BIOMOLECULES
МЕТАВOLITES AND BIOMACROMOLECULES
CHEMICAL
COMPOSITION
Chemical
Analysis of Biomolecules
To study the various biomolecules that are found in living
tissues, we perform a chemical analysis.
Procedure of chemical
analysis
Living tissue (a piece of liver or a vegetable, etc.) is
grounded in trichloroacetic acid (CCl3CCООН) with the help of a
mortar and a pestle, to obtain a thick slurry. This slurry is then strained
through a cheesecloth or cotton and two fractions were obtained. One is called
the filtrate or Acid soluble pool whereas the other fraction is called the
retentate or the acid-insoluble pool Filtrate consists of lower molecular
weight compounds whereas retentate consists of compounds like proteins, nucleic
acids, polysaccharides, etc., which have high molecular weight. Later on, the
compounds are extracted using various separation techniques from filtrate and
retentate. It finally leads to the complete isolation of a particular compound
from all other compounds. All these carbon compounds that we get from living
tissues are called biomolecules.
Ash analysis
Apart from organic compounds, living organisms also have
inorganic elements and compounds in their body. To analyse the inorganic elements
in the body of living organisms, we use a technique called Ash analysis. In
this technique, we take a small amount of living tissue, which is weighed and
dried. All the water evaporates and the remaining material gives dry weight.
This tissue is then fully burnt (the remaining are called ash) and the carbon
compounds present in them are oxidised to gaseous forms like carbon dioxide,
and water vapour and are removed and the remaining material is called ash. This
ash contains many inorganic elements like calcium, magnesium, sodium,
potassium, etc. Inorganic compounds like sulphate and phosphate are also present
in the acid-soluble fraction.
|
COMPONENT |
FORMULA |
|
SODIUM |
Na+ |
|
POTASSIUM |
K+ |
|
CALCIUM |
Ca2+ |
|
MAGNESIUM |
Mg2+ |
|
WATER |
H2O |
|
COMPOUNDS |
NaCl, CaCO3, H3PO4,
H2SO4 |
Functional groups such as aldehydes, ketones. aromatic
molecules, and others can be identified based on chemistry. However, we will
divide them into amino acids, nucleotide bases, fatty acids, and other
biological categories.
Important
The acid-insoluble fraction has only four types of organic
compounds that are protein, nucleic acid. polysaccharides and lipids. These
classes of compounds with the exception of Lipids have molecular weights in the
range of ten thousand daltons and above. For this reason, biomolecules Le
chemical compounds found in living organisms are of two types.
(1) Biomolecules that have a molecular weight less than 1000
Da are usually known as micro molecules or simple biomolecules.
(2) Biomolecules which are found in the add fraction are called macromolecules or biomacromolecules.
Biomacromolecules
The biomacromolecules present in living organisms are
Monosaccharides, Amino acids, Fatty acids, and Nucleotides. They have a
molecular weight of around 18 to 800 daltons (Da) approximately.
Amino acids
Amino acids are a type of biomolecule that contains a
carboxyl and an amino group attached to the same carbon (a-carbon) as
substituents. That's why they are called a-amino acids. The four valency
positions of a-carbon are occupied by four substituent groups, which are
hydrogen, amino group, carboxyl group. and a variable R-group.
(1) Amino acids are classified into various groups based on
the nature of the R-group. For example. when the R-group is hydrogen, then the
amino acid is called glycine. When the R-group is a methyl group (-CH3)
then the amino acid is called alanine.
(2) The proteins in the human body are made up of 20
different types of amino acids.
(3) The amino group. carboxyl group, and R-functional group
determine the chemical and physical properties of amino acids.
(4) Based on the number of amino and carboxyl groups, amino
acids are classified into three types:
(i)Acidic amino acid:
An amino acid in which the number of the carboxyl groups is greater as compared
to amino groups, e.g. glutamic acid.
(ii) Basic amino
acid: An amino acid in which the number of the amino group is more than the
number of the carboxyl group, e.g. lysine.
(iii) Neutral amino
acid: An amino acid in which the number of amino and carboxyl groups are
the same, e.g. valine.
(5) Similarly, there are aromatic amino acids (amino acids
whose structure contains an aromatic ring. e.g., phenylalanine, tyrosine,
tryptophan).
(6) Amino acids show a property in which -NH2 and
-COOH are ionisable. Therefore, the structure of amino acids changes in
solutions of different pH.
(7) Amino acids form zwitter ion (a molecule that contains
an equal number of positively and negatively charged functional groups).
Lipids
Lipids are water-insoluble and soluble in non-polar solvents
(Benzene, chloroform), whose basic unit is a fatty acid. A fatty acid consists
of a carboxyl group attached to an R-group, where the R-group could be a methyl
(-CH3) or ethyl (-C2H5) or a higher number
of-CH2 groups.
Lipids
= fatty acid + glycerol
Types of fatty acids are based on the presence of a double
bond between two carbon atoms. They are:
Saturated fatty acid:
A fatty acid in which there is no double bond between two carbon atoms. They
have high melting and boiling point and exist in solid form at room
temperature. E.g. Palmitic acid (16:0), Stearic acid (18:0) and Arachidic acid
(20:0)
Unsaturated fatty
acid: A fatty acid in which there is one or more than one double bond
between two carbon atoms. They have low melting and boiling point and exist in
liquid form at room temperature. E.g. Palmitoleic acid, oleic acid, linoleic
acid. arachidonic acid, etc.
Fatty acids can also be classified as:
Simple lipids:
These are esters of fatty acids with various kinds of alcohol E.g.
Triglycerides, suberin, wax, etc.
Compound lipids:
These are esters of fatty acids containing groups in addition to alcohol and
fatty acid. E.g. Phospholipids, glycolipids, lipoprotein, etc.
Derived lipids:
Fatty acids which are produced by hydrolysis of simple and compound lipids.
E.g. Steroids, prostaglandin, etc.
Nucleotides
Nucleic acids are a type of biomolecule found in living
organisms that are composed of basic units called nucleotides.
A nucleotide consists
of ribose sugar, nitrogenous base, and phosphoric acid. A nucleoside consists
of ribose sugar and nitrogenous base only. The nitrogenous base includes
adenine, guanine, cytosine, uracil, and thymine. Adenosine, guanosine,
thymidine, uridine, and cytidine are nucleosides.
Nucleotides are-Adenylic acid, guanylic acid, thymidylic
acid, uridylic acid, and cytidylic acid. Nucleic acids are present in DNA and
RNA which function as genetic material.
Primary and
Secondary Metabolites
Metabolites are intermediate or end products of metabolism.
Since every living organism shows metabolism, the products formed during the
process of metabolism or after it are called metabolites.
There are two types of metabolites:
Primary metabolites
It is required for basic metabolic activities like
respiration, photosynthesis, lipids and protein metabolism, etc. It is produced
in large quantities and its extraction is very easy. It is almost the same in
all plants. E.g. Enzymes, amino acids, vitamins, etc.
Secondary metabolites
It has no direct function in the growth and development of
living organisms. It is produced in small quantities and extraction is
difficult. It is unique to different plant species. E.g. pigments, antibiotics,
drugs, alkaloids, rubber, flavonoids, essential oils, scents, gums, spices,
etc.
POLYSACCHARIDES
Polysaccharides are chains of polymers of monosaccharides.
Monosaccharides are simple sugars or carbohydrates which cannot be further
hydrolysed into smaller components. Monosaccharides are composed of 3-7 carbon
atoms. Polysaccharides are composed of more than 10 monosaccharides. These
polysaccharides contain different monosaccharides and can be branched or
unbranched. The individual monosaccharides are Joined by a glycosidic bond in a
polysaccharide.
There are two types of polysaccharides:
Homopolysaccharides
They are made up of only one type of monosaccharide, Le. all
the monosaccharide units are the same. E.g. Starch, glycogen, inulin,
cellulose, etc.
(1) Glycogen:
Branched homopolysaccharide formed by glucose a-1,4 linkage at unbranched part
and a-1,6 linkage at branching points. When reacted with iodine it gives red
colour. It is the storehouse of energy in animal cells.
(2) Starch: Its
structure is the same as glycogen, but shows less branching frequency than
glycogen. It acts as the storehouse of energy in plant cells. It forms helical
secondary structures in which iodine molecules get trapped and gives blue
colour.
(3) Cellulose:
They are the structural component of plants, and these do not form helices, so
they cannot hold iodine molecules.
(4) Inulin: This
is a polymer of fructose. The metabolism of inulin does not occur in the human
body so it gets filtered out through the kidney. Due to this, they are used in
the testing of kidney function.
(5) Chitin: This
is a polymer of Nitrogen-containing glucose derivative called N-acetyl
glucosamine. It is found in the exoskeleton of arthropods.
Heteropolysaccharide
They are made up of more than one type of monosaccharide,
Le., monosaccharide units are different E.g. Peptidoglycans, hyaluronic acid,
etc.
NUCLEIC
ACIDS
Nucleic acids are polymers of nucleotides. There are two
types of nucleic Acids in nature, i.e. Deoxyribonucleic Acid (DNA) and
Ribonucleic Acid (RNA). A nucleotide is composed of a phosphate group, a
five-carbon sugar or pentose sugar, and a nitrogenous base. A nucleoside is
composed of pentose sugar and nitrogenous base only. The nitrogenous base is
joined with pentose sugar via a glycosidic bond. The bond between the hydroxyl
group of sugar and phosphate group is called an ester bond. Since there is one
such ester bond on either side, it is called a phosphodiester bond.
Caution
Students usually get confused between nucleotides and
nucleosides. They both are different Nucleosides are shorter than nucleotides.
Nitrogenous bases are of 5 types-Adenine, Guanine, Thymine,
Cytosine, and Uracil Adenine and Guanine are purines, whereas Thymine,
Cytosine, and Uracil are pyrimidines. Uracil is absent in DNA and thymine is
absent in RNA. In DNA, the sugar is deoxyribose sugar, and in RNA, the sugar is
ribose sugar.
Important
DNA contains - Adenine Guanine. Cytosine and Thymine
RNA contains - Adenine, Guanine, Cytosine and Uracil
Caution
Pay attention to the spelling of Thymine: Thymine is a
pyrimidine whereas Thiamine is Vitamin B.
PROTEINS
PROTEIN AND ITS
STRUCTURE
Protein is an essential biomolecule made up of monomers of amino acids. Amino acids are Joined together by a peptide bond and hence proteins are also called polypeptides, meaning a molecule made up of a number of peptide molecules. The amino acids are joined by peptide bonds when arranged in a linear fashion give rise to the basic structure of protein.
There are many amino acids present in nature, but only a few
are essential that need to be taken through the diet which cannot be synthesised
by the human body or organisms themselves. Such amino acids are called
essential amino acids like histidine, isoleucine, leucine, lysine, methionine,
etc. Essential amino acids must be taken in a diet for proper growth and
development of cells and hence are also called dietary proteins.
The non-essential amino acids are not important to be taken
in the diet as the body can synthesise them as per its need.
Proteins are found everywhere in the environment in various
forms and they have many essential roles in the biosystem and ecosystem.
Proteins have various functions and are abundant in nature.
The most abundant protein on the earth is called Ribulose Bisphosphate
Carboxylase-Oxygenase (RuBisCO) present in plants. Similarly, collagen is
abundantly found in animals and is the most abundant protein among animals.
Structure
The amino acid contains a central carbon atom linked with an
amino group (positively charged group). a carboxyl group (negatively charged
group), a hydrogen atom and an 'R'-group. There are 20 amino acids which have a
similar structure but only vary in their 'R-group. The R-group can be acidic,
basic, polar, non-polar, neutral, aliphatic or aromatic and it decides the
nature of amino acids.
The amino acids in the aqueous environment are present in
zwitter ion form. The hydrogen from the carboxyl group moves to the basic amino
group making carboxyl group negative and amino group positive and yet, the
overall charge on the zwitter ion remains zero and is only determined by distinct
'R-group.
Taking a long rope with numerous knots might give an idea of
the actual structure of protein's primary structure. The knots represent the
amino acids, the knots may vary in shape and size which represent the different
amino acids and the length of rope in between two knots represents the bond
which is present in between the amino acids to join them. The amino acids when
bound to one another in a linear fashion through peptide bonds make up the
primary structure of protein.
(1) The first amino acid has a free amino group and hence is
called N-terminus whereas the last amino acid has a free carboxyl group and is
hence called C-terminus.
(2) When the linear amino acid chain turns into a
right-handed helix then the secondary structure of protein is formed. It is
mainly due to the presence of hydrogen bonds within them. The linear chain can
be turned so that amino acids at some distance can have hydrogen bonding to
make an alpha-helix or two polypeptide chains can be linked to one another through
hydrogen bonding, forming beta-pleated sheets.
(3) When the linear structure of protein is folded into a
stable three-dimensional structure due to other forces of interactions like
sulphide bonds, Van der Waal forces of interaction, hydrophobic bonds, etc, the
structure is called tertiary structure of protein like globular proteins.
(4) Also, when two or more polypeptides interweave with each
other to form a complex structure. it is called quaternary structure of
protein, like haemoglobin is made up of four polypeptide chains or subunits;
two alpha and two beta.
ENZYMES
Many complicated reactions occur in the human body at
temperatures of 37.5°C. Food digestion is an example of this, as it involves
progressive oxidation producing CO2 and water, as well as energy
generation. Because of the existence of particular compounds known as enzymes,
these processes take place in such benign circumstances. They serve as
biochemical catalysts in living cells. Almost every enzyme is a globular
protein.
Even some nucleic acids have enzyme-like properties. These
are known as ribozymes. An enzyme, like any other protein, has a fundamental
structure, which is the amino acid sequence. An enzyme, like any other protein,
has secondary and tertiary structures.
Chemical Reactions
There are two sorts of modifications that occur in chemical
compounds. A physical change is merely a deformation that does not involve the
breaking of connections. This is a physical procedure. One physical process
could be a change in states of matter, such as evaporation and fusion of
substances. Whenever bonds are formed or broken during transformation, this is
referred to as a chemical reaction. An example of this is represented as
follows:
Ba(OH)2 + H2SO4
------> BaSO4 + 2H2O
(This represents a neutralisation reaction: H₂SO4
is an add while Ba(OH)2 is a base. This is a precipitation process,
and the precipitate created is BaSO4).
This is an example of a chemical process that takes place in an inorganic environment. Similarly, starch breakdown into glucose is the result of an organic chemical process. The rate of a physical or chemical process depends on the quantity of product created per unit time. It may be expressed as follows:
The rate of the reaction is the place where the products of
a chemical reaction are created from the reactants. It provides some
information about the time range wherein the reaction can be accomplished. To
provide an example, the combustion of cellulose is an extremely rapid reaction;
it only takes a few seconds. A general guideline is that for every 10°C shift in
either direction, the rate doubles or reduces by half. Catalysed processes have
been observed to proceed at significantly faster rates than uncatalysed ones.
When enzyme-catalysed reactions are seen, the rate is much higher than the
identical but uncatalysed process. An example of this is shown as follows:
In the absence of an enzyme, processes can be very
inefficient, producing just around 200 molecules of H2CO3
each hour. However, by utilising a cytoplasmic enzyme called carbonic
anhydrase. the reaction is speed up substantially, with around 600,000
molecules generated every second. The enzyme has thus increased the rate of the
reaction by about 10 million times.
A metabolic pathway is a multistep chemical process in which each step is regulated by an enzyme (or a combination of them).
This reaction is part of a metabolic pathway that allows the
conversion of glucose into energy in the human body. It is a step-by-step
reaction, involving specific conditions as well as enzymes that serve as
catalysts.
How do Enzymes bring
about such High Rates of Chemical Conversions?
When a protein chain's backbone folds upon itself, the chain criss-crosses itself, and many crevices or pockets are formed, the protein is then said to possess a tertiary structure. The 'active site' is one such pocket. An enzyme's active site is a socket into which the substrate fits. Thus, enzymes catalyse processes at a rapid pace via their active site. In many aspects, enzyme catalysts vary from inorganic catalysts, but one key distinction stands out Inorganic catalysts perform well at high temperatures and pressures, but enzymes are destroyed at high temperatures (over 40°C).
Enzymes obtained from organisms that ordinarily live at
extreme temperatures (e.g., heat vents and sulphur springs) are more stable and
keep their catalytic potency even at high temperatures (up to 80°C-90°C).
Thermal stability is therefore a critical property of enzymes derived from
thermophilic species. For example, Taq polymerase enzyme is present in Thermus
aquaticus.
Properties of Enzymes
(1) Enzymes can accelerate biological processes up to 10
million times faster than uncatalysed reactions.
(2) Enzyme catalysed processes reach equilibrium quickly.
(3) Human enzymes work best in dilute aqueous solutions at
moderate temperatures and pН.
(4) Their impact on substrates is exceedingly particular and
selective.
(5) Enzymes are very efficient and are only required in
trace amounts.
(6) In addition to the protein structure, most active enzymes are linked to a non-protein component essential for their function, known as a coenzyme. For example, nicotinamide adenine dinucleotide (NAD) is a coenzyme that is involved in the activity of several dehydrogenation enzymes.
Action of Enzymes
A reaction is defined as a chemical or metabolic change. A 'substrate'
is a chemical that is transformed into a product. As a result, enzymes, which
are mostly proteins with three-dimensional structures that include an 'active
site, transform a substrate (S) into a product (P). This can be represented
symbolically as:
It is now known that the substrate 'S' must bind the enzyme
at its 'active site' within a specific socket. The substrate must diffuse to
the 'active site.' As a result. the establishment of a 'ES' complex is
unavoidable. The letter E stands for the enzyme. This complicated structure is
a passing occurrence. When the substrate is attached to the active site of the
enzyme, a new structure of the substrate known as the transition state
structure is produced. The product is removed from the active location as soon
as the planned bond breaking/making is finished. The substrate structure is
changed into the product structure(s).
There are two things you would notice. The difference in
energy levels between S and P. When 'P' is smaller than 'S, the reaction is
exothermic. There is no need to supply energy (through heating) In order to
create the product, the substrate (S) must pass through a much higher energy
state. This is also called the transition stage.
The gap in mean energy content between the substrate and this transition is known as 'activation energy. It is here that enzymes finally break through this energy barrier, allowing the shift from substrate (S) to product (P) easier.
Nature of Enzyme
Action
Each enzyme (E) contains a substrate (S) binding domain in
its molecule, allowing a substrate to attach to the enzyme. This results in the
formation of a reactive enzyme-substrate complex (ES).
E+S --------> ES
This complex has a brief lifetime and decomposes into its
final product(s) (P) and the unmodified enzyme with intermediate enzyme-product
complex (EP). The formation of the 'ES' complex is absolutely essential for the
process of catalysis.
ES -------> EP ------> E + P
The following stages explain the catalytic cycle of an
enzyme action:
(1) The substrates attach to the enzyme's active site.
fitting into it.
(2) This binding of the substrate causes the enzyme to
change shape, causing it to fit more closely around the substrate.
(3) The enzyme's active site, which is now in close vicinity
to the substrate, destroys the chemical bonds of the substrate, resulting in
the formation of a new enzyme-product complex.
(4) The enzyme releases the reaction products, and the free
enzyme is ready to attach to some other molecule of the substrates and repeat
the catalytic cycle.
Factors Affecting
Enzyme Activity
The activity of an enzyme can be affected by a change in the
conditions which can alter the tertiary structure of the protein. These include
temperature, pH, change in substrate concentration or binding of specific
chemicals that regulate its activity.
Temperature and pH
Enzymes generally function in a narrow range of temperature and pH. Each enzyme shows its highest activity at a particular temperature and pH called the optimum temperature and optimum pH. Activity declines both below and above the optimum value. Low temperature preserves the enzyme in a temporarily inactive state whereas high temperature destroys enzymatic activity because proteins a denatured by heal.
Concentration of Substrate
With the increase in substrate concentration, the velocity
of the enzymatic reaction rises at first. The reaction ultimately reaches a
maximum velocity (Vmax) which is not exceeded by any further rise in
concentration of the substrate. This is because the enzyme molecules are fewer
than substrate molecules and after saturation of these molecules, there are no
free enzyme molecules to bind with the additional substrate molecules.
The activity of an enzyme is also sensitive to the presence
of specific chemicals that hind to the enzyme. When the binding of the chemical
shuts all enzyme activity, the process is called inhibition and the chemical is
called an inhibitor.
When the inhibitor closely resembles the substrate in its
molecular structure and inhibits the activity of the enzyme, it is known as
competitive inhibitor. Due to its close structural similarity with the
substrate, the inhibitor competes with the substrate for the substrate binding
site of the enzyme. Consequently, the substrate cannot bind and as a result,
the enzyme action declines, e.g. Inhibition of succinic dehydrogenase by
malonate which closely resembles the substrate succinate in structure. Such
competitive inhibitors are often used in the control of bacterial pathogens.
Classification and Nomenclature of Enzymes
Enzymes are biological catalysts made up of proteins (and
sometimes RNA ribozymes) that speed up biochemical reactions.
To bring uniformity, the International Union of Biochemistry
(IUB) and later the International Union of Biochemistry and Molecular Biology
(IUBMB) established a systematic classification and nomenclature.
Enzyme Classification (Based on the nature of reaction)
Enzymes are divided into 6 major classes (plus subclasses)
depending on the type of reaction they catalyse.
1. Oxidoreductases
Catalyse oxidation–reduction (redox) reactions.
Transfer of electrons or hydrogen atoms.
Examples:
Dehydrogenases (e.g., Lactate dehydrogenase)
Oxidases, peroxidases, reductases
2. Transferases
Transfer a functional group (methyl, amino, phosphate) from
one molecule to another.
Examples:
Transaminases (transfer amino group)
Kinases (transfer phosphate from ATP to substrate)
3. Hydrolases
Catalyse hydrolysis of bonds by adding water.
Examples:
Proteases, amylase, lipases, nucleases
4. Lyases
Remove or add groups to substrates, without hydrolysis or
oxidation.
Often form or break double bonds.
Examples:
Decarboxylases
Aldolase
5. Isomerases
Catalyse intramolecular rearrangements → formation of
isomers.
Examples:
Racemases, mutases, epimerases, phosphohexose isomerase
6. Ligases
(Synthetases)
Join two molecules using energy from ATP.
Examples:
DNA ligase
Carboxylases
Cofactors –
Definition, Types, Examples
What are
Cofactors?
Cofactors are non-protein chemical components required by
some enzymes to become active.
They help the enzyme in catalysing biochemical reactions by
assisting in substrate binding or stabilizing the active site.
👉 Enzyme (protein part) + Cofactor
(non-protein part) → Active enzyme (Holoenzyme)
If the cofactor is absent, the inactive enzyme is called Apoenzyme.
Types of Cofactors
Cofactors are classified into three major types:
1. Prosthetic Groups
Tightly or permanently bound to the enzyme (covalently or
strongly bound).
Do not dissociate during the reaction.
Example:
FAD in succinate dehydrogenase
Haem group in catalase & cytochromes
Biotin in carboxylases
2. Coenzymes
Organic molecules
Loosely bound to enzymes (not permanent).
Often derived from vitamins.
Participate directly in the reaction (carry electrons,
atoms, functional groups).
Examples
NAD⁺ / NADP⁺ (from Vitamin B₃)
FAD (from Vitamin B₂)
Coenzyme A (CoA) (from Vitamin B₅)
TPP – Thiamine pyrophosphate (from Vitamin B₁)
3. Metal Ions or
Activators
Inorganic metal ions that improve enzyme activity.
May bind temporarily or permanently.
Examples
Mg²⁺ – activates ATP-utilizing enzymes, kinases
Zn²⁺ – carbonic anhydrase, alcohol dehydrogenase
Fe²⁺ / Fe³⁺ – catalase, peroxidase
Cu²⁺ – cytochrome oxidase