BIOLOGICAL

MOLECULES
 TOPICS
• Structure and Functions of Biological Molecules
– Carbohydrates
– Lipids
– Proteins
– Enzymes
– Nucleic acids
 Learning Competencies
(objectives)
• Categorize the biological molecules (lipids, carbohydrates,
proteins, and nucleic acids) according to their structure and
function
• Explain the role of each biological molecule in specific metabolic
processes
• Describe the components of an enzyme
• Explain oxidation and reduction reactions
• Determine how factors such as pH, temperature and substrate
concentration affect enzyme activity
 Monomers, polymers, and
macromolecules
Key terms
• Molecule  a particle made of two or more atoms
bonded together
• Macromolecules  “Macro”  big or up close
– Big molecules, many can be seen by the naked eye
• Micromolecules  “Micro”  very small
– Very small molecules, cannot be seen by the naked eye or
even under the microscope
• Polymer  “Poly” means “ many”. “Mer” = unit
– Long and complex molecule composed of small molecules
called monomers bonded together in repetitive ways
• Monomers  “Mono” means one or alone
– Basic units / building blocks of polymer
 Categories of Macromolecules
There are 4 categories of macromolecules:
• Carbohydrates
• Proteins,
• Lipids,
• and Nucleic acids
 Important properties of
macromolecules you need to
familiarize
• What they are made up of
• their polarity
• The type and strength of interaction they
utilize
• their structure, size and shape
• Their classifications
• Their importance in the body
 Carbon is the central element
• All biomolecules contain a Carbon chain or ring
• Carbon has 4 outer shell electrons (valence = 4)
• Therefore it’s bonding capacity is great
• It forms covalent bonds –hence, has strong bonds
• Once bound to other elements (or to other Carbons), it is
very stable
 Special Catenation
• This is carbon’s special ability
• Catenation is the ability of an atom to form chemical bond
with another identical atom. Ex. C—C , H—H, O—O,
N—N.
• Aside from carbon, a handful other elements also have that
ability but its limited to two atoms
• As for carbon, this ability is almost unlimited!
• Thus, 10 million strong (and counting) compounds exist
today using catenated carbon atoms as their backbone.
This very large family of compounds is called organic
compounds
• And biomolecules belong to this family
 What are biomolecules?
• Molecules, almost all organic, that are
acquired, utilized or synthesized by a living
organism to the maintenance of its life
 Molecules of Life
• When atoms bond together, the result is a
molecule
• Biomolecules  special molecules needed for the
maintenance of life.
• Biochemistry  special field of chemistry that
study biomolecules
• Almost all biomolecules belong to a bigger family
of substances called organic compounds
 Atoms and Element
• Element  the simplest form of a substance. It can no longer be
broken down into simpler substances by any means
• Atoms  basic unit or basic building blocks of an element.
Identical atoms have identical properties, and they belong to the
same element
• Elements are divided into three groups: the metals, the metalloids
(also called semi-metals) and the non-metals.
• Metals have loose valence electrons and hence have reducing
property
• Non-metals have tight valence electrons and hence possess
oxidizing property
• Electronegativity  the measure of the capacity of an atom to
attract electron to itself. The more non-metallic is an atom, the
higher is the value of its electronegativity
 Chemical bond
• It is the “glue” that bonds atoms together to form a molecule
• There are 3 kinds of chemical bond
 Ionic bond
 Covalent bond
 Metallic bond
• Ionic bond  formed by transfer of electrons
• Covalent bond  formed by sharing of electrons
 Non-polar covalent bond  electrons are equally shared
 Polar covalent bond  electrons are unequally shared
• Metallic bond  formed between metal atoms
 Organic Compounds
• Organic compounds  compounds of carbon or compounds
containing carbon
• Compounds pure substances formed by two or more elements
• There are now 10 million organic compounds and counting
• Organic compounds are grouped into families
• Each organic compound family (also called organic family) has
identification mark: its functional group.
• Functional group  atom or group of atoms in the structure of an
organic compound that determines and controls the behavior,
properties and reactions of that organic compound
• Molecules belonging to the same organic family have the same
functional group. Molecules from different families have different
functional group
 Carbon binds to more than just
hydrogen!!
• To OH groups in sugars
• To NH2 groups in amino
acids
• To H2PO4 groups of
nucleotides of DNA,
RNA, and ATP

Amino acid

OH, NH2, PO4 are called ‘functional groups’!

Fig. 3.1

Functional groups:
Functional group  atom or group
of atoms in the structure of an organic
compound that determines and
controls the behavior, properties and
reactions of that organic compound

Some functional groups

• Multiple bonds (double &
triple bonds)
• Hydroxyl group
• Ether group
• Sulfhydril group
• Carbonyl group
• Carboxyl group
• Amino group
• Phosphate group
• Amide group
 Monomers and polymers
• Polymers  long and complex molecules made by linking simple,
small molecules together to form a chain
• Monomers are made into polymers via condensation reactions
• Polymers are broken down into monomers via hydrolysis reactions
• Many biomolecules have polymeric and monomeric form
Polymeric and Monomeric Forms
of Biomolecules
biomolecule Polymeric form Monomer Special bond that
connects monomers
Carbohydrates Polysaccharide Monosaccharide Glycosidic
• Ex. Starch, • Ex. Glucose, bond/linkage
cellulose, fructose,
glycogen ribose
Proteins Protein/polypeptides Amino acids Peptide bond/linkage
• Ex. Insulin, • Ex. Glycine,
muscle proteins alanine etc
Nucleic acid Nucleic acid Nucleotides Phosphodiester bond
/polynucleotides • Ex.
Ex. DNA, RNA Adenoside,
Lipids Up to few monomers Glycerol, fatty Ester bond/linkage
only acids
• Triglycerides
Fig. 3.3
Manufacturing sites of different
biomolecules inside the cell
• Nucleic acid (DNA & RNA)  nucleus
• Proteins  ribosomes
• Fats  smooth endoplasmic reticulum
• Carbohydrates  stroma of chloroplasts (for plants)
• Carbohydrates  smooth endoplasmic reticulum and
golgi apparatus (for animals)
– actually, these carbohydrates were just absorbed by animal cell, and
modified in this organelle to suit its need
CARBOHYDRATES
 Carbohydrates
• most abundant organic molecules in nature
• aldehyde or ketone derivatives of higher
polyhydroxy alcohols
• Cn(H2O)n
• “saccharides”; sugar
• hydrates of carbon
 Monosaccharides - simple sugars with
multiple OH groups. Based on number of
carbons (3, 4, 5, 6), a monosaccharide is a
triose, tetrose, pentose or hexose.
 Disaccharides - 2 monosaccharides
covalently linked.
 Oligosaccharides - a few monosaccharides
covalently linked.
 Polysaccharides - polymers consisting of
chains of monosaccharide or disaccharide
units.
 Functions of Carbohydrates
important source of energy production for living
cells. Providing 4 kcal/gram
 storage form of energy in the body (glycogen for
animals, starch for plants)
 cell membrane components that mediate some
forms of intercellular communication
(glycoprotein)
 structural component of many organisms
including the cell walls of bacteria, the
exoskeleton of many insects, and the fibrous
cellulose of plants
Important Monosaccharides

D-glucose, also known as

dextrose; found in large quantities
throughout the living world;
primary fuel for living cells.
In animals, it is the preferred energy
source of brain cells and cells that
have few or no mitochondria,
such as erythrocytes.
Dietary sources include plant starch
and the disaccharides lactose,
maltose, and sucrose.

24
 Important Monosaccharides

D-fructose, or levulose; CH 2OH

often referred to as fruit C O
sugar; also found in HO C H
some vegetables as well
H C OH
as honey; important
member of the ketose H C OH
family of sugars; on a per CH 2OH
gram basis, fructose is
twice as sweet as
sucrose; sperm use this D-Fructose
sugar as an energy
source.

3/24/2018 proteins, Fej Jose 25

Important Monosaccharides
Galactose – necessary to H
C
O

synthesize a variety H C OH
of biomolecules— HO C H
lactose, glycolipids, HO C H
phospholipids, H C OH
proteoglycans, CH 2OH
glycoproteins

3/24/2018 proteins, Fej Jose 26

Carbohydrates (or sugars)
• Simple sugars
(monosaccharides)
• Only one 3-C, 5-C, 6-
C chain or ring are
involved
 Monosaccharides involved in
biochemical rxns
• Triose (3 carbon monosaccharide)
– Glyceraldehyde Important intermediate products of
– Dihydroxyacetone metabolic pathways (ex. Glycolysis)
• Pentose (5 carbon monosaccharide)
– Ribose and deoxyribose  used to form nucleotides, ATP
– Ribulose  important intermediate in hexose
monophosphate shunt/pathway (or HMP)
• Hexose (6 carbon monosaccharide)
– Galactose, fructose, glucose  absorbed by small intestine
– Glucose  used in glycolysis
• Heptose (7 carbon monosaccharide)
– Heptose phosphate  important intermediate product in HMP
Fig. 3.5

Examples of monosaccharides*

*these are the important

monosaccharides
Important Disaccharides
• Maltose = Glucose + Glucose
• Maltose is the disaccharide of D- glucose having an a-linkage
• Maltose results from hydrolysis of starch by the enzyme diastase
– Maltose has a hemiacetal group in one glucose moiety; it is a reducing sugar
– The two glucose units of maltose are joined by an a-glucosidic linkage

• Lactose = Glucose + Galactose

milk sugar; composed of one molecule of galactose & glucose; β(1,4)
linkage

• Sucrose = Glucose + Fructose

• Sucrose is a disaccharide formed from D-glucose and D-fructose
– The glycosidic linkage is between C1 of glucose and C2 of fructose
– Sucrose is a nonreducing sugar because of its acetal linkage

3/24/2018 proteins, Fej Jose 30

 Carbohydrates (sugars)

• Double sugars
(disaccharides)
• Two 6-C chains or
rings bonded together
Structure of Lactose, a disaccharide

Structure of sucrose, another disaccharide

 OLIGOSACCHARIDES
composed of 2 -10
monosaccharide units

often found attached to

polypeptides in glycoproteins

attached to membrane and

secretory proteins found in the
endoplasmic reticulum

e.g. high mannose

3/24/2018 proteins, Fej Jose 32

 Polysaccharides
• used as storage forms of energy or as structural materials
• composed of large numbers of monosaccharide units
connected by glycosidic linkages
• may be divided into two classes:
• a. homopolysaccharides – composed of one type of
monosaccharide
• b. heteropolysaccharides – are high-molecular-weight
carbohydrate polymers that contain 2 or more types of
monosaccharide. Because many of the sugar residues are
amino derivatives, tese substances are often referred to as
glycosaminoglycans (GAG’s)

3/24/2018 proteins, Fej Jose 33

Homopolysaccharides

• Starch
Amylose
Amylopectin

• Glycogen

• Cellulose

3/24/2018 proteins, Fej Jose 34

Fig. 3.9
Polysaccharides
Starch structure vs Glycogen structure

• Starch  stored carbohydrates of plants

• Amylose  starch that is made of straight chains of glucose units
• Amylopectin  starch with branched structure
• Glycogen  stored carbohydrates of animals. Made and stored in
the liver. More branching & more complex compared to
amylopectin
Fig. 3.10

Polysaccharides: Cellulose structure

 Glycogen
• Glycogen is the major carbohydrate storage molecule in animals
• Glycogen is similar to amylopectin except that glycogen has far more
branching
– Branching occurs ever 10-12 glucose units in glycogen
• Glycogen is a very large polysaccharide
– The large size of glycogen prevents if from leaving the storage cell
– The storage of tens of thousands of glucose molecules into one
molecule greatly relieves the osmotic problem for the storage cell
(this would be caused by the attempted storage of many individual
glucose molecules)
– The highly branched nature of glycogen allows hydrolytic
enzymes to have many chain ends from which glucose molecules
can be hydrolyzed
• Glucose is the source of “ready energy” for the body
– Long chain fatty acids of triacylglycerols are used for long term
energy storage

3/24/2018 proteins, Fej Jose 37

 DIGESTION OF
CARBOHYDRATES
1. Digestion of carbohydrates begins in the
mouth
2. Further digestion of carbohydrates (by
pancreatic enzymes) occurs in the small
intestine
3. Absorption of monosaccharides (by
intestinal mucosal cells)

3/24/2018 proteins, Fej Jose 38

PROTEIN
 • Composed of chains
Proteins of amino acids
• 20 amino acids exist.
10 of which are called
essential amino acids
• Amino acid structure
has two parts: the
“head” and the “tail”
• The “head” of amino
acid is always polar
while the “tail” may
Protein = from the Greek be non-polar, polar but
word “proteus” w/c means
uncharged, acidic or
“first”
basic
 Proteins
Central “tail”
• The “head” of amino
Carbon
acids has the ff:
– Central Carbon
– Amine group
– Carboxyl group
– Alpha hydrogen
• All amino acids have
identical “head” but
Carboxyl
Amino
group
varied “tail”
group Alpha-
• Amino acids form
hydrogen
chain through their
“heads”
Fig. 3.20

The 20 Amino Acids

All differ with respect
to their R group
 Peptide bonds occur between amino acids
• The COOH group of 1
amino acid binds to
the NH2 group of
another amino acid

• Forms a peptide bond!

Fig. 3.21

The chain (polymer) of amino acids forms a variety of

loops, coils, and folded sheets from an assortment of
bonds and attractions between amino acids within the
chain(s)
 There are at least 9 functions of proteins

• Enzyme catalysts – specific for 1 reaction

• Defense – antibody proteins, other proteins
• Transport- Hgb, Mgb, transferrins, etc
• Support – keratin, fibrin, collagen
• Motion – actin/myosin, cytoskeletal fibers
• Regulation- some hormones, regulatory proteins on
DNA, cell receptors
• Storage – Ca and Fe attached to storage proteins
• Messenger  hormones, neurotransmitters
• Source of energy of last resort: 4 kilocalories/gram
Classification of amino acids based on
the properties of their “Tail”
1. Amino acids with non-polar
side chain
 Gly, Ala, Leu, Ileu, Met, Phe,
Pro, Trp, Val
2. Amino acids with polar but
uncharged side chain
 W/ OH = Thr, Tyr, Ser
 w/ SH = cysteine
 w/ amide = Asn, Gln
3. Amino acids with acidic
side chain
 Glut acid, Asp acid
4. Amino acids with basic side
chain
 Arg, Lys, His
Amino acids w/ interesting properties
• Glycine
– Smallest amino acid
– Does not have “tail”
– The only amino acid that does not have optical activity
– Causes bending in the polypeptide chain
• Cysteine
– Has sulfhydryl group in the “tail” (--S—H group)
– This tail forms very strong disulfide bond (--S—S--) with another
cysteine tail
– The more disulfide bond, the stronger is the protein
• Proline
– With imino group instead of amino group in the “head”
– Its “tail” attaches to its “head”
– Causes kink in the polypeptide chain
Glucogenic and ketogenic amino acids
• Amino acids can be metabolized to produce ATP by entering some
catabolic pathways
• Glucogenic A.A.  AA that can be used to synthesize glucose
• Ketogenic AA  AA that form ketone bodies when metabolized
• Ketone bodies  make fluid (including blood) acidic  acidosis
• Leu, ileu, trp, lys, tyr, phe  can enter kreb cycle via acetyl CoA
• Arg, pro, gln, his, glu  can enter kreb cycle via a-ketoglutarate
• Val, ileu, met, thr  can enter the kreb cycle via succinyl CoA
• Phe, tyr  can enter the kreb cycle via fumarate
• Asn, asp  can enter kreb cycle via oxaloacetate
• Gly, ser, trp, ala, cys  can be converted to pyruvate
• Only leucine is purely ketogenic. The rest are glucogenic
• 5 are both ketogenic and glucogenic  ileu, lys, phe, tyr, trp
STRUCTURE OF
PROTEIN
There are four levels of protein structure
• Primary = specific
sequence of amino acids
in the chain
• Secondary = the different
ways by w/c the chain
twists, folds and bends.
Forms pleated sheet, helix,
or coil
• Tertiary = 3D shape
formed by an entire length
of an AA chain
• Quaternary = several aa
chains or sequences linked
together
 Chemical Properties of Proteins
In protein hydrolysis, the reverse of protein
formation, peptide bonds are hydrolyzed to yield
amino acids.
 Denaturation: The loss of secondary, tertiary,
or quaternary protein structure due to
disruption of noncovalent interactions and/or
disulfide bonds that leaves peptide bonds and
primary structure intact.

Prentice Hall © 2007 Chapter Eighteen 52

• Agents that cause denaturation include heat,
mechanical agitation, detergents, organic solvents,
extremely acidic or basic pH, and inorganic salts.
• Heat: The weak side-chain attractions in globular
proteins are easily disrupted by heating, in many
cases only to temperatures above 50°C.
• Mechanical agitation: The most familiar example of
denaturation by agitation is the foam produced by
beating egg whites. Denaturation of proteins at the
surface of the air bubbles stiffens the protein and
causes the bubbles to be held in place.
• Detergents: Even very low concentrations of
detergents can cause denaturation by disrupting the
association of hydrophobic side chains.

Prentice Hall © 2007 Chapter Eighteen 53

• Organic compounds: Organic solvents can interfere
with hydrogen bonding or hydrophobic interactions.
The disinfectant action of ethanol results from its
ability to denature bacterial protein.
• pH change: Excess H+ or OH- ions react with the basic
or acidic side chains in amino acid residues and disrupt
salt bridges. An example of denaturation by pH change
is the protein coagulation that occurs when milk turns
sour because it has become acidic.
• Inorganic salts: Sufficiently high concentrations of
ions can disturb salt bridges.
• Most denaturation is irreversible. Hard-boiled eggs do
not soften when their temperature is lowered.
NUCLEIC ACID
 Nucleic acids: DNA and RNA
Structure of DNA
• DNA & RNA are both nucleic acids
• DNA = deoxyribonucleic acid
• RNA = Ribonucleic acid
• DNA is a double polymer (chain),
RNA is single chain polymer
• Each chain is made of nucleotides
• The 2 chains of DNA interact
together to form a double helix,
which looks like a long twisted
1st 2nd ladder
strand strand
 • Nucleotides are monomers
Nucleotides of nucleic acids
• The structure of a nucleotide
“head” may be divided into 3 parts:
“tail” “head”, “body” & “tail”
Nitrogen-
phosphat • The “head” refers to any of
“body” ous base
the ff 5 nitrogenous bases
e
– Adenine (A)
– Cytosine (C)
Pentose – Guanine (G)
sugar – Thymine (T) = for DNA only
– Uracil (U) = for RNA only
• The “body” refers to the
OH X pentose (5-carbon) sugar
– Ribose  for RNA
X = OH for Ribose
– Deoxyribose  for DNA
X = H for Deoxyibose • “tail” = phosphate group
 DNA nucleotides
• Each nucleotide in
“head”
“tail” DNA contains:
Nitrogen- – 5-C pentose sugar
phosphat “body” ous base (deoxyribose) (“body)
e
– Phosphate (“tail”)
– Nitrogen base (“head”)
Pentose
-adenine (A)
sugar
-guanine (G)
-cytosine (C)
OH X -thymine (T)
X = OH for Ribose
X = H for Deoxyibose
Fig. 3.14

One polymer of nucleotides on one “backbone” of nucleic acid

“heads” protruding at the

side of the backbond
Fig. 3.15

The DNA “double helix”

• Adenine will only interact w/
thymine
• Guanine will only interact w/
Cytosine
LIPIDS
 Lipids: Hydrophobic non-polar
molecules
• All insoluble in water
• Central backbone is glycerol, a 3-carbon compound
• Each carbon of glycerol can accept a fatty acid to form triglyceride
(also called fats and oil)
• They exhibit a high number of C-H bonds – therefore high energy
and non-polar
• When placed in water, lipids spontaneously cluster together
• They help organize the interior content of cells  “phospholipids”
• Some lipids do not use glycerol as backbone. A quite few do not
have fatty acid in their structure
• Lipids have variety of functions in the body, including insulation
(myelin sheaths in nerve cells) water proofing (waxes), regulation
(steroid hormones), but most are as stored energy (9 kcal/gram)
 Glycerol and fatty acid chains

Fatty
acid
chains

Glycerol
backbone
What specific bonds form between glycerol and each fatty acid
chain?  ans. Ester linkage
Would you think this to be an hydrolysis or a condensation rxn?
 ans. Condensation rxn forms the linkage
 Description of Fatty Acid
Palmitic acid, a 16-carbon saturated fatty acid

Carboxyl group “head” Hydrocarbon “tail”

• Fatty acid is a relatively long organic molecule with a “head” w/c is
made of carboxyl group and a “tail” of hydrocarbon
• Its “head” is polar while its “tail” is non-polar, therefore it is an
amphipathic molecule.
• A fatty acid is said to be saturated if there is no double bond in its tail.
If there is at least one, it is unsaturated.
• Its hydrocarbon “tail” is energy rich
• Hydrocarbon refers to an organic compound or portion of a compound
made purely of carbon and hydrogen.
 Saturated and unsaturated fats

Double
bonds form
kinks

• Saturated fatty acid = fatty acid w/ no carbon to carbon double bond/s

• Unsaturated fatty acid = w/ carbon-to-carbon double bond
• The more double bonds, the higher is the unsaturation
• Higher unsaturation = lower boiling pt and melting pt
Saturated vs unsaturated fats and diet
• Saturated fats raise LDL-cholesterol levels in the
blood (animal fats, dairy, coconut oil, cocoa butter)
• Polyunsaturated (2 double bonds) fats leave LDL-
cholesterol unchanged; but lower HDL-cholesterol
(safflower and corn oil)
• Monounsaturated (1 double bond) fats leave LDL and
HDL levels unchanged (olive oil, canola, peanut oil,
avocados)
• One variety of polyunsaturated fat (Omega-3 fatty
acids) guards against blood clot formation and reduce
fat levels in the blood (certain fish, walnuts, almonds,
and tofu)
• Omega-3 means there is a double bond at 3rd carbon
from the end of the molecule
 Phospholipids and cell membranes
• P-lipids make up the majority of cell
membranes including:
– The plasma membrane
– Nuclear envelope
– Endoplasmic reticulum (ER)
– Golgi apparatus
– Membrane-bound vesicles
Structure of single P-lipid

The 3 C’s of glycerol are bound to:

2 fatty acid chains
phosphate
Cell environment organizes P-lipid
bilayer to proper orientation

Hydrophilic (polar) “heads” of P-lipid oriented to the

exterior; hydrophobic (non-polar) “tails” oriented to
the interior
ENZYMES
 In the next slides we’ll be studying
enzymes. Enzymes in the body are used
in chemical reactions, and many of these
are reactions that extract energy from
biomolecules. These are redox reactions.
So before we proceed to enzymes, let us
first take a glimpse on an important kind
of chemical reactions called the REDOX
reactions.
 What is a Redox Reaction?
• Redox rxn refers to the inseparable pair of losing (oxidation) and
gaining (reduction) electrons as electrons are transferred from one
substance to another
– Oxidation = loss of electron/s
– Reduction = gain of electron/s
• When electrons are transferred from one substance to another, one
substance has to lose electrons (the donor) and the other substance has
to gain electrons (the recipient)
• A substance is said to be oxidized if it lost electrons in the transfer of
electrons in redox reactions
• A substance is said to be reduced if it gained electrons in the transfer of
electrons in redox reactions
• Oxidizing agents  are substances that tend to receive electrons.
They cause other substances to be oxidized (lose electrons)
• Reducing agents  are substances that tend to give away their
electrons. They cause other substances to gain electrons
• Reduction is the reverse of oxidation and vice versa
From his side
REDOX ANALOGY From her side
its oxidation its reduction

The donor The recipient

Reducing agent Oxidizing agent
oxidized reduced
 In a complex molecule, how would I
know if the flow of redox reaction is
that of oxidation or that of reduction?
• It is in the direction of oxidation if:
 The reactant has additional oxygen
atom/s as shown in the product
 The reactant lost hydrogen atom/s as
shown in the product
 Or both
• It is in the direction of reduction if:
 The reactant lost oxygen atom/s as
shown in the product
 The reactant has additional hydrogen
atom/s as shown in the product
 Or both
 Oxidation of methanol
( CH4O ) ( CH2O )
H O

H C OH + ½ O  C + H2O
Oxidizing
H H
H agent Reduced
form of
Oxidized
Reducing the
form of the
agent oxidizing
reducing
agent
agent
 Overall Equation for Cellular
Respiration of Glucose

C6H12O6 + 6O2
Loss of H Gain of H

YIELDS

6CO2 + 6H20 + e- + 36-38ATP’s

 10
Enzymes
• Enzymes are special proteins because they serve as catalysts
• Catalysts = special substances that can speed up chemical
reaction w/out themselves being transformed in the process
• Enzymes are also called biological catalysts because they
are used to catalyse biological reactions
• They are present in the cytoplasm of all cells
• There are hundreds of different enzymes but each one
speeds up only one kind of reaction
• Almost all enzymes have names ending in “ase”
• There are physical and chemical factors that can affect—
positively or negatively—the activity of an enzyme. The
chemical factors are collectively called as effectors.
• Enzymes can also be regulated. It can be activated and
deactivated.
• Enzymes can also be inhibited, temporarily or permanently
 Characteristics of Enzymes
• They all have a special portion where the catalytic activity takes
place. It’s called active site
– Active site is a pocket in the structure of an enzyme, a “mouth” of an
enzyme
– A substrate has to enter and attach itself inside the active site to be
transformed into a product
• Sometimes, enzymes also use “helpers” called cofactors
– There are three kinds of cofactors: inorganic ions, coenzymes and
prosthetic groups
– Coenymes and prosthetic groups are non-protein organic compounds.
Coenzymes can detach from enzymes but prosthetic groups cannot because
they are tightly bound
– Many coenzymes are made from vitamins
• Some enzymes have another important portion, called allosteric
binding site, where effectors attach to change the shape of the
“mouth” of an enzyme
 Catalytic activity is measured by turnover
number, the maximum number of substrate
molecules acted upon per enzyme per unit
time. Most enzymes turn over 10–1000
molecules per second.

Prentice Hall © 2007 Chapter Nineteen 79

Prentice Hall © 2007 Chapter Nineteen 80
 How do enzymes increase the speed of
reaction?
Intermediate • All organic rxns have to hurdle
product energy barrier to proceed
– Energy barrier is the difference in the
energy of the reactant and the
intermediate product
Energy
barrier • The higher the energy barrier, the
more difficult it is for the reaction to
Reactant take place, and the slower is the
process
• Enzymes lower the energy barrier
Intermediate product  by introducing a “detour”,
the unstable, temporary Product formation of a less energy-
semi-product formed
before it finally converts
demanding intermediate product,
into a final product the ES (enzyme-substrate) complex
 How Do Enzymes Work?
• Two models are invoked to represent the interaction
between substrates and enzymes.
• Historically, the lock-and-key model came first. The
substrate is described as fitting into the active site as a
key fits into a lock.
• Enzyme molecules are not totally rigid like locks. The
induced-fit model accounts for changes in the shape
of the enzyme active site that accommodate the
substrate and facilitate the reaction. As an enzyme
and substrate come together, their interaction induces
exactly the right fit for catalysis of the reaction.
 The induced-fit model model of enzyme action
has a flexible active site that changes shape to
best fit the substrate and catalyze the reaction.

Prentice Hall © 2007 Chapter Nineteen 83

 12
The substrate molecules fit the shape of the enzyme

enzyme

substrate A

substrate B
 13

Lock and key

model

Induced fit
model
 14

substrates combine temporarily with enzyme

Intermediate
ES Complex product w/
lower energy
demand

enzyme joins substrates together

 15
enzyme unchanged new compound released
and ready for by enzyme
next reaction
Effect of Concentration on Enzyme Activity
• Under most conditions the rate of an enzyme
catalyzed reaction is controlled by the amount of
substrate and the overall efficiency of the enzyme.
• If the enzyme–substrate complex is rapidly converted
to product, the rate at which enzyme and substrate
combine to form the complex becomes the limiting
factor.
• Enzyme and substrate molecules moving at random in
solution can collide with each other no more often
than about 108 collisions per (mole/liter) per second.
• One of the most efficient enzymes is catalase; this
enzyme can break down H2O2 at a rate of up to 107
catalytic events per second.
• At low substrate
concentration, the
reaction rate is directly
proportional to the
substrate concentration.
• With increasing
substrate concentration,
the rate drops off as
more of the active sites
are occupied.
• With all active sites
occupied, the rate
reaches a maximum.
• In the presence of excess
substrate, the
concentration of an
enzyme can vary
according to our
metabolic needs.
• If the concentration of
substrate does not
become a limitation, the
reaction rate varies
directly with the enzyme
concentration.
Prentice Hall © 2007 Chapter Nineteen 90
 Effect of Temperature and pH
on Enzyme Activity
• Enzyme catalytic activity is highly dependent on pH
and temperature.
• Optimum conditions vary slightly for each enzyme but
are generally near normal body temperature and the pH
of the body fluid in which the enzyme functions.
• Pepsin, which initiates protein digestion in the highly
acidic environment of the stomach, has its optimum
activity at pH 2.
• Trypsin, which acts in the alkaline environment of the
small intestine, has optimum activity at pH 8.
91
 (a) The rate increases with increasing temperature until
the protein begins to denature; then the rate decreases
rapidly. (b) The optimum activity for an enzyme
occurs at the pH where it acts.

Optimum temperature Optimum pH

Denaturation = alteration of the shape of protein w/out “cutting” it.
 Enzyme Regulation: Feedback and
Allosteric Control

• A variety of strategies are utilized to adjust the

rates of enzyme-catalyzed reactions.
• Any process that starts or increases the action of
an enzyme is an activation.
• Any process that slows or stops the action of an
enzyme is an inhibition.
• Feedback and allosteric control are two strategies
for enzyme regulation.

Prentice Hall © 2007 Chapter Nineteen 93

• Feedback control: Regulation of an enzyme’s
activity by the product of a reaction later in a
pathway.
• If a product near the end of a metabolic pathway
inhibits an enzyme that functions near the beginning
of that pathway, then no energy is wasted making the
ingredients for a plentiful substance.
• Allosteric control: An interaction in which the
binding of a regulator at one site on a protein affects
the protein’s ability to bind another molecule at a
different site.
• Allosteric control can be either positive or negative.
• Binding a positive regulator changes the active sites
so that the enzyme becomes a better catalyst and the
rate accelerates.
• Binding a negative regulator changes the active sites
so that the enzyme is a less effective catalyst and the
rate slows down.

Prentice Hall © 2007 Chapter Nineteen 95

 Enzyme Regulation: Inhibition
• Enzyme inhibition can be reversible or irreversible.
• In reversible inhibition, the inhibitor can leave,
restoring the enzyme to its uninhibited level of
activity.
• In irreversible inhibition, the inhibitor remains
permanently bound and the enzyme is permanently
inhibited.
• The inhibition can also be competitive or
noncompetitive, depending on whether the inhibitor
binds to the active site or elsewhere.
Prentice Hall © 2007 Chapter Nineteen 97
 A competitive inhibitor can eventually be overcome
by higher substrate concentrations. With a
noncompetitive inhibitor the maximum rate is
lowered for all substrate concentrations.

Prentice Hall © 2007 Chapter Nineteen 98

• Hg+2 and Pb+2 ions are irreversible inhibitors that
bond to the S atoms in cysteine residues.
• Organophosphorus insecticides such as parathion and
malathion, and nerve gases like Sarin are irreversible
inhibitors of the enzyme acetylcholinesterase.

Prentice Hall © 2007 Chapter Nineteen 99

 Enzyme Regulation: Covalent
Modification and Genetic Control
• There are two general modes of enzyme regulation
by covalent modification, removal of a
covalently bonded portion of an enzyme, or
addition of a group.
• Some enzymes are synthesized in inactive forms
known as zymogens or proenzymes, activation
requires a chemical reaction that splits off part of
the molecule.
• Genetic (enzyme) control: Regulation of enzyme
activity by hormonal control of the synthesis of
enzymes is especially useful for enzymes needed
only at certain times.
 Enzymes that cause blood clotting or digest
proteins are examples of enzymes that must
not be active at the time and place of their
synthesis.

Prentice Hall © 2007 Chapter Nineteen 101

 Glycogen phosphorylase, the enzyme that initiates
glycogen breakdown, is more active when
phosphorylated. When glycogen stored in muscles
must be hydrolyzed to glucose for quick energy, two
serine residues are phosphorylated. The groups are
removed once the need to break down glycogen for
quick energy has passed.

Prentice Hall © 2007 Chapter Nineteen 102

Thank you for
listening!