Chemicals of Life 1 3
Chemicals of Life 1 3
Chemicals of Life 1 3
CHEMICALS OF LIFE
These are building blocks of life. Organisms are made up
of both inorganic and organic molecules.
Biological molecules
Living organisms are made of atoms that combine to form
molecules which are the building blocks of life. The Hydrogen bond
molecules vary from being simple to large molecules.
Many simple molecules are soluble and can easily be
transported within the cells. Large molecules are used for Water molecules have negative and positive ends so they tend
storage or structural purposes. These molecules are either to be pulled together by hydrogen bonding
organic (fats, starch, proteins) or inorganic (carbon
dioxide, water, nitrogen).
Water is a universal solvent
The dipolar molecules make water an excellent solvent. It
Water is referred to as a universal solvent because it dissolves
Water is a vital chemical constituent of living cells and it many things. Polar and ionic substances have an
also provides an environment for those organisms that live electrostatic charge, so they are attracted to the charges on
in water. water molecules. They dissolve readily in water and are
Water has unusual properties which are mainly due to its therefore called hydrophilic (water-loving). Non-polar
small size, polarity and the hydrogen bonding between its substances, such as oil, have no charge on their molecules.
molecules. Polarity is the uneven distribution of charge They do not dissolve readily in water and are called
within a molecule. hydrophobic (water-hating). When any salt or ionic
compound dissolves in water, the ions separate and layers
of water molecules form around the ions. These layers of
Arrangement of atoms in a water molecule water molecules stop ions or polar molecules from
clumping together and keep the particles in solution.
Hδ+ Hδ+
Water is a good solvent because its molecules form around
ions or molecules. In a solution of sodium chloride, the
O2δ+ positive (hydrogen) ends of water molecules point towards
the negative chloride ion, and the negative (oxygen) ends
The oxygen atom has a tendency to draw point towards the positive sodium ion.
electrons closer it. This gives the oxygen end of Layers of water molecules form around many non-ionic
organic substances such as sugars because they contain
a water molecule a slightly negative charge and polar side groups.
the hydrogen end a slightly positive charge.
Chloride ion, Cl- Sodium ion, Na+
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RONALD SIKU
Properties of water than in water. This is why water expands when it freezes.
High heat capacity. Heat capacity of water is the amount Although individual hydrogen bonds are weak, combined
of heat required to raise the temperature of 1 kg of water in their thousands they make ice as solid rock.
by 1 0C. Water has a high heat capacity. A large increase
in heat energy results in a relatively small rise in Other properties of water
temperature. This is because much of the energy is used in It is difficult to compress water. This enables
breaking the hydrogen bonds which restrict the movements water to form an important structural agent,
of the molecules. Temperature changes within the water forming hydrostatic skeleton in worms and turgor
are minimized as a result of its high heat capacity. in plants.
Biological processes, therefore, operate over a smaller It has a relatively high density compared with
temperature range, proceeding at more constant rates and air. Water supports organisms as large as whales;
are less likely to be inhibited by extremes of temperature. it also supports and disperses reproductive
structures such as larvae and large fruits such as
The high heat of vaporization. The latent heat of coconuts.
vaporization is the amount of energy required to vaporize Water is colourless and transparent.
a liquid, i.e. to overcome the attractive forces between its Transmission of sunlight enables aquatic plants to
molecules so that they can escape as a gas. A relatively photosynthesize.
large high amount of energy is needed to vaporize water. It conducts electricity. However, pure water has
The energy transferred to water molecules to allow them to a low conductivity but dissolved ions make it a
vaporize results in a loss of energy from their surroundings good conductor. This enables the transmission of
causing cooling. This is made use of in the sweating and impulses in organism.
panting of mammals. A large amount of heat can be lost Water is a liquid at room temperature. This
with minimal loss of water from the body. provides a liquid environment inside cells and
aquatic environments for organisms to live in.
The high heat of fusion. The latent heat of fusion is the Water is the universal solvent. It dissolves more
amount of heat energy required to melt a solid, in this case, substances than any other solvent. This enables
ice. With its high heat capacity, water requires relatively chemical reactions inside cells to take place in
large amounts of heat energy to melt it. At the same time, aqueous solution; water also forms the main
liquid water must lose a relatively large amount of heat transport medium in organisms.
energy to freeze. Contents of cells and their environments Water has a low viscosity. It flows freely, its
are therefore less likely to freeze. Ice crystals are molecules can easily slide over each other. This
particularly damaging if they develop inside cells. makes water to freely flow through narrow
vessels. Watery solutions also form lubricants for
High surface tension and cohesion. Cohesion is the force example mucus which allows food to move easily
that makes water molecules stick together. At the surface down the oesophagus.
of a liquid, a force called surface tension exists between Water has a high tensile strength caused by
the molecules as a result of cohesive forces between water combined hydrogen bonds between its molecules.
molecules. This forms a firm ground for some organisms It therefore continuously flows in columns through
which can rest on the water surface. Such organisms can the xylem vessels up to the top of a tree during
exploit different niches. transpiration.
The cohesion of water molecules is also important in cells
and in translocation of water through the xylem in plants. Importance of water
Structure: high water content of cells (70-95%).
Density and freezing properties. The density of water Solvent and medium for diffusion.
decreases below 4 0C. This makes ice to float. It first forms Reagent in hydrolysis.
at the surface and the bottom last. Ice insulates the water Support for aquatic organisms.
below it, thus increasing the chances of survival of Fertilisation by swimming gametes.
organisms in the water. This is important in cold climates Dispersal of seeds, gametes and larval stages of
and cold seasons and must have been particularly so in the aquatic organisms, and seeds of some terrestrial
past. species e.g. coconut.
Osmosis and turgidity (important in many ways,
In liquid water hydrogen bonds are constantly forming and such as growth (cell enlargement), support, guard
reforming. When water freezes, each molecule forms cell mechanism).
hydrogen bonds with four other molecules. This makes a Reagent in photosynthesis.
rigid lattice, which holds water molecules further apart Transpiration.
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Translocation of inorganic ions and organic Carbohydrates
compounds. These are substances which contain the elements carbon,
Germination of seeds; water causes the swelling hydrogen and oxygen and have the general formula
and breaking open of the testa and further Cx(H2O)y, where x and y are variable numbers; their name
development. (hydrate of carbon) is derived from the fact that hydrogen
Transport in the blood vascular system, lymphatic and oxygen are present in the same proportions as in water,
system, excretory system. namely two hydrogen atoms to one oxygen atom. They are
Osmoregulation. all aldehydes or ketones and all contain several hydroxyl
Cooling by evaporation, such as sweating, panting groups.
Lubrication, as in joints. Carbohydrates are divided into three main classes:
Support. A hydrostatic skeleton of e.g. annelid monosaccharides, disaccharides, and polysaccharides.
worms Protection, for example, lachrymal fluid
(tears), mucus Migration in ocean currents. Monosaccharides. These are simple sugars. They have the
general formula (CH2O)n. Letter n can be any number from
Acids, Bases and Salts 3 to 7. They are grouped according to the value of n.
When n=3, trioses; n=4, tetroses; n=5, pentoses; n=6,
Acid is a substance that ionizes in aqueous solution to hexoses.
release hydrogen ions as the positively charged ions. It is a Aldoses and ketoses
proton donor. The strength of an acid is determined by the In monosaccharides, all the carbon atoms except one have
easy it can release hydrogen ions; strong acids ionize a hydroxyl group attached. The remaining carbon atom is
completely while weak acids partially ionize in aqueous either part of an aldehyde group. This monosaccharide is
solutions. called an aldose or aldo sugar. For a keto group then the
H2SO4(aq) 2H+ (aq) + SO42-(aq) monosaccharide is called a ketose or keto sugar. All
A base is a substance that accepts protons from the acid. monosaccharides are aldoses or ketoses.
Sodium carbonate dissociates and releases hydrogen The simplest monosaccharides are the trioses,
carbonate ions. These ions accept protons from the acid. In glyceraldehyde, and dihydroxyacetone. Glyceraldehyde
this way, it acts as a buffer by resisting change in pH. has an aldehyde group and dihydroxyacetone has a keto
Na2CO3(aq) H+(aq) + HSO4-(aq) group.
H H
Even if moderate amounts of the base are added, it accepts Aldehyde
the OH- ions to form water and carbonate ions. C O group H C OH
In the human body, many substances play a role in
H C OH C O keto
buffering the body. This is important to enable chemical group
reactions to proceed without alteration of pH. H C OH H C OH
Phosphate salt is one of the salts used during the regulation H H
of blood pH by the kidney. Organic substances like glyceraldehyde dihydroxyacetone
proteins and haemoglobin also accept ions. Classification of monosaccharides
The biological importance of this is that cells and tissues Category Example
can only function properly at round neutrality; they cannot Aldotriose Glyceraldehyde
tolerate fluctuations in pH. Aldopentose Ribose, deoxyribose
Aldohexose Glucose, galactose
Macromolecules Ketohexose Fructose
A macromolecule is a giant molecule made from many
repeating units of simple molecules. Molecules built like The carbonyl group on all monosaccharides readily
this are known as polymers. The individual units are donates electrons. This is the property that makes
known as monomers. The units are joined by a process monosaccharides reducing sugars. When heated with
known as condensation polymerization, which means loss Fehling’s or with Benedict’s reagents they reduce copper
of water occurs. (ii) ions to copper (i), forming a brick-red precipitate of
They can be broken down again by the opposite process copper (i) oxide.
called hydrolysis. Macromolecules may include
polysaccharides, proteins, lipids, and nucleic acids. Hexoses. Glucose is the most abundant hexose. Its
chemical formula is C6H12O6. Glucose exists in different
shapes. This phenomenon is known as isomerism. Each
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isomer has the same chemical formula but a different Used in the synthesis of Ribulosebisphosphate, a
structural formula. carbon dioxide acceptor in photosynthesis.
α and β glucose are the common isomers of glucose. Ring
structures are the same but only the positions of hydrogen Hexoses (C6H12O6)
and hydroxyl groups on carbon atom 1 are different. In
three-dimensional, glucose structure -CH2OH group is Source of energy when oxidized in respiration
above the ring in both alpha and beta glucose. The -OH (glucose).
group is below carbon atom 1 in alpha glucose but above Synthesis of disaccharides; two monosaccharides
carbon atom 1 in beta glucose. units can link together to form a disaccharide.
Synthesis of polysaccharides.
H
Disaccharides
1C O These are formed when two monosaccharides combine by
means of a chemical reaction known as condensation. A
H 2C OH
water molecule is given off during the reaction.
HO 3C H
C6H12O6 + C6H12O6 ↔ C12H22O11 + H2O
H 4C OH
H 5C OH The bond formed between two monosaccharides as a result
of condensation is called a glycosidic bond and it normally
6CH2OH
forms between carbon atoms 1 and 4 of neighbouring units.
Open chain form The process can be repeated many times to build up the
giant molecules of polysaccharides. The monosaccharide
units are called residues once they have been linked. A
6 CH2OH
maltose molecule contains two glucose residues. The most
H 5C O H common disaccharides are maltose, lactose, and sucrose.
H
4C OH H C
1 Maltose. This occurs mainly as a breakdown product
OH C C OH
3 2 during digestion of starch by enzymes called amylases.
H OH This commonly occurs in animals and in germinating
seeds. In seeds, it is made use of in brewing beer when
α-glucose barley grain is used as the source of starch. Germination of
the barley is stimulated and this results in the conversion
6 CH2OH of the starch to maltose, a process known as malting.
H 5C O OH
H Lactose, or milk sugar. This is found exclusively in milk
4C OH H C and is an important energy source for young mammals. It
1
OH C
3
C H is digested slowly and steadily releases energy.
2
H OH
Sucrose, or cane sugar. This is the most abundant
β-glucose disaccharide in nature. It is most commonly found in
plants, where it is transported in large quantities through
The different arrangements of glucose have important phloem tissues. It makes a good transport sugar because it
biological consequences for example; alpha glucose is very soluble, and can, therefore, be moved efficiently in
molecules combine to form starch whereas beta glucose high concentrations. It is also chemically unreactive.
molecules combine to form cellulose. It is consumed in large amounts to sweeten many foods.
Functions of monosaccharides
Trioses. C3H6O3e.g glyceraldehyde, dihydroxyacetone. It is formed when one α-glucose and one β-fructose join in
They form intermediates in respiration and photosynthesis. a condensation reaction. A bond is formed between the
Pentoses C5H10O5 carbon atom 1 of the α-glucose ring and carbon atom 2 of
Used in the synthesis of nucleic acids, ribose is a the β-glucose. It is thus called an α-1, 2-glycosidic linkage.
constituent of RNA, deoxyribose of DNA. It is at these atoms that the carbonyl groups occur in both
Used in the synthesis of some coenzymes, e.g. glucose and fructose. There are no free carboxyl groups in
ribose is used in the synthesis of NAD and NADP sucrose which are therefore a non-reducing sugar. Sucrose
Synthesis of ATP. This requires ribose. can be easily hydrolysed into monosaccharides by boiling
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with dilute hydrochloric acid or by incubating it with the Formation of glycosidic bond in sucrose by condensation
enzyme sucrase (invertase)
6 CH2OH
6 CH2OH
H 5C O H H 5C O H
4C
H
OH H C
1
+ 4C
H
OH H C
1
OH C C C C
3 2 OH OH 3 OH
2
H OH H OH
α-glucose α-glucose
H2O
6 CH2OH 6 CH2OH
H 5C O H H 5C O H
H H
4C OH H C1 4 C C maltose
OH H
1
OH C
3
C C C OH
2 3
O 2
H OH H OH
1,4-glycosidic bond
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by 1, 4-glycosidic bonds. These bonds cause the
H H H
chain to coil helically into a more compact shape.
Plants store glucose as amylose or amylopectin, 4 1 4 1
glucose polymers collectively called starch. o o
Glucose storage in polymeric form minimizes 1-4
osmotic effects. o 1-6
6
H H H H H H
Amylopectin is also compact as it has many
branches, formed by 1, 6-glycosidic bonds. It has 4 1 4 1 4 1
O o o O
up to twice as many glucose residues as amylose.
A suspension of amylose in water gives a blue- 1-4 1-4
black colour with iodine-potassium iodine
solution, whereas a suspension of amylopectin The long chains in starch are coiled into a helix and the
gives a red-violet colour. This forms the basis of orientation of the glucose sub-units is such that most of
the test for starch. The branches produce a the OH groups potentially capable of forming hydrogen
compact structure & provide multiple chains ends
bonds projecting inwards. So there are no cross-linkages
at which enzymatic cleavage can occur.
in starch making it not suitable to form structures. The
chain is coiled into a helix forming, in effect a cylinder in
which most OH groups capable of forming cross-linkages
projects into the interior. There are six glucose units for
every complete turn of the spiral.
Starch molecules accumulate to form starch grains. These to provide energy in the form of ATP. Starch is
are visible in many plant cells, notably in the chloroplasts never found in animal cells.
of leaves. It is used in storage organs such as the potato Test for starch
tuber, and in seeds and legumes. The grains appear to be
Starch is easily detected by its ability to turn the iodine in
made of layers of starch and are usually of characteristic
potassium iodide solution from a yellow colour to blue-
size and shape for a given species.
black. The colouration is due to the iodine molecules
becoming fixed in the centre of the helix of each starch
Suitability of starch as a storage substance
molecule. It is important that this test is carried out at
It is insoluble and therefore does not have any
room temperature (or below), as high temperatures cause
osmotic effects within cells, i.e. it does not tend to
the starch helix to unwind, releasing the iodine, which then
draw water into the cells.
returns to its usual yellow colour.
Being insoluble, it does not easily diffuse out of
cells.
It is compact, so a lot of it can be stored in a small
Glycogen
space.
This is the animal equivalent to starch. It is a
When hydrolysed it forms glucose, which is both
polysaccharide made from α-glucose and stored by many
easily transported and readily used in respiration,
fungi. In vertebrates, glycogen is stored in the liver and
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muscles, both are centers of high metabolic activity, where
it provides a useful energy reserve. Its conversion back to When two β glucose molecules line up, the -OH group on
glucose is controlled by hormones, particularly glucagone. carbon atom 1 can only line up alongside the -OH group
on carbon atom 4 if one of the molecules is rotated at 1800
Cellulose. This is made up of many straight chains each to the other. This is because of the -OH group on carbon
containing as many as 10,000 sugar units. Each chain is atom 1 projects below the ring and the -OH group on atom
made up of many β glucose units joined together in such a 4 projects above the ring. This rotation of successive
way that the OH groups are on both sides of the chain. residues is the underlying reason why cellulose has a
These are capable of forming hydrogen bonds with different structure to starch.
neighbouring OH groups resulting in the formation of
bundles of cross-linked parallel chains.
6 CH2OH OH H OH 6 CH2OH
3 2 H
H 5 O H 5 O OH
O OH H
4 H 1 4 1 4 H
OH H H OH H 1
3 2 H 3 2 H
OH H 5 O O
H OH 6 CH2OH H OH
cellulose
H OH CH2OH H OH CH2OH
O
O O
O O
OH H OH H
OH H OH H
O O
O O
CH2OH H OH CH2OH H OH
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when water enters by osmosis and also helps to determine They are not broken down by human enzymes, but instead
the shapes of cells. can be metabolized (or fermented) by bacteria present in
the large intestine. Pectin is a fiber made of galacturonic
It is fully permeable to water and solutes. This is because acid and other monosaccharides. Because it absorbs water
the matrix is made up of minute water-filled channels and forms a gel, it is often used in jams and jellies. Sources
through which free diffusion of salts, sugars can take place. of pectin include citrus fruits, apples, strawberries, and
The molecules of the matrix are hydrophilic. carrots. Mucilages and gums are similar in structure.
Cellulose is also an important food source for some Mucilages are dietary fibers that contain galactose,
animals, bacteria, and fungi. manose, and other monosaccharides; and gums are dietary
fibers that contain galactose, glucuronic acid, and other
monosaccharides. Sources of gums include oats, legumes,
Lignin. This is a polymer of various sugars and amino guar, and barley
acids. It is deposited in the spaces between the cellulose
molecules which makes the cell wall rigid rendering it Other sugar compounds
impermeable. It serves as a waterproof cement. This is
called lignification and occurs in plant cell walls Sugars like hexoses and pentoses readily link up with other
concerned with providing strength and conducting water. molecules to form more elaborate compounds. Some
Once lignification is complete the protoplasm can no sugars contain nitrogen: they are called amino sugars. A
longer absorb materials from outside the cell, which polysaccharide that contains amino sugars is called a
therefore dies. The lignified tissue is always dead. Its mucopolysaccharide. They are found in the basement
function of providing mechanical strength is entirely due membrane of epithelia, the matrix of connective tissue, the
to its lignocellulose composition. It can transport water and synovial fluid in vertebrate joints, and in the cell wall of
salts, this is because lignification involves loss of the prokaryotes. They also occur in chitin.
protoplasm, resulting in the formation of a hallow-
waterproof tube. Chitin. This is a strong carbohydrate chemically related to
cellulose. It is a polymer made up of many glucosamine
units (glucose in which one –OH is replaced by –
The commercial importance of cellulose NHCOCH3).
It is used in the manufacture of paper, cellophane, Glucosamine is one of the simplest amino sugars. The OH
celluloid, rayon and various plastics. group at position 2 is replaced by an amino group (NH2).
Cellulose derivatives such as cellulose nitrate are Amino sugars can form long chains like other sugars.
used in the manufacture of lacquers, films, and Chitin is a polymer of acetylglucosamine.
explosives. Glucosamine
Cellulose in cotton is used to make fabrics.
6 CH2OH
Dietary fiber. They don’t undergo digestion. Fibers H 5 O OH
contain sugars linked by bonds that cannot be broken down
4 H
by human enzymes. OH H 1
3 2 H
Pasta and whole-grain pieces of bread contain complex OH
carbohydrates, which are long strands of glucose H NH2
molecules. A fiber derived from plant sources contains
polysaccharides such as cellulose, hemicellulose, pectin,
Chitin forms long, straight chains similar to cellulose.
gums, mucilages, and lignins.
Chitin is the second most abundant carbohydrate. Chitin is
The indigestible fibers do not provide energy. Cellulose, found in the exoskeleton of insects and other arthropods.
hemicellulose, and lignin make up the structural part of Chitin is also found in the wall of fungal hyphae.
plants and are classified as an insoluble fiber because they
usually do not dissolve in water. Hemicellulose is a non-
starch carbohydrate polymer made of glucose, galactose,
xylose, and other monosaccharides; it can be found in
whole grains.
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LIPIDS chief constituent of olive oil and is liquid at normal
These are water-insoluble organic substances. Lipids are temperatures (melting point 13.40C), whereas palmitic and
formed by condensation reactions between fatty acids and stearic acids (63.1 0C and 69.6oC) are solid at normal body
alcohol. temperatures.
Classification of lipids
1. Simple lipids (Fats & Waxes). Essential fatty acids. These are fatty acids that cannot be
2. Compound or conjugated lipids. synthesized in the human body and must be taken in
3. Derived Lipids. adequate amounts in the diet. They are required for normal
4. Lipid-associating substances. growth and metabolism. They include linoleic, linolenic,
arachidonic, eicosapentaenoic acid, docosahexaenoic.
Constituents of lipids
Fatty acids. These contain the acidic group –COOH and The location of the first double bond in unsaturated fatty
are so named because some of the larger molecules in the acids affects omega-3 fatty acids and omega-6 fatty acids.
series occur in fats. They have the general formula R- Omega-3 fatty acid, the first double bond is between the
COOH where R is hydrogen or a group such as –CH3, - third and fourth carbon from the omega end, Example:
C2H3. The long chain of carbon and hydrogen atoms forms Alpha-linolenic acid, one of the two essential fatty acids.
the hydrocarbon chain. Omega-6 fatty acid, the first double bond is between the
Many of the properties of all lipids are determined by this sixth and seventh carbon from the omega end, Example:
tail, including their solubility in water. The tails are said to Linoleic acid, one of the two essential fatty acids
be hydrophobic, meaning water-hating (hydro, water, Omega-3, Linolenic found in coldwater fish, dissolves
phobos, fear) blood clots, lowers blood pressure, dilates the arteries.
Fatty acids contain one or more double bonds, such as oleic Source: vegetable oils such as corn oil, linseed oil, peanut
acid they are then said to be unsaturated. Fatty acids and oil, olive oil, cottonseed oil, soybean oil, and many other
lipids lacking double bonds are called saturated. plant oils, cod liver oil and animal fats.
Unsaturated fatty acids melt at much lower temperatures Name and occurrence of some fatty acids
than saturated fatty acids. Oleic acid, for example, is the
Glycerol The carboxyl groups of fatty acids react with the hydroxyl
This is an alcohol that contains three carbon atoms each groups of glycerol to form acylglycerols (glycerides) and
linked to a hydroxyl group. water. The bonds formed between the two components are
called ester linkages and the process is known as
H esterification. If only one hydroxyl group is esterified,
the product is a monoacylglycerol (monoglyceride), if
H C OH
two a diacylglycerol (diglyceride), and if three a
H C OH triglycerol (triglyceride).
H C OH
H Most lipids are triglycerides. They are made from the
alcohol glycerol.
Formation of lipids Glycerol has three hydroxyl groups, all of which can
combine with a fatty acid. Usually, all three undergo
condensation reactions. And the lipid formed is therefore
called triglyceride.
H H
H C O H HO OC (CH2)nCH3Condensation H C O OC (CH2)nCH3
H C O H HO OC (CH2)nCH3 H C O OC (CH2)nCH3
H C O H HO OC (CH2)nCH3 Hydrolysis H C OC (CH2)nCH3
O
H H
Ester bond
+
3H2O 3H2O
Functions of triglycerides
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Waxes
Simplified steroid
Waxes are esters of long-chain saturated and unsaturated
fatty acids (having 14-36 carbon atoms) with long-chain
alcohol (having 16-30 carbon atoms).
They are low- melting, stable solids which appear in
nature in both plants and animals.
The test for lipids is known as the emulsion test. Using a N CH COOH
completely dry and grease-free test tube, 2 cm3 of the H
sample being tested is added plus 5 cm3 of ethanol. The The simplest amino acid is glycine, where R is simply
contents are mixed thoroughly to dissolve any lipid in the hydrogen.
sample. When 5 cm3 of water is added and the mix shook
gently, a cloudy-white colour is formed. This confirms the The table below shows the 20 common amino acids
presence of lipids. Essential amino Non-essential amino acids
acids
For the control, the procedure is repeated using water Leucine Alanine (R-group is -CH3)
instead of the sample; the final solution remains clear. Arginine Asparagine
Lysine Aspartic acid (R-group is
CH2-COOH)
Methionine Cysteine (R-group is CH2-SH)
The cloudy colour is due to any lipid in the sample being Phenylalanine Proline
finely dispersed in the water to form an emulsion. Light Threonine Glutamic acid
passing through this emulsion is refracted as it passes Tryptophan Serine (R-group is CH2-OH)
Histidine Glutamine
from oil droplets to water droplets, making it appear
Isoleucine Glycine (R-group is -H)
cloudy. Valine Tyrosine
PROTEINS
They are polymers from amino acids. Some proteins form Rare amino acids. A small number of rare amino acids
complexes with other molecules containing phosphorus, occur in proteins of an organism. They are made from
iron, zinc, and copper. There are 20 different amino acids some of the common amino acids. For example,
that are commonly found in naturally occurring in hydroxylproline is made from proline, and is found in the
proteins. protein collagen, hydroxylysine is made from lysine, and
is also found in collagen. There is no DNA code for the
Amino acids rare amino acids, and they are made from their parent
Amino acids are the basic units from which proteins are amino acids.
made. There are over 170 amino acids in cells and tissues,
but 20 are commonly found in proteins. Plants make all Amphoteric nature of amino acids
amino acids they require from a simpler substance. They contain both an acid and a basic part. They exist as
Animals are unable to synthesise all the proteins they ions and can carry both a positive charge on the basic part
need. They obtain some amino acids directly from their and a negative charge on the acid part. They form a dipole
diet. These are termed essential amino acids. and therefore described as zwitterions.
Non-essential amino acids can be synthesized by animals The acidic property is derived from the carboxyl group
from essential amino acids by the transamination which can donate a proton so the molecule becomes
process. negatively charged when in an alkaline solution.
Essential amino acids are only described as essential The basic properties are derived from the amino group
because they cannot be synthesized. which can take up a proton so the molecule becomes
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positively charged in an acidic solution. They buffer the
Illustration of ionic bond
body because they can donate or receive protons.
NH3+
Ionic bond
Formation of a protein COO-
A protein is formed by condensation polymerization of
amino acids bonded by polypeptide bonds. Two amino
acids form dipeptide, and more than two amino acids Polypeptide chain
bonded together for a polypeptide. A polypeptide forms
the primary structure of proteins; the linear arrangement
of amino acids bonded together by only peptide bonds. Disulphide bond. This is formed when amino
acids containing sulphydryl groups are close to
Formation of a dipeptide each other in a protein. When two molecules of
H R cysteine line up alongside each other,
H R
neighbouring sulphydryl are oxidised and form a
N CH CO OH H N CH COOH sulphide bond.
H Formation of a disulphide bond
H2O
H2O S H H S
Hydrolysis
Condensation
disulphide bond
Hydrogen bond. The hydrogen part of the -OH
or -NH groups are usually slightly positively
Bonds used in protein structure charged. This is because the oxygen and nitrogen
atoms pull the bonding pair of electrons leaving
Apart from the peptide bonds which are formed from the hydrogen atom positively charged. The hydrogen
carboxylic and the amino groups of amino acids, other is then attracted towards a neighbouring
bonds exist as a result of variations in the R-groups. They electronegative oxygen or nitrogen atom, such as
include the following: the O of a C=O and NH groups, contained in
Ionic bond. Acidic and basic R groups exist in an another amino acid in the protein. Hydrogen
ionized (charged) state at a certain pH. The bonds are common in the alpha-helix and silk
negatively charged acidic R groups and the protein.
positively charged basic R groups in protein,
attract each other forming ionic bonds. These
bonds are much weaker than a covalent bond Formation of hydrogen bond
(peptide bonds). They can be broken by changing
the pH of the medium. Therefore, changes in pH δ+ δ-
can disrupt the structure of a protein. N H O C
Hydrogen
bond
Polypeptide chain
13
Polypeptide chain
Hydrophobic interactions. These are formed
when a polypeptide contains amino acids with Hydrogen bond Hydrogen bond
non-polar (hydrophobic) R groups. For example,
those in the amino acid tyrosine and valine. When
a polypeptide chain containing a number of these
groups is in aqueous solution, the chains tend to
fold so that the maximum number of hydrophobic
groups come into close contact and exclude
water. The hydrophobic groups tend to point
inwards towards the center of the roughly
spherical molecule while thee hydrophilic groups
face outwards into the aqueous environment,
making the protein soluble. This is how many
globular proteins fold up.
Illustration of hydrophobic interaction
14
Protein Conformation
This is determined by the primary structure, physical and
Renaturation of proteins. A protein can
chemical conditions. Alternations in pH, salt
spontaneously refold into its original structure after
concentration, temperature, or other environmental
denaturation, provided conditions are suitable.
factors can cause a protein to unravel. This loss of a
protein’s native conformation is called denaturation. A
denatured protein is biologically inactive. Classification of proteins according to structure
Denaturation is the loss of the specific three- dimensional Globular protein. They include enzymes, haemoglobin,
shape of a protein molecule. The change may be hormones, and antibodies. Tertiary structure is the most
temporary or permanent, but the amino acid sequence of common in globular proteins. The polypeptide chains are
the protein remains unaffected. During denaturation, the folded to form a spherical shape. They carry out metabolic
molecule unfolds and can no longer perform its normal functions.
biological function Fibrous proteins
They form long chains that run parallel to one another.
Causes of denaturation of proteins
The chains are linked by cross-bridges and so form very
Heat or radiation. e.g. infra-red or ultraviolet light. stable molecules. An example is collagen and keratin.
Kinetic energy is supplied to the protein causing its atoms Collagen is found in tissues requiring physical strength,
to vibrate violently, so disrupting the weak hydrogen and e.g tendons, and walls of blood vessels, bone and the
ionic bonds. Coagulation of the protein then occurs. fibres that hold teeth in place. Keratin is found in nails,
Strong acids and alkalis and high concentrations of hooves, and hair.
salts. Ionic bonds are disrupted and the protein is Intermediate proteins. These are fibrous but soluble.
coagulated. Breakage of peptide bonds may occur if the They include fibrinogen which forms insoluble fibrin
protein is allowed to remain mixed with the reagent for a when blood clots.
long period of time.
Comparison between fibrous and globular proteins
Heavy metals. The positively charged ions of heavy Fibrous proteins Globular proteins
metals (cations) form strong bonds with the negatively Repetitive regular Irregular amino acid
charged carboxyl groups on the R groups of proteins and sequences of amino sequences
often disrupt ionic bonds. They also reduce the protein's acids
electrical polarity and thus increase its insolubility. This Insoluble Water-soluble; form colloidal
causes the protein to precipitate out of the solution. suspensions
Organic solvents and detergents. These reagents Support and structural Metabolic functions
disrupt hydrophobic interactions and form bonds with functions
hydrophobic (non-polar) groups. This, in turn, causes the Stable structure Relatively unstable
disruption of hydrogen bonding. When alcohol is used as Polypeptide chains Polypeptide chains folded into
a disinfectant it functions to denature the protein of any form long parallel a spherical shape
bacteria present. strands
Examples include Examples include all
collagen and keratin enzymes, some hormones(like
insulin) and haemoglobin
18
SSABAKRISTU RONALD SIKU 0783-686735
Pyrimidine
5CH2OH H
O
4C C1
H H OH
H
3C 2C
OH OH
Ribose sugar Purine
5CH OH O H
2
4C C1
H H OH
H
3C 2
C
OH H
Deoxyibose sugar
3. Phosphoric acid (H3PO4). This gives nucleic
acids their acid character.
2. Bases. Each nucleic acid contains four different
bases. Two derived from purine and two from OH
pyrimidine. The nitrogen in the rings gives the
molecules their basic nature.
O P OH
Purines are adenine (A) and guanine (G).
Pyrimidines are thymine (T) and cytosine (C) in DNA,
OH
with uracil (U) in place of thymine in RNA.
Thymine is chemically very similar to uracil (it is 5-
methyl uracil, that is uracil with a methyl group, -CH3, on
carbon atom 5).
Purines have two rings and pyrimidines have one ring in Formation of nucleotide
their structure.
These bases are commonly represented by their initial The combination of a sugar with a base occurs with the
letters A, G, T, U, and C. elimination of water and therefore is a condensation
reaction. A nucleotide is formed by further condensation
with phosphoric acid. Different nucleotides are formed
C N according to the sugars and bases used.
H N C
C C
19
OH A NUCLEOTIDE OF DNA
OH PHOSPHORIC ACID
O P OH
O P OH
O
OH
5CH H
H2O 2 O C N
5CH OH O H
2 1C
H2O
4C N C
4C C1 H H C
C
C N H
H H OH 3C 2C
H H N C OH H
3C 2
C
OH H C C
DEOXYRIBOSE ORGANIC BASE
Phosphate group
base
sugar
Nucleotides are not only used as building blocks for
nucleic acids, but they form several important coenzymes,
including adenosine triphosphate (ATP), cyclic AMP,
coenzyme A, nicotinamide adenine dinucleotide (NAD)
and its phosphate NADP, and flavine adenine dinucleotide
(FAD).
Formation of dinucleotides
and polynucleotides
Two nucleotides join to form a dinucleotide by
condensation between the phosphate group of one with the
sugar of the other. The process is repeated up to several
million times to make a polynucleotide. An unbranched
sugar-phosphate backbone is thus formed 3' end
Structure of DNA
DNA is made up of two helical chains of polynucleotides
held together by the pairing of bases between
neighbouring chains. The bases are held together by
hydrogen bonds. Adenine pairs with thymine, and guanine
with cytosine; the adenine-thymine pair has two hydrogen
bonds.
Each chain forms a right-handed helical spiral and the two
chains coil around each other to form a double helix. The
chains run in opposite directions, that is are antiparallel.
Each chain has a sugar-phosphate backbone with bases
which project at right-angles and hydrogen bond with the
20
bases of the opposite chain across the double helix. The 5' 3'
width between the two backbones is constant and equal to
the width of a base pair that is the width of a purine plus a
pyrimidine.
Along the axis of the molecule, the base pairs are 0.34 nm
apart, accounting for the regularity indicated by X-ray anti parallel chain
diffraction. A complete turn of the double helix comprises 3.4 nm
3.4 nm, or ten base pairs. Basing on the rules of base
One complete turn =
pairing, the sequence in one chain determines that in the
bases ten base pairs (0.34
other. The two chains are thus said to be complementary.
nm between base
Diagrammatic structure of DNA pairs)
sugar-phosphate
Complementary base pairs 3' backbones
5'
A T 3' 5'
2 nm
Structure of RNA
G C
Ribonucleic acid (RNA) is a polymer made up of
repeating mononucleotide sub-units. It forms a single
strand in which the pentose sugar is always ribose and the
T A
organic bases are adenine, guanine, cytosine, and uracil.
There are three types of RNA, all of which are important
in protein synthesis:
21
there is a different sequence of organic bases on the Messenger RNA (mRNA). It is made up of thousands of
anticodon. During protein synthesis, this anticodon pairs mononucleotides. It is a long strand that is arranged in a
with the complementary three organic bases that make up single helix. It is formed by the DNA in the nucleus in the
process called transcription. There is a great variety of
the triplet of bases on mRNA, known as the codon.
different types of mRNA according to the part of DNA
being transcribed.
Clover-leaf structure of tRNA
Once formed, mRNA leaves the nucleus via pores in the
A nuclear envelope and enters the cytoplasm, where it
binding site for
C associates with the ribosomes. There it acts as a template
C anamino acid upon which proteins are built. It possesses the correct
sequence of many triplets of organic bases that code for
specific polypeptides. It is also easily broken down and
therefore exists only for as long as it is needed to
manufacture a given protein.
messenger-RNA
codons
A C U G G U A C
22
SSABAKRISTU RONALD SIKU 0783 686735
ENZYMES
An enzyme is a biological catalyst protein in nature that
Energy level
speeds up biochemical reactions in living cells. The
without enzyme
chemical (or chemicals) which an enzyme works on is
called its substrate. Enzymes control and catalyse all
Energy barrier
metabolic processes. with enzyme
Free energy
Metabolism is the sum total of all the chemical reactions Energy level
Substrate of substrate
going on in cells. It is divided into two types: anabolism
and catabolism. Catabolic reactions involve the Lower activation
energy
breakdown of molecules and usually release energy.
Anabolic reactions involve the synthesis of molecules and
usually require energy. Energy level
of the products
Products
Properties of enzymes
1. Oxidoreductases. This group of enzymes oxidizes substrates. There are two kinds of these enzymes.
Oxidases which catalyse the transfer of hydrogen to molecules of oxygen. An example is the cytochrome
oxidase which catalyse the oxidation of reduced cytochrome.
Dehydrogenases. These catalyse the oxidation of substrates by transferring hydrogen to coenzymes such as
NAD and NADP. An example is alcohol dehydrogenase which controls the rate at which ethanol is oxidized
to ethanol.
23
Ethanol + 2NAD+ ethanal + 2NADH
In reactions catalyzed by oxidoreductases, substrates are oxidized whereas oxygen or coenzymes are reduced.
2. Lysases. These catalyse the addition of a group across a double bond. For example pyruvate
decarboxylase. Pyruvic acid is converted into ethanal and carbon dioxide by breakage of its double
bond and the addition of a new group to the ‘freed’ bonds. Ethanal is then converted to alcohol.
pyruvic decarboxylase
Pyruvic acid ethanol + carbon dioxide
3. Isomerases. These catalyse rearrangements within a molecule, converting one isomer to another. Isomerases
control the conversion of one isomer of a compound to another isomer of the same compound.
phosphoglucomutase
Glucose-1-phosphate Glucose-6-phosphate
Glucose-6-phosphate fructose-6-phosphate
4. Ligases. These catalyse bond formation between two compounds. The reaction uses energy that comes from
hydrolysis of ATP to ADP and phosphate.
5. Hydrolases. These catalyse the splitting of a large substrate molecule into smaller products in the presence of
water. For example, a disaccharide is broken down into two monosaccharides by the addition of water by the
enzyme lactase.
lactase
Lactose + water Glucose + galacose
6. Transferases. These catalyse the transfer of a group from one compound to another. For example
aminotransferase.
aminotransferase
Glutamic acid + pyruvic acid α-ketoglutaric acid + alanine
The R group on the amino acid, glutamic acid, is exchanged with the R group on a keto acid. A new amino acid, alanine
is formed along with a new keto acid, alpha-ketoglutaric acid. This specific type of process is called transamination and
it is used to make non-essential amino acids from essential amino acids.
Another example of transferases are the phosphotransferases which control the transfer of phosphate groups in
respiration.
Transferases can also be transaminases which control the transfer of amino groups from one substrate to another.
24
Summary of classification of enzymes
Optimum temperature
26
Apart from the effect in denaturing enzymes, changes in H+
ENZYME INHIBITION
can alter the ionisation of the amino acid side chains at the
active centres of enzymes. Ionisation of substrate molecules Enzyme inhibitors are substances that reduce the activity
can also be affected. The formation of enzyme-substrate of enzymes. Inhibition is a normal part of the regulation
complexes sometimes depends on the active centres and of enzyme activity within cells. Many drugs and poisons
substrate molecules having opposite electrostatic charges. If are enzyme inhibitors. Inhibition may be competitive or
the charges are altered by changes in pH, some enzymes fail non-competitive.
to work.
One way in which pH affect an enzyme 1. Competitive inhibition. This occurs when a
compound has a structure which is sufficiently
similar to that of the normal substrate to be able to
fit into the active site. The inhibitor occupies the
active site and prevents the true substrate from
entering the active site. The genuine substrate and
the inhibitor, therefore, compete for the active site.
positively A characteristic feature of competitive inhibition
enzyme with charged Enzyme-substrate
negatively- substrate complex formed is that if the substrate concentration is increased,
charged active the rate of reaction increases.
centre
+
Competitive
+ +
+ inhibitor
+ unused
enzyme hydrogen ions substrate
+ +
+ enzyme Enzyme-inhibitor
+ substrate complex
27
Non-competitive inhibition Comparative effects of a non-competitive and
competitive inhibitor of an enzyme-catalysed reaction
substrate molecule
occupying the active
site of the enzyme no inhibitor
Rate of reaction
enzyme molecule
shape is changed competitive inhibitor
due to presence of
the inhibitor
molecule non-competitive inhibitor
30