Biomolecules

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Chemicals or molecules present in the living organisms are known as Biomolecules

The sum total of different types of biomolecules, compounds and ions present in a cell is called as cellular pool

Biomolecules are compounds of carbon. Hence the chemistry of living organisms is organized around carbon

Carbon is the most versatile and the most predominant element of life.

ELEMENT Non living (Earth crust)

Living Matter

Hydrogen 0.14 0.5

Carbon 0.03 18.5

Oxygen 46.6 65.0

Nitrogen Very less 3.3

Sulphur 0.03 0.3

Sodium 2.8 0.2

Calcium 3.6 1.5

Magnesium 2.1 0.1

Silicon 27.7 Very less

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BIOMOLECULES

Inorganic Organic

MineralsGasesWater

CarbohydratesLipidsAmino acidsProteinsEnzymesNucleotidesNucleic acidsVitamins

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BIOMOLECULES

Micro molecules

MineralsGasesWaterSugarsAmino acidsnucleotides

CarbohydratesLipidsProteinsNucleic acids

Macromolecules

Small sized, low mol wtBetween 18 and 800 daltonsFound in the acid soluble pool

Large sized, high mol wtAbove 10000 daltonsFound in the acid insoluble pool

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Biomolecule Building block Major functions

Protein Amino acid Basic structure and function of cell

DNA Deoxyribonucleotide Hereditary information

RNA Ribonucleotide Protein synthesis

Polysaccharide Monosaccharide Storage form of energy

Lipids Fatty acids & glycerol Storage form of energy to meet long term demands

The major complex biomolecules of cells

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NUCLEOTIDES

SUGAR

N2 BASES

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DNA

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m- RNA r- RNA t- RNA

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Carbohydrates

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CARBOHYDRATES

Carbohydrates are the most abundant organic molecules in nature.

The term carbohydrate is derived from the French term hydrate de carbone i.e. it is a hydrate of carbon or Cn(H2O)n

Carbohydrates are defined as organic substances having C, H & O Wherein H and O are in the ratio 2:1 as found in H2O

FUNCTIONS OF CARBOHYDRATES

- Most abundant source of energy (4 cal/g)- Precursors for many organic compounds (fats, amino acids)- Present as glycoproteins and glycolipids in the cell

memebrane and functions such as cell growth and fertilization- Present as structural components like cellulose in plants,

exoskeleton of some insects, cell wall of microorganisms- Storage form of energy (glycogen) to meet the energy

demands of the body.

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CARBOHYDRATES

MONOSACCHARIDES OLIGOSACCHARIDES POLYSACCHARIDES

Basic units of carbohydratesCannot be hydrolysed into smaller units

They can be further hydrolysed

Non crystalline, non soluble in water, tasteless, on hydrolysis gives mol of monosaccharidese.g. starch , cellulosea. Based on the no. of

C-atomsb. Based on the type of

functional group

a. Disaccharidesb. Trisachharidesc. Tetrasachharides

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MONOSACCHARIDES

Based on the no of C-atoms Based on the functional group

- Trioses (C3H6O3) e.g. Glyceraldehyde, Dihydroxyacetone- Tetroses (C4H8O4) e.g. Erythrose, Threose

- Pentoses (C5H10O5) e.g. Ribulose, Xylose Arabinose(deoxyribose – C5H10O4)

- Hexoses (C6H12O6) e.g. glucose, fructose galactose, mannose- Heptoses (C7H14O7) e.g. sedoheptulose glucoheptose

- Aldoses : the functional group is Aldehyde –CHOe.g. Glyceraldehyde, glucose

- Ketoses : the functional group is ketone ( C = O)e.g. Dihydroxyacetone, fructose

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Derivatives of Monosaccharides

1. Deoxy Sugars : Deoxygenation of ribose produces deoxyribose, which is a structural component of DNA

2. Amino Sugars : When 1 or more –OH groups of monosaccharides are replaced by –NH2 (amino group) it forms an amino sugar e.g. Glucosamine, which forms chitin, fungal cellulose, hyaluronic acid. 3. Sugar Acid : Oxidation of –CHO or –OH group forms sugar acids. Ascorbic acid is a sugar acid

4. Sugar alcohols : Reduction of aldoses or ketoses. Glycerol and Mannitol.

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OLIGOSACCHARIDES

They are formed by condensation of 2-9 monosaccharides

Depending upon the no. of monosachharide molecules they are :

a. Disaccharides (sucrose, lactose)

b. Trisaccharides (raffinose)

c. Tetrasaccharides (stachyose)

The smallest and the commonest oligosaccharides are Disaccharides

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DISACCHARIDESA disaccharide consists of 2 monosaccharide units (similar or dissimilar)held together by a glycosidic bond

They are crysatalline, water soluble and sweet to taste.

MALTOSE : - is also called as malt sugar. - made up of 2 glucose molecules

LACTOSE : - is also called as milk sugar as it is found naturally in milk - made up of glucose and galactose - souring of milk is due to conversion of lactose to lactic acid

SUCROSE : -is also called as cane sugar. It is the sugar found in sugar cane and sugar beet - most abundant among naturally occuring sugars. - Important source of Dietary carbohydrates - made up of glucose and fructose

POLYSACCHARIDES- Also called as GLYCANS- Made up of repeating units of monsaccharides held by glycosidic

bonds- During its formation a water molecule is released at each

condensation This helps reduce the bulk making it almost insoluble decreasing its effect on the water potential or osmotic potential of the cell - Unlike sugars they are not sweet.- They are ideal as STORAGE AND AS STRUCTURAL COMPONENTS- They are of 2 types Homoglycans and Heteroglycans.

HOMOGLYCANS-Made up of only 1 type of monosaccharide monomers-For eg starch, glycogen, cellulose -Glucan (made up of glucose)-Fructan(made up of fructose) -Galactan (made up of galactose)

HETEROGLYCANS-Made up condensation of2 or more types of monosaccharides- For eg Hyaluronic acid, agar, Chitin, peptidoglycans etc

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STORAGEPOLYSACCHARIDES

STARCH1. Carbohydrate reserve of plants and the most important dietary source

for animals2. High content of starch in cereals, roots, tubers, vegetables etc.3. Homopolymer made up of GLUCOSE units. Also called as GLUCAN.4. Starch = Amylose + Amylopectin (polysaccharide components)

GLYCOGEN1. Carbohydrate reserve in animals. Hence referred as animal starch2. High concentration in Liver, muscles and brain.3. Also found in plants that do not have chlorophyll (yeast and fungi)4. GLUCOSE is the repeating unit.

INULIN1. Polymer of fructose i.e. fructosan2. Found in Dahlia, bulbs, garlic, onion etc3. Easily soluble in water4. Inulin is not readily metabolised in the human body and is readily filtered through the kidney. Hence used for testing kidney function (GFR)

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STRUCTURALPOLYSACCHARIDES

CHITIN1. Second most abundant organic substance.2. Complex carbohydrate of Heteropolysaccharide type.3. Found in the exoskeletons of some invertebrates like insects and

crustaceans. Provides both strength and elasticity.4. Becomes hard when impregnated with calcium carbonate.

CELLULOSE1. Occurs exclusively in plants and is the most abundant organic

substance in plant kingdom.2. Predominant constituent of plant cell wall.3. It is totally absent in animals.

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Proteins

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PROTEINS

Most abundant organic molecules of the living system. They form about 50% of the dry weight of the cell. They are most important for the architecture and functioning of the cell.

Proteins are polymers of amino acids

Proteins on complete hydrolysis yields Amino Acids There are 20 standard amino acids which are repeatedly found in the structure of proteins – animal, plant or microbial. Collagen is the most abundant animal protein and Rubisco is the most abundant plant protein Protein Synthesis is controlled by DNA.

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AMINO ACIDS

Amino acids are group of organic compounds having 2 functional groups (-NH2) and (-COOH)

(-NH2) group is basic whereas (-COOH) is acidic

R- can be H in glycine, CH3 in alanine, Hydroxymethyl in serine

in others it can be hydrocarbon chain or a cyclic group

All amino acids contain C, H, O and N but some of them additionally contain S

Physical and chemical properties of amino acids are due to amino, carboxyl and R functional groups

Amino acids are differentiated into 7 groups

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No. Nature Amino acids

1. NEUTRAL : Amino acids with 1 amino and 1 carboxyl group

Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile)

2. ACIDIC : 1 extra carboxyl group Aspartic acid (Asp), Asparagine (Asn), Glutamic acid (Glu), Glutamine (Gln)

3. BASIC : 1 extra amino group Arginine (Arg), Lysine (Lys)

4. S – CONTAINING : Amino acids have sulphur Cysteine (Cys), Methionine (Met)

5. ALCOHOLIC : Amino acids having –OH group Serine (Ser), Threonine (Thr), Tyrosine (Tyr)

6. AROMATIC : Amino acids having cyclic structure

Phenylalanine (Phe), Tryptophan (try)

7. HETEROCYCLIC : amino acids having N in ring structure

Histidine (His), Proline (Pro)

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Aspartic acid (acidic)Alanine (neutral)Lysine (basic)

Serine (alcoholic) Cysteine (suphur) Phenylalanine (aromatic)

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PEPTIDE FORMATION

Amino acids are linked serially by peptide bonds (-CONH-) formed between the (-NH2) of one amino acid and the (-COOH) of adjacent amino acid

Chain having 2 amino acids linked by a peptide bond is called as a DIPEPTIDE

The sequence of amino acids present in a polypeptide is specific for a particular protein.

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STRUCTURE OF PROTEIN

4 basic structural levels are assigned to proteins – primary, secondary, tertiary and quaternary

PRIMARY

The primary structure refers to the number and linear sequence of amino acids in thepolypeptide chain and the location of thedisulphide bridges

The primary structure is responsible for thefunction of the protein.

The N-terminal amino acid is written on the left side whereas the C- terminal amino acid is written on the right side

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SECONDARY

The folding of the linear chain into a specific coiled structure is called as secondary structure.

3 types : α- helix, β- pleated sheet and collagen helix

α- helix β- pleated sheet Collagen helix

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TERTIARY

The helical polypeptide may fold upon itself and assume a complex but specific form – spherical, rod like or something in between.

These geometrical shapes are known as tertiary (30) structure

QUATERNARY

Proteins are said to be quaternary in structureIf they have 2 or more polypeptide chains

Haemoglobin is an excellent example

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PROTEINS

Function Chemical nature and solubility

Nutritional importance

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Fun

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Structural proteins e.g. keratin, collagen

Enzymatic proteins e.g. pepsin

Transport proteins e.g. Haemoglobin

Hormonal proteins e.g. Insulin, Growth hormone

Contractile proteins e.g. Actin, myosin

Storage proteins e.g. Ovalbumin

Genetic proteins e.g. Nucleoproteins

Defence proteins e.g. Imunoglobulins

Receptor proteins e.g. for hormones and viruses

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Classification based on chemical nature and

solubility

1. Simple proteins : They are composed only of amino acid residues

2. Conjugated proteins : Along with amino acids , there is a non-protein prosthetic group.3. Derived proteins : They are denatured or degraded products of the above two

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Proteins

Simple ConjugatedDerived

Nucleoproteins

Glycoproteins

Mucoproteins

Lipoproteins

Phosphoproteins

Chromoproteins

Metalloproteins

Globular Fibrous

Globulin

Histones

Albumin

Elastin

Keratin

Collagen

Primary Secondary

Proteans

Metaproteins

Coagulatedproteins

protones

Peptides

Proteoses

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With the water, I say, Touch me not,

To the tongue, I am tasteful,

Within limits, I am dutiful,

In excess, I am dangerous

LIPIDS

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Lipids are the chief concentrated storage form of energy forming about 3.5% of the cell content.

Lipids are organic substances relatively insoluble in water but soluble in organic solvents (alcohol, ether)

Functions : 1. They are the concentrated fuel reserve of the body.2. Lipids are constituents of membrane structure and regulate the membrane permeability.3. They serve as source of fat soluble vitamins4. Lipids are important cellular metabolic regulators5. Lipds protect the internal organs and serve as insulating materials

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LIPIDS

Simple ComplexDerived

Phospholipids

Glycolipids

Lipoproteins

Fats & Oils Waxes

Steroids

Terpenes

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SIMPLE LIPIDS

They are esters of fatty acids with alcohol. They are of 2 types :

1. Neutral or true fats : Esters of fatty acids with glycerol 2. Waxes : Esters of fatty acids with alcohol other than glycerol.

Neutral / True fats

True fats are made up of C, H, & O but O is lessA fat molecule is made up of 2 components : a) GLYCEROL b) FATTY ACIDS (1-3 mol, of same or diff long chained)

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Glycerol

A glycerol mol has 3 carbons each bearing a –OH group

Fatty acid

A fatty acid mol is an unbranched chain of C-atoms.

It has a –COOH group at one end and a H bonded to almost all the C-atoms

Fatty acids may be saturated or unsaturated

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WAXES

Lipids which are long chain saturated fatty acids and a long chainSaturated alcohol of high mol wt other than glycerol

Example : 1. Bees wax : secretion of abdominal glands of worker honey bees2. Lanolin or wool fat : Secretion of cutaneous glands and obtained from the wool of sheep3. Sebum : secretion of sebaceous glands of skin4. Cerumen : soft and brownish waxy secretion of the glands in the external auditory canal. Also called as Earwax5. Plant wax : Coating formed on the plant organs to prevent transpiration6. Paraffin wax : A translucent waxy substance obtained from petroleum

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COMPLEX LIPIDSThey are derivatives of simple lipids having additional group like phosphate, N2-base,Protein etc. They are further divided intoPhospholipids, Glycolipids, Lipoproteins.

Phospholipid They are made up of a molecule of glycerol Or other alcohol having1. A phos group at 1 of its –OH groups2. 2 fatty acid molecules at other 2 –OH groups3. A nitrogen containing base attatched to phos group

A phospholipid molecule has a hydrophobic tail (fatty acids) and a hydrophilic head(phos group)

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Glycolipid

They are components of cell membranes, particularly myelin sheath and chloroplast membranes

CEREBROSIDE are the most simplest form of glycolipids

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Lipoprotein

They contain lipids and proteins in their molecules.They are main constituent of membranes.They are found in milk and Egg yolk.

Lipids are transported in blood and lymph as lipoproteins.

5 types of lipoproteins : 1. chylomicrons 2. VLDL 3. LDL 4. HDL 5. Free fatty acid albumin complex

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DERIVED LIPIDS

They are derivatives obtained on the hydrolysis of the simple and complex lipids.e.g. steroids, terpenes and prostaglandins

Steroid The steroids do not contain fatty acids but are included in lipids as they have fat-like properties.

They are made up of 4 fused carbon rings

Cholesterol, Vit D, testosterone, adrenocortical hormones.

The most common steroids are STEROLS.

Common sterols are Cholesterol and ergosterol

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Terpenes

Terpenes are a major component of essential oils produced by plants. They give fragrance to the plant parts.

Vitamins A, E and K contain a terpenoid called phytol

Carotenoid pigment is precursor for Vitamin A

Lycopene, a pigment present in tomatoes is a terpenoid

Gibberellins, the plant hormone is also a terpene

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ENZYMES

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Enzymes are a group of catalysts functioning in a biological system

They are usually proteinaceous substances produced by the living cellWithout themselves getting affected.

Enzymes enhance the rate of reaction and are formed in the cell under the instructions of genes

ENZYMOLOGY is the branch of science that deals with the study ofEnzymes in all the aspects like nomenclature, reactions and functions

Enzymes occur in colloidal state and are often produced in inactive form called proenzymes (zymogen), which are converted to their active forms by specific factors like pH, substrate etc.

The enzymes that are produced within a cell for metabolic activities are known as endoenzymes and those which act away from the site of synthesis are called exo-enzymes

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GENERAL PROPERTIES OF ENZYME AND FACTORS AFFECTING THEIR ACTIVITY

1) Enzymes accelerate the reaction but do not initiate it.

2) Enzymes themselves do not participate in the reaction and remain unchanged at the end of the reaction. Enzymes, are therefore, needed in small amounts.

3) The molecule of an enzyme is larger than that of substrate molecule and hence during reaction a specific part of enzyme molecule comes in contact with the substrate molecule. That part is called active site of enzyme.

4) Amphoteric nature: Chemically most of the enzymes are proteins and, therefore, show amphoteric nature. The enzymes can react with acidic substances as well as alkaline substances.

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5) Specificity: Most of the enzymes are specific in their action. A single enzyme acts upon a single substrate or a group of closely related substrates.

For example, the enzyme urease can act only upon urea invertase can act upon sucrose only

A slight change in the configuration of the substrate molecule requires action by a different enzyme.

6) Colloidal nature: All enzymes are colloidal in nature and thus provide large surface area for reaction to take place. Colloids (colloids- gel like) are mixtures of two components i.e. dispersed particles and dispersion medium. The size of the dispersed particles is larger than dispersion medium.

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7) Enzyme optima : Enzymes generally work best under certain narrowly defined conditions referred to as optima. These include appropriate temperature and PH.

a) Temperature sensitivity : Since the enzymes are proteins, they are affected by change in temperature. With increase in temperature, increase in enzyme activity takes place (up to 40°C). However, when temperature increases above 60°C the proteins undergo denaturation or even complete breakdown. When the temperature is reduced to freezing point or below freezing point the enzymes become inactivated but they are not destroyed. The rate of reaction is more at optimum temperature.

b) pH sensitivity : Most of the enzymes are specific to pH and remain active within particular range of pH. The strong acid or strong base denatures enzymes. Most of the intracellular enzymes function best around neutral pH

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8) Concentration of enzyme and substrate : The rate of reaction is proportionate to the concentration of the reacting molecules. If the substrate concentration is increased the rate of enzyme action also increases up to certain limit. Beyond a certain concentration, the enzyme molecules remain saturated with substrate molecules and the activity becomes steady.

9) Enzyme inhibitors : Enzyme inhibitors are certain products which inhibit enzyme activity. During the reaction, if the active site of enzyme is occupied by these inhibitors instead of substrate molecules and the activity of enzyme is lost. These substances are like substrate molecules in their structure and are called competitive inhibitors.

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Group of Enzymes Reactions catalysed Examples

1. Oxidoreductases Transfer of O2 or H2 atoms or electrons from one substrate to another

DehydrogenaseOxidases

2.Transferases Transfer of a specific group from one substrate to another

Transaminase

3.Hydrolases Hydrolysis of a substrate Digestive enzymes

4. Isomerases Change of the molecular form of the substrate

Phospho Hexo isomerase

5.Lyases Non hydrolytic removal or addition of a group to a substrate

DecarboxylaseAldolase

6. Ligases Joining of 2 molecules by formation of new bonds

Citric acid synthetase

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