Natural Products
Natural Products
Purines Pyrimidine
O NH2 NH2
O H N CH3
HN N N
N
HN
H2N N N O N O N
H2N N N H
H H
guanine Cytosine 5-methylcytosine
2. Sugars: The sugar present in the nucleic acids are pentoses: D(–)-ribose and 2-deoxy-D-(–)-ribose.
CHO CHO
H OH H H
H OH H OH
H OH H OH
CH2OH CH2OH
D(–)-ribose 2-deoxy-D-(–)-ribose
H O HO H H OH
C
H OH H OH H OH
O + O
H OH
H OH H OH
H OH
CH2OH H H
CH2OH CH2OH
Ribose
-anomer -anomer
5
HOH2C O OH HOH2C O H
4 1
H H H H
H H H OH
3 2
OH OH OH OH
-anomer -anomer
112 Chemistry of Natural Products
3. Deoxy Ribose:
H O HO H H OH
C
H H H H H H
O + O
H OH
H OH H OH
H OH
CH2OH H H
-anomer -anomer
5
HOH2C OH HOH2C H
O O
4 1
H H H H
H H H OH
3 2
OH H OH H
-anomer -anomer
Remark: In nucleic acid sugars are in -anomeric, furanose form and it is hemiacetal.
4. Phosphate Group :
HO OH
P
HO O
H H 2 PO4 ;
H3 PO 4
H PO34
HPO 24
Nucleoside: The combination of a base (either a purine or pyramidine with a sugar(ribose or deoxyribose) are
called nucleosides. For example
NH2
NH2
N
N N
N
O O
HN CH3
HN CH3
–H2O
O N O N
H
HOH2C HOH2C O
O OH
H H
H H H H
H H OH H
OH H
Ribonucleic Acids(RNA):
• RNA is a polymer of ribonucleotides.
• The individual ribonucleotides are linked together by phosphodiester bonds.
• The attachment of the phosphate is at the 3' position in the ribose molecules.
• The common bases in RNAs are adenine, guanine, uracil and cytosine.
• According to the source of nucleic acid there are three types of nucleic acid:
Ribosomal RNA (r–RNA), Transfer RNA(t–RNA) and Messenger RNA (m–RNA).
O P O CH2
O G
O
H H
H H
O OH
O P O CH2
O U
O
H H
H H
O OH
O P O CH2
O A
O
H H
H H
O OH
O P O CH2
O C
O
H H Tetranucleotide
H H
OH OH
3' end
The secondary structure of RNA has been investigated and it appears that RNAs exist as a single strands
which contain helical segments established by hydrogen bond.
114 Chemistry of Natural Products
Nucleotide:
Nucleotides are the combination of a nucleoside and phosphoric acid i.e. nucleotides are nucleosides phos-
phate. For example
Adenosine + phosphate Adenylic acids
Guanosine + phosphate Guanylic acids
Cytidine + phosphate Cytidylic acids
Uridine + phosphate Uridylic acids
NH2
NH2
N
N N
N O
H3PO4 N
N
N N HO P OH 2 C O
–H2O
HOH2C O OH H
H
H H H H
H H H O OH
OH OH
On the basis of sugar present in the nucleic acid, it can be classified into two parts:
Ribonucleic acids (RNA) and the deoxyribonucleic acid (DNA).
Deoxyribonucleic acid:
• DNA are polymers of the deoxyribonucleotides and hydrolysis by certain enzymes result in a mixture of
monomers.
• The common bases DNAs are Adenine(A), Guanine (G), Thymine (T) and Cytosine (C).
Secondary Structure of DNA: (Double helix model by Watson & Crick):
20Å
A .. T
3.4Å
G .. C
T .. A
C .. G
34Å
(a)
• Two strands are antiparallel.
Chemistry of Natural Products 115
• The X-ray studies have shown that the pairs are planar and that the hydrogen bonds are almost collinear, their
lengths lying between 2.8 and 2.9 Å.
• Each turn of the helix contains ten nucleotide pairs and the diameter of the helix is about 20 Å.
• The spacing between adjacent pair is 3.4 Å.
O N
H H H
N O
N N N N
R H N R H N
N N
O O
H
N N N N N
A-T pair R R
H
G-C pair
MgO,
Nucleosides + H3PO4
soln.
aq.NH3
AMP Adenosine H 3PO4
Nucleotides 175o C
? aq.NH3 HCl
Problem: RNA CMP X Y
175oC
aq.NH3 aq.NH3 Nucleoside HCl N base + Sugar
Soln. RNA CMP
115 C o 175oC (cytidine) (Cytosine + Sugar)
Ribose
Replication Tanscription
DNA DNA m–RNA Protein
Reverse
Transcription
116 Chemistry of Natural Products
t-RNA OH H O C CH NH2
O R
m-RNA :
It brings the information regarding the sequence of amino acid to the ribosomes. The four base in m-RNA exist
in form triplet called as CODON with code for one specific amino acid. (an amino acid can have more than one
codon).
eg. : UCU serine GCA + AGC (more than 1 codon is used for 1 amino acid)
3.4. Proteins :
• Proteins are nitrogenous substances which occurs in protoplasm of all animal and plants cells. Their compo-
sition varies with the source: carbon, 46-55%; hydrogen, 6-9%; oxygen, 12-30%; nitrogen, 10-32%; sul-
phur, 0.2-0.3%. Other elements may also be present, for example phosphorus (nucleoproteins),
iron(homeoglobin).
• Proteins can be broken down into smaller and smaller fragments until, the final products are amino acids.
Protein polypeptides peptides amino acids.
• There are no sharp dividing lines between peptides, polypeptides and proteins. Generally–
If the molecular weight above ~ 10, 000 = Proteins.
If the molecular weight below ~ 10, 000 = Peptide and polypeptide.
• The physical and chemical properties of proteins and peptides are different.
• Proteins are amphoteric in nature.
• All proteins are optically active, and may be coagulated and precipitated from aqueous solution by heat, the
addition of acids, alkalies, salts, organic solvents miscible with water.
• Proteins in precipitated state are called denatured and the process of reaching this state, denaturation occurs
most readily near the isoelectric point.
• Denaturation is generally irreversible, but in many cases the process has been reversed this reversal of
denaturation is called renaturation.
Classification of proteins:
(A) Simple Proteins (B) Conjugated Proteins
(A) Kind of simple proteins:
(i) Albumins: These are soluble in water, acids and alkalis. It is coagulated by heat.
(ii) Globulins: These are insoluble in water, but are soluble in dilute salt solution and in dilute solutions of
strong inorganic acids and alkali.
(iii) Prolamins: These are insoluble in water or salt solution but are soluble in dilute acids and alkalies.
(iv) Glutelins: These are insoluble in water or dilute salt solution, but are soluble in dilute acids alkalies. They
are coagulated by heat, glutelins are rich in arginine, proline and glutamic acids.
(v) Scleroproteins: These are insoluble in water or salt solution, but are soluble in concentrated acid. For
example: keratin(from hair, hoof), fibroin (from silk).
(vi) Basic Proteins: These are strongly basic, and are of the two kinds: (a) Histones (b) Protamines
Chemistry of Natural Products 117
(B) Conjugated proteins: These are proteins which contains a non-protein group(i.e. a compound not con-
taining amino acid residues) attached to the protein part. The non protein group is known as prosthetic
group and it may be separated from the protein part by careful hydrolysis.
Kinds of conjugated proteins.
(i) Nucleoproteins: In nucleoproteins the prosthetic group is a nucleic acid.
(ii) Chromoproteins: Their prosthetic group are coloured. For example, chlorophyll and haemoglobin.
(iii) Glycoproteins: In glycoproteins the prosthetic group contains a carbohydrates or a derivative of carbo-
hydrate. It is also known as mucoproteins.
(iv) Phosphoproteins: In phosphoproteins the prosthetic group contains phosphoric acids.
(v) Lipoproteins: In lipoproteins the prosthetic group is lecithin, kephalin etc.
(vi) Metalloproteins: The metalloproteins contain metal which is an integral part of the structure.
Structure of Proteins:
1. Primary Structure: The primary structure of proteins are the particular sequence of amino acids ,that is the
backbone of a peptide chain or protein. CH3
CH3 S
CH CH3 SH CH2
CH3 O CH2 O CH2 O CH2 O
H3N CH C NH CH C NH CH C NH CH C O
H
H
N
N
The helix model for the conformation of protein was proposed by Pauling and it suggest that:
(i) The peptide group is planar
118 Chemistry of Natural Products
(ii) Intramolecular hydrogen bonding stabilises the conformation and the strength of this bond is a maximum,
when the atoms concerned C O H N are collinear or, failing this ideal situation do not deviate by
more than 30º.
The – conformation, was proposed by Pauling. In this, the Pauli peptide chain is extended and chains are
held together by inter molecular hydrogen bonds. There are two types of -conformation(Pleated sheet):
parallel and anti-parallel.
3. Tertiary Structure :
• The tertiary structure of protein deals with folding of entire molecule which envolves hydrogen bonding, ionic,
chemical and hydrophobic bonds.
• The tertiary structure that a protein assumes under the normal condition of temperature and pH will be its
most stable arrangement. This has been refered to as the native conformation of that protein.
• There are two major molecular shapes of naturally occuring proteins: Globular and fibrous.
• Fibrous proteins have a large helical content and are essentially rigid molecules of rod-like shape.
• Globular proteins have a peptide chain which consist partly helical section and folded about the random coil
section to give a spherical shape.
• In globular proteins most polar groups lies on the surface of the molecule and most hydrophobic side change
lies inside the molecules.
• The tertiary structure of protein have been elucidated by X-ray analysis, viscosity measurements, diffusion,
light-scattering, ultracentirifuge methods and electromicroscopy.
• When a protein undergoes denaturation, the changes that occur involve changes in secondary and/or tertiary
structure of proteins.
3.5. Carbohydrate :
Carbohydrates are polyhydroxy aldehydes, polyhydroxy ketones or compound that can be hydrolyzed to
them.Carbohydrates are the ultimate source of most of the food.
Classifications of Carbohydrate:
(i) Monosaccharide (ii)Disaccharide (iii) Polysaccharide
(i) Monosaccharide: Carbohydrate that can not be hydrolyzed to simpler compounds is said to be monosac-
charide. For example: Glucose, Fructose etc.
(ii) Disaccharide: A carbohydrate that can be hydrolyzed to two monosaccharide molecule is said to be
disaccharide. For example: Lactose, Maltose, Sucrose, Cellobiose etc.
(iii) Polysaccharide: A carbohydrate that can be a hydrolyzed to many monosaccharide molecules is said to
polysaccharide. For example: Starch, Amylose, Amylopectin, Cyclodextrine, Cellulose etc.
Monosaccharide may be further classified as aldoses, if it contain aldehyde and ketose, if contains ketonic
group. On the basis of numbers of carbon atoms monosaccharides are also classified as: triose, tetrose, pen-
tose, hexose and so on.
Reducing and Non-Reducing: Carbohydrate that reduce Fehling’s solution (or Benedict’s solutions) Tollen’s
are known as reducing sugar. All monosaccharide whether aldoes or ketose are reducing sugars. Most disac-
charides are reducing sugars, for example lactose, maltose, cellobiose etc. except sucrose which is non-reduc-
ing sugar.
Chemistry of Natural Products 119
CHO
H OH
CH2OH
D(+)-glyceraldehyde
CHO CHO
H OH HO H
H OH H OH
CH2OH CH2OH
D(–)-erythrose D(–)-threose
D-xylose D-lyxose
1. Mono Saccharides :
These are the sugars which can’t be hydrolysed in to smallar molecules. CnH2nOn (n = 2 – 6)
2H O
C6 H12O 6 No Reaction
H
Configuration : In carbohydrates configurational differences are associated with different spatial arrange-
ment of tetrahedrally disposed ligands attached to chiral carbon atoms. The presence of asymmetric carbon
makes possible the formation of stereo isomers. Glyceraldehyde [CHO–CHOH–CH2OH] is selected as the
standard of reference to assign the configuration of carbohydrate because it is the simplest carbohydrate which
is capable of optical isomerism. It is a aldotriose.
CHO CHO
H OH HO H
CH2OH CH2OH
D(+)–glyceraldehyde L(–)-glyceraldehyde
4. Glucose reacts with one mole of HCN to form cyanohydrin and with NH2OH to form oxime. This indicate
presence of a carbonyl group.
NH2OH
C O C NOH
5. Oxidation of glucose with Br2/H2O give gluconic acid having same number of carbon atom as that of glucose.
C6 H12O7 . This indicates that carbonyl group is on –CHO (aldehyde) group (keto group containing sugars
give acid with less C-atoms).
O O
C H –C OH
6. Oxidation of gluconic acid with HNO3 produces a dicarboxylic acid (Glucaric acid) with molecular formula
C6H10O8. This indicates a presence of alcohol group (CH2OH) and oxidation occures with loss of 2Hs and
gain of one oxygen atom.
7. Glucose dissolve in H2O to produce a neutral solution shows that it don’t contain –COOH.
8. Glucose on reduction with H2/Ni, produces a hexa-hydric alcohol (Glucitol) (–CHO CH2OH). This on
reaction with HI/red P first yield 2-iodohexane at 100oC and then n-hexane on prolonged heating.
It indicate that all six C atoms in glucose are in a straight chain.
9. Glucose on reaction with HCN, form cyanohydrin, which on hydrolysis and followed by reduction with HI/red
phosphorus yields n-heptanoic acid which indicates the presence of six C atoms in straight chain.
Chemistry of Natural Products 121
10. Periodate or Pb(CH3COO)4 oxidation of Glucose produces five molecule of HCOOH and HCHO group.
Optical activity in monosaccharide:
CHO
H OH
CH2OH
D(+)-glyceraldehyde
Reactions of Fructose:
D-ribose D-arabinose
H OH HO H H OH HO H
H OH H OH HO H HO H
H OH H OH H OH H OH
H OH H OH H OH H OH
CH2OH CH2OH CH2OH CH2OH
D(+)–allose D(+)–altrose D(+)–glucose D(+)–mannose
[O] [O] [O] [O]
H OH HO H H OH HO H
H OH H OH HO H HO H
H OH H OH H OH H OH
H OH H OH H OH H OH
D-xylose D-lyxose
H OH HO H H OH HO H
H OH H OH HO H HO H
HO H HO H HO H HO H
H OH H OH H OH H OH
CH2OH CH2OH CH2OH CH2OH
D(+)–glyose D(+)–idose D(+)–galactose D(+)–talose
Reactions of Aldohexose:
HC NHNHC 6 H 5
C 6 H 5 NHNH 2
(CHOH)4
(1 equivalent)
CH 2 OH
Glucose phenylhydrazone
COOH
Br2 + H 2 O
(CHOH)4
CH 2 OH
Gluconic acid
COOH
HNO 3
(CHOH)4
COOH
Glucaric acid
CHO (Saccharic acid)
CHOH
Ac 2O
CHOH
C 6 H 7 O(OAc)5
Penta-O-acetylglucose
CHOH
CHOH
CH 2 OAc
CH 2 OH Ac 2 O
(+)–Glucose (CHOAc)4
CH 2 OAc
CH 2 OH
H exa-O-acetylglucitol
H 2/Ni
(CHOH)4 (H exa-O-acetylsorbitol)
COOH CH 3
Glucitol HI/P CHI
(Sorbitol)
(CH 2 )3
CH 3
2-Iodohexane
COOH
H 2, Ni hydrolysis HI, heat
CH 2
(CH 2 )4
CH 3
Heptanoic acid
OSAZONE FORMATION OF KETOSE AND HEXOSE:
CO CO C NNHC6H5 H OH
HO H HO H C6H5NHNH2 HO H C6H5NHNH2 HO H
Zn
H OH H OH H OH H OH
CH3CO2H
H OH H OH H OH H OH
CH2OH CH2OH
CH2OH CH2OH
Osone D(–)–fructose Osazone D(+)–glucose
124 Chemistry of Natural Products
CN COOH C O CHO
H OH H OH H OH H OH
HO H H2O HO H –H2O HO H O Na(Hg) HO H
H OH H+ H OH H H OH
H OH H OH H OH H OH
CH2OH CH2OH CH2OH CH2OH
CHO
HO H
H OH HCN
H OH
CH2OH
CN COOH C O CHO
An aldopentose
HO H HO H HO H HO H
HO H H2O HO H –H2O HO H O Na(Hg) HO H
H OH H+ H OH H H OH
H OH H OH H OH H OH
CH2OH CH2OH CH2OH CH2OH
Diastereomeric Diastereomeric Diastereomeric Diastereomeric
cyanohydrins aldonic acids aldonolactones aldohexoses Epimers
Shortening the carbon chain of Aldose: Ruff degradation:
H OH H OH HO H
H OH H OH H OH
O
CHO
C HO H
HO H
Na(Hg) HO H
HO H O
H OH
H
H OH
H OH CH2OH
H OH HO H
H OH H OH
HO H O HO H O
H OH H OH
H H
CH2OH CH2OH
CH2OH CH2OH
O O
H H H OH
H H
OH H OH H Haworth Projection for -D-glucose
H and -D-glucose
OH OH OH
OH H OH
H
H
H CH2OH
CH2OH
O
O HO
HO H
H
H OH
H H HO
HO OH
OH H H
H OH
126 Chemistry of Natural Products
Problem:
H
CH2OH H
O CH2OH
HO H CH3OH, HCl O
HO (CH3)2SO4
H OH H
HO NaOH
H OMe
OH HO
H H OH
-D-(+)–Glucose H H
Methyl -D-(+)–Glucoside
H H H
CH2OMe CH2OMe
O O
MeO MeO
H dil. HCl H
H OMe H OH
MeO MeO
OMe OMe
H H H H
Methyl-2,3,4,6-tetra-O-methyl-D-glucoside
H H
CH2OMe CH2OMe
O OH
MeO H MeO
H CHO
H H H
MeO MeO
OMe OMe
H OH H
-2, 3,4,6-Tetra-O-methyl-D-glucose
HIO4 :
On treatment with HIO4 aquous solution or Pb(OAc)4 in organic solvent compounds containing two or more
C=O or C–OH groups adjacent to each other undergo oxidation with cleavage of the C–C bond.
O
C OH IO4 C O O
I C O + C O + IO3
C OH C O
O
CHOH
CHOH 5 IO4–
5HCOOH + HCHO
CHOH
CHOH
CH2OH
CH2OH
C O
HO H
5IO4–
H OH HCHO + CO2 + HCOOH + HCOOH + HCOOH + HCOH
H OH
CH2OH
Limitation:
Periodate oxidation don’t occur in which – OH group or C=O group are separated by a CH2 group. It also do
not cleave the compounds in which OH group is adjacent to a ether or acetyl group.
CH2OH CH2 OCH3
IO4– IO4–
H2C No reaction ; HO HC No reaction
CH2OH CH3
Disaccharides:
Sucrose: Sucrose is a non-reducing sugar. Upon hydrolysis with dilute acids or by enzyme invertase it gives
an equimolar mixture of D-glucose and fructose.
O
CH2OH
H C CH2OH
CH2OH
C O H O
H OH H H H
HO H
HO H O O or OH H H OH
H OH O CH2OH
OH
H OH
H H OH OH H
H
CH2OH
CH2OH
128 Chemistry of Natural Products
H C
CHOH CH2OH CH2OH
H C OH O H
H OH H O
HO H H H
H
O O or H H, OH
HO H O OH H OH
H OH O
OH
H
H H OH H OH
H
CH2OH
CH2OH
Cellobiose: The Cellobiose is 4-O- -D-glucopyranosyl-D-glucopyranose. Cellobiose upon hydrolysis with
dilute acid gives two molecules of D-glucose. Since this hydrolysis is effected by emulsin, the glycocidic link
must be beta. Cellobiose is reducing sugar.