Introduction to bio chemistry

 The branch of biology which explain the biochemical basis of life is called biochemistry
 Most important branch of biology
 1)it provide information about all the process carried out in the living organisms
 2)It also provides about abnormal mechanism which lead to disease and also the
development of medicine and medical equipment to eradicate these abnormalities.
 3) all about the question of the cell disease and it’s medicine are Answered In this
branch
 Organisms are made up to tissues and cell while cells are made up of molecules Those
molecules are chemically bonded atoms
 Fundamentally living things or organism are made up to chemicals Which explain the
second postulate of cell theory
 Structure and function of cell are dependent upon their chemical composition

CHEMICAL COMPOSITION OF CELL:

 Living organism are structurally composed of cell and living cell contains a living matter
called protoplasm
 Chemical composition of protoplasm is still not known perfectly
 Protoplasm Contains 70 to 90 Percentage of Water(H2O) if water is Removed from
protoplasm the remaining mass of cell is called dry weight of cell
 Dry weight of cell consists of many carbon containing long chain molecule called
biomolecules which are the types of organic molecules
 Compound produced by living organism are called biomolecules
 The elements or compound which are involved in the synthesis of biomolecule are
mainly 6 (Six) Which are Carbon,Hydrogen,Nitrogen,oxygen,phosphorus and sulphur
 These elements from 98 Percentage of the biomolecules

FUNDAMENTAL TYPES OF BIO MOLECULE:

 Biomolecules are divided into 5 Types according to changing in there structure and
function in cells These 5 Types are
 Carbohydrates 2)Proteins 3)Lipids 4)Nucleic acids 5)Conjugated molecules
TABLE 1.1
 Biomolecules. Unit. Linkage
 Carbohydrates. Mono. Glycoside
  Saccharides linkage
 2)Proteins. Amino acids. Peptide
 Linkage
 3)Lipids
 Fats and oils. Glycerol and. Ester
 Fatty acid. Linkage
 Phospholipids. Glycerol,fatty. Ester and
 Acids,phosphat. Cc
 And choline. Linkages
 Terpenoids. Isoprenoids. Cc linkage
 Units
 4)Nucleic acids
 DNA. Deoxyribo. Phospho
 Nucleotides. Ester
 Linkages
 RNA. Ribonucleo. Same as
 Tides. DNA
 5)Conjugated. Different. Different
 Molecules. Biomolecules Linkage
 TABLE NO 1 ENDED
 Different cells within the same body have different amount of biomolecule
TABLE NO 2 CHEMICAL COMPOSITION OF CELLS IN PERCENTAGE
 Molecules. Bacterial cell. Mammalian cell
 Water. 70. 70
 Protein. 15. 18
 Carbohydrates. 3. 4
 Lipids. 2 3
 DNA. 1. 0.25
 RNA. 6. 1.10
 Other organic. 2. 2
 Compounds
 Inorganic ions. 1. 1
Synthesis and breakdown of macromolecules
A)Synthesis of macromolecules (polymers by condensation):
 Molecules which from the structure and carry out the activities of the cells and are large
in size and highly organized are called Macromolecules
 Macromolecules are made up of large number of low molecular weight,small molecules
the subunits called monomers or building blocks

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  Macromolecules also called Polymers
 Macromolecules are formed from monomer
 Process of joining two monomers by removing water molecule is called condensation or
dehydration synthesis
 Basic structure of each Group of macromolecule is very similar in all organism from
bacteria to human beings
 Covalent bond is formed in condensation
 Condensation always takes place or happen by proper enzymes and energy expense
B) breakdown of macromolecule by hydrolysis
 Process where macromolecule or polymer are broken down into their sub units
monomer by addition of H2O or water molecule is called Hydrolysis
 Just reverse of condensation
 During metabolism, macromolecules are either formed or broken down in the cell
 Autotroph cells produce monomers form inorganic molecules like CO2,H20,NO3,SO4
IMPORTANCE OF WATER
 Water is most abundant component in living cells
 In living cell it is 70 to 90 Percentage
 It is the medium of life
 Almost all reaction of a cell occur in the presence of water
 It is a polar molecule
 It has partial negative charge on oxygen and partial positive charge on hydrogen Due to
electronegativity difference
 This separation of electrical charge is called dipole
Hydrogen bond
 The force of attraction between positive hydrogen atom of water and negative atom of
oxygen called Hydrogen Bond
A)Cohesion or Cohesive Force of attraction
 The attractive force between similar molecules is called cohesive Force Of attraction
 Polar nature cause attraction of water molecule which help to form a long chain of
water molecule
B) Adhesive force of attraction or adhesion
 The attractive force between dissimilar molecule is called adhesive force of attraction

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 High specific heat
 Specific heat of a substance is the amount of heat required to raise the temperature of
1g of any substance by 1 celcius
 Specific heat of water is high due to its polar nature and hydrogen bonding between
there molecule
High heat of vaporization
 The amount of heat required to change liquid state of water to vapour state is called
heat of vaporization
 Greater the heat of vaporization higher will be the chances of stability in state or vice
versa
 Water has high heat of vaporization about 574 kcal/kg
 It require high heat to change its state from liquid to vapours
 High heat of vaporization give stability to water molecule
 High heat of vaporization plays important role in thermoregulation also provide cooling
effect when evaporate during transpiration or sweating
Hydrophobic exculsion
 The ability of water to make new hydrogen bond when old are destroyed due to entry of
non polar molecule is called hydrophobic exculsion
Ionization of water
 The water molecule ionize into H+ And OH-
 This ionization reaction of water is reversible and also maintain equilibrium
 Due to ionization property water is amphoteric in nature amphoteric means water can
also act as acid or base
 Also behave as buffer and maintain PH For enzymatic activities in cells and organs
Anomalous behavior of water
 Water shows anomalous means different behavior below 4 celcius
 Matter contract at low temperature
 But in case of water due to hydrogen bond below 4 celcius it expands rather than
contracting this expanding decrease it’s density
 At 0 celcius water expand maximum in ice condition
 The low density of water in ice become Low ice come above the surface of high density
water of liquid it makes the life possible in frozen water
Carbohydrates

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  The literal meaning of word carbohydrates is hydrated carbon means water containing
carbon
 Thus biomolecules contain C,H And O as element in which hydrogen and oxygen are
present in the simple ration of 2:1 as present in water
 General formula of carbohydrates is CnH2nOn
 In Iupac carbohydrates are defined as the Poly hydroxy carbonyl compound
 Main source of carbohydrates are plants
 They are sweet in taste called sachrum or sachride
 They are Found abunduntly in All organism
 Cellulose is find in cell wall of plant while starch is stored in cereal
grains,tubers,sugarcane etc
 They plays both structural And functional Role
Classification of Carbohydrates
 They are also classified as saccharides and are classified into 3 groups which are
Mono,oligo and poly saccharides
Monosaccharides
 The group of carbohydrates which contain only one sugar molecule
 They cannot hydrolyse Because of only 1 number of molecule
 There emperical formula is same as general formula of carbohydrates
 They are Found in white crystalline solids with sweet taste and soluble in water
 Class. Formula. Example
 Triose. C3H6O3 Glycerose dihyroxy acetone
 Tetrose. C4H8O4. Erythrose erythrulose
 Pentose. C5H10O5 Ribose ribulose
 Hexose. C6H12O6 G,F,G etc
 Heptose. C7H14O7 glucoheptase
 Glycerose and dihydroxy acetone are important triose produced during respiration
 Tetrose like erythrose and erythrulose are rare in nature occurs in some bacteria
 Pentose sugar form basic skeleton of nucleic acid
 The most important sugars are hexose in which glucose is found in ripe fruit,sweet corn
and honey also found in all poly saccharides in combined state while second hexose
sugar is Fructose which is also called Fruit sugar Found in ring structures

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  These hexose are further divided into aldohexose isomers like
glucose,galactose,mannose and ketohexose isomers like fructose,sorbose,psicose etc
2)Oligo saccharides
 The type of carbohydrates which are made up to 2 to 10 monosaccharides
 Less sweat in taste and less soluble in water
 They can hydrolyze due to polymonomers
 The most common type of oligosaccharides is disaccharide on hydrolysis yeilds two
monosaccharides
 The covalent bond between these monosaccharides is glycosidic bond or linkage
 Glycoside simply a ring shaped sugar molecules attach to another molecule
 The sugar ring may be either 5 or 6 membered ring
 Sucrose us a disaccharide composed of two sugar that are glucose and fructose
 The disaccharide may be reducing or non reducing sugar
 Reducing sugar is the carbohydrates which has the ability of being oxidized and cause
the reduction of other substance without hydrolysis due to the presence of free
aldehyde or free ketone group reducing sugar example is maltose,lactose
 The non reducing sugar are carbohydrates which are not able to being oxidized or to
reduce other substance due to the absence of free aldehyde or free ketone group
example is sucrose or refinose etc
 Plant transport there sugar in the from of non reducing sugar in which glycosidic bond is
formed between carbonyl group of two sugars
Polysaccharide
 These are high molecular weight carbohydrates on hydrolysis yeilds many mono
saccharides
 These are formed by the condensation of hundred or thousands of Monosaccharides it's
examples are given Below
1)Starch:
 Most abundant reserve food material of higher plants Found in various vegetables
 Made up by condensation of many glucose molecules in a straight chain
 Staright chain is amylose which is soluble in hot water
 Branched chain is amylopectin which is insoluble in hot and cold water amylopectin give
blue colour to iodine
2)Glycogen

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  Poly saccharides
 Molecular structure similar to starch but found in animals called animal starch
 Mainly Found in bacteria,Fungi,Animals abundantly found in liver and muscles
 Glycogen gives redcolour with iodine
3)Cellulose
 Polymer of glucose
 Most abundant carbohydrates found in nature
 Highly insoluble in water and not digested in human body
 No branch chain only straight chain Which become spirally coiled
 Give no colour to iodine
4)Chitin (C8H13O5N)n
 Long chain polymer of N-acetyl glucosamine
 It is an amide derivative of glucose
 Structure similar to cellulose
 Comparable to keratin and protein
 It is modified polysaccharide also contain nitrogen
 In it’s pure and un modified from chitin is translucent also tough found in some
arthropods
 It froms exoskeleton of insect with CaCO3
 All the things related to exoskeleton is associated with chitin
Sterioisomers in carbohydrates
 Many sugar molecules have sterioisomers which means molecules are image of each
other
 Most of the sugar in our body is right handed
 Taste are same in left and right handed sugar
 Proteins and enzyme are also left and right handed the enzyme which is in our body are
right handed and right handed enzymes form right handed sugars only
 They are unable to digest or metabolize left handed sugar
 Artificial sweeteners used by sugar or diabetic patient usually are left handed and has 0
calories this sugar not digested in our body because of no left handed enzymes
Protein

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  It is the polymer of specific amino acids arrange in a particular manner
 Protein are the most important organic compounds of the cells which carry out virtually
all activity of the cell
 They constitute the major part of the dry weight of the cell
 They are complex organic compound contain C,H,O and N elements sometime they
contain sulphur too
 In protein amont of nitrogen is high due to which they are also called nitrogenous
compound
 Protein are the building blocks of tissue
 Many parts of the body such as nails hairs and feather are also protein
 The source of protein are meat,fish,milk and pulses are the main sources of protein
Amino acid as a building block of protein
 Protein are macromolecules and are the polymer of amino acid
 They are also linked through covalent bond which is called peptide bond or peptide
linkage in case of protein
 Twenty basic amino acid form different or each types of proteins
 Amino works as base while carboxalic acid work as acid and are attached to asymmetric
carbon also called alpha carbon
 20 amino acid have same formula except R group radical which is variable
Formation and breakdown of peptide linkage
 The protein is formed by linking 20 amino acid with the peptide or covalent bond
 The resultant dipeptide us glyclyanine has two amino acid subunit called dipeptide
 The polypeptide chain can be broken by breaking peptide bonds by Hydrolysis with the
help of hydrolytic enzymes
 Protein chain can be broken into small chain of more than 10 amino acid called peptone
 Peptone can be hydrolysis further into small unit of few amino acids called peptide
which are further hydrolysis into amino acid
Significance of the sequence of amino acids
 F.sanger was the first sceintist who discovered the sequence of amino acid in a protein
molecule
 Insulin is composed of 51 amino acid in 2 chain the one chain has 21 amino acid while
the second one has 30 amino acids which are held together by dishulphide bond

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  Haemoglobin is composed of 4 chain Two are alpha and Two are beta chains each alpha
chain has 141 amino acid while each beta chain has 146 amino acids
 Human body has more than 10,000 proteins
 If the sequence of amino acid go upright then it would affect the protein function
Classification of protein
 Protein on the basis of shape is classifieds in two types
Fibrous Protein
 These are the long fibers of proteins
 In this protein the secondary protein (spiral)chains intertwine with each other
 They are insoluble in water non crystalline and elastic in nature
 Perform structural role in cells and organisms
B)Globular protein
 These are spherical or ellipsoidal due to three dimensional fold of secondary protein
 They are either tertiary or quaternary in structure soluble in slats
 Can be crystallized
 Work as enzyme antibiotics hormones and haemoglobin
o Necessary to remember Table 1.4 list of structural protein
Lipids
 Important diverse group of biological molecules
 The term lipid was proposed by Bloor in 1943
 These biomolecules are insoluble in water and soluble in non polar organic solvents like
ethers and alcohal etc
 These compounds are made of C,H,O like carbohydrates but contain much lesser ratio of
oxygen than carbohydrates example is stearin has molecular formula (C57H110O6)
 High quantity of carbon and hydrogen they contain almost double amount of energy
than carbohydrates
Aclyglycerol (Fats and Oil)
 These are the condensation product of one glycerol and three fatty acid called fats and
oils
 Can be defined as the esters of glycerol and fatty acid
 Ester is the bond or linkage formed between alcohal and organic acid by removing water
this reaction is called esterification

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  Glycerol is a trihydroxy alcohol made of three carbon atom each contain on OH group
 Fatty acid is a type of organic acid containing one carboxalic acid group with long
hydrocarbon chain
 When three fatty acid and one glycerol combine they form three ester bonds Also a
compound called triglycerol is formed
 The triglycerol are neutral in nature
 Two types of aclyglycerol or triglycerol
Saturated aclyglycerol (Fats)
 They contain saturated fatty acid do not contain any double bonds between carbonyl
atoms of hydrocarbon chain
 It’s example is stearin
Unsaturated Aclyglycerol (Oils)
 They contain unsaturated fatty acid contain more than one bond double bond between
carbon atoms of hydrocarbon
 Have stable physical state usually found at liquid state at ordinary means roam
temperature
 It is found in plants also called oil
 It’s example is linolin found in seed
 Aclyglycerol are very rich in chemical energy
 Twice amount of energy content than carbohydrates
 16 Kg of fats which contain 144x10 power 3 Kcal of energy
Phospholipids
 Condensation product of glycerol and two fatty acid one choline and one phosphate
 Phospholipids is similar to aclyglycerol except it’s one fatty acid is replaced by
phosphate
 Contain two end the one fatty acid which is non polar and are hydrophobic and it’s
another part is phosphate and choline which behave as hydrophilic part of
phospholipids
WAXES
 These are esters of long chain mono alcohol and long chain fatty acid
 Simple lipid and found as protective coating
 Water repellant and non reactive due to non polar nature

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  Two types of wax
 1)Natural like beewax and cutin from cuticle of leaves
 2)Synthetic waxes
 Dervied from petroleum or polyethylene
 Sperm whales are the principle source of wax
Terpenoids
 It is a large unit and important class of lipids
 Made up of isoprenoids units(C5H8)
 Terpenes,steroids,cartenoids and prostaglandins are types of terpenoids
 Found in cell membrane as cholesterol
Terpenes
 They contain few isoprenoids units
 Small type terpenes are volatile in nature and produce special fragrance
 Are used in perfumes
 1)Mycerens from oil of bay
 2)Menthol from peppermint oil
 3)Geraniol From rose
 4)Limonene from lemon oil
Steroids
 Made up of isoprenoids units contain 17 carbon atoms arranged in four attached rings
 Three rings are hexagonal and one it’s pentagonal in shape
 Cholesterol is the type of steroid
 It’s example are testosterone,progesterone and nitrogens
Cartenoids
 Poly terpenes consist of long chain of isoprenoids units
 Which contian isoprenoids rings at both or at one terminal
 These compounds are pigments Producing red,orange,yellow and brown colour in plants
 Cartenoids are plant pigments like chlorophyll, cytochrome,phytochromes,latex,rubber
etc
Prostaglandins

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  Group of lipids made by mammalian tissues at the site of tissue damages or infection
 Involved in dealing with injuries and illness
 We use aspirin to reduce fever and decrease pain it inhibit of prostaglandins synthesis
Nucleic acids
 Fried rich Meicscher a swiss physician isolated a new compound from the nucleus of pus
cells
 It was first named nuclein and after that we know it has acidic properties than it was
renamed as Nucleic acids
 They are polymer of fiver sugar based compounds called nucleotide
 Nucleic acid have high molecular weight
 Present in all living from virus to man
 Two kinds of nucleic acids
o 1)DNA
o 2)RNA
 These 2 types are linear unbranch polymers
 DNA is the polymer of deoxyribonucleotide and RNA is the polymer of ribonucleotide
Composition of Nucleotides
 They are the monomer of nucleic acid
 Nucleotides are pentose sugar based in which the nitrogenous base is attached it's first
carbon and phosphate is attached at 5th carbon of pentose sugar
 Nucleotides without phosphate called nucleoside
 DNA and RNA are made up of four types of nucleotides and these types are variable on
the basis of nitrogenous bases
 these are two groups of nitrogenous bases
o 1)Purines
o 2)Pyramidines
 Purines are of two types Adenine and guanine while Pyramidines includes three
nitrogenous bases which are Cytosines,thymine and uracil
MonoNucleotides
 MonoNucleotides have extra phosphate group as ADP or ATP
 ATP work as energy storing,carrying and energy providing molecules to metabolic
reactions

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  During conversion of ATP into ADP 7.3kcal/mole or 31.81 kj/mole energy is released
Dinucleotides
 One of the well knows dinucleotides is NAD(Nicotinamide adenosine di nucleotide)
 It work as co-enzymes for redox reaction
 NAD carries 2 electron and 2 proton and energy
 It’s example are NADH2 And FADH2 etc
Formation of phosphodiester bond
 The two nucleotide are link together by a bond called phosphodiester bond
 It is considered as the back bone of nucleic acid
 It is a bond which is formed as a result of condensation reaction between phosphate
group of pentose sugar
Polynucleotide
 Nucleotides are joined together to from a polymer like DNA and RNA
 DNA perform function of transformations and heredity genetic information is encoded
in DNA
Structure of DNA
 Structure of DNA was explained by James Watson and Francis crick in 1953 by making
model
 The DNA is a double helical structure each helix is made up to 4 types of Nucleotides
 Both helix are complementary to each other For example
 if one helix contain adenine the opposite or complimentary helix will contain thymine
 cytosine is complementary to guanine
 Each helix is consist of two parts
 Upright which is made up of deoxyribose sugar and phosphate
 Rung: made up of Nitrogenous bases
 Both helix are held together by H-Bond and are opposite in direction and the distance
between two helix remain same from one end to another end of 20 Angston
 Each turn of the duplex consist of 10 base pairs
What is gene
 DNA carries genetic information from parents to offspring in the form of genes
 A gene is a part of DNA which has information to synthesis a protein

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  Gene is a functional unit of heredity material
 Genetic information flow in a cell from DNA to mRNA than to cytoplasm in two step for
protein synthesis
Transcription
 In this step the information of gene is copied in the form of RNA example mRNA which
carries information from nucleus to the ribosome in the from of genetic code
Translation
 In this step the mRNA attach to ribosome twi other type of RNA i.e tRNA and rRNA
translate the information of mRNA into specific sequence of amino acid which help to
synthesize the protein
Ribonucleic Acid (RNA)
 It is the polymer of nucleotides
 It’s one of the nitrogenous base i.e A,G,C and U it means instead of thymine it contains
the nucleotide of uracil
 There are three types of RNA
1)Messanger RNA (mRNA)
 It consist of single strand
 Length depend on the size of gene
 Contain information in the form of genetic code , Codon
 These codons are triplets of nucleotide of mRNA which encode one amino acid
 It is about 3 to 4 percentage of total RNA in the cell
2)Transfer RNA
 The smallest sized RNA consist of only 70 to 90 nucleotides
 Basically single standard but in some region double or duplex in duplex region
complementary bases are present
 It has anticodons
 It transfer related amino acid from cytosol to ribosome
 tRNA are sixty in numbers
 While human cell consist only 45 different types of tRNA
 It is about 10 to 20 percentage of total RNA
3)Ribosomal RNA (rRNA)
 It is present in ribosome and is largest among all three RNA

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  80 percent of total of RNA in a cell is rRNA
 Involved in peptide linkage during protein synthesis
Conjugated molecules
 Conjugate molecules are formed when biomolecules of two different group combine
chemically with each other acting as one unit
1)Glycolipids or cerebrosidea
 Conjugate of lipid and carbohydrate
 Also called cerebroside bcz they are present in white matter of brain and mylein sheat
of nerve fiber also found in the inner membrane of chloroplast
2)Glycoproteins or mucoids
 They are formed by combining of carbohydrates and protein molecule
 Most of the oligo and polysaccharide in animal are covalently linked to protein molecule
 It is one of the part of egg albumin and gonado tropins
3)Lipoprotein
 Conjugate of lipids and protein
 They help in transportation of lipids in blood plasma
4)Nucleoprotein
 Nucleoprotein are formed by simple basic protein and nucleic acid
 Main component of chromatin material,chromosomes and ribosmes

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