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F212 Molecules, biodiversity,

food and health



Biological
molecules
Water
Intro to biological
molecules
Proteins
Carbohydrates
Lipids
Practical
biochemistry
Nucleic acids
Enzymes

describe how hydrogen bonding
occurs between water molecules,
and relate this, and other properties
of water, to the roles of water in living
organisms
Covalent bond
Formed when atoms share electrons
Strong bonds
Hydrogen bond
Weak interaction that occurs when a
negatively charged atom is bonded to a
positively charged hydrogen
60 70 % of mammals
About 90% of plants
Life originated in water
Good solvent

What else do you know about little
old dihydrogen monoxide (DHMO)
A polar molecule
Made up of two positively charged hydrogen
atoms and one negatively charged oxygen
Covalent bonds form between oxygen and
hydrogen with electrons shared between them.
Hydrogen bonds form between water molecules
Up to four may form clusters which break and
reform all the time

Hydrogen
bonds
Key features of water as a
constituent of living organisms
Good solvent
High specific heat capacity
High latent heat of vaporisation
High cohesion
Reactive
Incompressibility
To be able to
Define metabolism
State the functions of biological
molecules
Name monomers and polymers of
carbohydrates, fats, proteins and
nucleic acids
Describe general features of
condensation and hydrolysis reaction
Molecular biology
the study of structure and functioning of
biological molecules.
Metabolism
sum total of all biochemical reactions in
the body.
To maintain a healthy body
Carbohydrates
Lipids
Proteins
Vitamins and minerals
Nucleic acid
Water
fibre
There are 4 key biological molecules
Carbohydrates
lipids
proteins
nucleic acids
4 most common elements in the
living organisms
hydrogen
carbon
oxygen
nitrogen
Covalent bonds join atoms together to
form molecules
Carbon is able to make 4 covalent bonds
Carbon can bond to form chains or rings
with other atoms bonded to the chain
Carbon can also form double bonds
E.g. C=C or C=O
poly means many = polymers

Macromolecules are made up of
repeating subunits that are joined end to
end, they are easy to make as the same
reaction is repeated many times.

Polymerisation is the making of polymers.
Macromolecule Subunit (monomer)
polysaccharide monosaccharide
proteins amino acids

nucleic acids nucleotides
Metabolism is the sum of all of the
reactions that take place within organisms
Anabolism
Build up of larger, more complex molecules from
smaller, simpler ones
This process requires energy
Catabolism
The breakdown of complex molecules into simpler
ones
This process releases energy
In a condensation reaction
A water molecule is released
A new covalent bond is formed
A larger molecule is formed by bonding
together of smaller molecules
In hydrolysis reactions
A water molecule is used
A covalent bond is broken
Smaller molecules are formed by the
splitting of a larger molecule
Hydrolysis and condensation
O
OH HO
CONDENSATION
HYDROLYSIS
describe, with the aid of diagrams,
the structure of an amino acids
describe, with the aid of diagrams,
the formation and breakage of
peptide bonds in the synthesis and
hydrolysis of dipeptides and
polypeptides
50% of the dry mass of cells is protein
Important functions include
Cell membranes
Haemoglobin
Anti-bodies
Enzymes
Keratin (hair and skin)
collagen
All proteins are made up of the same
basic components amino acids
There are 20 different amino acids,
which alter by having different
residual groups (R groups)
A single chain of amino acids makes
a polypeptide
Amino acids contain
Amine group (NH
2
)
Carboxylic acid group (COOH)
Joined at the same C atom
H
H
OH
N
H
R
C C
O
Amine
group
Carboxyl
group
R group varies in different amino acids
Build an amino acid using the molymod
models

Glycine is an amino acid where the R
group is hydrogen change you
molecule into glycine

Build a dipeptide using the molymod
models
Glycine R group = H
Alanine R group = CH
3

Valine R group = C
3
H
7


You will be expected to learn how to
draw the basic structure of an amino
acid. Remember that each Amino
acid has its own specific R group
explain, with the aid of diagrams, the
term primary structure
explain, with the aid of diagrams, the
term secondary structure with
reference to hydrogen bonding
H
H
N
H
R
C C
O
H
N
H
R
C C
O
OH
Peptide
bond
Peptide bonds are formed in
condensation reactions
Primary structure
The primary structure of a polypeptide is
its amino acid sequence
This is determined by the gene that
codes for the polypeptide
Amino
acid
Peptide Bond
Polypeptides become twisted or
coiled
They fold into one of two structures
Alpha helix (right handed helix)
Beta-pleated sheet
Hydrogen bonds hold coils in place
Weak but give stability to the parts of a
protein molecule.
C O H N
explain, with the aid of diagrams, the
term tertiary structure with
reference to hydrophobic and
hydrophilic interactions, disulphide
bonds and ionic interactions
Folding of the polypeptide to give a
more complex 3-D shape, the shape
is specific to the function of the
polypeptide.
Examples
Hormone must fit into the hormone
receptor in a target cell
Enzymes have a complementary active
site to its substrate

Four types of bond help to hold the
folded proteins in their precise
shape.
Hydrogen Bonds
Disulphide bonds
Ionic bonds
Hydrophobic interactions
Between polar groups
Electronegative oxygen atoms of the CO
Electropositive H atoms on either the OH
or NH groups.
Between sulfur-containing R groups
of the amino acid cysteine.
Covalent bonds
Form strong links which make the
tertiary protein structure very stable.
This bond can be broken by
reducing agents
Between R groups, which ionise to
form positively and negatively
charged groups that attract each
other.
Hydrophobic Interactions
These are interactions between the non-
polar side chains of a protein molecule.
The bond forms between non-polar,
hydrophobic R groups on the amino
acids.
Once the two hydrophobic molecules are
close together the interaction is reinforced
by Van der Waals attractions (which
provide the weak bond).
Van der Waals attractions
Electrons are always in motion, and
are not always evenly distributed
about a molecule.
This results in areas of positive and
negative charge, which are
continuously changing, and enables
molecules to stick to one another.
The Polar R groups of proteins interact with
water forming hydrogen bonds that face
outwards, This creates a hydrophobic core
to the molecule
When proteins are heated these bonds
break, the tertiary structure changes and
the protein does not function.
The destruction of shape or loss of function
is denaturation.
Frying an egg
explain, with the aid of diagrams, the
term quaternary structure, with
reference to the structure of
haemoglobin
Association of different polypeptide
chains bonded together to form
intricate shapes
Sometimes contain prosthetic
groups, which are a permanent part
of a protein molecule but not made
of amino acids
Globular protein
Molecules curl up into a ball shape
Examples myoglobin, haemoglobin
Metabolic roles
Fibrous Proteins
Form long strands
Usually insoluble
Have a structural role
Examples keratin, collagen
Function oxygen carrying pigment found
in red blood cells
Structure
4 polypeptides
2 x -globin
2 x -globin
Each polypeptide has a 3
o
structure stabilised
by hydrophobic interactions in the centre
In the middle each polypeptide in a haem
group
Protein structure and
diversity
It is difficult to describe in a simple
sentence the role of proteins.
when there is something to do, it is a protein
that does it.
Therefore proteins are
important
numerous
very diverse
very complex,
able to perform actions and reactions under
some circumstances
Some examples of
proteins
Antibodies:
they recognise molecules of invading organisms.
Receptors:
part of the cell membrane, they recognise other
proteins, or chemicals, and inform the cell...
Enzymes:
assemble or digest.
Neurotransmitters and some hormones:
Trigger the receptors...
Channels and pores:
holes in the cell membrane
Primary Structure
Amino acids linked in a linear sequence
Secondary Structure
folding or coiling of polypeptide
Tertiary structure
Folding of polypeptide by disulphide bonds,
ionic bonds, hydrogen bonds or hydrophobic
interactions
Quaternary structure
Two or more polypeptides bonded together
describe, with the aid of diagrams,
the structure of a collagen molecule
compare the structure and function
of haemoglobin (and example of a
globular protein) and collagen (an
example of a fibrous protein)
Collagen is found in skin, teeth,
tendons, cartilage, bones and the
walls of blood vessels, making it an
important structural protein.
3 identical polypeptide chains
wound into a triple helix; this is a left-
handed helix.
Each polypeptide is about 1000
amino acids long
Primary structure
Every 3 amino acids = glycine

Sequences of polypeptide chains are
staggered so that glycine is found at
every position along the triple helix.
The three polypeptide chains are held
together by hydrogen bonds.
Adjacent molecules of collagen are held
together by covalent bonds formed
between the carboxyl group of one amino
acid and the amine group of another.
Using your brains and what you have
been taught
compare the structure and function of
haemoglobin and collagen

Try to make a bullet point list of at least 10
things
Collagen
Repeating sequence of
amino acids
Most of molecule has
left handed helix
structures
Does not contain
prosthetic group
Insoluble in water
Metabolically
unreactive
Structural role
Haemoglobin
Precise 1
o
structure
2
o
structure wound into
alpha helix
Contains prosthetic
group
Soluble in water
Metabolically reactive

describe, with the aid of diagrams,
the molecular structure of alpha-
glucose as an example of a
monosaccharide carbohydrate
state the structural difference
between alpha and beta glucose
contain carbon, hydrogen & oxygen
organic compounds
general formula C
x
(H
2
O)
y

glucose C
6
H
12
O
6
3 main groups
monosaccharides
disaccharides
polysaccharides
dissolve easily in water to form sweet
solution
general formula (CH
2
O)
n
, where n is
the number of carbons
3 main types
Trioses (3C)
Pentoses (5C)
Hexoses (6C)
Glucose is made of a chain of atoms
long enough to close up upon itself
and form a stable ring structure.
Carbon atom 1 (
1
C) joins to the O on
5
C.
The six sided structure formed is
known as a pyranose ring.
1
C
2
C
3
C
4
C
5
C
6
CH
2
OH

OH
OH
OH
OH H
H
O
H
H
H

1
C
2
C
3
C
4
C
5
C
6
CH
2
OH

OH
OH
OH
OH
H
H
O
H
H
H
O
H
OH
Isomers
possess the same molecular formula
but differ in arrangement of atoms.
-glucose and -glucose are isomers
of glucose.
Depending on whether the OH of 1C is
above or below the plane of the ring.
-glucose -glucose

O
OH
H
O
H
OH
describe, with the aid of diagrams,
the formation and breakage of
glycosidic bonds in the synthesis and
hydrolysis of a disaccharide
(maltose) and a polysaccharide
(amylose)
Monosaccharides combine in pairs to
give a disaccharide, this involves the loss
of a single water molecule
This reaction is called condensation
The bond formed is known as a glycosidic
bond.
To break a disaccharide the addition of
water is needed, this reaction is called
hydrolysis.
Final molecules maybe 1000s of
monosaccharides, the size of these
molecules make them insoluble.
Polysaccharides are NOT sugars
The most important polysaccharides are
built up entirely of glucose molecules.
These are starch, glycogen and cellulose.
describe, with the aid of diagrams,
the structure of starch
describe, with the aid of diagrams,
the structure of glycogen

A mixture of two substances amylose and
amylopectin.
Starch granules are insoluble in water.
The form of carbohydrate used for storage
in plants.
Starch grains build up in chloroplasts, or in
storage organs such as potato tubers.
Long unbranching chains
1-4 glycosidic bonds
formed by condensation reactions.
The chains curve and coil into helical
structures.
1,4 linked -glucose molecules form
chains
shorter
branch out to the sides.
The branches form by 1-6 linkages
Comparison of the structure of
amylose and amylopectin molecules
The form in which carbohydrate is stored in the
animal body.
Glucose is converted to glycogen in the liver and
muscles,
it is kept until required
then it is broken down again into glucose.
Formed by -glucose molecules joining in 1-4
and 1-6 links
There are more branches containing a smaller
number of glucose molecules than amylopectin
Starch and Glycogen are energy
storage molecules
which take up little space due to
their compact shapes
They help to prevent too high
concentrations of glucose in cells.
describe, with the aid of diagrams,
the structure of cellulose

Most abundant organic molecule on the planet
due to its presence in cell walls.
Slow rate of breakdown in nature.
Polymer of about 10,000 -glucose molecules in
a long unbranched chain.
Many chains run parallel to each other and have
cross linkages between them, giving increased
stability.
hydrogen bonds form these links between chains,
which collectively give the structure increased
strength.
To join together one -glucose molecule
must be rotated at 180
0
relative to the
other.
Successive glucose molecules are linked
at 180
0
to each other.
Cellulose molecules become tightly cross-
linked with each other to form bundles
called micro fibrils.
Micro fibrils form cellulose fibres by
hydrogen bonding giving a high tensile
strength similar to steel.
compare and contrast the structure
and functions of starch (amylose)
and cellulose
explain how the structures of
glucose, starch (amylose), glycogen
and cellulose molecules relate to
their functions in living organisms

Comparing polysaccharides
Characteristic amylose amylopectin glycogen cellulose
Found in
Found as
Function
Monomer
Bonds
chain
Discuss the structures of glucose,
starch, glycogen and cellulose in
relation to their functions; include
diagrams to illustrate your answer
compare, with the aid of diagrams,
the structure of a triglyceride and a
phospholipids
explain how the structure of a
triglyceride, phospholipids and
cholesterol molecules relate to their
functions in living organisms
are not
Large molecules
few oxygen atoms
many carbon and hydrogen atoms
hydrophobic
Less dense than water

Two important groups
Triglycerides
Fats solid at room temperature
Oils liquid at room temperature
phospholipids
A source of energy
Store of energy (adipose tissues)
Biological membranes
Thermal insulators / insulation
Buoyancy
Protection
Cuticle of a leaf
Internal organs
Metabolic source of water
hormones
glycerol Fatty acid
H
H
C
C
C
H
H
H
OH
OH
OH
C
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
HO
H
OH O
C
Fatty acids have
an acid group at one end (COOH)
Hydrocarbon chain (2 20 carbons
long)
Fatty acids can be
Saturated
Unsaturated
All possible bonds are made with
hydrogen
HO
C
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
H
One or more double bond between
carbon atoms
HO
C
H
C
H
C
H
C
H
H
C
H
H
C
H
O
H
Saturated and
unsaturated fatty acids
Polyunsaturated
more than one double bond
Monounsaturated
only one double bond
Animal lipids are often saturated and
occur as fats
plant lipids are often unsaturated
and occur as oils
Most common form of lipid
Combination of 3 fatty acid
molecules and one glycerol
molecule.
Glycerol is a type of alcohol
Fatty acids are organic molecules with
a COOH group attached to a
hydrocarbon tail.
Each of the glycerol molecules 3 -
OH groups reacts with the carboxyl
group of a fatty acid.
This is a condensation reaction, and
an ester bond is established.

Glycerol + 3 fatty acids
H
H
C
C
C
H
H
H
OH
OH
OH
HO
HO
HO
C
O
C
O
C
O
Condensation reaction and
formation of an ester bond
H
H
C
C
C
H
H
H
O
O
O
C
O
C
O
C
O
Ester bond
Triglycerides are
insoluble in water,
soluble in some organic solvents, e.g.
ether or ethanol.
non-polar
hydrophobic.
Energy reserve
Insulator against heat loss
Buoyancy
Protection (vital organs)
Metabolic source of water.
Special type of lipid
one of the fatty acid groups is
replaced by phosphoric acid.
phosphoric acid is hydrophilic
(attracts water)
Biological significance of this
molecule is its role in the cell
membrane.
Structure of a phopholipid
H
H
C
C
C
H
H
H
O
O
O
P
O
C
O
C
O
Phosphate group
OH
Small molecule
-OH group is polar
4 carbon rings and hydrocarbon tail
are non polar
Found in biological membranes
Steroids e.g. testosterone, oestrogen
and progesterone are made from
cholesterol
Excess cholesterol
Form gallstones in bile
Cause atherosclerosis in blood vessels
describe how to carry out chemical
tests to identify the presence of the
following molecules: protein (Biuret
test), reducing and non-reducing
sugars (Benedicts test), Starch
(iodine solution) and lipids (emulsion
test)
Chemical tests can be done to
confirm the presence of various
biological molecules within a
sample
These tests are qualitative tests
They indicate presence of a molecule
not how much is present
Starch
Reducing sugar
Non reducing sugar
Iodine solution
iodine in potassium iodide
Add to solution will turn blue-black
quickly if comes into contact with
starch.
Starch molecules curl up into long
spirals, with a hole down the middle
of the spiral, just the right size for an
iodine molecule.
The starch-iodine complex forms a
strong blue-black colour.

Benedicts Reagent (copper II
sulphate in alkaline solution)
Add benedicts reagent to the solution
testing
Heat in a water bath (80
o
C) for 3
minutes
If added to a reducing agent Cu
2+
ions are
reduced to Cu
+
, and the change in colour to red
of Copper (I) sulphate.
All monosaccharides are reducing sugars;
Reducing sugars have an aldehyde group (H-
C=0) somewhere in their molecule, which
contribute an electron to the copper.
Reducing sugars become oxidised.

Reducing sugar + Cu
2+
= oxidised sugar + Cu
+
Heat sugar solution with acid to hydrolyse
any glycosidic bonds present
Neutralise solution by adding sodium
hydroxide
Add benedicts reagent
Heat in a water bath
If it goes orange/red a non-reducing
sugar is present.
Not all disaccharides are reducing sugars.
To check for the presence of a reducing
sugar, the disaccharide needs to be
broken down into its constituent
monosaccharides,
monosaccharides are reducing sugars
and will react with benedicts solution.
Biuret reagent
copper sulphate and potassium or
sodium hydroxide
Add Biuret solution to the substance
If protein present get a purple colour
All proteins have several amine, NH
2
,
groups within their molecules.
These groups react with copper ions
to form a complex that has a strong
purple colour.
Emulsion test
Shake substance (lipid) with absolute
ethanol
Pour ethanol into a tube containing
water
If no lipid is present mixture looks
transparent
If lipids are present looks white and
cloudy.
Lipids are insoluble in water, but soluble in
ethanol.
As the ethanol mixture is poured into
water, lipid molecules cannot remain
mixed in water and clump together to
form little groups.
The lipid molecules impede light and we
see an emulsion (white cloudiness).
describe how the concentration of
glucose in a solution may be
determined by using colorimetry

Bananas, at each of five different stages of
ripeness.
The stages must range from very green (inedible) to
very ripe (brown skin).
Each student will require an approximately 5 cm length
of each banana.
The bananas must be labelled or presented on labelled
watch glasses.
50cm
3
fresh iodine in potassium iodide solution in
a beaker labelled iodine solution.
50cm
3
fresh Benedicts solution in a beaker
labelled Benedicts solution.
Module 1 Biological Molecules
Unit 2 Molecules, Biodiversity, food and health

state that deoxyribonucleic acid (DNA) is
a polynucleotide, usually double stranded
and made up of the nucleotides adenine
(A), thymine (T), cytosine (C) and guanine
(G)
state that ribonucleic acid (RNA) is a
polynucleotide usually single-stranded
and made up of the nucleotides adenine
(A), uracil (U), cytosine (C) and guanine
(G)
The nucleic acids have
The ability to carry instructions
The ability to be copied

DNA and RNA are polymers; the individual
nucleotides are the monomers that build
up the polynucleotides.
DNA = deoxyribonucleic acid
RNA = ribonucleic acid
Nucleotides are made up of three smaller
components
Nitrogen containing base
Pentose sugar (5 carbon atoms)
Phosphate group
Phosphate
sugar
base
There are 5 different nitrogen-containing
bases:
A Adenine
T Thymine (DNA only)
U Uracil (RNA only)
G Guanine
C Cytosine

DNA A, G, C and T
RNA - A, G, C and U
Purines (larger)
These have double rings of carbon and nitrogen atoms
adenine
Guanine

Pyrimidines (smaller)
These have a single ring of carbon and nitrogen atoms
Thymine
uracil
cytosine
Polynucleotides strands are
formed of alternating sugars
and phosphates
Cut and paste activity
Cut out the nucleotides and stick them
down to form a double stranded DNA
molecule
describe, with the aid of diagrams,
how hydrogen bonding between
complementary base pairs (A-T, G-C)
on two anti-parallel DNA
polynucleotide leads to the formation of
a DNA molecule,
how the twisting of DNA produces its
double-helix shape outline, with the
aid of diagrams,
2 strands
side-by-side
running in
opposite
directions
(antiparallel)
The two
strands are
held together
by hydrogen
bonds.
Complementary base
pairs
A purine in one strand is always opposite
a pyramidine in the other strand.
Adenine thymine
Guanine - cytosine
DNA forms a double helix, the strands are
held in place by hydrogen bonds.
These bonds can be broken relatively
easily, this is important for protein
synthesis and DNA replication.
Build your own DNA molecule
Equipment needed:
2 purple pipe cleaners
2 white pipe cleaners
6 red beads
6 yellow beads
12 aqua beads
12 purple beads
Follow the instructions on the handout
Two polynucleotides held together by
hydrogen bonds
Complementary base pairs
AT (2 hydrogen bonds)
GC (3 hydrogen bonds)
Polynucleotides are anti-parallel
Parallel but with chains running in opposite
directions
3 to 5direction
5 to 3direction
Information storage
Long molecules
replication
Base-paring rules
Hydrogen bonds
Stable

how DNA replicates semi-
conservatively, with reference to the
role of DNA polymerase
Each polynucleotide acts as a
template for making a new
polynucleotide
This is known as semi-conservative
replication
Experimental Evidence for the semi-
conservative replication of DNA
Three ways were suggested for DNA
replication
Conservative replication
Semi-conservative replication
Dispersive replication
Scientists thought that semi-conservative
replication was most likely but there was
no evidence to support this theory.
1958 Matthew Meselsohn and Franklin
Stahl demonstrated that DNA replication
was semi-conservative following
experiments with E. Coli.
E. Coli were grown in a medium
containing a heavy isotope nitrogen
(
15
N).
The bacteria used 15N to make the
purine and pyrimidine bases in its
DNA.
After many generations, they were
then transferred to light isotope
nitrogen (
14
N)
Bacteria were taken from the new
medium after one generation, two
generations and later generations.
DNA was extracted from each group
of bacteria,
samples were placed in a solution of
caesium chloride and spun in a
centrifuge.
Generation 1 2 3
1. Explain why the band of DNA in the first
generation is higher than that in the parental
generation.
2. If replication were conservative what results
would you expect in the first generation?
3. If the DNA had replicated dispersively what
results would you expect in the first generation?
4. Explain how the second generation provides
evidence that the DNA has reproduced semi-
conservatively and not dispersively
5. What results would you expect to see from a third
generation, draw a diagram of the results?
Parental generation - both strands
made with
15
N


First generation DNA made of one
strand
15
N and one strand
14
N


Second generation some DNA made
of 2 strands of
14
N and some made of
15
N and
14
N.
Double helix unwinds and the DNA unzips as
hydrogen bonds break
Existing polynucleotides acts as a template for
assembly of nucleotides
Free nucleotides move towards exposed bases of
DNA
Base pairing occurs between free nucleotides
and exposed bases
Enzyme DNA polymerase forms covalent bonds
between free nucleotides
Two daughter DNA molecules form separate
double helices.
state that a gene is a sequence of
DNA nucleotides that codes for a
polypeptide
outline the roles of DNA and RNA in
living organisms (the concept of
protein synthesis must be considered
in outline only)
single strand, containing
uracil not thymine
Ribose sugar

There are 3 forms of RNA
Messenger RNA mRNA
Transfer RNA tRNA
Ribosomal RNA rRNA
DNA and Protein Synthesis
All chemical reactions are controlled by
enzymes, all enzymes are proteins, DNA
codes for proteins, therefore DNA controls
all the activities of a cell.
The shape and behaviour of a protein
depends on the exact sequence of amino
acids in the primary structure
(polypeptide).
DNA determines the exact order in which
amino acids join together.
The genetic code
sequence of bases along the DNA molecule,
There are 20 different amino acids, only 4 bases,
a sequence of 3 bases codes for an amino acid.
This is called the triplet code.
A gene is the part of a DNA molecule,
which codes for just one polypeptide.
The process of protein synthesis
occurs in four stages:
transcription of DNA to make
messenger RNA (mRNA)
movement of mRNA from the nucleus to
the cytoplasm
amino acid activation
translation of mRNA to make a
polypeptide
This is the process by which mRNA is built
up against one side of an opened up
piece of DNA.
The relevant section of DNA unwinds, the
hydrogen bonds between base pairs are
broken and the two strands split apart.
Free nucleotides then assemble against
one strand of DNA.
The enzyme RNA polymerase moves
along the DNA adding on RNA nucleotide
at a time.
mRNA leaves the nucleus through a
nuclear pore into the cytoplasm, and
attaches to a ribosome.
Enzymes attach amino acids to their
specific tRNA molecule.
This needs energy supplied by ATP.
An anti-codon is a triplet of bases
forming part of a tRNA molecule and
it is complementary to a codon.
Amino acid attaches to the ribosome
Adjacent amino acids are joined together
by peptide bonds and a polypeptide
chain is built up.
This carries on until the ribosome reaches
a stop codon, the polypeptide breaks
loose from the ribosome and translation is
complete.
state that enzymes are globular
proteins, with a specific tertiary
structure, which catalyse metabolic
reactions in living organisms;
What is metabolism?
sum total of all biochemical reactions in
the body.
All enzymes are
globular proteins
catalysts
Specific
affected by temperature and pH
Two basic functions within cells:
Act as biological catalysts
Provide a mechanism whereby
individual chemical reactions can be
controlled
Enzyme molecules have a specific
3D shape and all possess an active
site.
Follow the progress of an enzyme-
catalysed reaction;
The enzyme catalase breaks down hydrogen
peroxide into water and oxygen.

2H
2
O
2
=> 2H
2
O + O
2

Hydrogen peroxide is formed continually as a bi-
product of various chemical reactions in living
cells.
It is toxic and if the cells did not immediately
break it down it would kill them.
Catalase is the fastest enzyme known.
In this investigation you will be able to watch the
action of catalase and compare it with an
inorganic catalyst that catalyses the same
reaction.
1. Pour hydrogen peroxide into two test tubes to a depth
of about 2cm.
2. Into one test tube sprinkle about 0.1g of manganese
dioxide.
3. Into the 2nd test tube put in a 1cm
2
piece of potato.
4. Observe the two test tubes and record what happens.
Describe the difference in reaction
with the inorganic catalyst and the
organic catalyst
Graduated
measuring
cylinder
15ml
Hydrogen
peroxide
water
Design a results table to record the
oxygen produced every 10 seconds.
cut up 4cm
3
piece of potato into this
slices into the conical flask, and start
recording results immediately.
Take a reading for the amount of oxygen
produced every 10 seconds, until the
oxygen is no longer being produced.
If you have time, you could repeat
the above experiment, but this time
grind up the 4cm
3
of potato with
some fine sand. How do the results
compare?

Draw a graph of oxygen produced against
time.
Describe the graph in terms of interaction
between the molecules of catalase and
hydrogen peroxide.
How could you adapt this experiment to
investigate the effect of the following on the
rate of the reaction.
temperature
pH
substrate concentration
enzyme concentration
state that enzyme action may be intracellular or
extra cellular;
describe, with the aid of diagrams, the
mechanism of action of enzyme molecules, with
reference to
specificity,
active site,
lock and key hypothesis,
induced-fit hypothesis,
enzyme-substrate complex,
enzyme-product complex
lowering of activation energy
The Active site is the region to which
another molecule or molecules can bind.
This molecule is the substrate of the
enzyme.
The enzyme and substrate form an
enzyme-substrate complex.
When enzyme and substrate collide in the
correct orientation, the substrate becomes
attached and held temporarily in position
at the active site.
Substrate end products
Enzyme and substrate molecules
then interact so that a chemical
reaction involving the substrates
takes place and the appropriate
products are formed.
When the reaction is complete, the
product or products leave the active
site.
Enzyme Specificity
Active sites are specific for one type of
molecule
Examples of specificity
Amylase breaks down glycosidic bonds in
starch to form maltose
Catalase breaks down hydrogen peroxide into
water and oxygen
Trypsin is a protease that only breaks peptide
bonds next to the amino acids arginine and
lysine
Some part of the enzyme has an
active site, which is exactly the
correct shape to fit the substrate.
Active site = lock
Substrate = key

Active site is a cavity of a particular shape
initially the active site is not the correct
shape in which to fit the substrate.
As the substrate approaches the active
site, the site changes and results in being
a perfect fit.
After the reaction has taken place and
the products have gone.
The active site returns to its normal shape.
A catabolic reaction
substrate has been broken down
An anabolic reaction
substrate used to build a new molecule
Activation energy is the energy given
temporarily to a substrate to convert it into
a product.
The higher the activation energy the
slower the reaction.
Enzymes help to decrease activation
energy by providing an active site where
reactions can occur more easily than
elsewhere.
Activation
energy
without
enzyme



Activation
energy
with
enzyme
To follow the progress of an enzyme-
catalysed reaction;
Follow the time course of an enzyme-catalysed
reaction by measuring
rates of formation of products (for example using
catalase),
rate of disappearance of substrate (for example using
amylase).
When an enzyme and a substrate are mixed
together, a reaction begins. Substrate molecules
collide with the enzyme and bind to its active
site; product molecules are formed.
As the reaction proceeds the number of
substrate molecules decreases and the
number of product molecules increase.
The number of enzyme molecules remains
constant.
We can measure the rate of a reaction by
measuring either:
Increasing product
Decreasing substrate
Increasing Product
Example: catalase breaks down hydrogen
peroxide into water and oxygen
Decreasing Substrate
Example: amylase breaks down starch into
maltose
As the reaction proceeds there is less
substrate available, therefore less product
gets released.
Rate of reaction is quickest at the
beginning when there is a high
concentration of substrate.
Later the substrate becomes the limiting
factor and the reaction slows down.
Eventually all substrate is used up, so the
reaction stops
describe and explain the effects of pH,
temperature, enzyme concentration and
substrate concentration on enzyme
activity;
describe how the effects of pH,
temperature, enzyme concentration and
substrate concentration on enzyme
activity can be investigated
experimentally
Enzyme Concentration
Substrate concentration
Temperature
pH

The rate of reaction is directly
proportional to the enzyme
concentration
assuming that there are plenty of
substrate molecules and enzymes
are the only limiting factors.

For a given amount of enzyme, the
rate of an enzyme controlled
reaction increases with substrate
concentration, up to a certain point.
This point is Vmax, which is the
maximum rate of reaction; the
amount of enzyme becomes the
limiting factor.
An increase in temperature affects the
rate of reaction in two ways
Factor 1
As the temperature increase the kinetic
energy of the substrate and enzyme
molecules increases and they move faster.
The faster the molecules move the more often
they collide and the greater the rate of
reaction.
Factor 2
As temperature increases, more atoms
which make up the enzyme molecules
vibrate.
This breaks down the bonds which hold
the molecules in the precise shape.
The enzyme becomes denatured and
loses catalytic properties.
OPTIMUM TEMPERATURE
temperature at which an enzyme
catalyses a reaction at a maximum
rate.

Temperature
The precise 3-D shape of an enzyme is
partly a result of hydrogen bonding.
These bonds maybe broken down by high
concentrations of H+ ions.
When pH changes from the optimum
shape of enzyme changes
affinity of substrate for the active site
decreases
Online simulation of practical available at
http://mvhs.mbhs.edu/coresims/enzyme/inde
x.php

Good simulation of the theory of temp/pH
available at AS guru
www.bbc.co.uk

Chemistry for biologists
www.chemsoc.org/networks/learnnet/cfb/
explain the effects of competitive
and non-competitive inhibitors on
the rate of enzyme-controlled
reactions,
with reference to both reversible and
non-reversible inhibitors;
Inhibitors prevent enzymes from
working
There are two types of inhibitor
competitive
non-competitive.
Competitive Inhibitors
Have a similar shape to the normal
substrate and are able to bind to the
active site.
Do not react with the active site but leave
after a time without any product forming.
The rate of reaction decreases because
the substrate molecules have to compete
with the inhibitor for the active site.
It is possible to reduce the effect of the
inhibitor by adding more substrate
Effect of concentrations of inhibitor
and substrate on the rate of an
enzyme controlled reaction
No inhibitor
With fixed
concentration
of competitive
inhibitor
Substrate concentration
R
a
t
e

o
f

r
e
a
c
t
i
o
n

Competitive inhibitor
Reversible
Statins compete with a liver enzyme which
helps to make cholesterol
Non-reversible
Penicillin inhibits an enzyme that makes cell
walls in some bacteria
Molecules bind to some part of an
enzyme other than the active site.
This changes the active site so that the
substrate can no longer fit.
If the concentration of this type of inhibitor
is high enough, all enzymes maybe
inhibited and the reaction slows to
nothing.
Increasing the concentration of the
substrate has no effect on this type of
inhibition.
Rate of an enzyme controlled reaction
with and without a non-competitive
inhibitor
No inhibitor
With non-competitive
inhibitor
Substrate concentration
R
a
t
e

o
f

r
e
a
c
t
i
o
n

Non-competitive inhibitor
Potassium cyanide bind to haem, which
is part of cytochrome oxidase
This is non-reversible
Metabolic reactions must be finely
controlled and balanced;
end product inhibition regulates
certain enzyme-catalysed processes
in organisms.
This is an example of non-
competitive inhibition
product 3 binds to another part of the
enzyme other than the active site.
It is also an example of a feedback
mechanism.
explain the importance of cofactors and
coenzymes in enzyme-controlled
reactions;
state that metabolic poisons may be
enzyme inhibitors, and describe the
action of one named poison;
state that some medicinal drugs work by
inhibiting the activity of enzyme
A non-protein component
Required by enzymes to carry out
reactions
Examples
Metal ions in carbonic anhydrase
Haem in catalase
Chloride ions and amylase
Organic, non protein molecules
Role is to carry chemical groups
between enzymes, linking together
enzyme controlled reactions
Examples
NAD, FAD and coenzyme A involved
in respiration
NADP involved in photosythesis
A coenzyme that is a permanent
part of the enzyme
Example
Carbonic anhydrase contains a zinc-
based prosthetic group
Metabolic poisons can be enzyme
inhibitors
Example
Potassium cyanide
inhibits cell respiration
Non-competitive inhibitor for the enzyme
cytochrome oxidase
Decreases the use of oxygen so that ATP can not be
made
The organism respires anaerobically and lactic acid
builds up in the blood
Infection by viruses are treated by
using chemicals that act as protease
inhibitors which the virus needs to
build new viral coats.
Antibiotics
Penicillin inhibits a bacterial enzyme
which makes bacterial cell walls
Measure the effect of different
independent variables and
independent variable ranges on an
enzyme-catalysed reaction;
Measure the effect of an inhibitor on
an enzyme-catalysed reaction.