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2 CHEMICAL FOUNDATION OF LIFE

2.1 Properties of water

•biological medium on Earth


•Cells surrounded by water (70-
95%)
•main reason the Earth is
habitable

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2.1.1 Polarity of water and hydrogen
bonding

• a polar molecule

• form hydrogen bonds


with each other

2
• Oxygen is mo re e le ctro negative
than hydrogen
• Oxygen – 2 partial negative charge (δ-)

• Hydrogen - partial positive charge (δ+)


• negative and positive attract each
other.
• forces of attraction (between water
molecules) = hydrogen b onds.
(pg.47-48)

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2.1.2 Heat Capacity

• Specific heat - amount of heat that


must be absorbed or lost for 1 gram of
that substance to change its
temperature by 1ºC
• minimizes temperature fluctuations
• Heat is absorbed
• Heat is released

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Importance
• heats up more slowly & hold its
temperature longer
• major component in bodies of living
organisms
• Biochemical reactions
• Aquatic environments have relatively
stable temperatures.
(previous notes)

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2.1.3 Heat of vaporization

• transformation of a substance from


liquid to gas
• the heat a liquid must absorb for 1
gram to be converted to gas
• remaining surface cools - evaporative
cooling
• helps stabilize temperatures

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Importance
• cooling mechanism during sweating
and during transpiration.
• Large amount of heat is lost during
evaporation - minimal lost of water
(previous notes)

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2.1.4 Density

• Ice floats - hydrogen bonds more


“ordered,” making ice less dense
(Figure 3.5, pg.50 - 51)

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• Density of water decreases - between 4
°C and 100°C.
• density of water increases - between 0°
C and 4°C.
• Maximum density is at 4°C
• liquid water - hydrogen bonds are not
stable, constantly break and reform
• Below 0ºC (H bonds are more stable); H
bonds are locked into crystal
latticework (molecules relatively far) to
form ice (less dense and float)
(previous notes)
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2.1.5 Solvent Properties

• versatile solvent due to its polarity


• an effective solvent - forms hydrogen
bonds
• ion is surrounded by a sphere of water
molecules, a hydration shell
(Figure 3.6, pg.51)
• dissolve nonionic polar molecules
• Hydrophilic- has an affinity for water
• Hydrophobic- does not have an affinity
for water
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2.1.6 Adhesion and Cohesion

• Cohesion- hydrogen bonds hold water


molecules together
• Plants- helps transportation of water
against gravity
• Adhesion of water to plant cell walls
also helps to counter gravity
• Surface tension - measure of how hard
it is to break the surface of a liquid
• related to cohesion
(Figure 3.3 & 3.4, pg.48-49)
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Importance
• aquatic organisms to land and “walk” on
water.
– Water sticks strongly to most surfaces.
Capillary action
- glass tube with a narrow diameter is
placed in a beaker of water, the water will
rise in the tube.
– Adhesion of water to the glass surface
pulls the water upward because an
adhesive force is stronger than the force of
gravity.
(previous notes)

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2.1.7 Viscosity

• a measure of a fluid's resistance to


flow
• very low viscosity.
Importance
• Transport systems of living organisms.
• For example, blood is mostly water -
can flow easily through vessels.
• flow of water in xylem and phloem to
transport substances.
• Less energy used by aquatic organisms
when swimming in water.
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2.1.8 Other properties

• Colorless and transparent:


Transmission of sunlight is possible –
aquatic plants can photosynthesize.
• Difficult to compress: Important
structural agent - hydrostatic skeleton.
• Involved in many chemical reactions:
Major raw material for photosynthesis;
takes part in digestive reactions,
breaking down food molecules by
hydrolysis.
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2.2 The Chemistry of Carbon
2.2.1 Definition of organic compound

• Organic compounds = compound


containing carbon, can come from
living and non-living sources
• Cells- carbon-based compounds
• unparalleled
• ability to form large, complex, and
diverse molecules
• Proteins, DNA, carbohydrates

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2.2.2 Structure of carbon and formation
of covalent bond in carbon
• Electron configuration
• four valence electrons - can form four
covalent bonds
• tetravalence makes large, complex
molecules possible
• covalent compatibility with many
different elements
• Carbon chains - skeletons of most
organic molecules

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• vary in length and shape
(Figures 4.3, 4.4, 4,5, pg. 60-61)

• properties of organic –carbon skeleton


& component attached to it

• Functional groups- components of


organic molecules involved in chemical
reactions

• The number and arrangement of


functional groups- unique properties
(Figure 4.10, pg. 64-65)

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2.2.3 Macromolecules

• larger molecules
• composed of thousands of covalently
connected atoms
• Polymer- long molecule consist of building
blocks called monomers
• polymers:
– Carbohydrates
– Proteins
– Nucleic acids
• Monomers form larger molecules-
condensation (dehydration reaction)
• Polymers are disassembled to monomers-
by hydrolysis (Figure 5.2, pg. 69)

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2.3 Important Organic Compounds
2.3.1 Carbohydrates

• sugars and the polymers of sugars


• Simplest- monosaccharides, or single sugars
• Macromolecules- polysaccharides
• Monosaccharides - molecular formulas (CH2O)
• Glucose- common monosaccharide
• classified by carbonyl group location and
number of carbons
• major fuel for cells and raw material for
building molecules
• linear skeleton
• Ring form

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•A disaccharide - dehydration reaction
joins two monosaccharides
•covalent bond - glycosidic linkage

Dehydration reaction
in synthesis
of maltose

glucose glucose maltose

Dehydration reaction
in synthesis
of sucrose

glucose fructose sucrose

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• Polysaccharides - polymers of sugars
• storage and structural roles
• determined by its monomers and
positions of glycosidic linkages
• storage polysaccharide
1 plants- starch - consists entirely of
glucose monomers (α- glycosidic)
2 animals- glycogen (α- glycosidic)
(Figure 5.6, pg.72)

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• Cellulose- component of plant cell wall
• polymer of glucose, but the glycosidic
linkages differ (β- glycosidic)
• Difference - based on two ring forms for
glucose: alpha (α) and beta (β)
• alpha glucose are helical
• beta glucose are straight
• straight structures, H atoms on one strand
can bond with OH groups on other strands
• Parallel cellulose- grouped into microfibrils,
- strong building materials for plants
(Figure 5.7 & 5.8, pg. 73)

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• Enzymes that hydrolyzing alpha
linkages can’t hydrolyze beta linkages
in cellulose
• Cellulose- insoluble fiber
• Herbivores -have symbiotic
relationships with microbes to digest
cellulose
• Chitin - exoskeleton of arthropods
• provides structural
• cell walls of many fungi
• used as surgical thread

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2.3.2 Lipids
• large biological molecules
• not form polymers
• little or no affinity for water
• Hydrophobic- hydrocarbons,
nonpolar covalent bonds
• Lipids - fats, phospholipids, and
steroids
• Fats - constructed from two types
of smaller molecules: glycerol and
fatty acids
28
• Glycerol- three-carbon alcohol with a
hydroxyl group attached to each
carbon
• fatty acid- a carboxyl group attached to
a long carbon skeleton
• Fats separate from water because
water molecules form hydrogen bonds
with each other and exclude the fats
• triacylglycerol, or triglyceride - three
fatty acids joined with glycerol by an
ester linkage (Figure 5.11, pg.75)

29
Use of Triglycerides
• Energy source; Energy used as ATP
during respiration.
• Energy store; 38 kJ per g.
• Stored as insoluble droplets inside
cells or in adipose tissues (mammals).
• Adipose tissue – heat insulator.
• Fats – bad conductor of heat.
• Shock absorption.
• Buoyancy for aquatic organisms.
• Fats – relatively low density
(previous notes)
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• Saturated fatty acids - maximum
number of hydrogen atoms possible
and no double bonds
• Unsaturated fatty acids - one or more
double bonds
• Function - energy storage
• Fats made from saturated fatty acids
-saturated fats

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• animal fats - saturated
• solid at room temperature
• diet rich in saturated fats-
cardiovascular disease
• Fats made from unsaturated fatty acids
- unsaturated fats
• Plant fats and fish fats- unsaturated
• liquid at room temperature (oil)
(Figure 5.12, pg. 75)

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• Phospholipid - two fatty acids and a
phosphate group are attached to
glycerol
• fatty acid tails – hydrophobic
• phosphate group and its attachments
-hydrophilic head

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• structure of phospholipids - bilayer
arrangement
• Phospholipids- major component of all
cell membrane
• Example of phospholipid in cell
membrane : lecithin
(Figure 5.14, pg.77)

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• Steroids- a carbon skeleton consisting
of four fused rings
• important steroid- cholesterol
• component in animal cell membranes
• essential in animals
• high levels in the blood may contribute
to cardiovascular disease

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Importance:
• Raw material for manufacturing of vitamin D
• Component of mammalian membrane cells –
strengthens membranes at high body
temperatures.
• Steroid abuse
Example: Anabolic steroids
• Synthetic androgens (male reproductive
hormones)
Used especially by sportsmen to increase:
• Muscle mass (to “bulk up”)
• Physical strength
• Endurance
• Aggressiveness

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Signs of abuse:
• Mood swings
• Suicidal thoughts or suicide attempts
• Restlessness
• Fatigue, sleeplessness
• Loss of appetite
Changes in physical appearance:
• In males - baldness, impotence, Shrinking
testes and development of breasts
• In females - growth of facial hair, deepening
of the voice, and reduction of breast size
• In both sexes - acne, oily hair and skin, cysts,
jaundice (yellowing of the skin) swelling of
feet and ankles, aching joints, bad breath,
nervousness and trembling
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• Risks from taking steroids:
– Possibility of heart attack and
stroke.
– Increase in anger, hostility and
violent behavior.
– Increased risk of getting AIDS from
sharing needles

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2.3.3 Protein
• 50% of the dry mass of most cells
• structural support, storage, transport,
cellular communications, movement,
and defense against foreign
substances
• consists of one or more polypeptides
• Polypeptides - polymers of amino acids
• organic molecules with carboxyl and
amino groups
• properties due to differing side chains,
called R groups
• Cells use 20 amino acids to make
thousands of proteins
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α
carbon

Amino Carboxyl
Group Group

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Example of amino acid based on the side chain:
• polar, eg: Serine
• non polar, eg: glycine
• acidic, eg: aspartic acid
• basic, eg: lycine

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Pro pertie s of A mino Acids
• Amphote ric - both acidic and basic
properties.
• zw itterio ns in water.
• carries both positive charge (-NH3+)
and negative charge (-COO-) at a
specific pH(7.4)
Amino and carboxyl groups ionization in
solution:
• -COOH ↔ -COO- + H+ (donates H+)
• -NH2 + H+ ↔ -NH3+ (accepts H+)

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• Amino acids- linked by peptide bonds
• Polypeptide- polymer of amino acids
• range in length
• Each polypeptide - unique linear
sequence of amino acids
(Figure 5.18, pg.80)

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Protein Structure
• primary structure - sequence of amino
acids
• Secondary structure - found in most
proteins, coils and folds in the
polypeptide chain
• Tertiary structure - interactions among
various side chains (R groups)
• Quaternary structure - consists of
multiple polypeptide chains

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• Primary structure - inherited genetic
information
• coils and folds of secondary structure
result from hydrogen bonds between
repeating constituents of the
polypeptide backbone
• a coil - alpha helix
• a folded - beta pleated sheet

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• Tertiary structure - interactions
between R groups
• include hydrogen bonds, ionic bonds,
hydrophobic interactions, and van der
Waals interactions
• Strong covalent bonds- disulfide
bridges may reinforce the protein’s
conformation
• Quaternary structure - two or more
polypeptide chains form one
macromolecule

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• Collagen - fibrous protein consisting of
three polypeptides coiled like a rope
• Hemoglobin - globular protein
consisting of four polypeptides: two
alpha and two beta chains
(Diagram: Levels of protein structure,
pg.82-83)
Types of bond in protein structure:
• hydrogen bonds, ionic bonds,
disulphide bonds, hydrophobic
interactions & van der Waals
interactions
47
Fibrous and Globular Protein
• Fibrous - elongated molecules,
secondary structure - dominant
structure.
• insoluble, supportive role in the body,
and involved in movement (as in
muscle and ciliary proteins). 
• often have regular repeating
structures.
Example:
i.Keratin which is a helix of helices (2
pairs of α-helices wound around one
another) consisting of 7repeating
amino acid
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ii.Silk which is composed of only
β-sheets (glycine-alanine-serine
repeats)
• Globular - soluble and form spheroidal
molecules in water
• typically consist of relatively straight
runs of secondary structure joined by
stretches of polypeptides that
abruptly change direction. 
Example:
– Enzymes, transport proteins and
receptor proteins
– Myoglobin
49
• physical and chemical conditions can
affect conformation
• pH, salt concentration, temperature, or
other environmental factors - protein to
unravel
• denaturation
• protein is biologically inactive

Denaturation

Renaturation Denatured protein


Normal protein

50
2.3.4 Nucleic Acid
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• polynucleotides
• made of monomers called nucleotides
• Each nucleotide - a nitrogenous base, a
pentose sugar, and a phosphate group
• without the phosphate group
-nucleoside

51
• Nucleotide monomers - nucleosides
and phosphate groups
• Nucleoside = nitrogenous base + sugar
• two families of nitrogenous bases:
– Pyrimidines - single six-membered
ring
– Purines - six-membered ring fused to
a five-membered ring
• DNA - deoxyribose
• RNA - ribose

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• Nucleotides - phosphodiester linkages
between the —OH group on the 3’
carbon of one nucleotide and the
phosphate on the 5’ carbon of the next.

• Refer these as the 5’ end and the 3’


end, respectively.

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The DNA double Helix

• 1953 - James Watson and Francis Crick,


proposed the double helix as the three-
dimensional structure of DNA
• DNA double helix - two backbones run in
opposite 5´ to 3´ directions from each other -
antiparallel
• sugar-phosphate backbones are on the
outside of the helix, and the nitrogenous
bases are paired in the interior of the helix.
• two polynucleotides, or strands, held together
by hydrogen bonds between the paired bases
and by van der Waals interactions between
the stacked bases.

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Chargaff’s rules of complimentary base
pairing:
• A with T: the purine adenine (A) always
pairs with the pyrimidine thymine (T)
• C with G:  the pyrimidine cytosine (C)
always pairs with the purine guanine
(G)
• 2 H bonds between A–T; 3 H bonds
between C–G

57
RNA (structure mRNA & tRNA, pg.320-
321)
• mRNA - delivers the information
encoded in genes from DNA to
ribosome, a specialized structure, or
organelle, where that information is
decoded into a protein.
• tRNA – serves as adapter molecule in
protein synthesis; translates mRNA
codons into amino acids.
• rRNA - are the structural components
of the ribosome - active role in
recognizing conserved portions of
mRNAs and tRNAs - assist protein
synthesis. 58
2.4 Techniques of Analysis
2.4.1 Chromatography
• separate and analyze complex
mixtures.
• involves a sample (or sample extract)
being dissolved in a mobile phase
(which may be a gas, a liquid or a
supercritical fluid).
• mobile phase is then forced through an
immobile, immiscible stationary phase.
• The phases are chosen such that
components of the sample have
differing solubilities in each phase.

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• A component which soluble in the stationary
phase - take longer to travel through it than a
component which is not very soluble in the
stationary phase but very soluble in the
mobile phase.
• differences in mobilities - sample components
will become separated from each other as
they travel through the stationary phase.
Paper chromatography (PC)
• stationary phase is liquid soaked into a sheet
or strip of paper
– mobile phase is a liquid solvent
– some components spend more time in the
stationary phase than others
– components appear as separate spots
spread out on the paper after drying or
"developing" 60
What is the Retention Factor, Rf?
• The retention factor, Rf, is a quantitative
indication of how far a particular compound
travels in a particular solvent.
• The Rf value is a good indicator of whether an
unknown compound and a known compound
are similar, if not identical.
• If the Rf value for the unknown compound is
close or the same as the Rf value for the
known compound then the two compounds
are most likely similar or identical.

61
• The retention factor,
Rf, is defined as
Rf = distance the
solute (D1) moves
divided by the
distance traveled by
the solvent front (D2)
• Rf = D1 / D2 where D1
= distance that color
traveled, measured
from center of the
band of color to the
point where the food
color was applied
• D2 = total distance
that solvent traveled
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2.4.2 Electrophoresis
• Electro refers to the energy of
electricity. Phoresis, from the Greek
verb phoros, means "to carry across.“
• This technique uses a gel as a
molecular sieve to separate nuclei
acids or proteins by size
(Figure 20.8, pg.393)

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Mixture Longer
of DNA molecules
Cathode molecules
of differ-
ent sizes

Shorter
Power molecules
source Gel

Glass
plates

Anode

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2.4.3 X-ray diffraction
• used to determine crystalline compound in
a given sample.
• The analysis is based on that X-ray will be
diffracted by crystal planed and minerals
can be identified by measuring this
diffraction at different angles.
• The diffraction pattern of unknown material
is compared with that of the reference
database in order to identify its chemical
compound.
• Each crystalline compound has its unique
characteristic X-ray pattern which may be
used as a fingerprint for its identification.

65
From diffraction patterns we can:
• measure the average spacings between
layers or rows of atoms;
• determine the orientation of a single crystal
or grain;
• find the crystal structure of an unknown
material; and
• measure the size, shape and internal stress of
small crystalline regions.
(example : Figure 5.24, pg.86)

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2.4.4 Centrifugation
• Cell fractionation takes cells apart and
separates the major organelles from
one another
• Ultracentrifuges fractionate cells into
their component parts
• enables scientists to determine the
functions of organelles
(Figure 6.5, pg.97)

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Tissue
cells Homogenization

Homogenate

Differential centrifugation

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1000 g
(1000 times the
force of gravity)
10 min
Supernatant poured
into next tube

20,000 g
20 min

80,000 g
60 min
Pellet rich in
nuclei and
cellular debris
150,000 g
3 hr
Pellet rich in
mitochondria
(and chloro-
plasts if cells
are from a plant)
Pellet rich in
“microsomes”
(pieces of plasma
membranes and
cells’ internal
membranes) Pellet rich in
ribosomes

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2.4.5 Microscopy
Light Microscopy
• visualize cells too small to see with the
naked eye
• light microscope (LM) - visible light
passes through a specimen and then
through glass lenses, which magnify
the image
• minimum resolution- 200 nanometers
(nm), the size of a small bacterium
(Figure 6.2, pg.95)

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• magnify effectively to about 1,000
times the size of the actual specimen
• Various techniques enhance contrast
and enable cell components to be
stained or labeled
• Most subcellular structures, or
organelles, are too small to be resolved
by a LM
(Figure 6.3, pg.96)

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Electron Microscopy
• used to study subcellular structures
• Scanning electron microscopes (SEMs)
focus a beam of electrons onto the
surface of a specimen, providing
images that look 3D
• Transmission electron microscopes
(TEMs) focus a beam of electrons
through a specimen
• TEMs are used mainly to study the
internal ultrastructure of cells
(Figure 6.4, pg.96)
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2.5 Enzyme
• catalytic protein - speeds up a
reaction without being consumed by
the reaction
Endergonic
• chemical reaction that consume/USE
energy
• product contain more energy than
reactant
Exergonic
• chemical reaction that release energy
• product contain less energy than
reactant
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2.5.1 Properties of enzyme

• Specific
• not destroyed by the reactions they
catalyzed
• Sensitive to high temperature and pH
• reversible
• can be inhibited

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2.5.2 Catalysis and activation energy
• chemical reaction- involves bond
breaking and bond forming
• initial energy needed to start a
chemical reaction - activation energy
(EA)
• in a form of heat from the surroundings
• Enzymes catalyze reactions by
lowering the EA barrier
• Enzymes do not affect the change in
free-energy (∆G)

75
Course of EA
reaction without
without enzyme
enzyme EA with
enzyme
is lower
Reactants
Free energy

Course of ∆G is unaffected
reaction by enzyme
with enzyme

Products

Progress of the reaction

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2.5.3 Mechanism of action and kinetics
• Substrate - reactant that an enzyme
acts on
• enzyme binds to its substrate - enzyme-
substrate complex
• active site - region on the enzyme
where the substrate binds
• Induced fit of a substrate brings
chemical groups of the active site into
positions that enhance their ability to
catalyze the reaction
(Figure 8.16 & 8.17, pg.153)
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2.5.4 Factors affecting enzyme activity
– General environmental factors, such
as temperature and pH
– Chemicals that specifically influence
the enzyme
• optimal temperature
• optimal pH
(Figure 8.18, pg.154)

79
2.5.5 Inhibitor
• interfere, reduce or destroy enzyme
activity
Competitive inhibitors
• bind to the active site of an enzyme,
competing with the substrate
• has shape resemble enzyme’s
substrate
• inhibitor occupy the site - prevent
enzyme from combine with substrate,
no product is generating.
• Reversible
(Figure 8.19, pg.155)
80
Noncompetitive inhibitor
• bind to another part of an enzyme -
enzyme to change shape and active
site less effective
• Irreversible – example: toxin and
poisons (bind permanently)
• Reversible – allosteric regulation
• Allosteric regulation - protein’s
function at one site is affected by
binding of a regulatory molecule at
another site
• inhibit or stimulate an enzyme’s
activity
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Example of allosteric inhibition:
Feedback inhibition
• end product of a metabolic pathway
shuts down the pathway
• prevents a cell from wasting chemical
resources by synthesizing more
product than is needed
(Figure 8.21, pg.157)

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2.5.6 Enzyme cofactors
• Non-protein enzyme helpers (pg.155)

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2.5.7 Nomenclature of enzymes (IUB)
• Produced by the Nomenclature
Committee of the International Union
of Biochemistry and Molecular Biology
(NC-IUBMB), in consultation with the
IUPAC-IUB Joint Commission on
Biochemical Nomenclature (JCBN)
• Enzyme Nomenclature is a resource
providing general information on
enzyme nomenclature.

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2.5.8 Enzyme technology

• Biosensor- analytical device which


converts a biological response into an
electrical signal
• cover sensor devices used in order to
determine the concentration of
substances and other parameters of
biological interest even where they do
not utilise a biological system directly.

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• The biocatalyst must be highly specific for
the purpose of the analyses, be stable under
normal storage conditions.
• The reaction should be as independent of
such physical parameters as stirring, pH and
temperature as is manageable. This would
allow the analysis of samples with minimal
pre-treatment.
• The response should be accurate, precise,
reproducible and linear over the useful
analytical range, without dilution or
concentration.
• The complete biosensor should be cheap,
small, portable and capable of being used by
semi-skilled operators.

87
Schematic diagram showing the main components of a biosensor.
The biocatalyst (a) converts the substrate to product.
This reaction is determined by the transducer (b)
which converts it to an electrical signal.
The output from the transducer is amplified (c),
processed (d) and displayed (e).

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• Immobilized enzyme - an enzyme that is
physically attached to a solid support over
which a substrate is passed and converted to
product.
• advantages
• Multiple or repetitive use of a single
batch of enzymes
• The ability to stop the reaction rapidly by
removing the enzyme from the reaction
solution (or vice versa)
• Enzymes are usually stabilized by
bounding
• Product is not contaminated with the
enzyme  (especially useful in the food
and pharmaceutical industries)

89
• Application: example, lactose hydrolysis
• The main purpose of using immobilized
enzymes here is to convert the disaccharide
lactose via hydrolysis into its
monosaccharide components, glucose and
galactose.
• Lactose is a disaccharide that occurs
naturally in both human and cow's milk. It is
widely used in baking and in commercial
infant-milk formulas.
• One large problem with lactose is that many
people are lactose intolerant - meaning that
their body is incapable of digesting lactose.
• So it must be hydrolyzed into its
monosaccharide components, allowing
digestion which is the purpose of products
today such as LACTAID. 90