Acid-base concentration

– pH scale is measurement of concentration of
hydrogen ions [H+] in a solution
– The more hydrogen ions in a solution, the more
acidic that solution is
– The scale ranges from 0 to 14.

pH
• pH: Acid-base concentration (cont.)

– Acidic solutions have high [H+] but low pH
– Neutral solutions have equal numbers of H+ and
OH– ions
• All neutral solutions are pH 7
• Pure water is pH neutral
– pH of pure water = pH 7: [H+] = 10–7 m
– Alkaline (basic) solutions have low [H+] but high
pH

ABG
• The Respiratory System (Acid); CO2 is a volatile acid

– If you increase your respiratory rate
(hyperventilation) you "blow off" CO2 (acid)
therefore decreasing your CO2 acid—giving you
ALKALOSIS
– If you decrease your respiratory rate
(hypoventilation) you retain CO2 (acid) therefore
increasing your CO2 (acid)—giving you ACIDOSIS

• The Renal System (Base); the kidneys rid the body of
the nonvolatile acids H+ (hydrogen ions) and maintain a
constant bicarb (HCO3). Bicarbonate is the body’s base
– You have Acidosis when you have excess H+ and decreased
HCO3- causing a decrease in pH.
– You have Alkalosis when H+ decreases and you have excess (or
increased) HCO3- base.

• Compensation
– The respiratory system can effect a change in 15-30
minutes
– The renal system takes several hours to days to have
an effect.

The Big Four
❑ Respiratory Acidosis: pH < 7.35 (Normal: 7.35 - 7.45) CO2 > 45

(Normal: 35 – 45)
❑Respiratory Alkalosis: pH > 7.45 (Normal: 7.35 - 7.45) CO2 < 35
(Normal: 35 – 45)
❑Metabolic Acidosis pH < 7.35 (Normal: 7.35 - 7.45) HCO3- < 22
(normal: 22 – 26)
❑Metabolic Alkalosis pH > 7.45 (Normal: 7.35 - 7.45) HCO3- > 26

Organic Compounds: Synthesis and Hydrolysis
• Organic molecules contain carbon

• Carbon is electroneutral
• Major organic compounds: carbohydrates,
lipids, proteins, and nucleic acids
• Many are polymers
– Chains of similar units called monomers (building
blocks)
• Synthesized by dehydration synthesis
• Broken down by hydrolysis reactions

Carbohydrates
• Carbohydrates include sugars and starches

• Contain C, H, and O
– Hydrogen and oxygen are in 2:1 ratio
• Three classes
– Monosaccharides: one single sugar
• Monomers: smallest unit of carbohydrate
– Disaccharides: two sugars
– Polysaccharides: many sugars
• Polymers are made up of monomers of
monosaccharides

Monosaccharides
• Monosaccharides
– Simple sugars containing three to seven carbon
atoms
– (CH2O)n: general formula
• n = number of carbon atoms
– Monomers of carbohydrates
– Important monosaccharides
• Pentose sugars
– Ribose and deoxyribose
• Hexose sugars
– Glucose (blood sugar)
Dissacharides
• Disaccharides
– Double sugars
– Too large to pass through cell membranes
– Important disaccharides
• Sucrose, maltose, lactose
– Formed by dehydration synthesis of two
monosaccharides
• glucose + fructose → sucrose + water

Polysaccharides
• Polysaccharides
– Polymers of monosaccharides
• Formed by dehydration synthesis of many monomers
– Important polysaccharides
• Starch: carbohydrate storage form used by plants
• Glycogen: carbohydrate storage form used by animals
– Not very soluble

Lipids
• Contain C, H, O, but less than in carbohydrates,

and sometimes contain P
• Insoluble in water
• Main types:
– Triglycerides or neutral fats
– Phospholipids
– Steroids
– Eicosanoids

Triglycerides
• Triglycerides can be constructed of:

– Saturated fatty acids
• All carbons are linked via single covalent bonds,
resulting in a molecule with the maximum number of H
atoms (saturated with H)
• Solid at room temperature (Example: animal fats,
butter)

– Unsaturated fatty acids
• One or more carbons are linked via double bonds,
resulting in reduced H atoms (unsaturated)
• Liquid at room temperature (Example: plant oils, such
as olive oil)
• Trans fats – modified oils; unhealthy
• Omega-3 fatty acids – “heart healthy”

Phospholipids
• Phospholipids
– Modified triglycerides
• Glycerol and two fatty acids plus a phosphorus-
containing group
– “Head” and “tail” regions have different
properties
• Head is a polar region and is attracted to water
• Tails are nonpolar and are repelled by water
– Important in cell membrane structure

Steroids
• Steroids
– Consist of four interlocking ring structures
– Common steroids: cholesterol, vitamin D, steroid
hormones, and bile salts
– Most important steroid is cholesterol
• Is building block for vitamin D, steroid synthesis, and
bile salt synthesis
• Important in cell plasma membrane structure

Eicosanoids
• Eicosanoids
– Many different ones
– Derived from a fatty acid (arachidonic acid)
found in cell membranes
– Most important eicosanoids are prostaglandins
• Play a role in blood clotting, control of blood pressure,
inflammation, and labor contractions

Proteins
• Comprise 20–30% of cell mass

• Have most varied functions of any molecules
– Structural, chemical (enzymes), contraction
(muscles)
• Contain C, H, O, N, and sometimes S and P
• Polymers of amino acid monomers held
together by peptide bonds
• Shape and function due to four structural
levels

• All proteins are made from 20 types of amino
acids
– Joined by covalent bonds called peptide bonds
– Contain both an amine group and acid group
– Can act as either acid or base
– Differ by which of 20 different “R groups” is
present

Glycine Alanine Glycylalanine

Enzymes and Enzymes Activity
• Enzymes: globular proteins that act as

biological catalysts
– Catalysts regulate and increase speed of
chemical reactions without getting used up in the
process
– Lower the energy needed to initiate a chemical
reaction
• Leads to an increase in the speed of a reaction
• Allows for millions of reactions per minute!

• Characteristics of enzymes
– Most functional enzymes, referred to as
holoenzymes, consist of two parts
• Apoenzyme (protein portion)
• Cofactor (metal ion) or coenzyme (organic molecule,
often a vitamin)
– Enzymes are specific
• Act on a very specific substrate
– Names usually end in –ase and are often named
for the reaction they catalyze
• Example: hydrolases, oxidases
Animation:
How Enzymes Work
99
Nucleic Acids
• Nucleic acids, composed of C, H, O, N, and P,

are the largest molecules in the body
• Nucleic acid polymers are made up of
monomers called nucleotides
– Composed of nitrogen base, a pentose sugar,
and a phosphate group
• Two major classes:
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)

DNA
• DNA holds the genetic blueprint for the

synthesis of all proteins
– Double-stranded helical molecule (double helix)
located in cell nucleus
– Nucleotides contain a deoxyribose sugar,
phosphate group, and one of four nitrogen
bases:
• Purines: adenine (A), guanine (G)
• Pyrimidines: cytosine (C) and thymine (T)

DNA
• DNA holds the genetic blueprint for the

synthesis of all proteins (cont.)
– Bonding of nitrogen base from strand to opposite
strand is very specific
• Follows complementary base-pairing rules:
– A always pairs with T
– G always pairs with C

Animation:
DNA Structure
103
Figure 2.21 Structure of DNA.
Sugar: Base:
Phosphate Deoxyribose Adenine (A) Thymine (T) Sugar Phosphate
Adenine nucleotide Thymine nucleotide

Hydrogen
bond
A T
C G
Deoxyribose A
Sugar-
phosphate sugar
G
backbone Phosphate
G
T A
G C
Adenine (A)
G C
Thymine (T)
Cytosine (C) T A
Guanine (G)
Animation:
DNA Replication
105
RNA
• RNA links DNA to protein synthesis and is

slightly different from DNA
– Single-stranded linear molecule is active mostly
outside nucleus
– Contains a ribose sugar (not deoxyribose)
– Thymine is replaced with uracil
– Three varieties of RNA carry out the DNA orders
for protein synthesis
• Messenger RNA (mRNA), transfer RNA (tRNA), and
ribosomal RNA (rRNA)

Animation:
Stages of Transcription
107
Animation:
How Translation Works
108
Animation:
Protein Synthesis
109
ATP
• Chemical energy released when glucose is

broken down is captured in ATP (adenosine
triphosphate)
• ATP directly powers chemical reactions in cells
– Offers immediate, usable energy needed by
body cells
• Structure of ATP
– Adenine-containing RNA nucleotide with two
additional phosphate groups

Figure 2.22 Structure of ATP (adenosine triphosphate).
High-energy phosphate
bonds can be hydrolyzed
to release energy.
Adenine
P P P
Phosphate groups
Ribose
Adenosine
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)

Cellular respiration
• Anaerobic phase
- In the absence of oxygen, glucose is partially
broken down by a series of catabolic reactions
into pyruvic acid.
• Aerobic phase
- In the presence of oxygen, glucose is
completely broken down into carbon dioxide and
water.


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By Maria Katrina L.

Costiniano, RN, MAN

The Chemistry of Life

• Body is made up of many chemicals

Free PowerPoint Templates

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• Energy is the capacity to do work or put matter

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• Kinetic versus potential energy

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• Energy form conversions

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• All matter is composed of elements

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

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• Atoms are composed of three subatomic

• Number of positive protons is balanced by

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• Different elements contain different numbers of

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• Radioisotopes are isotopes that decompose to

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Molecules and Compounds

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• Most matter exists as mixtures: two or more

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• Chemical bonds are “energy relationships”

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• Electrons can occupy areas around nucleus

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• Outermost electron shell is called valence shell

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• Three major types of chemical bonds

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• Three main types of chemical reactions:

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2. Decomposition reactions involve breakdown