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Welcome to Biology!
Unit 1: Biochemistry
Chapter 1: The Molecules of Life
Chapter 2: The Cell and its Components
Chapter 1: The Molecules of
Life
 Molecules
 Interactions between and within molecules
 Structure and shape of molecules
 Macromolecules
 The 4 major types
 Roles in biological organisms
 Biochemical reactions
 The 4 major types
 The role of enzymes in reactions
Section 1.1: Chemistry in Living
Systems
 All matter is composed of elements
 Cannot be broken down into simpler substances by ordinary
chemical methods
 Approximately 92 naturally occurring elements
 Only 6 elements serve as the chemical foundation for life
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Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorous
Sulfur
Atoms
 An atom is the smallest
particle of an element that
retains the element’s
properties
 Atomic mass = sum of
protons and neutrons
 All atoms of an element
have the same number of
protons, but the number of
neutrons can vary
Isotopes
 Isotopes are atoms of the same element that have
different numbers of neutrons
 Radioisotopes are unstable and their nucleus decays
over time
 They are valuable diagnostic tools in medicine
Studying the Interactions of
Molecules
 A molecule is composed of two
or more atoms and is the
smallest unit of a substance that
retains the chemical and
physical properties of the
substance
 Organic molecules are carbonbased
 Carbon atoms often bind to each
other or hydrogen
 May also include nitrogen,
oxygen, phosphorous, and/or
sulfur
Biochemistry
 Biochemists study the properties and interactions of
biologically important organic molecules
 Biochemistry forms a bridge between chemistry
(the study of the properties and interactions of atoms
and molecules) and biology (the study of properties
and interactions of cells and organisms).
 Understanding the physical and chemical principles
that determine the properties of these molecules is
essential to understanding their functions in the cell
and in other living systems
Interactions within Molecules
 Intramolecular forces (“intra” = within) hold the atoms
within a molecule together
 These forces are generally thought of as the chemical
bonds within a molecule
 Chemical bonds within a molecule are called covalent
bonds.
 A covalent bond forms when the electrons of two atoms
overlap so that the electrons of each atom are shared
between both atoms
Interactions within Molecules
 Some atoms attract electrons much more strongly than
other atoms
 This property is referred to as an atom’s electronegativity
 Oxygen, nitrogen, and chlorine have high electronegativity
 Hydrogen, carbon, and phosphorus have low electronegativity
 When two atoms share electrons, the electrons are more
attracted to the atom with the higher electronegativity
 Electrons have a negative charge, so that atom would assume a
slightly negative charge (∂-)
 The atom with lower electronegativity assumes a partial positive
charge (∂+)
Interactions within Molecules
 This unequal sharing of electrons in a covalent
bond creates a polar covalent bond
 Ex: A water molecule contains two polar covalent O-H
bonds, where the electrons in each bond are more
strongly attracted to the oxygen atom
 Molecules that have regions of partial negative and
partial positive charge are called polar molecules
Interactions within Molecules
 When covalent bonds are formed between atoms with
similar electronegativities, the electrons are shared
equally between the atoms
 These bonds are considered non-polar
 If these bonds predominate a molecule, the
molecule is considered a non-polar molecule
 Ex: Carbon and hydrogen
 The polarity of biological molecules greatly affects
their behaviour and functions in a cell
Interactions between
Molecules
 Intermolecular forces (“inter” = between) are forces
between molecules
 They form between different molecules or between
different parts of the same molecule (if it is very large)
 They are much weaker than intramolecular forces
 They determine how molecules interact with each other
and with different molecules
 They play a vital role in biological systems
Interactions between
Molecules
 Intermolecular forces are usually attractive and make
molecules associate together
 They can be broken fairly easily if enough energy is
applied
 Intermolecular forces are responsible for many of the
physical properties of substances
 Two types of intermolecular interactions are particularly
important for biological systems:
 Hydrogen bonding
 Hydrophobic interactions
Hydrogen Bonding
 A water molecule has two polar O-H bonds and is a polar
molecule
 The slightly positive hydrogen atoms of one molecule are
attracted to the slightly negative oxygen atoms of other
water molecules
 This type of intermolecular attraction is called a hydrogen
bond.
 Hydrogen bonds are weaker than ionic and covalent bonds and
are represented by a dotted line
 Many biological molecules have polar covalent bonds involving
a hydrogen atom and an oxygen or nitrogen atom.
Hydrogen Bonding
 A hydrogen bond is more easily broken than a covalent
bond, but many hydrogen bonds added together can
be very strong
 The cell is an aqueous environment so hydrogen
bonding between biological molecules and water is
very important
 They help maintain the proper structure and function of
the molecules
Hydrogen Bonding
 Ex: The 3-D shape of DNA,
which stores an organism’s
genetic information, is
maintained by numerous
hydrogen bonds
 The breaking and reforming of
these bonds plays an important
role in how DNA functions in the
cell
Hydrophobic Interactions
 Non-polar molecules do not form
hydrogen bonds
 When non-polar molecules
interact with polar molecules,
they clump together
 Non-polar molecules are
hydrophobic, literally meaning
“water-fearing”
 Polar molecules have a natural
tendency to form hydrogen
bonds with water molecules and
are hydrophilic, literally
meaning “water-loving”
Hydrophobic Interactions
 The natural clumping
together of non-polar
molecules is called the
hydrophobic effect
 This effect plays a central
role in how cell membranes
form and helps to determine
the 3-D shape of biological
molecules as proteins
Ions in Biological Systems
 When an atom or group of atoms gains or loses
electrons, it acquires an electric charge and becomes
an ion
 When it loses electrons, the resulting ion is positive
and is called a canion.
 When it gains electrons, the resulting ion is negative
and is called an anion.
 Ions can be composed of only one element, such as
a sodium ion, Na+, or of several elements, such as a
bicarbonate ion HCO3-
Ions in Biological Systems
 Ions are an important part of living systems
 Hydrogen ions, H+, are critical to many biological
processes, including cellular respiration (the process by
which cells break down nutrients into energy)
 Sodium ions, Na+, are part of transport mechanisms that
enable specific molecules to enter cells.
 Since the cell is an aqueous environment, almost all ions are
considered free or disassociated ions (Na+(aq)) since they
dissolve in water, rather than as ionic compounds such as
sodium chloride (NaCl(s)).
Functional Groups
 Organic molecules that are made up of only carbon and
hydrogen atoms are called hydrocarbons
 Hydrocarbons share similar properties including:
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Non-polar
Do not dissolve in water
Relatively low boiling points (depending on size)
Flammable
 The covalent bonds between carbon and carbon and
between carbon and hydrogen are “energy-rich”
 Breaking them releases a great deal of energy
 Most of the hydrocarbons you encounter in everyday life, such
as acetylene, propane, butane, and octane, are fuels
Functional Groups
 Though hydrocarbons share similar properties, other organic
molecules have a wide variety of properties
 Most organic molecules have other atoms or groups of other
atoms attached to their central carbon-based structure.
 A cluster of atoms that always behaves in a certain way is
called a functional group
 Functional groups contain atoms such as oxygen (O), nitrogen
(N), phosphorus (P), or sulfur (S).
 Certain chemical properties are always associated with
certain functional groups
Table 1.1
Structures and Shapes of
Molecules
 A molecular formula shows the number of each type of
atom in an element or compound
 Ex: H2O, C3H7NO2, and C6H12O6
 Structural formulas show how the different atoms of a
molecule are bonded together
 When representing molecules using a structural
formula, a line is drawn between atoms to indicate a
covalent bond
 A single line indicates a single covalent bond, double
lines indicate a double bond, and triple lines indicate a
triple bond
Structural Formulas
Structural Formulas
 Structural formulas can also
be presented in a simplified
form, particularly for biological
molecules
 Carbon atoms are indicated by a
bend in the line
 Their symbol, C, is omitted
 Hydrogen atoms attached to
these carbon atoms are omitted
but are assumed to be present
Shapes of Molecules
 Structural formulas are 2-D representations, but
molecules take up space in 3 dimensions
 In fact, the 3-D shape of a molecule influences its
behaviour
Ball-and-stick Model
Space-filling Model
Section 1.2: Biologically
Important Molecules
 Many of the molecules of living organisms are
composed of thousands of atoms
 These are called macromolecules, which are large
molecules that often have complex structures
 Many macromolecules are polymers
 Long chain-like substances composed of many smaller
molecules linked together by covalent bonds
 These smaller molecules are called monomers, which
can exist individually or as units of a polymer
 The monomers in a polymer determine the properties of
that polymer.
Protein
Nucleic Acid
Carbohydrate
Lipid
Carbohydrates
 Carbohydrates contain carbon, hydrogen, and oxygen
in the ratio of 2 hydrogen and 1 oxygen for every
carbon
 The general formula for carbohydrates is (CH2O)n where
“n” is the number of carbon atoms
 Sugar and starches are examples of carbohydrates
 They store energy in a way that is easily accessible by
the body
 Most carbohydrates are polar and dissolve in water
 Due to high proportion of hydroxyl functional groups, and
often carbonyl groups
Monosaccharides and
Disaccharides
 Monosaccharides are simple sugars that consist of 3 to 7
carbon atoms
 “Mono” = one and “saccharide” = sugar
 Common examples include:
 Glucose is the sugar the cells in the body use first for
energy (i.e. blood sugar)
 Fructose is a principal sugar in fruits
 Galactose is a sugar found in milk
Glucose
Fructose
Galactose
Monosaccharides and
Disaccharides
 These 3 simple sugars have the same molecular
formula (C6H12O6) but the 3-D shapes of their
structures and the relative arrangement of their
hydrogen atoms and hydroxyl groups differ
 Molecules that have the same molecular formula but have
different structures are called isomers
 Due to their different 3-D shapes, they’re treated very
differently by your body and in the cell
 Ex: Your taste buds detect fructose as being much
sweeter than glucose
Monosaccharides and
Disaccharides
 Two monosaccharides can join to
form a disaccharide.
 The covalent bond between them
is called a glycosidic linkage
 It forms between specific
hydroxyl groups on each
monosaccharide.
Sucrose
 Common table sugar is the
disaccharide sucrose (glucose
and fructose)
 Lactose (galactose and glucose)
is found in dairy products
Glycosidic linkage
Polysaccharides
 Many monosaccharides can join together by glycosidic
linkages to form a polysaccharide (“poly” = many)
 Three common polysaccharides are starch, glycogen,
and cellulose
 All three are composed of monomers of glucose, but
they differ in the ways the glucose units are linked
together
 This results in them having different 3-D shapes
Starch and Glycogen
 The differences in their 3-D shapes also leads to them
having different functions
 Plants store glucose in the form of starch and animals
store glucose in the form of glycogen
 They provide short-term energy storage, whereby glucose
can be easily accessed from their breakdown within the
cell
 Starch and glycogen differ in their number and type of
branching side chains
 Glycogen has more branches so it can be broken down
much more rapidly than starch
Cellulose
 Cellulose carries out a completely different function. It
provides structural support in plant cell walls.
 The type of glycosidic linkage between monomers of
cellulose is different from the type in starch and glycogen
 The hydroxyl group on carbon-1 of glucose can exist in 2
different positions
 These positions are referred to as alpha and beta
 The alpha form results in starch and glycogen, while the beta
form results in cellulose.
Lipids
 Like carbohydrates, lipids are composed of carbon,
hydrogen, and oxygen atoms
 However, lipids have fewer oxygen atoms and a
significantly greater proportion of carbon and hydrogen
bonds
 As a result, lipids are non-polar and hydrophobic (they
do not dissolve in water)
 Since the cell is an aqueous environment, the
hydrophobic nature of some lipids plays a key role in
determining their function
Lipids
 The presence of many energy-rich C-H bonds makes
lipids efficient energy-storage molecules
 Lipids yield more than double the energy per gram
that carbohydrates do
 However, they store their energy in hydrocarbon
chains so their energy is less accessible to cells
than energy from carbohydrates
 Lipids provide longer-term energy and are processed by
the body after carbohydrate stores are used up
Lipids
 Lipids are crucial to life in many ways:
 Lipids insulate against heat loss
 Lipids form a protective cushion around major
organs
 Lipids are a major component of cell membranes
 Lipids provide water-repelling coatings for fur,
feathers, and leaves
Triglycerides
 Triglycerides are composed
Ester Linkages
of 1 glycerol molecule and 3
fatty acid molecules
 The bond between the
hydroxyl group on a glycerol
molecule and the carboxyl
group on a fatty acid is called
an ester linkage because it
results in the formation of an
ester functional group
1 Glycerol
3 Fatty Acids
Triglycerides: Fatty Acids
 A fatty acid is a hydrocarbon chain that ends with an
acidic carboxyl group (-COOH)
 A saturated fatty acid has no double bonds between
carbon atoms
 An unsaturated fatty acid has one or more double
bonds between carbon atoms
 One double bond = monounsaturated
 Two or more double bonds = polyunsaturated
 Humans can’t synthesize polyunsaturated fats and must
consume them in their diet
Triglycerides: Saturated and
Unsaturated Fats
 The double bonds in a triglyceride
affects its 3-D shape, which alters
its behaviour in the body
 Triglycerides containing saturated
fatty acids are generally solid fats
at room temperature
 Ex: lard and butter
 Triglycerides containing
unsaturated fatty acids are
generally liquid oils at room
temperature
 Ex: olive oil and canola oil
Triglycerides: Health
 Saturated fat is linked with heart disease, while some
unsaturated fats, particular polyunsaturated fatty acids, are
known to reduce the risk of heart disease
 A food preservation process called hydrogenation involves
chemical addition of hydrogen to unsaturated fatty acids of
triglycerides to produce saturated fats
 A by-product of this reaction is the conversion of cis fats
to trans fats, whereby remaining double bonds are
converted to a trans conformation
 Consumption of trans fats is associated with increased risk of
heart disease
Phospholipids
 Phospholipids are the main components of cell
membranes
 They are similar in structure to triglycerides, but a
phosphate group replaces the third fatty acid
 Attached to the phosphate group is an R group which
defines the type of phospholipid
 The “head” portion is polar and hydrophilic
 The lower “tail” portion is non-polar and hydrophobic
Phospholipids
 In aqueous environments phospholipids form a lipid
bilayer
 In a phospholipid bilayer, the hydrophilic heads
face the aqueous solution on either side of the
bilayer, while the tails form a hydrophobic interior
 The inside of a cell is an aqueous environment, as
is the extra-cellular fluid surrounding cells
 Therefore the membranes of cells, which are made of
phospholipids, adopt this bilayer structure
Other Lipids
 Steroids are a group of lipids that are composed of 4
carbon-based rings attached to each other
 Steroids differ depending on the arrangement of the
atoms in the rings and the types of functional group
Other Lipids: Steroids
 Cholesterol is a steroid that is:
 A component of cell membranes
 Present in the blood of animals
 The precursor of several other steroids, such as sex
hormones testosterone and estrogen.
 Testosterone regulates sexual function and aids in building
bone and muscle mass
 Estrogen regulates sexual function in females and acts to
increase the storage of fat
 Mammals make cholesterol and it also enters the body as
part of the diet
Other Lipids: Steroids
 In medicine, steroids are used to reduce inflammation
 Ex: Topical steroid ointments to treat skin conditions and
inhalers to treat asthma.
 Anabolic steroids are synthetic compounds that mimic
male sex hormones
 They are typically used to build muscle mass in people
who have cancer and AIDS, but are also frequently
misused by athletes
Other Lipids: Waxes
 Waxes have a diversity of chemical structures, often with
long carbon-based chains, and are solid at room
temperature
 They are produced in both plants (ex: carnauba wax) and
animals (ex: earwax, beeswax, and lanolin)
 In plants, waxes coat the surfaces of leaves, preventing
water and solutes from escaping and helping to repel
insects
 In animals, waxes are present on the skin, fur, and
feathers of many species and on the exoskeletons of
insects
Proteins
 Proteins represent an extremely diverse type of macromolecules
that can be classified into groups according to their function
 Some of the functions of proteins include:
 Catalyzing chemical reactions
 Providing structural support
 Transporting substances in the body
 Enabling organisms to move
 Regulating cellular processes
 Providing defense from disease
 The functions of proteins depend on their 3-D
structures
Amino Acids: Monomers of
Proteins
 A protein is a macromolecule
composed of amino acid monomers
 An amino acid contains a central
carbon atom that is bonded to the
following four atoms or group of atoms:
 A hydrogen atom
 An amino group
 A carboxyl group
 An R group (which is also called a
side chain)
 The distinctive shape and properties of
an amino acid depend on its R group
Amino Acids
 All amino acids are somewhat polar, due to the polar
C=O, C-O, C-N, and N-H bonds
 Some amino acids are more polar than others,
depending on the polarity of the R group
 There are 20 common amino acids that make up most
proteins
 8 of these are essential amino acids and can’t be
produced by the human body and must be consumed as
part of the diet
 These are isoleucine, leucine, lysine, methionine,
phenylalanine, threonine, tryptophan, and valine.
Amino Acids
 In proteins, amino acids are joined by covalent bonds
called peptide bonds
 Form between the carboxyl group on one amino acid and
the amino group on another
 A polymer composed of amino acid monomers is called
a polypeptide
 Proteins are composed of one or more polypeptides
 Amino acids can occur in any sequence in a polypeptide
and since there are 20 possible amino acids for each
position, an enormous variety of proteins are possible
Levels of Protein Organization
 The structure of a protein can be divided into 4 levels of
organization
 Primary structure
 The linear sequence of amino acids
 The peptide bonds linking the amino acids are the
backbone of a polypeptide chain
 Since the peptide bonds are polar, hydrogen bonding
is possible between the C=O of one amino acid and
the N-H of another amino acid.
Levels of Protein Organization
 Secondary structure
 The result of the hydrogen bonds between amino
acids
 A polypeptide can form a coil-like shape (alpha helix)
or a folded fan-like shape (beta pleated sheet)
Levels of Protein Organization
 Tertiary structure
 The 3-D shape of proteins that results from a complex process
of protein folding
 This folding occurs naturally as the peptide bonds and the
different R groups interact with each other and with the
aqueous environment of the cell
 The hydrophobic effect had a large effect on structure
 The polar hydrophilic groups direct towards the aqueous environment
and non-polar hydrophobic groups direct towards the interior of the
proteins 3-D shape
 Hydrogen bonding and electrostatic attractions between R
groups of different amino acids also add stability
 One class of proteins have molecular chaperones that interact
with the polypeptide chain and produce the final folded protein
Levels of Protein Organization
 Quaternary structure
 The association of two or more polypeptides to form
a protein
Protein Denaturation
 Under certain conditions, proteins can completely
unfold in a process called denaturation
 This occurs when the normal bonding between R groups
is disturbed
 Intermolecular bonds break, potentially affecting the
secondary, tertiary, and quaternary structures
 Conditions that cause denaturation include extremes of
hot and cold temperatures and exposure to certain
chemicals
 Once a protein loses its normal 3-D shape, it is no longer
able to perform its usual function
Nucleic Acids
 There are two types of nucleic acids:
 DNA (deoxyribonucleic acid)
 RNA (ribonucleic acid)
 DNA contains the genetic information of an organism, which
is interpreted and decoded into particular amino acid
sequences of proteins, which carry out numerous functions
in the cell
 This conversion is carried out with the assistance of different
RNA molecules
 The amino acid sequence of a protein is determined by the
nucleotide sequences of both DNA and RNA
Nucleic Acids
 DNA and RNA are polymers made of
thousands of repeating nucleotide
monomers
 A nucleotide is made up of 3
components that are covalently bonded
together
 A phosphate group
 A sugar with 5 carbon atoms
 A nitrogen-containing base
 The nucleotide make-up of DNA and
RNA differs
 The nucleotides in DNA contain the
sugar deoxyribose
 The nucleotides in RNA contain the
sugar ribose
Nucleic Acids
 There are 4 different types of
nitrogenous bases in DNA:
 Adenine (A)
 Thymine (T)
 Guanine (G)
 Cytosine (C)
 In RNA all the same bases
are used, except thymine,
which is replaced with Uracil
(U)
Nucleic Acids
 A polymer of nucleotides is often
referred to as a strand
 The covalent bond between
adjacent nucleotides is called a
phosphodiester bond
 It occurs between the phosphate
group on one nucleotide and a
hydroxyl group on the sugar of the
next nucleotide
 A nucleic strand has a backbone
made up of alternating phosphates
and sugars with the bases
projecting to one side of the
backbone
Nucleic Acids
 DNA is composed of 2 strands twisted about each other to form a
double helix
 When unwound, it resembles a ladder
 The sides of the ladder are made up of alternating phosphate and
sugar molecules, and the rungs of the ladder are made up of pairs
of bases held together by hydrogen bonds
 Nucleotide bases always pair together in the same way:
 Thymine (T) pairs with Adenine (A)
 Guanine (G) pairs with Cytosine (C)
 These bases are said to be complementary to each other
 RNA is single-stranded
Section 1.3 Biochemical
Reactions
 The chemical reactions that are associated with
biological processes can be grouped in several types
 The four main types of chemical reactions that
biological molecules undergo in the cell are:
 Neutralization
 Oxidation-reduction
 Condensation
 Hydrolysis
Neutralization (Acid-Base)
Reactions
 In the context of biological systems, acids and bases
are discussed in terms of their behaviour in water
 An acid is a substance that produced hydrogen ions,
H+, when it dissolves in water
 It increases the concentration of hydrogen ions in an
aqueous solution
 A base is a substance that produces hydroxide ions,
OH-, when it dissolves in water
 It increases the concentration of hydroxide ions in an
aqueous solution
Neutralization (Acid-Base)
Reactions
 The pH scale ranks substances
according to the relative
concentration of their hydrogen
ions
 Substances that have a pH
lower than 7 are classified as
acids
 Substances that have a pH
higher than 7 are classified as
bases
 Substances that have a pH of 7
(that is, they have an equal
concentration of hydrogen and
hydroxide ions) are classified as
neutral
Neutralization (Acid-Base)
Reactions
 When an acid chemically interacts with a base, they
undergo a neutralization reaction that results in the
formation of a salt (an ionic compound) and water
 The acid loses its acidic properties and the base loses
its basic properties
 i.e. their properties have been cancelled out, or
neutralized
Neutralization (Acid-Base)
Reactions
 The normal pH of human blood ranges from 7.35-7.45
 If blood pH increases to 7.5 it can cause dizziness and
agitation
 This condition is called alkalosis
 If blood pH decreases to 7.3-7.1 it can cause disorientation,
fatigue, severe vomiting, brain damage, and kidney disease
 This condition is called acidosis
 Blood pH that falls below 7.0 or rises beyond 7.8 can be
fatal
Neutralization (Acid-Base)
Reactions
 To maintain optimum pH ranges, organisms rely on buffers
 Substances that resist changes in pH by releasing hydrogen ions
when a fluid is too basic and taking up hydrogen ions when a fluid
is too acidic
 Most buffers exist as specific pairs of acids and bases
 Ex: One of the most important buffer systems in human blood
involves the pairing of carbonic acid, H2CO3(aq), and hydrogen
carbonate ion, HCO3-(aq)
Oxidation-Reduction
Reactions
 Another key type of chemical reaction is based on the
transfer of electrons between molecules
 When a molecule loses electrons it becomes oxidized and has
undergone a process called oxidation
 Electrons are highly reactive and do not exist on their own or
free in the cell so when a molecule undergoes oxidation, the
reverse process must occur in another molecule
 When a molecule accepts electrons from an oxidized molecule,
it becomes reduced and has undergone a process called
reduction
 Because oxidations and reductions occur at the same time,
the whole reaction is called an oxidation-reduction reaction,
or redox reaction
Oxidation-Reduction
Reactions
 A common type of redox reaction is a combustion
reaction
 Ex: In the combustion of propane in your barbeque, the
propane becomes oxidized and the oxygen is reduced
 This reaction releases a lot of energy that is used to cook
food on the barbeque.
 Redox reactions also occur in cells, such as cellular
respiration
 Sugars such as glucose are oxidized through a series of
redox reactions to produce carbon dioxide and water.
Condensation and Hydrolysis
Reactions
 The assembly of all four types of biological
macromolecules involves a condensation reaction
between the monomers of each polymer
 In a condensation reaction, an H atom is removed
from a functional group on one molecule, and an OH
group is removed from another molecule
 The two molecules bond to form a larger molecule and
water
 Condensation reactions are also called dehydration
reactions because the reaction results in the release of
water
Condensation and Hydrolysis
Reactions
 The breakdown of macromolecules into their
monomers involves the addition of water to break the
bonds between the monomers
 In a hydrolysis reaction, an H atom from water is
added to one monomer, and an OH group is added to
the monomer beside that one
 The covalent bond between these monomers breaks
and the larger molecule is split into two smaller
molecules
Condensation
Enzymes Catalyze Biological
Reactions
 A certain amount of energy is required to begin a reaction,
which is referred to as the activation energy of a reaction
 If the activation energy for a reaction is large, the reaction will
occur very slowly
 One of the methods to speed up reactions is to increase the
temperature of the reactants
 However, the temperatures that chemical reactions would need
to reach in order to proceed quickly enough to sustain life are
so high that they would permanently denature proteins
 This is why long-lasting high fevers are so dangerous, as the
high temperature can cause major disruptions to cellular
reactions
Enzymes Catalyze Biological
Reactions
 A catalyst is a substance that speeds up a chemical
reaction but is not used up by the reaction
 Catalysts function by lowering the activation energy of a
reaction
 Cells manufacture specific proteins that act as catalysts,
called enzymes
 Ex: In red blood cells an enzyme called carbonic anhydrase
enables carbon dioxide and water to react to form about
600,000 molecule of carbonic acid each second!
 Enzymes facilitate almost all chemical reactions in
organisms, and each type of reaction is carried out by its
own characteristic enzyme
Enzymes Bind with a
Substrate
 Like other proteins, enzymes are composed of long
chains of amino acids folded into particular 3-D shapes,
with primary, secondary, tertiary, and often quaternary
structures
 Most enzymes have globular shapes, with pockets or
indentations on their surfaces called active sites
 The unique shape and function of an active site are
determined by the sequence of amino acids in that
section of the protein
Enzymes Bind with a
Substrate
 An active site on an enzyme interacts in a specific manner with the
reactant of a reaction, called the substrate
 During the reaction, the substrate joins with the enzyme to form an
enzyme-substrate complex
 The substrate fits closely into the active site because enzymes can
adjust their shapes slightly
 Intermolecular bonds, such as hydrogen bonds, form between the
enzyme and the substrate as the enzyme adjusts its shape
 This change in shape is called induced fit
Enzymes Bind with a
Substrate
 Enzymes lower the activation energy of the reaction by
changing the substrate, its environment, or both
 To accomplish this, the active site may:
 Contain amino acid R groups that cause bonds in the substrate
to stretch or bend, making the bonds weaker and easier to
break
 Bring two substrates together in the correct position for a
reaction to occur
 Transfer electrons to and from the substrate (reduce or oxidize
it), destabilizing it and making it more likely to react
 Add or remove hydrogen ions to or from the substrate (i.e. act
as an acid or base), destabilizing it and making it more likely to
react
Enzymes Bind with a
Substrate
 Once the reaction takes place, the products of the reaction
are released and the enzyme is able to accept another
substrate and begin the process again
 This cycle is known as the catalytic cycle
 Some enzymes require the presence of other molecules or
ions, known as coenzymes, to catalyze a reaction
 Some enzymes require the presence of metal ions, such as
iron or zinc, which are referred to as cofactors
 This is why your body requires small amount of minerals and
vitamins to stay healthy
Enzyme Classification
 Enzymes are classified according to the type of reaction
they catalyze
 The shape of an enzyme must match its substrate exactly,
so most enzymes catalyze only one specific reaction
 There are thousands of different enzymes to catalyze the
numerous reactions that take place within an organism,
each with a specific name to identify it
 The names of many enzymes consist of the first part of the
substrate’s name, followed by the suffix “-ase”
 Ex: The enzyme that catalyzes the cleavage of the glycosidic
linkage in lactose is named lactase.
Enzyme Activity and
Surrounding Conditions
 Enzyme activity is affected by any change in conditions that
alters the enzyme’s 3-D shape
 Temperature and pH are two important factors
 When temperatures are too low, the bonds that determine
enzyme shape are not flexible enough to enable substrate
molecules to fit properly
 When temperatures are too high, the bonds are too weak to
maintain the enzyme’s shape
 The optimal temperature and pH ranges of most enzymes
are fairly narrow
 Most human enzymes work best within the pH range of 6-8.
There are exceptions though (ex: stomach enzymes)
Enzyme Activity and
Surrounding Conditions
 The number of substrates available also affects the rate
of enzyme activity
 If there are too few substrates present, enzymes and
substrates will encounter each other much less
frequently, and the rate of reaction will decrease
 Therefore, enzyme activity increases as substrate
concentration increases
 This is true up to a point where the enzymes are working
at maximum capacity, after which adding more substrate
will not affect the rate of the reaction
Enzyme Activity Regulation
 Inhibitors are molecules that interact with an enzyme
and reduce its activity
 They reduce the enzyme’s ability to interact with its
substrate
 This can occur by two different mechanisms:
 Competitive inhibition
 Non-competitive inhibition
Competitive Inhibition
 These inhibitors interact with the active site of the
enzyme
 When both the substrate and inhibitor are present, they
will compete to occupy the active site
 When the inhibitor is present in high enough
concentration, it will out-compete the substrate and
block it from binding
 This prevents the reaction that the enzyme usually
catalyzes from occurring
Non-competitive Inhibition
 These inhibitors bind to an allosteric site, altering the
conformation or 3-D shape of the enzyme, which decreases
the activity of the enzyme
 Many biochemical reactions are grouped together in
pathways where the product of one reaction acts as a
substrate for the enzyme that catalyzes the next reaction in
the pathway
 These pathways are regulated by feedback inhibition
 The product of the last reaction in a pathway is a noncompetitive inhibitor of the enzyme that catalyzes the reaction
at the beginning of the pathway
 This ensures that the products of a pathway are not produced
unnecessarily
Enzyme Activity Regulation
 Activator molecules can also bind to an allosteric
site
 In this case, the conformation of the enzyme alters in
such a way as to cause an increase in enzyme activity
 The regulation of enzyme activity by activators and
inhibitors binding to allosteric sites is called
allosteric regulation