Chapter 1 – THE MOLECULES OF LIFE
(Taken from Biology 12, MHR, 2011)
1.1 – CHEMISTRY IN LIVING SYSTEMS
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Biochemistry is the study of the activity and properties of biologically important
molecules.
Organic molecules are carbon-based where the carbon atoms are usually bonded to
each other and hydrogen.
Many organic molecules also include atoms of nitrogen, oxygen, phosphorus, and/or
sulfur.
Inorganic molecules do not contain any carbon.
All organic molecules contain the element carbon however, not all carbon-containing
molecules are organic.
Carbon dioxide, carbonates and hydrogen carbonates are three examples of inorganic
carbon compounds.
The most common chemical elements found in living things are:
 carbon (C) – valence of 4 (can form 4 bonds)
 hydrogen (H) – valence of 1 (can form 1 bond)
 oxygen (O) – valence of 2 (can form 2 bonds)
 nitrogen (N) – valence of 3 (can form 3 bonds)
These elements, along with other less common elements, make up the molecular
structures of carbohydrates, lipids, proteins, and nucleic acids.
Living organisms also need other less common elements such as: sulfur, calcium,
phosphorus, iron and sodium.
The table below shows these elements and the role they play in living organisms.
Element
Sulfur
Calcium
Phosphorus
Iron
Sodium
Example role in
plants
in some amino acids
co-factor in some
enzymes
Example role in
animals
in some amino acids
co-factor in some
enzymes and component
of bones
phosphate groups in ATP phosphate groups in ATP
and DNA molecules
and DNA molecules
in cytochromes (proteins in cytochromes and in
used for electron
hemoglobin
transport during aerobic
cell respiration)
in membrane function
in membrane function
and sending nerve
impulses
(Damon, McGonegal, Tosto, Ward, 2007, pg 46-47)
Example role in
prokaryotes
in some amino acids
co-factor in some
enzymes
phosphate groups in ATP
and DNA molecules
in cytochromes
in membrane function
Water - The Universal Solvent
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Water is the most abundant molecule in any cell.
It has unique chemical properties due to its chemical structure.
Water, H2O, comprises two H atoms attached to one O atom.
Water’s polar covalent bonds and asymmetrical structure create a highly polar molecule.
One molecule of water attracts another at room temperature, to bond and make a liquid.
Water is essential in cell reactions, is a lubricant in the body, and carries dissolved
molecules into and out of a cell.
Water is considered the universal solvent (more substances dissolve in it than any other
liquid) because of its polarity - provides attachment for other polar molecules or ions.
All ionic and polar covalent substances dissolve in water.
Water and oil don’t mix because water is polar and oil is nonpolar: water & oil are
immiscible, while water & vinegar (both polar) are miscible.
Important properties of water include:
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Remains liquid over a large temperature range
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Dissolves most substances such as oxygen, carbon dioxide, and salt
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Protects cells from rapid temperature changes and provides a stable
environment for cell reactions
Interactions Within Molecules
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Intramolecular interactions occur between atoms within a molecule, forming covalent
bonds.
A covalent bonds form when two non-metal atoms share their valence electrons.
Some atoms attract electrons more strongly than other atoms (electronegativity).
electronegativity - a measure of an atom’s ability to attract a shared electron pair
when it is participating in a covalent bond
Oxygen (O), nitrogen (N), and chlorine (Cl) are atoms with high electronegativity.
Hydrogen (H), carbon (C), and phosphorus (P) are atoms with lower electronegativity.
The higher the electronegativity, the stronger the atom attracts the electrons of a
covalent bond.
A polar covalent bond is formed when there is an unequal sharing of electrons.
A water molecule contains two polar covalent O-H bonds.
See Figure 1.2, pg 11
Molecules, such as water, which have regions of partial negative (δ-) and partial positive
(δ+) charges, are referred to as polar molecules.
Non-polar bonds form when atoms equally share the electrons of a covalent bond. If
this type of bond predominates in a molecule, the molecule is considered a non-polar
molecule.
The polarity of biological molecules greatly affects their behaviour and functions in a cell.
Interactions Between Molecules
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The polarity of a molecule influences the intermolecular interactions that occur between
molecules.
Intermolecular interactions are much weaker than intramolecular interactions therefore
are responsible for many of the physical properties of substances.
Two important types of intermolecular interactions are hydrogen bonding and
hydrophobic interactions.
Hydrogen Bonding
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A hydrogen bond is a weak association between an atom with partial negative charge
and a hydrogen atom with partial positive charge.
Many biological molecules have polar covalent bonds involving a hydrogen atom and an
oxygen or nitrogen atom.
In water, hydrogen bonds (dotted lines) form between the partially positive hydrogen
atoms of one molecule and the partially negative oxygen atoms on other molecules.
See Figure 1.3, pg 12
Hydrogen bonds between molecules in cells help maintain the proper structure and
function of the molecule.
For example, the shape of DNA is maintained by numerous hydrogen bonds.
Hydrophobic Interactions
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Hydrophobic (water-fearing) refers to non-polar molecules that do not have
attractive interactions with water molecules.
Hydrophilic (water-loving) refers to polar molecules that have attractive
interactions with water molecules.
The hydrophobic effect plays a central role in how cell membranes form and helps to
determine the 3-D shape of biological molecules such as proteins.
Organic molecules consisting of only carbon and hydrogen are known as
hydrocarbons.
Hydrocarbons share similar properties: they are non-polar, do not dissolve in water,
have relatively low boiling points, are flammable, and most are fuels.
For example, acetylene, propane, butane, and octane are all fuels.
Ions in Biological Systems
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When an atom or group of atoms loses electrons, the ion produced is positive and is
called a cation.
When an atom or group of atoms gains electrons, the ion produced is negative and is
called an anion.
Ions play a critical role in many biological processes.
For example, hydrogen ions (H+) are critical to the process of cellular respiration and
sodium ions (Na+) play a role in the transport of materials across the cell membrane.
Functional Groups
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Functional groups are reactive groups of atoms attached to the carbon backbone of an
organic molecule that gives the molecule particular chemical and physical properties.
Functional groups contain atoms such as oxygen (O), hydrogen (H), nitrogen (N),
phosphorus (P), or sulfur (S).
Most of the reactions that occur in living organisms involve functional groups.
Hydroxyl group (-OH) and carboxyl group (-COOH) are polar because of the
electronegative oxygen atom they contain.
Carboxyl group (-COOH) makes a molecule acidic (carboxylic acids).
Amino group (-NH2) makes a molecule basic (amines).
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See Table 1.1, pg 14 For Important Functional Groups on Biological Molecules
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Structures and Shapes of Molecules
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Structural formulas are two-dimensional representations that indicate how different
atoms of a molecule are bonded together.
When using a structural formula, a single line drawn between atoms represents a single
covalent bond.
A double line represents a double covalent bond and a triple line represents a triple
covalent bond.
Space-filling models or ball and stick models are a common way to represent the
three-dimensional structures of molecules.
In space-filling models, each atom is assigned a particular colour by convention.
Carbon is black, hydrogen is white, and oxygen is red.
The 3-D shape of larger biological molecules influences its behaviour and function.
See Figure 1.6, pg 15
HOMEWORK:
pg 17 #1-13
1.2 – BIOLOGICALLY IMPORTANT MOLECULES
(Taken from Biology 12, MHR, 2011)
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Many macromolecules are polymers - very large, complex molecules, usually
composed of repeating units of smaller molecules (monomers) covalently linked together.
Carbohydrates, Lipids, Proteins and Nucleic Acids are examples of macromolecules.
A polymer is a large molecule composed of repeating units of smaller molecules
(monomers).
A monomer is the smallest repeating unit of a polymer.
See Figure 1.7, pg 18
CARBOHYDRATES (CH2O)n
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Carbohydrates are macromolecules that contain carbon, hydrogen and oxygen in the
ratio of 1:2:1.
Sugars and starches are examples.
Because they contain hydroxyl functional groups and many contain carbonyl groups,
most carbohydrates are polar molecules, and many dissolve in water.
Monosaccharides
 A monosaccharide is a carbohydrate composed of between three and seven carbon
atoms.
 “mono” meaning one
 “saccharide” meaning sugar
Examples:
 5C pentoses (eg ribose, deoxyribose)
 6C hexoses (eg glucose, fructose, galactose)
Isomers
 Glucose (blood sugar)
 Galactose (sugar found in milk)
 Fructose (sugar found in fruits)
 These three simple sugars have the same molecular formula: C6H12O6.
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Isomers are molecules that have the same molecular formula but have different
structures.
Glucose, fructose, and galactose are isomers of each other.
See Figure 1.8, pg 19
Disaccharides
 A disaccharide is a carbohydrate composed of two monosaccharides joined by a covalent
bond.
 The covalent bond between monosaccharides is called a glycosidic linkage and forms
between specific hydroxyl groups on each monosaccharide.
 The two sugars are joined by condensation and may be broken by hydrolysis.
Different Disaccharides
 sucrose (table sugar) = glucose + fructose
 lactose (sugar in milk) = glucose + galactose
 maltose = glucose + glucose
Polysaccharides
 Many monosaccharides can join together by glycosidic linkages to form a polysaccharide.
 “poly” meaning many
 “saccharide” meaning sugar
 Three common polysaccharides are: starch, glycogen, and cellulose.
Glycogen and Starch
 Glycogen and starch provide short-term energy storage.
 Plants store glucose in the form of starch while animals store glucose in the form of
glycogen in the liver to be used as quick energy.
 Glycogen consists of hundreds of glucose molecules strung together in a highly branched
chain whereas starch is much more linear.
Cellulose
 Cellulose provides structural support in plant cell walls.
 The glycosidic linkage between monomers of cellulose is different from the type for
starch and glycogen.
 The different linkages occur because the hydroxyl group on carbon-1 of glucose can exist
in two different positions.
 The alpha form results in starch and glycogen, while the beta form results in cellulose.
 See Figure 1.10, pg 20 and Figure 1.11, pg 21
 Starch and glycogen are digestible by humans and most other animals.
 Cellulose is indigestible because we lack the enzyme that recognizes the glycosidic
linkage in that macromolecule.
Functions of Carbohydrates
 main energy source for living things
 energy is stored for short term or long term
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have two important biological functions
1. Energy Storage (Starch and Glycogen)
2. Structural Support (Cellulose and Chitin)
Importance of Carbohydrates in Animals
Name
glucose
lactose
glycogen
Type
monosaccharide
disaccharide
polysaccharide
One Function
chemical fuel for cell respiration
makes up some of the solutes in milk
stores glucose in liver and muscles
(Damon, McGonegal, Tosto, Ward, 2007, pg 51)
Importance of Carbohydrates in Plants
Name
fructose
sucrose
Type
monosaccharide
disaccharide
cellulose
polysaccharide
One Function
found in many fruits (makes them sweet)
often transported from leaves of plants to other
locations in plants by vascular tissue
one of the primary components of plant cell walls
(Damon, McGonegal, Tosto, Ward, 2007, pg 52)
LIPIDS
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Lipids are biological molecules composed of carbon, hydrogen, and oxygen atoms, with a
high proportion of non-polar carbon-hydrogen bonds.
Lipids are hydrophobic – they are insoluble in water.
Lipids yield more than double the energy per gram that carbohydrates do.
There are 5 groups of lipids that are important to living things: Oils, Fats, Phospholipids,
Waxes and Steroids.
Functions of Lipids
 Long term nutrient and energy storage (fat in humans and oil in plants)
 Cushions vital organs in mammals
 Insulation against heat loss
 Hormones to send messages around the body
 Primary structure of cell membranes
 Provide water-repelling coatings for fur, feathers, and leaves
 Buoyancy (lipids are less dense than water so help animals to float)
Triglycerides: Lipids Used For Energy Storage
 Triglycerides are composed of one glycerol molecule and three fatty acid molecules
linked by ester bonds.
 The bond between the hydroxyl group on a glycerol molecule and the carboxyl
group on a fatty acid is called an ester linkage.
 Glycerol is a 3 carbon molecule with 3 hydroxyl groups (-OH).
 Fatty acids are hydrocarbon chains that end with a carboxyl group (-COOH).
 The carboxyl group of each fatty acid is linked to the glycerol molecule on one of three
reaction sites (hydroxyl groups). It is a dehydration synthesis reaction.
 See Figure 1.12, pg 22
Saturated Fatty Acids
 have no double bonds between carbon atoms (only single bonds)
 contain the maximum number of hydrogen atoms.
 are usually solid at room temperature
 the saturated fatty acid is straight
Monounsaturated Fatty Acids
 have one double bond between carbon atoms.
 tail ‘kinks’ at C=C so the molecules do not pack closely enough to be solid at room
temperature
 liquid at room temperature, usually are plant fats and referred to as oils (corn oil, olive
oil...)
Polyunsaturated Fatty Acids
 have two or more double bonds between carbon atoms.
 have low melting points
 are liquid oils at room temperature
Examples:
 -sunflower, canola, olive oil (all made from plants), margarine
 See Figure 1.13, pg 22
Phospholipids: Components of Cell Membranes
 A phospholipid is a lipid composed of a glycerol molecule bonded to two fatty acids and a
phosphate group with an R group.
 In water, phospholipids form a lipid bilayer.
 They arrange themselves so the non-polar “tails” are tucked away from the water, and
the polar “heads” are directed toward the water.
 See Figure 1.14 and Figure 1.15, pg 23
Steroids
 Structure- composed of four fused carbon rings with various functional groups attached
to them
 Function- makes many human hormones (ie) testosterone in males; cholesterol is
needed for nerve cells and other cells to function properly
 high concentration of cholesterol is known to lead to clogged arteries
 In medicine, steroids are used to reduce inflammation.
 Anabolic steroids mimic male sex hormones.
Waxes
 Waxes are lipids composed of long carbon-based chains that are solids at room
temperature.
 Function-waterproof, provide protective coatings, earwax prevents microorganisms from
entering the middle ear
PROTEINS
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Proteins are biological macromolecules composed of amino acid monomers linked by
covalent bonds.
An amino acid is composed of a central carbon atom bonded to a hydrogen atom, an
amino group, a carboxyl group and a variable R group (or side chain).
See Figure 1.18, pg 25
There are 20 possible amino acids.
In proteins, amino acids are joined by covalent bonds called peptide bonds.
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A peptide bond forms between the carboxyl group on one amino acid and the amino
group on another.
Forming a Dipeptide
 A polypeptide is a polymer composed of amino acid monomers.
 Proteins are composed of one or more polypeptides.
 See Figure 1.20, pg 26
Levels of Protein Organization
 There are four levels of protein organization: primary, secondary, tertiary, and
quaternary.
1) Primary Structure
 linear sequence of amino acids attached by peptide bonds
 polypeptide chains may include hundreds of amino acids
 This forms a – N – C – C – N – C – C – N – C – C – backbone to the molecules.
 The primary structure is read from the NH2 – terminal to the – COOH terminal.
 Each amino acid is identified by its specific R group.
2) Secondary Structure
 coil-like shape – α (alpha) helix
 folded fan-like shape – β (beta) pleated sheet
 caused by hydrogen bonding between C=O of one amino acid and N-H of another amino
acid
3) Tertiary Structure
 three-dimensional structure of proteins (folding of polypeptide chains)
 Interactions that cause tertiary organization include:
 covalent bonds between sulfur atoms to create disulfide bonds (disulfide bridges);
 hydrogen bonds between polar chains;
 Van der Waals interactions among hydrophobic side chains of the amino acids; polar
hydrophilic groups (outside of protein); non-polar hydrophobic groups (inside of protein);
 ionic bonds between positively and negatively charged side chains.
(Damon, McGonegal, Tosto, Ward, 2007, pg 208), (Burrell, J. G. (2002-11) Click4Biology
(version 0820.2011). Thailand: Bangkok; URL http://click4biology.info)
4) Quaternary Structure
 multiple polypeptide chains (each with its own primary, secondary, and tertiary
structures) combine to form a single structure
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See Figure 1.21, pg 27 for various structures of proteins
Denaturation of Proteins
 Denaturation occurs when proteins become completely unfolded.
 Conditions for denaturation include: extreme hot and cold temperatures and exposure to
certain chemicals.
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Once a protein loses its normal 3-D shape, it is no longer able to perform its usual
function.
Proteins Classified By Function
 Catalyzing chemical reactions: speed up reactions
 Providing structural support: bones, tendons, skin, hair, nails, claws, and beaks
 Transporting substances in the body: hemoglobin transports O2 in blood
 Enabling organisms to move: muscle contraction (interaction of actin and myosin)
 Regulating cellular respiration: hormones, regulate genetic activity of a cell
 Providing defense from disease: antibodies
NUCLEIC ACIDS
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There are two types of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic
acid).
DNA carries genetic information that determines the structure and functional
characteristics of organisms.
RNA contains instructions to make proteins.
Nucleic acids are polymers made up of monomers called nucleotides.
A nucleotide contains the following parts:
1) nitrogenous base
 (Double ringed purines - adenine, guanine; Single-Ringed pyrimidines - cytosine,
thymine and uracil)
2) five-carbon (pentose) sugar
 deoxyribose (DNA) and ribose (RNA)
3) phosphate group
See Figure 1.22, pg 28
DNA molecules of cells consist of two polynucleotide chains that spiral around an
imaginary axis to form a double helix – bases are T (thymine), C (cytosine), G (guanine)
and A (adenine)
RNA is a single-stranded molecule.
A always bonds with T and G always bonds with C along the double strand
Types Of Bonds in Nucleic Acids
1) Hydrogen Bonds
 Three hydrogen bonds occur between G and C base pairs, while two hydrogen bonds
occur between A and T base pairs.
2) Phosphodiester Bonds
 between the phosphate group on one nucleotide and a hydroxyl group on the sugar of
the next nucleotide in the strand
3) Glycosyl Bonds
 between a base and a sugar
DNA vs RNA
*
*
*
*
*
Deoxyribonucleic acid
(DNA)
contains deoxyribose sugar
double stranded
adenine pairs with thymine
guanine pairs with cytosine
resides in the nucleus
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See Figure 1.23, pg 29
Ribonucleic acid
(RNA)
* contains ribose sugar
* single stranded
* adenine pairs with uracil
* guanine pairs with cytosine
* resides both in the nucleus and in the
cytoplasm
HOMEWORK: pg 31 #1 – 12
1.3 – BIOCHEMICAL REACTIONS
(Taken from Biology 12, MHR, 2011)
Neutralization (acid-base) Reactions
 A neutralization reaction is a reaction between an acid and a base, producing water and
salt as products.
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Acid + Base  Water + Salt
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To maintain optimum pH ranges, organisms rely on buffers.
Buffers are substances that minimize changes in pH by donating or accepting H+ as
needed.
Oxidation-reduction (Redox) Reactions
 oxidation: chemical reaction in which an atom loses one or more electrons.
 reduction: chemical reaction in which an atom gains one or more electrons.
 redox reaction: is a chemical reaction involving the transfer of one or more electrons
from one atom to another.
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A series of redox reactions where energy is released in each step is the basis for the
electron transport chains in photosynthesis and cellular respiration.
Condensation Reactions (Making Bonds)
(water is removed, energy is required)
•
endergonic (endothermic) reaction  requires energy
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In a condensation reaction (dehydration synthesis), two or more molecules are linked
together and a water molecule is released per bond formed.
involves the removal of a hydrogen atom (H) from the functional group of one subunit
and an –OH group from another subunit’s functional group
The assembly of all four types of biological macromolecules involves condensation
reactions between the monomers of each polymer.
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Hydrolysis reactions (Breaking Bonds)
(water is added, energy is released)
•
exergonic (exothermic) reaction  energy is produced or released
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In a hydrolysis reaction, a large molecule such as a polymer is broken down into smaller
molecules, as water is added to bonds between monomers.
The water molecule provides an H atom to one subunit and an –OH group to another
subunit. The breakdown of macromolecules into their monomers involves hydrolysis
reactions.
The breakdown of macromolecules into their monomers involves hydrolysis reactions.
See Figure 1.27, pg 35
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Enzymes Catalyze Biological Reactions
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Enzymes are protein catalysts – they speed up a chemical reaction without being
consumed in the process.
The reactants are converted faster into products.
Enzymes provide the force needed for collisions to occur (they lower the activation
energy – the energy needed to start the reaction).
Activation energy (AE) is the energy needed to destabilize the chemical bonds in the
substrate of an enzyme-substrate catalyzed reaction. In other words, it is the energy
needed to initiate a chemical reaction.
Enzymes lower the activation energy required thereby speeding up the rate of reactions.
See Figure 1.28, pg 36
(Damon, McGonegal, Tosto, Ward, 2007, pg 212)
Enzymes Bind With a Substrate
 The name of enzymes usually end in –ase.
 The substrate is the reactant that an enzyme acts on when it catalyzes a chemical
reaction.
 Enzymes are substrate specific – they will only work with one particular reactant.
 For example, enzymes that break down proteins will not break down starch.
 The substrate binds to a particular site on the enzyme called the active site.
 Active sites match the shape and chemical properties of their substrates. Molecules of
substrate fit the active site and are chemically attracted to it.
 A substrate must fit into an active site, much like a lock-and-key situation. Once the
substrate (key) is in place in the enzyme (lock) the chemical reaction can begin.
 induced-fit model: a model of enzyme activity that describes an enzyme as a dynamic
protein molecule that changes shape to better accommodate the substrate.
 the attachment of the substrate to the enzyme’s active site creates the enzymesubstrate complex.
 See Figure 1.29, pg 37
Enzymes
 Polar and non-polar amino acids are important in determining the specificity of active
sites in enzymes.
 Active sites are substrate-specific meaning that only certain substrates can combine with
particular active sites.
 This combination relies on the general shape and polar properties of the substrate and of
the amino acids exposed at the active site.
 Polar amino acids within the active site of an enzyme allow a chemical interaction
between the substrate and the enzyme to form an enzyme-substrate complex. This
weakens the internal molecular structure and therefore reduces the activation energy.
(Damon, McGonegal, Tosto, Ward, 2007, pg 209), (Burrell, J. G. (2002-11) Click4Biology
(version 0820.2011). Thailand: Bangkok; URL http://click4biology.info)
Induced-Fit Model
 Recent knowledge about enzyme action has found that the lock and key model does not
fully explain the binding of the substrate to the active site.
 As the substrate approaches the active site and binds to it, the shape of the active site
changes and only then does it fit the substrate.
 induced-fit model: a model of enzyme activity that describes an enzyme as a dynamic
protein molecule that changes shape to better accommodate the substrate.
 The change in shape is due to changes in the R-groups of the amino acids at the active
site of the enzyme as they interact with the substrate.
 Mechanism of enzyme action:
1)
The surface of the substrate contacts the active site of the enzyme.
2)
The enzyme changes shape to accommodate the substrate.
3)
A temporary complex called the enzyme-substrate complex forms.
4)
Activation energy is lowered and the substrate is altered by the rearrangement of
existing atoms.
5)
The transformed substrate (the product) is released from the active site.
6)
The unchanged enzyme is then free to combine with other substrate molecules.
E + S  ES  E + P
E is the enzyme, S is the substrate, ES is the enzyme-substrate complex, P is the product
(Damon, McGonegal, Tosto, Ward, 2007, pg 211), (Allott, 2007, pg 69)
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Thousands of different chemical reactions must occur in cells to make life possible. Each
reaction requires its own specialized enzyme in order to proceed efficiently.
Cellular respiration and photosynthesis are both complex metabolic processes that
involve many reactions and therefore many enzymes.
Some enzymes require cofactors and coenzymes to catalyze a chemical reaction.
Cofactors are inorganic metal ions (e.g., iron and zinc) that help enzymes function
properly by accepting or donating atoms to the reactions.
Other enzymes need assistance of coenzymes, which are organic non-protein molecules
such as vitamins.
Factors Affecting Enzyme Activity
Effects of Temperature
 Enzyme activity increases as temperature increases. This is because collisions between
substrate and active site happen more frequently at higher temperatures due to faster
molecular motion.
 At high temperatures enzymes are denatured and stop working. This is because heat
causes vibrations inside enzymes which break bonds needed to maintain the structure of
the enzyme. The enzyme loses its three-dimensional shape.
(Allott, 2007, pg 19)
 Every enzyme has an optimal temperature at which it works best. Enzyme activity
decreases above and below the optimal temperature. Most human enzymes work best at
around 37oC.
Effects of pH
 At the optimal pH, the maximum rate of reaction is achieved.
 Above and below the optimal pH the rate decreases.
 The change in rate is because bonds are made and broken which change the shape of
the active site and therefore, decrease the rate of reaction.
 Different enzymes have very different optimal pH in which they work best.
 See Figure 1.30, pg 39
Effects of Concentration
 Enzyme activity increases as the substrate concentration increases because the
enzyme and the substrate encounter each other more frequently.
 After a certain point, adding more substrate does not increase the reaction rate because
all the enzymes are saturated (most active sites are oppucied) with substrates and
cannot work any faster.
Denaturation
 Denaturation is changing the structure of an enzyme (or other protein) so that it can no
longer carry out its function. Denaturation is usually permanent.
 Under extreme temperatures or pH conditions, denaturation can occur because of the
disruption in the bonding of the functional groups affecting the enzyme’s shape and
function.
(Carter-Edwards, Gerards, Gibbons, McCallum, Noble, Parrington, Ramlochan, Ramlochan,
2011), (Allott, 2007, pg 18)
Metabolic Pathways
 Here is an example of a very simple generalized metabolic pathway.
substrate A  substrate B  final product
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Each arrow represents a specific enzyme that causes one substrate to be changed to
another until the final product is produced.
Some metabolic pathways consist of cyclic pathways instead of chains of reactions.
Other involve a combination of both cyclic and chains of reactions.
(Damon, McGonegal, Tosto, Ward, 2007, pg 210-211)
Competitive Inhibition
 Competitive inhibitors – enter the enzyme’s active site and block the normal substrate
from binding.
 The substrate and inhibitor are chemically similar.
 This results in the substrate not being able to enter active site as often and the rate of
chemical reaction is decreased.
 One way to overcome competitive inhibition is to increase the substrate concentration.
When the substrate binds to the active site, the inhibitor cannot bind, so the proportion
of enzyme molecules that are inhibited is reduced.
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
Example:
Succinate is converted to fumerate by succinate dehydrogenase.
Succinate dehydrogenase
Succinate ---------------------------------------- Fumarate
o Succinate dehydrogenase can be inhibited by a later intermediate in the cycle called
malonate.
(Damon, McGonegal, Tosto, Ward, 2007, pg 212), (Allott, 2007, pg 70), (Burrell, J. G. (200211) Click4Biology (version 0820.2011). Thailand: Bangkok; URL http://click4biology.info)
Noncompetitive Inhibition
 Noncompetitive inhibitors – attach to an allosteric site (other site on the enzyme –
not the active site), causing a change in the enzyme’s shape. This changes the active
site in such a way that it loses affinity for its substrate.
 The substrate and the active site are not similar.
 Example:
 Metallic ions, such as mercury, binding to the sulfur groups of component amino acids of
many enzymes. This changes the shape of the protein which causes inhibition of the
enzyme.
 Example:
 Inhibition by metal ions, such as silver (Ag+).
 Silver ions inhibit the formation of sulphide brides at the amino acid cysteine. This
changes the protein bonding and in turn the active site changes preventing the substrate
from attaching.
(Damon, McGonegal, Tosto, Ward, 2007, pg 212), (Allott, 2007, pg 70), (Burrell, J. G. (200211) Click4Biology (version 0820.2011). Thailand: Bangkok; URL http://click4biology.info)
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See Figure 1.31, pg 40
End-Product Inhibition or Feedback Inhibition
 End-product inhibition helps regulate biochemical pathways by ensuring that only the
necessary products of a pathway are produced. It prevents the cell from wasting
chemical resources and energy by making more of a substance than it needs.
 The product of the last reaction of a pathway acts as a non-competitive inhibitor of the
enzyme that is involved in the reaction at the beginning of the pathway.
 When enough product is available, its synthesis and all the reactions related to its
synthesis are turned off or reduced.
 As the end-product gets used up by the cell, the first enzyme is reactivated.
 The enzyme that is inhibited and reactivated is an allosteric enzyme.
 When concentrations of the end-product are high, it binds with the allosteric site of the
first enzyme – causing inhibition to occur.
 When concentrations of the end-product are low, it binds less often with the allosteric
site of the first enzyme – causing activation of the enzyme.
(Carter-Edwards, Gerards, Gibbons, McCallum, Noble, Parrington, Ramlochan, Ramlochan,
2011, pg 40), (Damon, McGonegal, Tosto, Ward, 2007, pg 213)
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Activator molecules can also bind to an allosteric site.
An activator keeps an enzyme active or causes an increase in the activity of that enzyme.
HOMEWORK:
pg 42 #1-12