Download unit 2 – the chemistry of life

UNIT 2 – THE CHEMISTRY OF LIFE
(Chapters 2 – 5 and Chapter 8)
THEMES OF THE UNIT:
THEME 1 – SCIENCE AS A PROCESS – X-ray
crystallography helps scientists determine the 3D
structure of proteins and nucleic acids.
THEME 2 – EVOLUTION – Chemical evolution of the young
earth set the stage for the origin of live.
THEME 6 – REGULATION – In feedback inhibition, a
metabolic pathway is switched off by its end product.
THEME 7 – INTERDEPENDENCE – Prokaryotes play
essential roles in chemical cycling for plants and animals.
CHAPTER 2 – BASIC CHEMISTRY
YOU MUST KNOW:
 The three subatomic particles and their significance.
 The types of bonds, how they form, and their relative strength.
We will not spend any time on this chapter. If you are not familiar with
this, please check out the notes in your exam review book.
CHAPTER 3 – CHARACTERISTICS OF WATER
YOU MUST KNOW:
 The importance of hydrogen bonding to the properties of water.
 Four unique properties of water, and how each contributes to
life on Earth.
 How to interpret the pH scale.
 The importance of buffers in biological systems.
I. The Chemical Composition of Water
You must be able to draw the structural formula of water and
bind at least 4 water molecules together with hydrogen bonds.
Use proper chemical symbols not circles when you draw water.
II. The Characteristics of Water
Property of water
Ice is less dense than
water
Low viscosity
Liquid at room
temperature
Colorless with a high
transmission of visible
light
Strong adhesive and
cohesive forces
Water is classified as a
universal solvent
because many
substances can
dissolve in water
Significant amounts of
energy are required
before water will
change state (high
heat of fusion)
High heat of
vaporization
Structural
explanation
Ice takes on a more
regular, tetrahedral
structure so the
molecules are further
from each other
Small molecules
Significance for life
H-bonds
Heat is lost by
evaporation of water.
Sweating and
transpiration causes
rapid cooling.
Aquatic environments
are thermally stable.
Organisms have stable
internal temperatures
when external
temperatures
fluctuate.
Water forms droplets
Life under ice
Flows through very
small spaces,
capillaries
H-bonds
Medium for aquatic
life, inside cells
Small, stable molecule, Light penetrates
no excitable electrons
tissues and aquatic
environments
H-bonds
Water can be lifted and
does not pull apart
easily.
H-bonds, polar, small
Medium for the
molecules
chemical reactions of
life, main transport
medium
Hydrophilic and
hydrophobic
substances
H – bonds
Contents of cells are
unlikely to freeze.
Water can absorb a lot
of energy for only a
small rise in
temperature (high heat
capacity or specific
heat)
H – bonds
High surface tension
Close attraction
between water
molecules, H – bond
III.
on surfaces and runs
off.
Acids, Bases, pH, Buffers and Indicators
We will not spend any time on this section either. If you are not
familiar with this, please read your review book.
CHAPTER 4 – CARBON AND THE MOLECULAR DIVERSITY
OF LIFE
OBJECTIVES
YOU MUST KNOW:
 The properties of carbon that make it so important.
 The functional groups.
I.
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OVERVIEW
Every living organism is made up of chemicals based mostly on the
element carbon.
Carbon enters living organisms through plants via photosynthesis.
Other important elements in living organisms are:
o Oxygen
o Hydrogen
o Nitrogen
o Sulfur
o Phosphorous
II. CARBON COMPOUNDS AND FUNCTIONAL GROUPS:
 Organic compounds – molecules that contain carbon, except
carbonates, carbides, carbon dioxide and carbon monoxide.
 Special characteristics of carbon:
o Able to form long chains and rings
o Able to bind with other carbon atoms or other atoms in an
unlimited number
o Able to form stable covalent bonds (4 of them)
o Able to form double bonds and triple bonds
 Molecules that contain only hydrogen and carbon are called
hydrocarbons. Hydrocarbons are major components of petroleum
(fossil fuel) but not particularly important in living organisms.
 Functional groups (parts of organic molecules that are mostly
involved in chemical reactions that behave consistently in various
compounds and determine the chemical characteristics of those
compounds):
CHAPTER 5 – THE STRUCTURE AND FUNCTION OF
MACROMOLECULES
OBJECTIVE QUESTIONS:
YOU MUST KNOW:
 The role of dehydration synthesis in the formation of organic
compounds and hydrolysis in the digestion of organic
compounds.
 How to recognize the four biologically important organic
compounds (carbohydrates, lipids, proteins, nucleic acids) by
their structural formulas.
 The cellular functions of all four organic compounds.
 The four structural levels that proteins can go through to reach
their final shape (conformation) and the denaturing impact
that heat and pH can have on protein structure.
I.
OVERVIEW:
 A new level of hierarchy is reached when small molecules and
atoms combine to form very large molecules – macromolecules.
 The architecture (structure) of these molecules helps to
determine their function (how they work). – Theme of Biology
 The four major groups of macromolecule that are common in living
organisms are:
a. Nucleic acids
b. Carbohydrates
c. Lipids
d. Proteins
II.
MACROMOLECULES ARE BUILT FROM MONOMERS
 Three of the four groups of macromolecules (nucleic acids,
carbohydrates, proteins) are chains of smaller units called
monomers. When these chains combine, they form polymers – a
long molecule consisting of many similar or identical building
blocks linked together by covalent bonds.
 Some of the monomers have other functions. Example: some
amino acids are neurotransmitters or hormones, some nucleic
acids carry electrons, protons or high energy bonds.
 Condensation (dehydration) reaction – the chemical reaction
that connects monomers by covalent bonds to form polymers,
while water is released.
M – OH + H – M – M – M – OH → H2O + M – M – M- M – OH

Hydrolysis – Chemical reaction, in which polymers are
disassembled into their monomers. Water is inserted into the
reactants to get the products.
H2O + M – M – M- M – OH → M – OH + H – M – M – M – OH
 With the help of these reactions, a few monomers can give rise to a
huge number of polymers within each individual and among
species.
http://www.tvdsb.on.ca/westmin/science/sbioac/biochem/condense
.htm
III.
CARBOHYDRATES
 Include both sugars and the polymers of sugars. They are
molecules that contain carbon, hydrogen and oxygen
A. Monosaccharides
 The simplest form of carbohydrates are monosaccharides (CH2O),
the most important representatives of monosaccharides are
glucose (C6H12O6)
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Important functional groups in sugars are carbonyl group,
hydroxyl group.
Monosaccharides can be very diverse for three reasons:
o Location of the carbonyl group can be at the end of the chain
(aldose) or not at the end of the chain (ketose)
o Number of carbon atoms can vary (hexose, pentose, triose)
o Spatial arrangement of the parts of asymmetric carbon
atoms
Glucose as well as most monosaccharides form ring structures
Monosaccharides are generally used as sources of energy during
cellular respiration. If they are not immediately used than they are
stored as polysaccharides or disaccharides
B. Dissacharides:
 Molecules that consists of two monosaccharides joined by
glycosidic linkage (a covalent bond formed between two
monosaccharides by dehydration reaction)
 Most important representatives are:
o Maltose (two glucose) – ingredients of beer making
o Sucrose (glucose + fructose) – table sugar
o Lactose (glucose + galactose) – found in milk.
C. Polysaccharides:
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Macromolecules of a few hundred to a few thousand
monosaccharides joined by a glycosidic linkage
Most important representatives and their functions:
o Starch – a storage polysaccharide of plants that consists
entirely of glucose molecules that join by a 1-4 carbon
linkage by two α-glucose molecules. The molecule is helical.
Two subgroups of starches are amylose and amylopectin.
o Glycogen – a storage polysaccharide of animals that is like
amylopectin but more branched. In higher animals it is
mostly stored in the liver and the muscles.
o Cellulose – a structural polysaccharide that is the major
component of plant cell walls. A polymer of glucose
molecules but in this case the OH group on the first carbon
has a β orientation. This orientation results in long fiber-like
molecules that are very though. Enzymes in humans cannot
digest cellulose but can digest starch. Digestion of cellulose
in animals is frequently helped by microbes.
o Chitin – structural polysaccharide that is found in
arthropods shells (exoskeletons) and in many fungi.
IV. LIPIDS:
 These compounds are all hydrophobic and have little or no affinity
to water.
 They contain very few oxygen molecules but have long chains of
hydrocarbons.
 Their form and function varies greatly in each subgroup:
o Fats
o Phospholipids
o Steroids
A. FATS:
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These molecules are not polymers but large molecules that are
assembled from simpler units of 1 glycerol and 3 fatty acid
molecules by dehydration synthesis:
Important functional groups are hydroxyl and carboxyl groups.
But the long CH2 chains make the fats hydrophobic
 Fats vary in length and number of carbon atoms in the carbon
chain. They also can have varying number of double bonds. This
results in two types of fats:
o Saturated fats – don’t have any double bonds in the carbon
chain. These fats are mostly animal originated, harder and
mostly solid on room temperature.
o Unsaturated fats – they have one or more
(polyunsaturated) double bonds in the carbon chain. These
fats are mostly plant originated, liquid on room temperature.
Health issues.
 Biological function of fats:
o Fats are important energy storage molecules. 1 g of fat
stores more than 2x as much energy as 1 g of
polysaccharide.
o Adipose tissue (fat storage cells) also cushions vital organs
and provides thermal insulation.
B. PHOSPHOLIPIDS:
 Structure: similar to fats but one of the fatty acids are replaced by
a phosphate group:
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Because of the negative charge of the phosphate group,
phospholipids are polar and can be linked to other polar
molecules. Phospholipids form bilayers in water to shield their
hydrophobic portions:
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Biological function of phospholipids: Their bilayers are the basis of
the cell membrane structure that separates every cell from its
environment.
C. STEROIDS:
 Lipids that have a characteristic carbon skeleton of four fused
rings:
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Because of their multiple nonpolar rings, sterols are usually fat
soluble and insoluble in water.
The most common sterol is cholesterol.
Biological function of cholesterol:
o Cholesterol is a common component of cell membranes
that give the membrane more rigidity
o Many hormones including sex hormones are steroids
o Vitamin D is also made of sterol derivatives
IV.
PROTEINS:
 As the main structural components of all living organisms they
account for 50 % of the total dry mass of cells.
 Their functions are very diverse:
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Proteins’ diverse functions are supported by a very strictly
determined hierarchical arrangement of protein structure.
A. AMINO ACIDS AND THE PRIMARY PROTEIN STRUCTURE:
 All proteins are constructed from the same 20 different amino
acids.
 Amino acids are smaller organic molecules that have both
carboxyl and amino functional groups:
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The 20 amino acids are all different in the R group. The polarity
and other characteristics of this group will determine the 3
dimensional structure of the protein that is formed from amino
acids:
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Amino acids bind to each other by peptide bonds and form long
chains of polypeptides. This process is a type of condensation
reaction:
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The first protein that had its amino acid order determined was
insulin. Since than the science of proteomics determined many
more protein structures.
B. SECONDARY PROTEIN STRUCTURE:
 The repeated folding of the polypeptide chain and fixing this folding
by hydrogen bonds is called the secondary structure of a protein.
 This structure is fixed by hydrogen bonds between the oxygen and
nitrogen atoms and the hydrogen atoms of the main backbone of
the polypeptide chain.
 The secondary structure can take two different shapes:
o  - helix: a delicate coil that is fixed with a hydrogen bond
between every fourth amino acid. -helix provides flexibility
to proteins.
o  pleated sheet: two or more regions of polypeptide chains
lying side by side and connected by hydrogen bonds.  sheet provides strength to proteins
C. Tertiary Structure:
 Multiple sets of various secondary structures add up to the tertiary
structure of a protein. This structure constructs the protein’s
three dimensional shape and determines important sites that are
necessary for the normal functioning of the protein.
 The tertiary structure is fixed by various bonds of the side chains
of the amino acids. Potential bonds include covalent bond, ionic
bond, hydrogen bond, hydrophobic interactions, and van der
Waals interactions, disulfide bridges.
D. Quaternary structure:
 When two or more polypeptide chains aggregate into one functional
macromolecule, the quaternary structure of the protein is formed.
Ex. Collagen is formed from 3 long helical polypeptide chains. This
protein is found in the connective tissue of animals and gives the
tissue stability and resistance. Hemoglobin is an other complex
protein that is formed from 4 polypeptide chains. It is a protein
that is necessary to carry oxygen in the red blood cells.
A simple change in the primary structure of a protein can affect
the protein’s entire conformation and function. A good example is
sickle cell disease.
Watch:
http://www.pbs.org/wgbh/evolution/library/01/2/quicktime/l_012_
02.html on malaria and sickle cell anemia relationship
Protein conformation is mostly determined by the type and order of
amino acids in the protein molecule, however, there are other
factors that influence it, such as: temperature, pH, salt
concentration. If these factors are not ideal, denaturation of
proteins can take place. Denaturation is the loss or change of the
native conformation of the protein that makes the protein
temporarily or permanently inactive. Denaturation usually breaks
the bonds that form to keep up the protein’s tertiary structure.
V. NUCLEIC ACIDS:
 The primary structure of proteins is determined by the sequence of
genetic code in the genes. The biochemical representative of genes
are nucleic acids.
 There are two types of nucleic acids, deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA)
 DNA is a very unique molecule because it is able to provide
directions for its own replication and for the replication of RNA as
well, and through RNA it controls protein synthesis.
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Each chromosome in the nucleus of cells contains one single DNA
molecule with thousands of genes. These chromosomes are passed
on from one generation to the next during cell division.
We can summarize the flow of genetic information as DNA → RNA
→ protein. This route is universal in every living organisms,
among nonliving only some viruses break this order and can form
DNA from RNA.
A. The Structure of Nucleotides:
 Nucleic acids are polymers that are made up of monomers called
nucleotides by condensation
 Nucleotides are also complex and form from three parts:
a. Nitrogenous bases
b. Pentose (five-carbon sugar)
c. Phosphate group
 The unit without the phosphate group is called a nucleoside
 Each nitrogenous base can be either a purine base (two attached
carbon rings) or a pyrimidine base (one carbon ring). Purine bases
can be adenine (A) or guanine (G), while pyrimidine bases can be
cytosine (C), thymine (T) or uracil (U):
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Thymine is only found in DNA, while uracil is found only in RNA.
Pentose is also different in DNA and RNA. DNA has deoxyribose
while RNA has ribose:
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The numbering of the carbon atoms of the pentose determine
where the phosphate and the nitrogenous base binds. When
nucleotides form:
B. Nucleotide polymers:
 Nucleotides are linked together to form a polynucleotide chain by
forming a type of covalent bond called phosphodiester linkages
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between the –OH group of the 3’ carbon of the pentose and the
phosphate group of the other nucleotide on the 5’ carbon. This
repeated pattern forms the sugar-phosphate backbone of the
nucleic acid
The RNA molecule is made up of one single chain.
The DNA double helix was discovered by Watson and Crick in
the 1950’s. In this double helix the sugar-phosphate backbone runs
antiparallel. The sugar-phosphate backbones are on the outside,
while the nitrogenous bases turn inside and tie the two chains
together by hydrogen bonding. Most DNA molecules are very long,
with thousands or millions of bases.
Only certain bases in the double helix are compatible with each
other – base pairing rule. Adenine always binds with thymine while
cytosine binds with guanine.
 With this sequence of nucleotides, DNA is a perfect molecule to
store genetic information and inherit it from one generation to
the next.
CHAPTER 8 – AN INTRODUCTION TO METABOLISM
OBJECTIVES
Metabolism, Energy, and Life
1. Explain the role of catabolic and anabolic pathways in cellular
respiration.
2. Distinguish between kinetic and potential energy.
3. Explain why an organism is considered an open system.
4. Explain why highly ordered living organisms do not violate the second
law of thermodynamics.
5. Write and define each component of the equation for free-energy
change.
6. Distinguish between exergonic and endergonic reactions in terms of
free energy change.
7. Explain why metabolic disequilibrium is one of the defining features of
life.
8. List the three main kinds of cellular work. Explain in general terms
how cells obtain the energy to do cellular work.
9. Describe the structure of ATP and identify the major class of
macromolecules to which ATP belongs.
10. Explain how ATP performs cellular work.
Enzymes are Catalytic Proteins
11. Describe the function of enzymes in biological systems.
12. Explain why an investment of activation energy is necessary to
initiate a spontaneous reaction.
13. Explain how enzyme structure determines enzyme specificity.
14. Explain the induced-fit model of enzyme function.
15. Describe the mechanisms by which enzymes lower activation energy.
16. Explain how substrate concentration affects the rate of an enzymecatalyzed reaction.
17. Explain how temperature, pH, cofactors, and enzyme inhibitors can
affect enzyme activity.
The Control of Metabolism
18. Explain how metabolic pathways are regulated.
19. Explain how the location of enzymes in a cell may help order
metabolism.
I. OVERVIEW:
 The process of cellular respiration drives the cells to obtain
energy by breaking down organic molecules. This energy is
used to perform various functions such as the transport of
solutes, contraction of muscles, building up the cell’s own
biomolecules.
II.
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III.
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METABOLISM AND THE LAWS OF THERMODYNAMICS
Metabolism is the totality of an organism’s all chemical reactions.
These chemical reactions are organized into metabolic pathways
that begin with a specific molecule that will be altered in a series of
specific steps that result in a certain product. Each step has its
specific enzyme.
Enzymes are proteins that will regulate these metabolic pathways
at every step.
Some metabolic pathways release energy while breaking down
complex organic molecules into simpler ones – catabolic
processes
Anabolic processes – chemical reactions that consume energy to
build complex molecules from simpler ones.
Bioenergetics – the study of how organisms manage their energy
sources.
FORMS OF ENERGY:
Energy – the capacity to cause change.
Virtually all the energy for living things comes from the sun and is
captured by electrons.
Kinetic energy – the energy that is associated with the relative
motion of objects
Potential energy – energy that matter possesses because of its
location or structure. Chemical energy is a type of potential
energy that is available for release in a chemical reaction.
Generally, complex organic molecules are high in energy that can
be released during catabolic processes. The released energy is
used to fuel life processes.
During energy studies, scientists use the expression “system” to
denote the matter under study. Living organisms are considered
“open systems” because they interact with their surroundings and
exchange energy with them.
Whether a chemical reaction will take place spontaneously or not
is determined by the amount of available energy. The energy in a
system available for doing work under conditions of constant
temperature and pressure is called free energy. If energy is not
available it needs to be obtained from an outside source (First Law
of Thermodynamics – Law of Conservation of Energy).
The Second Law of Thermodynamics states that in the universe
as a whole the total amount of free energy is declining – heat is not
useful as a new energy source. With the decreasing free energy,
entropy is increasing in spontaneous processes. (Entropy is the
measurement of disorder or randomness).
The net charge in free energy that accompanies a reaction
determines whether a reaction is spontaneous or not (G = Gf – Gi).
If the reaction results in products with less free energy, the
reaction is spontaneous. These reactions are said to be
exothermic or exergonic (G is negative). If the reaction requires
the input of energy the reaction is said to be endothermic or
endergonic (G is positive). Energy changes in living organisms
tend to take place spontaneously in the direction that results in a
decrease in usable energy.
NEXT USE: http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookATP.html
IV.
THE ROLE OF ATP MOLECULES
 The cell does three main kinds of work:
o Mechanical work (beating of cilia, contraction of muscle
cells, movement of chromosomes)
o Transport work (pumping substances across the cell
membrane, carrying respiratory gases)
o Chemical work (forming polymers from monomers)
 Cells use energy coupling (pairing endergonic processes with
exergonic ones) to fuel all energy requiring processes.
 Adenosine triphosphate (ATP) plays a key role in these energy
coupling reactions as a mediator.
 The structure of ATP: an adenine + ribose + three phosphate
groups join together by dehydration synthesis.
 The phosphate groups of the molecule can be broken down by
hydrolysis. When the terminal phosphate breaks down ADP
(adenosine diphosphate) is produced. This reaction releases 7.3
kcal of energy per mole of ATP because of the lower free energy
level of the ADP molecules.
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The cell directly uses the energy that is released from the ATP by
transferring the phosphate group from ATP to some other molecule.
The recipient of the phosphate group is then phosphorylated and
becomes more reactive than the original reactant was.

ATP is a renewable resource that can be regenerated by the addition
of phosphate to ADP. The energy for building new ATP molecules
comes from exergonic reactions in the cell.
V. ENZYMES
 Enzymes – globular proteins that act in living organisms as catalysts.
 As catalysts, enzymes speed up chemical reactions by lowering the
activation energy of the reaction, without being consumed during the
reaction.
 The initial investment of energy for starting a reaction is known as the
activation energy (EA). The activation energy can be quite high for
many biological processes. Enzymes act by lowering this activation
energy so the reaction can take place with less of an energy
investment than before. Without enzymes these reactions would take
too long or would require high heat that would denature many organic
compounds.

Because enzymes are very sensitive to the reactions that they
catalyze, they will determine the type and direction of chemical
processes in the body.
 Enzymes are specific – a particular enzyme interacts with only one
type of reactant or pair of reactants – substrates (reactants of the
catalyzed reaction). Enzymes with substrates form enzyme-substrate
complexes, than the enzyme converts the substrate to a product.
They are very efficient – one enzyme may cause thousand or even
hundreds of thousands of molecules of reactants to react each
second. Enzymes are highly sensitive to changes in pH, temperature
and salt concentration. These characteristics depend on the enzyme’s
3D molecular conformation. This is the reason why denatured
proteins lose their enzymatic characteristics.
Show:
http://en.wikipedia.org/wiki/Image:GLO1_Homo_sapiens_small_fast.gif
 The reactive portion of the substrate molecule binds to the enzyme by
usually weak interactions at the active site and becomes temporarily
bonded.
 Binding energy is the energy that is released form all of the weak
interactions between the enzyme and substrate. This energy is used
to help substrates get together, orienting substrates in positions
favoring reaction, shutting out water or inducing changes in the
enzyme’s shape that pushes the substrates to a different shape as
well (induced fit model).
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Most metabolic processes are reversible and an enzyme can
catalyze both the forward and backward processes.
Because enzymes are proteins, many environmental factors will
influence their function. Most enzymes have a range of
environmental factors where they are the most efficient. These are
called optimal conditions. If the temperature or the pH increases or
decreases from the optimum, enzymes first slow down than
denature and become completely dysfunctional.
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Cofactor: A nonprotein component of enzymes. If the cofactor is
organic, then it is called a coenzyme. Coenzymes are relatively
small molecules compared to the protein part of the enzyme. Many
of the coenzymes are derived from vitamins. The coenzymes make
up a part of the active site, without the coenzyme the enzyme will
not function. Vitamins frequently act as coenzymes.
Enzyme activities are controlled by many ways. They frequently
depend on chemicals that mask, block, alter the active sites of the
enzymes:
i. Competitive inhibition: uses an inhibitor that is
similar to the substrate. It binds to the enzyme’s
active site but is not changed in the process and it
does not allow the substrate to bind to the active site –
carbon monoxide poisoning is an extreme example.
ii. Noncompetitive inhibition: depends on two kinds of
binding sites on the same enzyme. The usual active
site binds the substrate and another site binds the
inhibitor. Most noncompetitive inhibition is called
allosteric inhibition (different site, not the active
site). An allosteric enzyme usually exists in two forms.
One active form can bind the substrate the other,
inactive form is stabilized by inhibitor molecules
(negative modulators). Frequently the product is the
negative modulator – feedback inhibition. In other
allosteric enzymes there is more than one active site
for the substrate. When the first substrate molecule
binds to the enzyme it makes the remaining sites more
reactive – cooperativity (amplification of the response
of enzymes to substrates – one substrate makes the
enzyme accept an additional substrate).
Animations:
 http://highered.mcgrawhill.com/sites/0072495855/student_view0/chapter2/animation__h
ow_enzymes_work.html
 http://www.lpscience.fatcow.com/jwanamaker/animations/Enzym
e%20activity.html
 http://www.northland.cc.mn.us/biology/biology1111/animations/
enzyme.swf
 Biochemical pathway: http://highered.mcgrawhill.com/olc/dl/120070/bio09.swf
 Feedback inhibition: http://highered.mcgrawhill.com/olc/dl/120070/bio10.swf
THE END OF UNIT 2