A2 Chemistry Application Notes
Chemistry Applications
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Solubility decreases with the size and nature of
the Alkyl Chain which is hydrophobic (water
repelling).
Optical Activity
Amino Acids have Amino (-NH2) group and
Carboxylic Acid (-COOH) group
Few Examples of Amino Acids are given below.
Alpha Amino Acids have Amino and Acid Group
attached to the same Carbon Atom.
Almost all amino acids and zwitter ions are
optically active since a chiral carbon atom is
present attached to 4 different groups (amino
group, acid group, alkyl chain and hydrogen
atom). The central C atom is the chiral atom
which lacks a plane of symmetry. Two optical
isomers are known as enantiomers.
General formula of an Alpha Amino Acid:
Amino Acids have High Melting Points (They
generally decompose before melting)
Amino Acids form Zwitter Ions as they have
both an Acid group and a Basic group.
A Zwitter ion has no overall
charge but has separate
parts which contain both
positive and
negative
charges e.g.
Natural Systems generally work with one of the
two enantiomers. The spatial arrangement
hinders one of the enantiomers from fitting into
the active site of an enzyme.
Acid-Base Nature of Amino Acids
Zwitter ion as a base
Zwitter ion as an acid
The Basic Amino group gains H+ ions and the
Acid group loses H+ to form Zwitter Ion.
The high melting point is due to strong ionic
forces present between Amino Acids which are
existing as Zwitter Ions.
Solubility of Amino Acids
Due to Zwitter Ion formation, Amino acids are
highly soluble in water and other polar solvents
and insoluble in nonpolar solvents.
Zwitter ion will become positively charged if it’s
acting as a base (i.e. in an acidic environment)
and it will become negatively charged if its
acting as an acid (i.e. in a basic environment).
Since both reactions given above are reversible
and have different equilibrium positions hence
one of the two types of ions will be present in a
larger number even in a neutral environment.
A2 Chemistry Application Notes
ELECTROPHORESIS can distinguish between the
two ions. Place a drop of amino acid at the
center of a damp filter paper and attach two
oppositely charged battery terminals at
opposite ends of the filter paper. The drop of
amino acid will travel towards the negative
terminal if there are more positively charged
ions present and vice versa. Ninhydrin is used as
an indicator to make the colorless amino acid
visible.
ISOELECTRONIC POINT is the point when both
the negative ion of amino acid and the positive
ion of the amino acid are present in equal
amount in a solution. If Electrophoresis is done
at this point then the drop of amino acid will
remain stationary.
-NH3+1 in a zwitter ion acts as a stronger acid in
neutral conditions compared to the –COO-1
group. So in a neutral environment, a larger
quantity of zwitter ions are converted into
negative ions. To balance the positive and
negative ions to get an isoelectronic point, you
would need to shift the following reaction to
the left. This can be done by adding a small
quantity of acid.
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amino acids can join together as a chain in a
similar manner, these are known as
polypeptides (protein chain):
Protein chains or polypeptides have around 502000 amino groups joined together.
A Protein chain has two sides, N-Terminal is the
side which ends with the –NH2 group and CTerminal is the side ending with the –COOH
group. N-Terminal is always written on the left.
Some common amino acids are given below
based on the different –R group attached.
Non polar R-group Amino Acids
Alanine (ALA)
Valanine (VAL)
Hence, most amino acids, have an isoelectronic
point at around PH 6.
INTRODUCTION TO PROTEINS
Two different amino acids can combine to form
dipeptides in a condensation reaction.
The linkage highlighted in blue is known as
Amide Linkage or Peptide Linkage. Multiple
Polar R-group Amino Acids
The associated –R group in each of the amino
acid has polarity
A2 Chemistry Application Notes
Serine (SER)
Electrically Charged - Acidic or Basic –R group
Amino Acid
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Amide Link
Example of hydrogen bonding due to amide
linkage given below
Aspartic Acid (ASP)
Lysine (LYS)
PRIMARY STRUCTURE OF A
PROTEIN
Primary structure tells you the order in which
each amino acid joins
to form a protein. Each
Amino Acid is written in
a Three letter
abbreviation starting
from the N-terminal on
the left to the Cterminal on the right.
Secondary Structure of Proteins
The Amide Linkage is capable of forming
Hydrogen bonds. These Hydrogen bonds help
protein chains form regular arrangements.
ALPHA HELIX Arrangement due to Hydrogen
Bonding.
The Protein chain exists as a spiral with
overlapping chain forming hydrogen bonds
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between themselves. The R-chain always points
outwards. The N-H bond points upwards
whereas the C=O bond points downwards. Each
complete circular spiral has approximately 3.6
Amino Acid residues.
Tertiary Protein Structure
BETA PLEATED SHEETS due to hydrogen bonds.
The protein chain is folded as described below
with each chain lying in parallel and forming
hydrogen bonds parallel to each other.
Tertiary structures are formed when the entire
chain (including the secondary structures)
bends on itself usually to interactions involving
the R-group in amino acid residues.
For example Aspartic acid has an extra –COOH
group and Lysine has an extra -NH2 group. If
they are part a protein chain then the –COO-1
ion might form an ionic bond with the –NH2+1
group e.g.
Hydrogen bonds are shown in the following
structure where the black and red atoms show
C=O and the black and blue atoms represent NH.
Similarly some –R groups might contain –OH
functional group e.g. Serine. These –R groups
can then form hydrogen bonds themselves
bending the secondary structure in different
directions.
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Some –R groups could set up large van der
waals dispersion forces due to their large size.
These VDW forces would be strong enough to
fold the structure as well. E.g.
ENZYMES
Di sulfide bridges can also be formed by
residues of cysteine shown below
The following diagram shows all the possible
folding of Alpha-Helix due to different
interactions
Enzymes are globular (spherical) proteins. The
globular structure is caused by the tertiary
structure of the proteins which folds the
secondary structure. It is similar to a tangled
mass of string, where the string represents the
protein chain.
These globular proteins have excellent catalytic
properties which are much better than
inorganic catalysts like transition metals.
SPECIFICITY
Enzymes are very specific and only work with a
specific reactant molecule. Slight changes in the
shape and structure of the reactant molecule
will make the Enzyme redundant. E.g. Carbonic
Anydrase only catalyzes the following reaction
A2 Chemistry Application Notes
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and helps to remove CO2 from the blood
stream.
CO2
+
H2O

H2CO3
Enzymes have active sites which are
responsible for their specificity. These active
sites are usually cracks or openings in the
globular structure. These cracks or openings
result from the folding when the secondary
structure bends and folds. Therefore, the
reactant molecule also known as substrate,
needs to have a specific shape and structure to
fit into these active sites.
Apart from the shape, the active site must
contain the right arrangement of functional
groups and chains to chemically react with the
substrate in the right order.
A typical enzyme catalyzed reaction is shown by
following symbols where E represents Enzyme
and S represents substrate:
The E-S Complex is formed when the Enzyme
and Substrate join together. Eventually the
Enzyme breaks away leaving the Product P
behind. The E-S complex can also just break off
without anything happening hence the first
stage is reversible.
Properties of Enzyme Catalyses



e.g. groups in the active sites need to interact
with the groups in substrate as shown below,
some are forming ionic bonds, others are
forming hydrogen bonds, This would only be
possible if the groups were present in the right
order.

Speeds up reaction rates by 106 to 1012
Very specific
Only occurs in mild conditions,
Temperature<100
C, Atmospheric
Pressure, close to neutral pH.
Reaction rate could be regulated by
controlling concentration of enzyme.
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One example of competitive inhibitor
is the following catalysis carried out
by the enzyme succinate
dehydrogenase.
Enzymes lower Activation Energy
ENZYME INHIBITORS
A) COMPETITIVE ENZYME INHIBITOR
Inhibitors prevent or inhibit enzyme activity.
Competitive enzyme inhibitors are similar to
substrates in shape and can fit into the active
sites in the enzyme. But unlike substrates they
do not undergo any change, instead they block
the active site by occupying it and preventing
catalysis from happening. Competitive
inhibitors do not destroy the active site or the
This catalysis can be inhibited by the following
competitive inhibitor which has the exact same
shape and the exact same functional groups
interacting with the active site in the enzyme
B) NON COMPETITIVE INHIBITORS
Non Competitive inhibitors do not block
the active site but attach somewhere else
on the enzyme. This has two effects.
substrate but temporarily block it.
The substrate and competitive inhibitor both
are fighting for access to the site. If Substrate is
in higher concentration than it will get access to
the site more often compared to the
competitive inhibitor and enzyme catalysis
could proceed.
1) By attaching somewhere else, they
change the shape of the enzyme
2) By attaching somewhere else, they
alter the nature of the functional
groups/side chains in the active sites, so
when a substrate attaches to the active
site, no reaction is possible.
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 Temperature (speed of molecules)
 Activation energy of reaction
 Thermal
stability
of
enzyme/substrate
The following diagram shows how
enzyme activity increases.
One example of a non-competitive inhibitor:
+1
Ag poisoning leads to the replacement of H
atom in the S-H side chain in the cysteine amino
acid residue. This changes the structure of the
protein chain in the Enzyme as disulfide bonds
would no longer be possible. The significant
change in Enzyme shape makes the Enzyme
redundant and incapable of Catalysis.
FACTORS AFFECTING ENZYME
ACTIVITY
Enzyme activity is very specific and is severely
affected if the weak(or strong) interactions (e.g.
disulfide bonds, ionic interactions, van der
waals etc ) are altered. This will alter the
tertiary structure of proteins/enzymes, which
will then alter the shape of the active site.
Slight changes in PH and temperature will alter
these interactions and the shape/specificity of
the enzyme. Similarly, different chemical
substances would introduce irreversible
changes in the active sites. Following factors
would affect enzyme activity:
It is optimum at 40 C and decreases at high
temperature, as enzymes get denatured and
tertiary structures change due to high speed
collisions of enzymes which affect the weak
interactive forces holding the tertiary structure
together.
Changes in PH would also alter the tertiary
structure of the enzyme and therefore affect
the shape of the active site. A change in PH
would alter R groups in amino residues e.g –NH2
changes into –NH3+1 or –COO=1 would change
into –COOH.
Most enzymes therefore are active over a very
narrow (specific) PH range. The following
diagram shows PH ranges for certain enzymes.
A2 Chemistry Application Notes



Pepsin hydrolysis proteins to peptides
in very acidic condition in stomach
Amylase in saliva hydrolyses starch in
sugar and maltose in neutral
environment.
Trypsin hydrolyses peptides to amino
acids in alkaline small intestine.
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ENZYME COFACTORS
Some enzymes need a non-protein group or
cofactor so they can function as catalysts.
Apoenzyme + Cofactor  Holoenzyme
Apoenzymes are proteins, which become
functional enzymes called Holoenzymes due to
the presence of cofactor. These cofactors might
be permanently attached to the active sites, in
which case they are known as prosthetic group.


Enzymes can be chemically denatured



High salt concentration, increases ion
concentration which affects the ionic
interaction in the tertiary structure of
enzymes, changing its shape.
Urea denatures proteins by interfering
with hydrogen bonding which keeps the
secondary and tertiary structure of
enzyme intact.
Chemical inhibitors irreversible change
the enzyme by reacting with amino acid
residues at the active site.
Diagram shows serine amino acid residue at the
active site reacting with a chemical inhibitor
DFP.
Carbonic anhydrase has Zn2+ at the
heart of the active site (permanently
attached)
Cytochrome oxidase has the haem
group present as a cofactor. Example of
haem group is shown, generally useful
for respiration. Haem group shown
below:
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Proteins in cell membranes form water and ion
channels. They have small pores which work as
active sites in controlling the inflow/outflow of
ions. Proteins that form ion channel should be
hydrophilic (water loving) so that ions could be
transported.
Cofactors which only attach to an enzyme to
make it effective and then get removed once
the function is performed are known as
coenzymes. Their working is shown in the
previous diagram. Coenzymes are mostly
organic complex molecules which provide
electrons or help the active site take part in
redox reactions. Coenzymes are generally
derived from vitamins. NAD+, NADP+, FAD are
some important coenzymes that help enzymes
take
part
in
redox
reactions
by
+
accepting/donating H and electrons. They are
also known as H+ carriers.
Coenzyme A is useful in metabolism of fatty
acid and carry the ethanoyl group CH3CO-. It can
form esters with fatty acids.
ION CHANNELS IN BIOLOGICAL MEMBRANES
Example: A nerve cell at rest will have a higher
concentration of Na+ outside the cell membrane
and a higher concentration of K+ inside the cell.
It therefore has two separate Sodium and
Potassium channels. If the Sodium channel is
open then ions can flow through the
pore/channel. These ion channels are very
specific, and a sodium channel will only
transmit sodium ions as only they are capable
of fitting in the pore and the right interaction
with the channel wall would not hinder the flow
of ions. Similarly these channels could be
inhibited by inhibitors which would block these
channels.
ATP is needed for the proper function of these
channels which acts as a coenzyme. Without
ATP these channels would stop functioning.
A2 Chemistry Application Notes
DeoxyriboNucleic Acid (DNA)
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DeOxyRibose attached to a Phosphate Group
Two DNA strands running in opposite direction
and forming a Right handed helix, similar to a
twisted ladder
Organic Base
The final group attached to the above structure
is an organic base. There are 4 different types of
organic bases which are Cytosine (C), Thymine
(T), Adenine (A), and Guanine (G).
These bases attach on the OH group on the
right C atom on the deoxyribose .
Each DNA strand is a condensed polymer of
sugar molecules and phosphate groups. Organic
bases (ammines) are attached to these sugarphosphate backbone.
Construction of DNA Molecule
Sugar – DeOxyRibose
Together they form a nucleotide which is the
basic building block of a DNA strand.
Below is a nucleotide with a cytosine base.
Phosphate Group
Formation of DNA Strands by condensation
polymerization
Two nucleotides join together to form DNA
strands as shown below:
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Shown below is a GC base pair
joined together by three hydrogen
bonds.
Base Pairing
An AT base pair is shown below which has two
hydrogen bonds connecting them together.
Two DNA strands running in opposite direction
will have their organic bases (G,C,A,T) pointing
towards each other as shown below:
Another diagram showing the structure of two
DNA strands joined together by organic bases.
Where P and cyclic compound represents
deoxyribose (sugar) and phosphate groups
linked together in a DNA strand. Notice the 3’
and 5’ carbon atoms on deoxyribose.
AT base and GC base pair:
Due to the number of hydrogen bonds formed
and the size and shape of the bases, GC and AT
base pairs are more stable.
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RIBONUCLEIC ACID
DNA stores genetic information whereas RNA
transfers genetic information.
Three different types of RNAs
1. Messenger RNA (mRNA)
2. Ribosomal RNA (rRNA)
3. Transfer RNA (tRNA)
Differences between RNA and DNA
Sugar: Pentose sugar present in DNA is
deoxyribose. Pentose sugar present in RNA is
ribose.
Bases: Adenine, cytosine, guanine, thymine
bases present in DNA. Adenine, Guanine,
Cytosine, Urasil bases present in RNA.
Structure: Double Helix (two strands) present in
DNA. In RNA, single strand is present which may
fold on itself to form helical loops.
GENE EXPRESSION
DNA is capable of self-recognition and selfreplication.
DNA duplicates every time a cell divides and
produces daughter copies.
DNA is used as a blue print for the synthesis of
structural proteins, enzymes, antibodies.
Sequence of amino acid in a polypeptide chain
is determined by a certain stretch of DNA.
In RNA, instead of thymine base you have uracil.
Note there is only a difference of CH3.
The following image also shows the structure of
a tRNA strand forming a clover leaf structure.
This structure helps tRNA in protein thesis.
Polypeptide chain copies are generated through
a two stage process:
Stage 1 : TRANSCRIPTION
DNA template is copied into an intermediary
nucleic acid molecule (mRNA)
Stage 2 : TRANSLATION
mRNA directs the assemble of the polypeptide
chain. Ribosomes attach to and move along the
mRNA as the polypeptide chain is synthesized.
Formation of New DNA Strands
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Entire reaction is catalyzed by an enzyme called
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GENE SEQUENCING
The DNA sequence is coded by using only the
base letters. They are coded in the 5’ to 3’
direction.
Since both DNA strands are the same except
running in opposite direction and
complementing each other, hence one of the
strands is not written.
EXPRESSING THE MESSAGE : ROLE OF RNA
Each gene is a coded description for
synthesizing a particular protein. A specific
code from the DNA is first copied to the
messenger RNA (mRNA). mRNA then travels
out of the nucleus and into the cytoplasm of
the cell.
DNA polymerase.
The enzyme interferes with hydrogen bonding
in the base pair and unzips the DNA molecule,
separating the DNA strands, forming bubbles in
the double helix structure. Nucleotide
triphosphate shown above then attaches new
nucleotides. Each DNA molecule is replicated in
the 5’ to 3’ direction so one DNA strand is built
in the opposite direction to the other one. A
human DNA replicates 150 million base pairs.
RNA’s are much shorter than DNA and only
contain the code for one polypeptide chain. A
single protein consists of many polypeptide
chains (hence the process is way more
complicated). Enzyme RNA polymerase is used
for copying mRNA.
A small portion of the double helix unravels and
Semi-conservative replication shown below.
Each new DNA has new strand and one old
strand.
mRNA is copied:
A triplet of bases on the mRNA represents a
code for a specific amino acid. The message is
read again from the 5’ to the 3’. There are
A2 Chemistry Application Notes
generally 20 amino acids each represented by a
combination of three bases. These triplets are
known as codons.
The RNA sequence is exactly the same as the
DNA sequence, except the base Uracil has
replaced Thymine.
Example of an mRNA transcription.
A promoter sequence and a termination
sequence of bases in the DNA is present which
instructs the mRNA to start and stop copying, so
only a specific portion of DNA sequence is
copied.
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until a stop signal is read represented by codons
as well.
BUILDING THE PROTEIN FROM Mrna:
mRNA cannot interact directly with amino acids
so translating the code into a sequence of
amino acids is controlled by ribosomes which
are complicated proteins that have rRNA of
their own.
Ribosomes travel the mRNA from 5’ to 3’ and
then bind to the start point. The transfer RNA
then starts looking for Amino Acids and starts to
bind them in the right order based on the
sequence given by the mRNA.
WHAT THE CODE MEANS:
Each three letter base code (codon) represents
a specific amino acid. A single amino acid could
be represented by more than one Codon.
The start signal is 5’-AUG-3’ which represents
methionine amino acid. Hence each
polypeptide chain initially begins with
methionine. The initial methionine may break
away once the translation is complete. The
amino acids continue to add to the polypeptide
tRNA shown above has an anticodon side which
attaches to the mRNA chain. Meanwhile the
amino acid gets attached to the –OH group on
the other side forming an ester. The code
(anticodon) found at the bottom of tRNA (see
above) would be exactly complementary to the
code found on the mRNA.
Each tRNA molecule picks up the amino acid
determined by the anticodon code given at the
bottom. The process is complicated, no need
A2 Chemistry Application Notes
for going into details about how it picks up the
right amino acid.
Translation Process involves three steps:



Initiation
Elongation
Termination
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SICKE CELL ANAEMIA
Red blood cells have a crescent moon shape
instead of the normal disc shape.
Abnormality alters the sixth amino acid in 146
amino acid chain.
The change in shape does not allow red blood
cells to pass through small capillaries; hence
MUTATIONS
A single change in the replication of DNA could
result in a mutation and this change would then
be copied to all new generations. UV light,
cigarette smoke or different pollutants might
bring on mutations.
Most mutations are harmless, since each amino
acid is represented by multiple codes, hence a
change from CAA to CAG would still refer to an
valanine. But sometimes, a slight change in
code could result in a completely different
protein synthesis.
Examples of Mutation related Disorders
oxygen supply to organs is affected.
CYSTIC FIBROSIS
Affects normal fluid secretions. Thick sticky
mucus is released instead in vital body organs.
Lungs, pancreas and sweat glands are affected.
Infected children get frequent lung infections
and have digestive problems.
Chloride ion concentration in cell increases in
infected children. CTFR protein responsible for
controlling the ion channel and regulating
Chloride ion concentration is missing.
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