9.

BIOMOLECULES
 Biomolecules: All the carbon compounds that we get from living tissues
 Comparison of Elements Present in Non-living and Living Matter:

 A List of Representative Inorganic Constituents of Living Tissues

 BIOMACROMOLECULES:
- one feature common to all those compounds found in the acid soluble pool, have
molecular weights ranging from 18 to around 800 daltons (Da) approximately.
- acid insoluble fraction, has four types of organic compounds:
 proteins
 nucleic acids
 polysaccharides
  lipids
- less than one thousand dalton are usually referred to as micromolecules or simply
biomolecules
- which are found in the acid insoluble fraction are called macromolecules or
biomacromolecules
- Lipids are not strictly macromolecules

 α-Amino acids: organic compounds containing an amino group and an acidic group as
substituents on the same carbon i.e., the α-carbon
- substituted methanes
- four substituent groups occupying the four valency positions
 hydrogen
 carboxyl group
 amino group
 a variable group designated as R group
- Based on the nature of R group, there are many amino acids.
- amino acid those which occur in proteins are only of twenty types
- R group in these proteinaceous amino acids could be:
 Hydrogen: glycine
 a methyl group: alanine
 hydroxy methyl: serine

- chemical and physical properties of amino acids are essentially of the amino, carboxyl
and the R functional groups
- Based on number of amino and carboxyl groups
 Acidic: glutamic acid
 Basic: lysine
 Neutral: valine
- aromatic amino acids:
 tyrosine
 phenylalanine
 tryptophan
- A particular property of amino acids is the ionizable nature of –NH2 and –COOH
groups: in solutions of different pH, the structure of amino acids changes
 PROTEINS:
- Polypeptides
- linear chains of amino acids linked by peptide bonds
- protein is a polymer of amino acids
- protein is a heteropolymer and not a homopolymer
- essential amino acids: amino acids that we get through our diet/food
- non-essential amino acids: amino acids which our body can make
- Proteins carry out many functions:
 transport nutrients across cell membrane
 some fight infectious organisms
 some are hormones
 some are enzymes
- Collagen is the most abundant protein in animal world
- Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO) is the most
abundant protein in the whole of the biosphere

 STRUCTURE OF PROTEINS:
- are heteropolymers containing strings of amino acids
- the positional information in a protein – which is the first amino acid, which is second,
and so on – is called the primary structure
- protein is imagined as a line:
 the left end: first amino acid
 right end: last amino
- first amino acid – called as N-terminal amino acid
- last amino acid – called the C-terminal amino acid
- A protein thread does not exist throughout as an extended rigid rod. The thread is
folded in the form of a helix
- only some portions of the protein thread are arranged in the form of a helix
- In proteins, only right-handed helices are observed
 - Other regions of the protein thread are folded into other forms: secondary structure
- long protein chain is also folded upon itself like a hollow woolen ball, giving rise to the
tertiary structure
- Tertiary structure is absolutely necessary for the many biological activities of
proteins
- Some proteins are an assembly of more than one polypeptide or subunits.
- manner in which these individual folded polypeptides or subunits are arranged with
respect to each other is the architecture of a protein otherwise called the quaternary
structure
- Adult human haemoglobin consists of 4 subunits.
- Two of these are identical to each other.
- two subunits of α type and two subunits of β type together constitute the human
haemoglobin
 Lipids:
- water insoluble
- could be simple fatty acids
- fatty acid has a carboxyl group attached to an R group
- R group could be:
 methyl (–CH3)
 ethyl (–C2H5 )
 higher number of –CH2 groups (1 carbon to 19 carbons
- palmitic acid: 16 carbons including carboxyl carbon
- Arachidonic acid: 20 carbon atoms including the carboxyl carbon
- Fatty acids could be
 Saturated: without double bond
 Unsaturated: with one or more C=C double bonds
- Another simple lipid: glycerol which is trihydroxy propane
- Many lipids have both glycerol and fatty acids
- fatty acids are found esterified with glycerol:
 monoglycerides
 diglycerides
 triglycerides
- Oils have lower melting point
- Some lipids have phosphorous and a phosphorylated organic compound in them:
phospholipids – found in cell membrane
- Example: Lecithin
 Nitrogenous bases:
- Adenine
- Guanine
- Cytosine
- Uracil
- Thymine

- Nitrogenous bases found attached to a sugar: nucleosides

 Adenosine
 Guanosine
 Thymidine
 uridine
 cytidine
- phosphate group is also found esterified to the sugar: nucleotides
 Adenylic acid
 thymidylic acid
 guanylic acid
 uridylic acid
 cytidylic acid
- Nucleic acids like DNA and RNA consist of nucleotides
- DNA and RNA function as genetic material
 Polysaccharides:
- long chains of sugars
- threads containing different monosaccharides as building blocks.
- Example: cellulose is a polymeric polysaccharide consisting of only one type
of monosaccharide i.e., glucose.
 Cellulose is a homopolymer
 Cellulose does not contain complex helices and hence cannot hold I2

 Starch is a variant of this but present as a store house of energy in plant tissues.
 starch can hold I2 molecules in the helical portion
 Starch forms helical secondary structures.
 The starch-I2 is blue in colour.

 Animals have another variant called glycogen.

 Inulin: polymer of fructose.
- In a polysaccharide chain:
  right end: reducing end
 left end: non-reducing end.
 Nuclei Acids:
- Polynucleotides
- Together with polysaccharides and polypeptides these comprise the true
macromolecular fraction of any living tissue or cell
- For nucleic acids, the building block is a nucleotide
- nucleotide has three chemically distinct components:
 heterocyclic compound: nitrogenous bases -
 Purines: Adenine and Guanine
 Pyrimidines: uracil, cytosine, and thymine.
 Monosaccharide: ribose (a monosaccharide pentose) or 2’ deoxyribose
 A nucleic acid containing deoxyribose is called deoxyribonucleic acid
(DNA) while that which contains ribose is called ribonucleic acid
(RNA)
 phosphoric acid or phosphate
 secondary metabolites:
 alkaloids
 flavonoids
 rubber
 essential oils
 antibiotics
 coloured pigments
 scents
 gums
 spices
- primary metabolites have identifiable functions and play known roles in normal
physiological processes
- we do not at the moment, understand the role or functions of all the ‘secondary
metabolites’ in host organisms

 NATURE OF BOND LINKING MONOMERS IN A POLYMER

- polypeptide or a protein, amino acids are linked by a peptide bond
 which is formed when the carboxyl (-COOH) group of one amino acid reacts with the
amino (-NH2 ) group of the next amino acid with the elimination of a water moiety:
dehydration
 - In a polysaccharide the individual monosaccharides are linked by a glycosidic bond.
 bond is also formed by dehydration
 formed between two carbon atoms of two adjacent monosaccharides.
- In a nucleic acid a phosphate moiety links the 3’-carbon of one sugar of one nucleotide
to the 5’-carbon of the sugar of the succeeding nucleotide. The bond between the
phosphate and hydroxyl group of sugar is an ester bond.
- As there is one such ester bond on either side, it is called phosphodiester bond
- Nucleic acids exhibit a wide variety of secondary structures
- Example: one of the secondary structures exhibited by DNA is the famous:
Watson-Crick model:
 This model says that DNA exists as a double helix.
 The two strands of polynucleotides are antiparallel i.e., run in the opposite direction
 The backbone is formed by the sugarphosphate-sugar chain.
 The nitrogen bases are projected more or less perpendicular to this backbone but face
inside.
 A and G of one strand compulsorily base pairs with T and C, respectively, on the other
strand
 two hydrogen bonds between A and T and three hydrogen bonds between G and C.
 At each step of ascent, the strand turns 36°.
 biomolecules have a turn over
- means that they are constantly being changed into some other biomolecules and also
made from some other biomolecules.
 breaking and making is through chemical reactions constantly occuring in living organisms
 Together all these chemical reactions are called metabolism
 metabolites are converted into each other in a series of linked reactions called metabolic
pathways
 Flow of metabolites through metabolic pathway has a definite rate and direction
 There is no uncatalysed metabolic conversion in living system
 catalysts which hasten the rate of a given metabolic conversation are also proteins
 These proteins with catalytic power are named enzymes

 Anabolic pathways: lead to a more complex structure from a simpler structure

- Requires energy
- Example: acetic acid becomes cholesterol

 Catabolic pathway: lead to a simpler structure from a complex structure

- Releases enerrgy
- Example: glucose becomes lactic acid in our skeletal muscle
- glucose is degraded to lactic acid in our skeletal muscle, energy is liberated
- metabolic pathway from glucose to lactic acid which occurs in 10 metabolic steps is
called glycolysis
- The most important form of energy currency in living systems is the bond energy in a
chemical called adenosine triphosphate (ATP)

 the blood concentration of glucose in a normal healthy individual: 4.2 mmol/L– 6.1 mmol/L,
while that of hormones would be nanograms/mL
 Hence the living state is a non-equilibrium steadystate to be able to perform work
  ENZYMES:
- all enzymes are proteins
- There are some nucleic acids that behave like enzymes.
- These are called ribozymes
- inorganic catalysts work efficiently at high temperatures and high pressures
- enzymes get damaged at high temperatures (say above 40°C)
- Thermal stability is an important quality of such enzymes isolated from thermophilic
organisms
 Rate of a physical or chemical process refers to the amount of product formed per unit
time. It can be expressed as:

 Rate can also be called velocity if the direction is specified

 rate doubles or decreases by half for every 10°C change in either direction
 Catalysed reactions proceed at rates vastly higher than that of uncatalysed ones
Example:

In the absence of any enzyme this reaction is very slow, with about 200 molecules of H 2CO3 being
formed in an hour.
by using the enzyme called carbonic anhydrase, the reaction speeds dramatically with about
600,000 molecules being formed every second.

 The catalytic cycle of an enzyme action can be described in the following steps:
- First, the substrate binds to the active site of the enzyme, fitting into the active site
- The binding of the substrate induces the enzyme to alter its shape, fitting more tightly
around the substrate
- The active site of the enzyme, now in close proximity of the substrate breaks the
chemical bonds of the substrate and the new enzyme- product complex is formed
- The enzyme releases the products of the reaction and the free enzyme is ready to bind
to another molecule of the substrate and run through the catalytic cycle once again

 Factors Affecting Enzyme Activity:

- Temperature and pH
 function in a narrow range of temperature and pH
 highest activity at a particular temperature and pH called the optimum
temperature and optimum pH.
 - 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
 When the binding of the chemical shuts off enzyme activity: inhibition
 the chemical is called an inhibitor
 competitive inhibitor: When the inhibitor closely resembles the substrate in its
molecular structure and inhibits the activity of the enzyme
 Classification and Nomenclature of Enzymes:
- Oxidoreductases/dehydrogenases: Enzymes which catalyse oxidoreduction between
two substrates S and S’
- Transferases: Enzymes catalysing a transfer of a group, G (other than hydrogen)
between a pair of substrate S and S’
- Hydrolases: Enzymes catalysing hydrolysis of ester, ether, peptide, glycosidic, C-C,
C- halide or P-N bonds
- Lyases: Enzymes that catalyse removal of groups from substrates by mechanisms other
than hydrolysis leaving double bonds
- Isomerases: Includes all enzymes catalysing inter-conversion of optical, geometric or
positional isomers
- Ligases: Enzymes catalysing the linking together of 2 compounds, e.g., enzymes
which catalyse joining of C-O, C-S, C-N, P-O etc. bonds

 Co-Factors:
- Cofactors: there are a number of cases in which non-protein constituents bound to the
the enzyme to make the enzyme catalytically active.
- protein portion of the enzymes: apoenzyme.
- Three kinds of cofactors may be identified:
 prosthetic groups:
 organic compounds and are distinguished from other cofactors in that
they are tightly bound to the apoenzyme
 Example: peroxidase and catalase, which catalyze the breakdown of
hydrogen peroxide to water and oxygen
haem is the prosthetic group and it is a part of the active site of the
enzyme
 co-enzymes: organic compounds but their association with the apoenzyme is
only transient, usually occurring during the course of catalysis
  The essential chemical components of many coenzymes are vitamins,
e.g., coenzyme nicotinamide adenine dinucleotide (NAD) and NADP
contain the vitamin niacin
 metal ions.
 Example: zinc is a cofactor for the proteolytic enzyme carboxypeptidase.
- Catalytic activity is lost when the co-factor is removed from the enzyme which testifies
that they play a crucial role in the catalytic activity of the enzyme.