UNIT-I Biomolecules

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JAIPUR COLLEGE OF PHARMACY, JAIPUR B.PHARMACY, FIRST YEAR, SECOND SEMESTER

BIOCHEMISTRY Prepared by: Dr. Rakesh Kumar Gupta

UNIT-I

Biomolecules

Definition

Biomolecules are molecules that occur naturally in living organisms.

Biomolecules include macromolecules like proteins, carbohydrates, lipids and

nucleic acids. It also includes small molecules like primary and secondary

metabolites and natural products. Biomolecules consists mainly of carbon and

hydrogen with nitrogen, oxygen, sulphur, and phosphorus. Biomolecules are

very large molecules of many atoms, which are covalently bound together.

Classification of Biomolecules

There are four major classes of biomolecules:

i. Carbohydrates

ii. Lipids

iii. Proteins

iv. Nucleic acids

1. Carbohydrates

- Carbohydrates are good source of energy. Carbohydrates (polysaccharides)

are long chains of sugars.

Monosaccharides are simple sugars that are composed of 3-7 carbon atoms.

- They have a free aldehyde or ketone group, which acts as reducing agents

and are known as reducing sugars. Disaccharides are made of two

monosaccharides. The bonds shared between two monosaccharides are




the glycosidic bonds.

- Monosaccharides and disaccharides are sweet, crystalline and water

soluble substances. Polysaccharides are polymers of monosaccharides.

They are un-sweet and complex carbohydrates. They are insoluble in

water and are not in crystalline form.

- Example: glucose, fructose, sucrose, maltose, starch, cellulose etc.

2. Lipids

- Lipids are composed of long hydrocarbon chains. Lipid molecules hold a

large amount of energy and are energy storage molecules. Lipids are

generally esters of fatty acids and are building blocks of biological

membranes.

- Most of the lipids have a polar head and non-polar tail. Fatty acids can be

unsaturated and saturated fatty acids.

- Lipids present in biological membranes are of three classes based on the

type of hydrophilic head present:

Glycolipids are lipids whose head contains oligosaccharides with 1-15

saccharide residues.

Phospholipids contain a positively charged head which are linked to

the negatively charged phosphate groups.

Sterols, whose head contain a steroid ring. Example steroid.

- Example of lipids: oils, fats, phospholipids, glycolipids, etc.

3. Nucleic Acids




- Nucleic acids are organic compounds with heterocyclic rings. Nucleic

acids are made of polymer of nucleotides. Nucleotides consist of

nitrogenous base, a pentose sugar and a phosphate group. A nucleoside is

made of nitrogenous base attached to a pentose sugar. The nitrogenous

bases are adenine, guanine, thyamine, cytosine and uracil. Polymerized

nucleotides form DNA and RNA which are genetic material.

4. Proteins

- Proteins are heteropolymers of stings of amino acids. Amino acids are

joined together by the peptide bond which is formed in between the

carboxyl group and amino group of successive amino acids. Proteins are

formed from 20 different amino acids, depending on the number of amino

acids and the sequence of amino acids.

- There are four levels of protein structure:

(i) Primary structure of Protein - Here protein exist as long chain of

amino acids arranged in a particular sequence. They are non-functional

proteins.

(ii) Secondary structure of protein - The long chain of proteins are folded

and arranged in a helix shape, where the amino acids interact by the

formation of hydrogen bonds. This structure is called the pleated sheet.

Example: silk fibres.

(iii) Tertiary structure of protein - Long polypeptide chains become more

stabilizes by folding and coiling, by the formation of ionic or

hydrophobic bonds or disulphide bridges, these results in the tertiary

structure of protein.

(iv) Quaternary structure of protein - When a protein is an assembly of

more than one polypeptide or subunits of its own, this is said to be the




quaternary structure of protein. Example: Haemoglobin, insulin.

Functions of Biomolecules

- Carbohydrates provide the body with source of fuel and energy, it aids in

proper functioning of our brain, heart and nervous, digestive and immune

system. Deficiency of carbohydrates in the diet causes fatigue, poor

mental function.

- Each protein in the body has specific functions, some proteins provide

structural support, help in body movement, and also defense against

germs and infections. Proteins can be antibodies, hormonal, enzymes and

contractile proteins.

- Lipids, the primary purpose of lipids in body are energy storage.

Structural membranes are composed of lipids which form a barrier and

controls flow of material in and out of the cell. Lipid hormones, like

sterols, help in mediating communication between cells.

- Nucleic Acids are the DNA and RNA; they carry genetic information in

the cell. They also help in synthesis of proteins, through the process of

translation and transcription.

Carbohydrate

Definition:

Carbohydrates are products of plants and are a part of an extremely large group

of naturally occurring organic compounds. Cane sugar, glucose, starch and so

on are a few examples of carbohydrates.




The general formula for carbohydrates is Cy(H2O)z.

Carbohydrates are generally hydrates of carbon, which is where the name was

derived. So, carbohydrates on hydrolysis produce polyhydroxy aldehydes or

polyhydroxy ketones.

Carbohydrates are also known as saccharides, the word saccharide comes from

Greek word sakkron which means sugar.

Carbohydrates are good source of energy.

Classification of Carbohydrates

(A) On the basis of Hydrolysis

(i) Monosaccharides: A carbohydrate that can be hydrolyzed only once to

break down into simpler units of polyhydroxy aldehyde or ketone is called

monosaccharide. These include glucose, mannose, etc.

(ii) Oligosaccharides: Sugars that on hydrolysis produce two or nine molecules

of monosaccharides are called oligosaccharides. These are further classified as

di-, tri- or tetrasaccharides, etc.

(a) Disaccharides: These are sugars that produce two molecules of the

same or different monosaccharides on hydrolysis. Examples are sucrose,

maltose, and lactose. An example of disaccharides is sucrose, maltose :

C12H22O11.




(b) Trisaccharides: Sugars that yield three molecules of the same or

different monosaccharides on hydrolysis are called trisaccharides. An example

of trisaccharides is Raffinose: C18H32O16

(iii) Polysaccharides: On hydrolysis, polysaccharides yield a large number of

monosaccharides units. An example of a polysaccharide is starch, glycogen,

Dextrin, Cellulose etc.

- In general monosaccharides and oligosaccharides are crystalline solids,

soluble in water and sweet to taste, they are collectively known as sugars, the

polysaccharides on the other hand are amorphous, insoluble in water and

tasteless, they are called non-sugars.

(B) On the basis of Physical Characteristics

(i) Sugar: Characteristics of sugars are crystalline substances, taste sweet and

readily water soluble. Because of their fixed molecular weight, sugars have

sharp melting points. A few examples of sugars are glucose, fructose, sucrose,

lactose, etc.

(ii) Non-Sugars: Amorphous, Tasteless, water-insoluble substances with

variable melting points e.g., Starch.




(C) On basis of test with reagents (like Benedict’s solution, Tollen’s reagent

and Fehling’s solution):

(i) Reducing Sugars:

These have a free aldehyde (-CHO) or ketone group.

These have the ability to reduce the cupric ions (Cu2+; blue) in Fehling’s or

Benedict’s Solution to cuprous ions (Cu+; reddish) that separates out as cuprous

oxide (Cu2O) from the solution.

Examples include maltose, lactose, melibiose, gentiobiose, cellobiose,

mannotriose.

(ii) Non-reducing sugars:

A free aldehyde or ketonic group is absent.

No cuprous oxide (Cu2O) producing chemical reaction takes place.

Examples are sucrose, trehalose, raffinose, gentianose, melezitose.

Difference between monosaccharaides, oligosaccharides & Polysaccharides

Character Monosaccharaides Oligosaccharide

s

Polysaccharides

No. of sugar

molecules

1 2-9 More than 9

Glycoside bond Absent Present Present

Molecular Weight Low Moderate High

Taste Sweet Minimally sweet No taste




taste

Solubility Soluble Soluble Insoluble

Nature Always

reducing sugar

May or may not

be

Always non

reducing sugar

Example Glucose, fructose,

Galactose

Sucrose, Maltose Starch, Glycogen,

Dextrin, Cellulose

Biological Role of Carbohydrates

Carbohydrates are chief energy source, in many animals; they are instant

source of energy. Glucose is broken down by glycolysis/ kreb's cycle to yield

ATP.

Glucose is the source of storage of energy. It is stored as glycogen in animals

and starch in plants.

Stored carbohydrates act as energy source instead of proteins.

Carbohydrates are intermediates in biosynthesis of fats and proteins.

Carbohydrates aid in regulation of nerve tissue and are the energy source for

brain.

Carbohydrates get associated with lipids and proteins to form surface

antigens, receptor molecules, vitamins and antibiotics.

They form structural and protective components, like in cell wall of plants

and microorganisms.

In animals they are important constituent of connective tissues.

They participate in biological transport, cell-cell communication and

activation of growth factors.

Carbohydrates those are rich in fibre content help to prevent constipation.

Also they help in modulation of immune system.




Test for Carbohydrates

Properties of Carbohydrates

- General properties of carbohydrates

Carbohydrates act as energy reserves, also stores fuels, and metabolic

intermediates.

Ribose and deoxyribose sugars forms the structural frame of the

genetic material, RNA and DNA.

Polysaccharides like cellulose are the structural elements in the cell

walls of bacteria and plants.

Carbohydrates are linked to proteins and lipids that play important

roles in cell interactions.

Carbohydrates are organic compounds; they are aldehydes or ketones




with many hydroxyl groups.

- Physical Properties of Carbohydrates

Steroisomerism - Compound shaving same structural formula

but they differ in spatial configuration. Example: Glucose has

two isomers with respect to penultimate carbon atom. They are D-

glucose and L-glucose.

Optical Activity - It is the rotation of plane polarized light forming (+)

glucose and (-) glucose.

Diastereo isomeers - It the configurational changes with regard to

C2, C3, or C4 in glucose. Example: Mannose, galactose.

Annomerism - It is the spatial configuration with respect to the first

carbon atom in aldoses and second carbon atom in ketoses.

- Chemical Properties of Carbohydrates

Ozazone formation with phenylhydrazine.

Benedicts test.

Oxidation

Reduction to alcohols

Structure of Carbohydrates

- There are three types of structural representations of carbohydrates:

(i) Open chain structure.

(ii) Hemi-acetal structure.

(iii) Haworth structure.




Functions of Carbohydrates

Carbohydrates are chief energy source, in many animals; they are instant

source of energy. Glucose is broken down by glycolysis/ kreb's cycle to yield

ATP.

Glucose is the source of storage of energy. It is stored as glycogen in

animals and starch in plants.

Stored carbohydrates act as energy source instead of proteins.

Carbohydrates are intermediates in biosynthesis of fats and proteins.

Carbohydrates aid in regulation of nerve tissue and are the energy source

for brain.

Carbohydrates get associated with lipids and proteins to form surface

antigens, receptor molecules, vitamins and antibiotics.

They form structural and protective components, like in cell wall of plants




and microorganisms.

In animals they are important constituent of connective tissues.

They participate in biological transport, cell-cell communication and

activation of growth factors.

Carbohydrates those are rich in fibre content help to prevent constipation.

Also they help in modulation of immune system.

Example of Carbohydrates

- Monosaccharides - Glucose, galactose, glycerose, erythrose, ribose,

ribulose, fructose.

- Oligosaccharides - Maltose, lactose, sucrose, raffinose, stachyose.

- Polysaccharides - Starch, glycogen, cellulose, pectin, inulin, hyaluonic

acid.

Glucose:

Glucose is a simple sugar with the molecular formula C6H12O6. Glucose is the

most abundant monosaccharide, a subcategory of carbohydrates. Glucose is

mainly made by plants and most algae during photosynthesis from water and

carbon dioxide, using energy from sunlight, where it is used to

make cellulose in cell walls, which is the most abundant

carbohydrate. In energy metabolism, glucose is the most important source of

energy in all organisms. Glucose for metabolism is partially stored as

a polymer, in plants mainly as starch and amylopectin and in animals

as glycogen. Glucose circulates in the blood of animals as blood sugar. The

https://en.wikipedia.org/wiki/Amylopectin




naturally occurring form of glucose is D-glucose, while L-glucose is produced

synthetically in comparatively small amounts and is of lesser importance.

Preparation:

(a) From sucrose (cane sugar): Boiling sucrose with diluted HCl or H2SO4 in

alcoholic solution produces glucose and fructose in equal proportions.

(b) From starch: Industrially, glucose is manufactured by the hydrolysis of

starch by boiling it with dil. H2SO4 at 393 K under pressure.

Structures of Glucose

Glucose was assigned open chained structure on the basis of the following

evidence. Glucose has one aldehyde group, one primary (—CH2OH) group and

four secondary (—CHOH) hydroxyl groups, and gives the following reactions:

(a) Acetylation of glucose with acetic anhydride forms a pentaacetate, proving

the presence of five hydroxyl groups in glucose.

(b) Glucose reacts with hydroxylamine to form monoxime and adds up a

molecule of hydrogen cyanide to form a cyanohydrin.

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The above reactions validate the occurrence of a carbonyl group in glucose.

(c) On prolonged heating with HI, glucose forms n-hexane, indicating that all

the six carbon atoms in glucose are linked linearly.

(d) Reaction with Bromine water.

Cyclic Structures of Glucose

The open chain structure of glucose could not explain the following facts : –

Despite having the aldehyde group, it does not give the 2,4-DNP test, Schiff ‘s

test and it does not form the hydrogen sulphite addition product with NaHSO3.

The pentaacetate of it does not react with hydroxylamine indicating the absence

of free — CHO group in glucose pentaacetate. Glucose exists in two different

crystalline forms: α-form (obtained by crystallization from conc. solution of

glucose at 303 K) and β-form (obtained by crystallization from hot and

saturated aq.. solution at 371 K).

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α and β glucose have different configuration at anomeric (C-1) carbon atom,

hence are called anomers and the C-1 carbon atom is called anomeric carbon

(glycosidic carbon). The six-membered cyclic structure of glucose is called the

pyranose structure.

Fructose

It is a ketohexose as it contains six C- atoms and ketonic group.On the basis of

its reactions, it was found to contain a ketonic functional group at C-2 atom and

six carbon atoms in the straight chain as in the case of glucose. It belongs to D-

series and is a laevorotatory compound. It is appropriately written as D-(-)-

fructose.

Fructose also exists in two cyclic forms which are obtained by the addition of -

OH at C-5 to the (>C = 0) group. The ring, thus formed is a five-membered ring

and is named as furanose.

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Disaccharides

Maltose:

(a) Preparation: Fractional hydrolysis of starch by enzyme diastase.

(b) Units: Two units of α-D glucose.

(c) Reducing sugar

(d) Linkage: α glycosidic linkage between C1 and C4 carbon atoms.

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Sucrose:

(a) Preparation: Prepared from sugarcane and beetroot

(b) Units: α-D glucose and α-D fructose.

(c) Non-reducing sugar

(d) Linkage: α glycosidic linkage with reference to glucose and β glycosidic

linkage to fructose, both linked at C1 carbon.

Lactose:

(a) Preparation: Found in milk.

(b) Units: β-D glucose and β-D galactose.

(c) Reducing sugar.

(d) Linkage: β glycosidic linkage.





The levo rotation of fructose (–92.4°) is more than the rotation of glucose

(+52.5º), so the mixture is laevorotatory. Sucrose hydrolysis brings about a

change in the sign of rotation, from dextro (+) to laevo (–) and the product is

called invert sugar.

Polysaccharides

(a) Starch: It is the main storage polysaccharide of plants having the general

formula (C8H16O5)n. The main source is maize, wheat, barley, rice, and potatoes.

It is a polymer of α-glucose and consists of two components – Amylose and

Amylopectin. Amylose is made up of a long, unbranched chain of α-D-(+)-

glucose linkage. Amylopectin is a branched chain polymer of α-D-glucose

units, in which chain is formed by C1–C6 glycosidic linkage whereas branching

occurs by C1–C6 glycosidic linkage.

(b) Cellulose It occurs exclusively in plants and is the main constituent of the

cell wall of a plant cell. It is a linear polymer of β-D glucose in which glucose

units are linked together by C1–C4 glycosidic linkage. It is a non-reducing sugar.





(c) Glycogen

It is also known as animal starch because its structure is similar to amylopectin

and is rather more highly branched. It is found in the liver, muscles, and brain.

Glycogen breaks down to glucose by the action of enzymes when needed by the

body. It is also found in yeast and fungi.





Lipids

- Lipids are a heterogeneous group of water-insoluble (hydrophobic) organic

molecules that can be extracted from tissues by nonpolar solvents, because

of their insolubility in aqueous solutions, body lipids are generally found

compartmentalized, as in the case of membrane-associated lipids or

droplets of triacylglycerol in adipocytes, or transported in plasma in

association with protein, as in lipoprotein particles or on albumin.

- Lipids are a major source of energy for the body, and they provide the

hydrophobic barrier.

- Lipids serve additional functions in the body, for example, some fat-soluble

vitamins have regulatory or coenzyme functions, and the prostaglandins

and steroid hormones play major roles in the control of the body's

homeostasis.

General characters of lipids

- Lipids are relatively insoluble in water.

- They are soluble in non-polar solvents, like ether, chloroform, and

methanol.

- Lipids have high energy content and are metabolized to release calories.

- Lipids also act as electrical insulators, they insulate nerve axons.

- Fats contain saturated fatty acids; they are solid at room temperatures.

Example, animal fats.

- Plant fats are unsaturated and are liquid at room temperatures.

- Pure fats are colorless, they have extremely bland taste.

- The fats are sparingly soluble in water and hence are described are

hydrophobic substances.




- They are freely soluble in organic solvents like ether, acetone and benzene.

- The melting point of fats depends on the length of the chain of the

constituent fatty acid and the degree of unsaturation.

- Geometric isomerism, the presence of double bond in the unsaturated fatty

acid of the lipid molecule produces geometric or cis-trans isomerism.

- Fats have insulating capacity, they are bad conductors of heat.

- Emulsification is the process by which a lipid mass is converted to a

number of small lipid droplets. The process of emulsification happens

before the fats can be absorbed by the intestinal walls.

- The fats are hydrolyzed by the enzyme lipases to yield fatty acids and

glycerol.

- The hydrolysis of fats by alkali is called saponification. This reaction

results in the formation of glycerol and salts of fatty acids called soaps.

- Hydrolytic rancidity is caused by the growth of microorganisms which

secrete enzymes like lipases. These split fats into glycerol and free fatty

acids.

Classification of lipids

1. Simple lipids: Esters of fatty acids with various alcohols.

a. Fats: Esters of fatty acids with glycerol. Oils are fats in the liquid state.

b. Waxes: Esters of fatty acids with higher molecular weight monohydric

alcohols.

2. Complex lipids: Esters of fatty acids containing groups in addition to an

alcohol and a fatty acid.

a. Phospholipids: Lipids containing, in addition to fatty acids and an

alcohol, a phosphoric acid residue. They frequently have nitrogen

containing bases and other substituents, eg, in glycerophospholipids the




alcohol is glycerol and in sphingophospholipids the alcohol is

sphingosine.

b. Glycolipids (glycosphingolipids): Lipids containing a fatty acid,

sphingosine, and carbohydrate.

c. Other complex lipids: Lipids such as sulfolipids and aminolipids.

Lipoproteins may also be placed in this category.

3. Precursor and derived lipids: These include fatty acids, glycerol, steroids,

other alcohols, fatty aldehydes, and ketone bodies, hydrocarbons, lipid-

soluble vitamins and hormones.

Essential fatty acids

- Two fatty acids are dietary essentials in humans

(i) Linoleic acid, which is the precursor of arachidonic acid, the substrate

for prostaglandin synthesis.

(ii) α-linolenic acid is the precursor for growth and development.

- Essential fatty acid deficiency can result in a scaly dermatitis, as well as

visual and neurologic abnormalities.

Examples of Lipids

- Fatty acids - Oleic acid, Linoleic acid, Palmitoleic acid, Arachidonic acid.

- Fats and Oils - Animal fats - Butter, Lard, Human fat, Herring oil.

Plant oils - Coconut oil, Corn, Palm, Peanut, Sunflower oil.




- Waxes - Spermacti, Beeswax, Carnauba wax.

- Phospholipids - Lecithins, Cephalins, Plasmoalogens, Phosphatidyl

inositols, Sphingomyelins.

- Glycolipids - Kerasin, Phrenosin, Nervon, Oxynervon.

- Steroids - Cholesterol.

- Terpenes - Monoterpenes, Sesquiterpenes, Diterpenes, Triterpenes.

- Carotenoids - Lycopene, Carotenes, Xanthophylls.

Biological Role of Lipids

1. Food material: Lipids provide food, highly rich in calorific value. One

gram lipid produces 9.3 kilocalories of heat.

2. Food reserve: Lipids provide are insoluble in aqueous solutions and hence

can be stored readily in the body as a food reserve.

3. Structural component: Lipids are an important constituent of the cell

membrane.




4. Heat insulation: The fats are characterized for their high insulating

capacity. Great quantities of fat are deposited in the subcutaneous layers in

aquatic mammals such as whale and in animals living in cold climates.

5. Fatty acid absorption: Phospholipids play an important role in the

absorption and transportation of fatty acids.

6. Hormone synthesis: The sex hormones, adrenocorticoids, cholic acids and

also vitamin D are all synthesized from cholesterol, a steroidal lipid.

7. Vitamin carriers: Lipids act as carriers of natural fat-soluble vitamins such

as vitamin A, D and E.

8. Blood cholesterol lowering: Chocolates and beef, especially the latter one,

were believed to cause many heart diseases as they are rich in saturated

fatty acids, which boost cholesterol levels in blood and clog the arterial

passage.

9. Antibiotic agent. Squalamine, a steroid from the blood of sharks, has been

shown to be an antibiotic and antifungal agent of intense activity. This

seems to explain why sharks rarely contract infections and almost never get

cancer.

Some of the different types of lipids are described below in detail.

Fatty Acids

Fatty acids are carboxylic acids (or organic acid), often with long aliphatic tails

(long chains), either saturated or unsaturated.

Saturated fatty acids

When a fatty acid is saturated it is an indication that there are no carbon-carbon

double bonds. The saturated fatty acids have higher melting points than




unsaturated acids of the corresponding size due to their ability to pack their

molecules together thus leading to a straight rod-like shape.

Unsaturated fatty acids

If a fatty acid has more than one double bond then this is an indication that it is

an unsaturated fatty acid.

“Most naturally occurring fatty acids contain an even number of carbon atoms

and are unbranched.”

Unsaturated fatty acids, on the other hand, have a cis-double bond(s) that create

a kink in their structure which doesn’t allow them to group their molecules in

straight rod-like shape.

Role of Fats

Fats play several major roles in our body. Some of the important roles of fats

are mentioned below:

Fats incorrect amounts are necessary for the proper functioning of our

body.

Many fat-soluble vitamins need to be associated with fats in order to be

effectively absorbed by the body.

They also provide insulation to the body.

They are an efficient way to store energy for longer periods.




Waxes

Waxes are “esters” (an organic compound made by replacing the hydrogen with

acid by an alkyl or another organic group) formed from long-chain carboxylic

acids and long-alcohols.

Waxes are seen all over in nature. The leaves and fruits of many plants have

waxy coatings, which may protect them from dehydration and small predators.

The feathers of birds and the fur of some animals have similar coatings which

serve as a water repellent.

Carnauba wax is valued for its toughness and water resistance (great for car

wax).

Phospholipids

Membranes are chiefly made of phospholipids which are Phosphoacylglycerols.

Triacylglycerols and phosphoacylglycerols are similar however the terminal OH

group of the phosphoacylglycerol is esterified with phosphoric acid instead of

fatty acid which leads to the formation of phosphatidic acid.




The name phospholipid comes from the fact that phosphoacylglycerols are

lipids that contain a phosphate group.

Steroids

The chemical messengers in our bodies are known as hormones which are

organic compounds synthesized in glands and delivered by the bloodstream to

certain tissues in order to stimulate or inhibit the desired process.

Steroids are a type of hormone which is usually recognized by their tetracyclic

skeleton, consisting of three fused six-membered and one five-membered ring,

as shown in the diagram above. The four rings are designated as A, B, C & D as

noted in blue, and the numbers in red represent the carbons.

Cholesterol

Cholesterol is waxy like substance, found only in animal source foods.

Triglycerides, LDL, HDL, VLDL are different types of cholesterol found in

the blood cells.




Cholesterol is an important lipid found in the cell membrane. It is a sterol,

which means that cholesterol is a combination of steroid and alcohol. In the

human body, cholesterol is synthesized in the liver.

These compounds are biosynthesized by all living cells and are essential for

the structural component of the cell membrane.

In the cell membrane, the steroid ring structure of cholesterol provides a rigid

hydrophobic structure that helps boost the rigidity of the cell membrane.

Without cholesterol, the cell membrane would be too fluid.

It is an important component of cell membranes and is also the basis for the

synthesis of other steroids, including the sex hormones estradiol and

testosterone, as well as other steroids such as cortisone and vitamin D.

Regulating Blood Cholesterol Levels

- Fats and cholesterol cannot dissolve in blood and are consequently

packaged with proteins (to form lipoproteins) for transport

o Low density lipoproteins (LDL) carry cholesterol from the liver to the

rest of the body

o High density lipoproteins (HDL) scavenge excess cholesterol and carry

it back to the liver for disposal

- Hence LDLs raise blood cholesterol levels (‘bad’) while HDLs lower blood

cholesterol levels (‘good’)

- High intakes of certain types of fats will differentially affect cholesterol

levels in the blood

o Saturated fats increase LDL levels within the body, raising blood

cholesterol levels




o Trans fats increase LDL levels and decrease HDL levels within the

body, significantly raising blood cholesterol levels

o Unsaturated (cis) fats increase HDL levels within the body, lowering

blood cholesterol levels

Lipid Health Claims

- There are two main health claims made about lipids in the diet:

o Diets rich in saturated fats and trans fats increase the risk of CHD

o Diets rich in monounsaturated and polyunsaturated (cis) fats decrease the

risk of CHD

Health Risks of High Cholesterol

o High cholesterol levels in the bloodstream lead to the hardening and

narrowing of arteries (atherosclerosis)




o When there are high levels of LDL in the bloodstream, the LDL particles

will form deposits in the walls of the arteries

o The accumulation of fat within the arterial walls leads to the development of

plaques which restrict blood flow

o If coronary arteries become blocked, Coronary Heart Disease (CHD)

will result – this includes heart attacks and strokes




NUCLEIC ACIDS

Nucleic acids are vital biomolecules that present in the nuclei of all living cells

as nucleoproteins. These are long chain polymers with a high molecular mass.

Also called biopolymer, they have nucleotide as a repeating structural unit

(monomer). These play an important role in the transmission of the heredity

characteristics from one generation to the next and also in the biosynthesis of

proteins. Therefore, the genetic information coded in nucleic acid governs the

structure of protein during its biosynthesis and hence controls the metabolism in

the living system.

Structure of nucleic acids: The nucleic acid is the prosthetic component of

nucleoproteins. Nucleic acid on stepwise hydrolysis gives the following

products as shown in the chart.





Difference between DNA and RNA

The main points of difference between the two types of nucleic acids are given in

the table.

Ribonucleic acids

(a) The pentose sugar in RNA is ribose.

(b) Adenine and guanine represent the purine bases of RNA; the pyrimidine

bases are uracil and cytosine.

(c) The thymine in DNA is replaced by uracil in RNA.

(d) RNA is single-stranded, but double-stranded RNA is present in Reovirus

and wound tumour virus.

(e) There are three major classes of RNA, each with specific functions in

protein synthesis.





(i) mRNA

1. Messenger RNA is produced by DNA; the process is called transcription.

2. Messenger RNA encodes the amino acid sequence of a protein in their

nucleotide base sequence.

3. A triplet of nitrogenous bases specifying an amino acid in mRNA is called a

codon.

(ii) tRNA

1. tRNA is also known as soluble RNA (sRNA) as it is soluble in 1 molar

solution of sodium chloride.

2. Molecules of tRNA are single-stranded and relatively very small.

3. tRNA identifies amino acids in the cytoplasm and transports them to the

ribosome.

4. Anticodon is a three-base sequence in a tRNA molecule that forms

complementary base pairs with a codon of mRNA.

5. All transfer RNA possess the sequence CCA at their three ends; the amino

acid is attached to the terminal as residue.

(iii) rRNA

1. Ribosomal RNA is found in ribosomes of a cell and is also called insoluble

RNA.




2. The main function of rRNA is to provide a large surface for spreading of

mRNA over ribosomes during the translocation process of protein synthesis.

3. The relationship between the sequence of amino acids in a polypeptide with

the base sequence of DNA or mRNA is genetic code.

4. Genetic code determines the sequence of amino acids in a protein.

5. A triplet would code for a given amino acid as long as three bases are present

in a particular sequence.

6. Later in a cell-free system. Marshall Nirenberg and Philip (1964) were able to

show that GUU codes for the amino acid valine.

7. The spellings of further codons were discovered by R. Holley. H. Khorana

and M. Nirenberg.

8. They have been awarded the Nobel Prize in 1968 for researches in the genetic

code.

AMINO ACIDS

α-Amino Acids: Carboxylic acids in which one α-hydrogen atom of an alkyl

group is substituted by amino (–NH2) group are called α-Amino acids. The

general formula is





Structure of α-amino acids: The amino acids containing one carboxylic group

and one amino group behave as a neutral molecule. This is because in aqueous

solutions the acidic carboxylic group and basic amino group neutralize each

other intramolecularly to produce an internal salt structure known as a

zwitterion or dipolar ions.

However, the neutral zwitterion (dipolar ions) changes to the cation in an acidic

solution and exist as an anion in an alkaline medium. Thus amino acids exhibit

amphoteric character.

Therefore, amino acid exists as zwitterion when the solution is neutral or pH-7.

The pH at which the structure of an amino acid has no net charge is called its

isoelectric point.

Classification of Amino Acids: Based on the relative number of –NH2 and –

COOH group, α-amino acids are classified in three main groups

(a) Neutral Amino acids: Amino acids containing one –NH2 group and one –

COOH group. For example, glycine, valine, alanine etc.

(b) Basic amino acids: These contain one –COOH group and two –NH2

groups, such as lysine and arginine.

(c) Acidic amino acids: Amino acids containing two –COOH groups and one –

NH2 group are called acidic amino acids; for example, aspartic acid and

glutamic acid, etc.





PROTEINS

- Proteins are large biomolecules, or macromolecules, consisting of one or

more long chains of amino acid residues.

- Proteins are known as building blocks of life.

- Proteins are the most abundant intracellular macro-molecules. They

provide structure, protection to the body of multicellular organism in the

form of skin, hair, callus, cartilage, ligaments, muscles, tendons. Proteins

regulate and catalyze the body chemistry in the form of hormones,

enzymes, immunoglobulin’s etc.

General Characteristics of Proteins

- Proteins are organic substances; they are made up of nitrogen and also,

oxygen, carbon an d hydrogen.

- Proteins are the most important biomolecules; they are the fundamental

constituent of the cytoplasm of the cell.

- Proteins are the structural elements of body tissues.

- Proteins are made up of amino acids.

- Proteins give heat and energy to the body and also aid in building and

repair.

- Only small amounts of proteins are stored in the body as they can be used

up quickly on demand.

- Proteins are considered as the bricks, they make up bones, muscles, hair

and other parts of the body.

- Proteins like enzymes are functional elements that take part in metabolic

reactions.

- Antibodies, blood haemoglobin are also made of proteins.

- Proteins have a molecular weight of 5 to 300 kilo-Daltons.




Physical Properties of Proteins

- Proteins are colorless and tasteless.

- They are homogeneous and crystalline.

- Proteins vary in shape, they may be simple crystalloid structure to long

fibrilar structures.

- Protein structures are of two distinct patterns - Globular proteins and

fibrilar proteins.

- Globular proteins are spherical in shape and occur in plants. Fibrilar

proteins are thread-like, they occur generally in animals.

- In general proteins have large molecular weights ranging between 5 X 103

and 1 X 106.

- Due to the huge size, proteins exhibit many colloidal properties.

- The diffusion rates of proteins are extremely slow.

- Proteins exhibit Tyndall effect.

- Proteins tend to change their properties like denaturation. Many a times

the process of denaturation is followed by coagulation.

- Denaturation may be a result of either physical or chemical agents. The

physical agents include, shaking, freezing, heating etc. Chemical agents

are like X-rays, radioactive and ultrasonic radiations.

- Proteins like the amino acids exhibit amphoteric property i.e., they can act

as Acids and Alkalies.

- As the proteins are amphoteric in nature, they can form salts with both

cations and anions based on the net charge.

- The solubility of proteins depends upon the pH. Lowest solubility is seen

at isoelectric point, the solubility increases with increase in acidity or

alkalinity.

- All the proteins show the plane of polarized light to left, i.e., laevorotatory.




Chemical Properties of Proteins

- Proteins when hydrolyzed by acidic agents, like conc. HCl yield amino

acids in the form of their hydrochlorides.

- Proteins when are hydrolyzed with alkaline agents leads to hydrolysis of

certain amino acids like arginine, cysteine, serine, etc., also the optical

activity of the amino acids is lost.

- Proteins with reaction with alcohols give its corresponding esters. This

process is known as esterification.

- Amino acid reacts with amines to form amides.

- When free amino acids or proteins are said to react with mineral acids like

HCl, the acid salts are formed.

- When amino acid in alkaline medium reacts with many acid chlorides,

acylation reaction takes place.

- Xanthoproteic test - On boiling proteins with conc. HNO3, yellow color

develops due to presence of benzene ring.

- Folin's test - This is a specific test for tyrosine amino acid, where blue

color develops with phosphomolybdotungstic acid in alkaline solution

due to presence of phenol group.

Function of Proteins

- Proteins are seen in muscles, hair, skin and other tissues; they constitute

the bulk of body's non-skeletal structure.

Example: The protein keratin is present in nails and hair.

- Some proteins are hormones and regulate many body functions. Example:

Insulin hormone is a protein and it regulated the blood sugar level.




- Some proteins act enzymes, they catalyze or help in biochemical reactions.

Example: Pepsin and Tripsin.

- Some proteins act as antibodies; they protect the body from the effect of

invading species or substances.

- Proteins transport different substances in blood of different tissues.

Example: Haemoglobin is an oxygen transport protein.

- Contractile proteins help in contraction of muscle and cells of our body.

Example: Myosin is contractile protein.

- Fibrinogen a glycoprotein helps in healing of wounds. It prevents blood

loss and inhibits passage of germs.




Classification of proteins

Proteins are classified on the basis of two different methods. The first mode of

classification, proteins are of two types is based on their shape and functions:

(a) Fibrous proteins (b) Globular proteins

(a) Fibrous proteins: They are thread-like molecules that lie side by side to

form fibers. They are held together by hydrogen bonds. These are insoluble in

water but soluble in concentrated acids and alkalis. A few examples are keratin

(present in hair, nails, wood, feather, and horns). Muscles have myosin, silk is

composed of fibroin, bones and cartilages have collagen.

(b) Globular proteins: These proteins have molecules folded into compact

units that often acquire spheroidal shape. Such proteins are soluble in water,

diluted acids and alkalis, such as insulin, haemoglobin, albumin, etc.

Classification of Proteins on Biological Function

i. Enzymic Proteins

- They are the most varied and highly specialized proteins with catalytic

activity. Enzymes catalyze a variety of reactions.

- Example: Urease, catalase, cytochrome C, etc.

ii. Structural Proteins

- These proteins aid in strengthening or protecting biological structures.

- Example: Collagen, elastin, keratin, etc.




iii. Transport or Carrier Proteins

- These proteins help in transport of ions or molecules in the body.

- Example: Myoglobin, hemoglobin, etc.

iv. Nutrient and Storage Proteins

- These proteins provide nutrition to growing embryos and store ions.

v. Contractile or Motile Proteins

- These proteins function in the contractile system.

- Example: Actin, myosin, tubulin, etc.

vi. Defense Proteins

- These proteins defend against other organisms.

- Example: Antibodies, Fibrinogen, thrombin.

vii. Regulatory Proteins

- They regulate cellular or metabolic activities.

- Example: Insulin, G proteins, etc.

viii. Toxic Proteins

- These proteins hydrolyze or degrade enzymes.

- Example: snake venom, ricin.




Structure of Proteins:

The structure of proteins is quite complex. Study of its structure is carried out

under the following headings.

(a) Primary structure of a protein:

The primary structure of a protein refers to its covalent structure, that is, the

sequence in which various α-amino acid are arranged in protein or in the

polypeptide structure of a protein.

The linkage (–CO–NH–) is known as peptide linkage.

The dipeptide still has free amino and carboxyl groups that can react with other

molecules of amino acid resulting in polypeptide formation. In the polypeptide

chain, the free amino end is termed as N–terminal and the free carboxyl end is

called C–terminal end.

(b) Secondary structure of a protein:

This refers to the arrangement of polypeptide chains into a definite three-

dimensional structure that protein assumes as a result of hydrogen bonding.

Depending upon the size of the R-group of the amino acids in polypeptides, two

different types of secondary structure are possible:

(i) α-helix structure (ii) β-Pleated structure





(i) α-Helix structure: This type of secondary structure is possible when the

alkyl groups present in amino acids are large and involved in coiling of the

polypeptide chains. The intramolecular hydrogen bond between the >C = O

group of one amino acid and –NH group of the fourth amino acid stabilizes the

helical pattern in a right-handed coil and the shape.

(ii) β-Pleated structure: Such secondary structure is acquired when the alkyl

groups of amino acids are small. In this kind of structure, the linear polypeptide

chains are arranged side by side and are held together by the intermolecular

hydrogen bond between the (>C=O) and –NH group.

(c) Tertiary structure of a protein:

The tertiary structure of a protein is the most stable shape that a protein assumes

under the normal temperature and pH conditions. Attractive forces between the

amino acid chains are involved in acquiring tertiary structure. These attractive

forces, like hydrogen bond, disulphide bonds, ionic, chemical and hydrophobic

bonds, results in a complex and compact structure of the protein. The two





important tertiary structures of proteins are fibrous structures and globular

structure. Fibrous proteins have largely helical structure and are rigid molecules

of rod-like shape. Globular proteins show a polypeptide chain that consists

partly of helical sections and partly β-pleated structure and remaining in random

coil form. These different segments of secondary structure then fold up to give

protein a spherical shape.

(d) Quaternary structure of proteins:

The quaternary structure of proteins develops when the polypeptide chains,

which may or may not be identical, are held together by hydrogen bonds. It

results in the increase of molecular mass of protein greater than 50,000 amu.

For example, haemoglobin contains four subunits, two identical α-chains

containing 141 amino acids each and the other two identical β-chains containing

161 amino acids each.




Denaturation of proteins

Proteins when subjected to the action of heat, mineral acids or alkali, the water-

soluble form of globular protein changes to water-insoluble fibrous protein

resulting in the precipitation or coagulation of protein. This is called the

denaturation of proteins.

Enzymes

These are the essential biological catalysts which are needed to catalyze

biochemical reactions. Almost all the enzymes are globular proteins. Enzymes

have specificity, i.e., specific for a particular substrate and reaction.

The enzymes which catalyze the oxidation of one substrate with simultaneous

reduction of another substrate are named as oxidoreductase enzymes.

Vitamins

Certain organic substances required for regulating some of the body processes

and preventing certain diseases are called vitamins. These compounds cannot be

synthesized by an organism. On the basis of solubility, the vitamins are divided

into two groups.

(1) Fat soluble; Vitamin A, D, E and K.

(2) Water soluble; Vitamin B and C.




Bioenergetics

Bioenergetics – Bioenergetics can be defined as energy transfer mechanisms

occurring within living organisms.

Energy, the ability to do work or bring about change, occurs in a variety of

forms including heat, light, chemical and electrical. According to the first law of

thermodynamics, energy can change form, but it cannot be created and

cannot be destroyed. Microorganisms cannot produce energy, but they can

form high-energy compounds (ATP) by transferring energy from external

sources. Since during such transfers, a certain amount of energy is lost due to

entropy, an external energy source is essential to life. Energy flows through

living systems.

Metabolism – Metabolism can be defined as all the chemical reactions

occurring within living organisms, and can be divided into two categories,

anabolic reactions or anabolism (building reactions), and catabolic reactions or

catabolism (breakdown reactions).

Metabolism and bioenergetics are linked, because chemical reactions involve

energy transfers. Although catabolic reactions require energy to initiate, they

ultimately release more energy than they require, so are exergonic. Anabolic

reactions require or take in energy, so are endergonic.

As described earlier, living organisms obtain energy either from chemicals or

from light. In either case they use these external energy sources to form ATP,

and then use ATP to drive their metabolic processes.




Adenosine triphosphate (ATP)

Adenosine triphosphate is a high -energy compound or nucleoside

triphosphate (NTP) formed by adding two additional phosphate groups to a

nucleotide containing the base adenine and the pentose monosaccharide ribose.

Sometimes referred to as the energy currency within cells, ATP is formed and

used on a regular basis. According to some sources, a typical eukaryotic cell

may use as many as 1 million ATP molecules per second. Energy is stored in

the covalent bonds holding the phosphate groups together, particularly in the

one between the 2nd and 3rd phosphates. This is called a pyrophosphate bond,

and releases considerable energy when broken.

Though cells use ATP on a regular basis, they do not store it, so it is constantly

being made. The chemical equation representing ATP synthesis looks

something like this,

ADP + Pi + Energy = ATP.

In this equation, Pi represents inorganic phosphate and ADP is adenosine

diphosphate. The energy is provided by chemicals (which hold potential

energy in their bonds), or by light. When ATP is used, the pyrophosphate bond

is broken and ADP, Pi and energy are released. The energy released is used to

drive cellular processes such as active transport, flagellar movement (in

eukaryotic cells), the “walking” of kinesin and a wide variety of synthesis

reactions.

Chemical reactions that yield ATP are called phosphorylation reactions and

may be categorized as substrate level, oxidative and photophosphorylation.

Chemoheterotrophs such as fungi, protozoa, animals and many bacteria use




either substrate level or oxidative phosphorylation (or both) to make ATP

depending on whether their metabolism is fermentative or respiratory

(oxidative). Photoautotrophs such as algae and cyanobacteria use

photophosphorylation when light is available, but can also use oxidative

phosphorylation during periods of darkness.

Though ATP is the most common form of nucleoside triphosphate, it is not the

only one. Nucleotides containing the bases guanine, cytosine, thymine and

uracil can also take on extra phosphate groups to

form high-energy compounds. Nucleoside triphosphates (NTPs) may contain

either ribose or and are sometimes referred to as r-NTPs and d-NTPs

respectively. Other high-energy compounds associated with metabolic processes

in prokaryotes include acetyl-coenzyme A (acetyl-CoA) and succinyl-coenzyme

A (succinyl-CoA).

Biochemical Catalysts:

The chemical reactions of metabolism occur very rapidly (a single eukaryotic

cell can use 1 million ATP molecules per second), because cells contain

millions of biochemical catalysts. Most of these are proteins called enzymes

(recall that proteins are polymers composed of amino acids). Enzymes are

typically globular in form and often contain multiple polypeptides (are proteins

with both tertiary and quaternary structure). A second group of catalysts are

called ribozymes and are ribonucleic acid (RNA) molecules (recall that nucleic

acids are polymers composed of nucleotides). These are typically folded, and

associated with proteins in granular bodies, e.g, spliceosomes and ribosomes.




Enzymes and ribozymes catalyze biochemical reactions and interact

specifically with only certain types of substrate molecules, i.e. each different

type of chemical reaction requires a different type of catalyst. Catalysts

increase the rate of chemical reactions (speed them up) hundreds or

thousands of times, but they cannot cause chemical reactions to occur that

would not otherwise be possible. Enzymes and ribozymes are not changed by

the reactions they catalyze, so can be used over and over again.

Though molecular interactions cannot be directly observed, models have been

used to explain enzyme activity. In one example, known as the lock and key

model enzymes are described as increasing the interactions between

molecules as explained below (ribozymes function in a similar manner).

Each enzyme has an active or reactive site on its surface that fits with a

specific set of substrate molecules or reactants like a lock fits with a specific

key. Though the substrates rarely interact on their own, when held within the

enzyme's reactive site, they bind together forming a product. When the product

is released, the enzyme is free to bind more substrate and the reaction is

repeated. According to the induced fit model for enzyme activity, the active

sites of enzymes change somewhat to accommodate specific substrates. The

three-dimensional conformation of the protein changes slightly when the

substrate interacts with functional groups on the enzyme surface.

Enzymes also influence chemical reactions by decreasing the increments of

activation energy necessary to initiate them. For example, glucose can interact

with oxygen to form carbon dioxide and water, but the reaction is unlikely to

occur if a spoonful of glucose is simply exposed to the oxygen present in air.

The energy required to initiate the interaction is called activation energy or the

energy of activation. Raising the energy level by heating the glucose, e.g., by




holding the spoon over a Bunsen burner, will cause the reaction to occur, with

energy released in the form of heat and light. Most of the glucose will be

converted into carbon dioxide and some oxygen will be bound in water (though

some carbon is likely to remain in the spoon in the form of ash).

Since heating protoplasm over a Bunsen burner is not conducive to maintaining

life processes, an energy form other than heat is required for metabolism.

Enzymes allow chemical reactions to proceed with activation energy provided

by the catabolism of ATP (breaking of pyrophosphate bonds). When cells

convert glucose and oxygen into carbon dioxide and water, they use 2

molecules of ATP per glucose as activation energy and gain 36 to 38 molecules

of ATP in return. Without enzymes, this would not be possible

Enzyme categories:

Enzymes can be categorized in a variety of ways depending on their

composition, regulation, the types of reactions they catalyze and where they are.

Some examples of enzyme categories are listed below.

1. Endoenzymes Vs exoenzymes – Endoenzymes are those active within

living cells, while exoenzymes are active outside. Metabolic processes involve

endoenzymes, but exoenzymes are often required to break down food materials

needed as a source of energy. Bacteria, fungi and many types of multicellular

organisms, including humans, release digestive enzymes into their environments

so that nutrient materials (reduced to small molecules) can be taken through

their cell membranes more readily.

2. Simple enzymes Vs conjugated enzymes – Simple enzymes are those

active as protein along, i.e., those that do not require non-protein "helpers".

Conjugated enzymes are those requiring some form of non-protein helper in




order to be active. The protein portion of a conjugated enzyme is called an

apoenzyme and is inactive; the active form of a conjugated enzyme is called a

holoenzyme and includes both protein and non-protein constituents. Helper

groups (sometimes called cofactors) occur in three basic forms including:

a) Coenzymes – Coenzymes are non-protein organic groups that can bind

with apoenzymes and convert them into holoenzymes. Some examples of

coenzymes include NAD, FAD, NADP, coenzyme A and coenzyme Q

(ubiquinone). NAD and FAD are derived from B-complex vitamins,

niacin and riboflavin respectively.

b) Cofactors – Cofactors are inorganic groups that can bind with

apoenzymes and convert them into holoenzymes. Minerals such as

calcium, magnesium and manganese often serve as cofactors.

c) Prosthetic groups – Prosthetic groups are inorganic and permanently

bound to their enzyme conjugates. Iron and copper often serve in

prosthetic groups. An important group of conjugated enzymes called

cytochromes (cytochrome = cell color) are pigmented enzymes with iron

prosthetic groups. These play an essential role in the electron transport

chains associated with oxidative and photophosphorylation.

Although these enzyme helpers can serve a variety of functions, they often act

as electron acceptors and so play an essential role in oxidation and reduction

reactions. Unlike enzymes, coenzymes and cofactors are not specific, and the

same ones can be found interacting with a variety of different enzymes. Like

enzymes they can be used over and over again, but they are changed during

many reactions because they are alternately oxidized and reduced. NAD is

commonly associated with enzymes involved in catabolic processes, while

NADP is associated with enzymes involved in anabolism.




Oxidation reactions – Oxidation reactions are those involving the addition of

oxygen to or the removal of electrons and hydrogen protons from atoms or

molecules.

Reduction reactions – Reduction reactions are those involving the removal of

oxygen from or the addition of electrons and hydrogen protons to atoms or

molecules

In biological systems, the transfer of electrons and hydrogen protons often

occurs in association with energy transfers, so oxidation-reduction reactions

(redox reactions) occur frequently. Though different in outcome, the two

processes are linked because when one type of molecule is reduced, another is

oxidized. Students may find it helpful to remember the saying "LEO the lion

goes GER" when studying oxidation and reduction reactions. When atoms or

molecules lose electrons they are oxidized (LEO), and when they gain electrons

they are reduced (GER).

Coenzymes in their reduced form (NADH + H+ and FADH2) have a higher

energy potential than they do when in their oxidized form (NAD and FAD).

3. Constitutive Vs repressible Vs inducible enzymes - Enzymes can be

categorized as constitutive, repressible or inducible on the basis of regulatory

mechanisms associated with their production.

a) Constitutive enzymes – Constitutive enzymes are those essential to cell

function and so always being made. The synthesis of constitutive

enzymes is not repressible, i.e., it cannot be blocked at the gene level.

b) Repressible enzymes – Repressible enzymes are those coded for by

repressible genes, i.e., those for which transcription can be repressed.




Inducible enzymes – Inducible enzymes are those coded for by inducible

genes, i.e., those for which transcription can be induced

Factors influencing enzyme activity:

A variety of factors influence enzyme activity and the rate at which metabolic

processes can occur. Some of these are listed below.

1. Temperature – Temperature influences enzyme activity in part by

increasing the number of collisions occurring between enzymes and substrate

molecules; however, multiple other factors can be involved. Different types of

enzymes have different temperature optimums, i.e., temperature ranges within

which they work best. This is why different organisms grow best at different

temperatures (e.g., psychrophiles, mesophiles, thermophiles, etc.). Excess heat

will cause enzyme activity to be lost because the proteins are denatured.

2. pH – The pH of the environment can significantly influence enzyme activity

by changing the charge on various groups along the enzyme surface. Increases

in the production of acidic or alkaline substances associated with metabolic

processes can vary how readily enzymes bind with their substrates. Different

enzymes have different pH optimums, i.e., work best at different pH levels.

3. Concentration – The concentration of either enzyme or substrate present in

an environment can influence enzyme activity. If substrate is plentiful,

increasing enzyme concentration will increase reaction rate, but if the substrate

is limited, many enzymes have nothing to interact with and they can catalyze no

reactions.

4. Light – Some enzymes are activated or inactivated by exposure to light.

Enzymes involved in light repair (a process used to repair damaged DNA

molecules), are activated by visible light. Some enzymes involved in pigment

production are also activated by light.




5. Inhibitors and enhancers (activators) – Inhibitors are substances that

decrease or block enzyme activity, while enhancers or activators are those that

increase enzyme activity. Inhibitors can exert their influence in different ways.

a) Competitive inhibition – Competitive inhibition involves an inhibitor

binding to the active site of an enzyme in place of the normal substrate.

When the inhibitor is bound, the substrate cannot be acted upon and

enzyme activity is blocked. A variety of substances recognized as toxic,

including arsenic, cyanide and sarin (nerve gas) act as competitive

inhibitors of important enzymes.

b) Allosteric inhibition – Allosteric inhibition involves an inhibitor binding

to a site on an enzyme other than the active site, i.e., the allosteric site.

When the inhibitor binds, it changes the molecular configuration of the

enzyme so that the active site is no longer active, i.e., can no longer bind

the normal substrate.

c) Allosteric regulation of enzyme activity can involve inhibition,

enhancement/activation, or other interactions. Allosteric inhibitors block

enzyme activity, while enhancers or activators typically bind to

allosteric sites on enzymes and thereby increase the enzymes ability to

interact with substrate molecules. A complete summary of allosteric

regulation is beyond the scope of this presentation.

Enzyme names:

Enzyme names typically (though not always) end in "ase" and often provide

information about the enzyme, e.g., what it does or what it acts on. Recall that

luciferase enzymes are associated with bioluminescence or light production. In

this case the enzymes are named for Lucifer, the angle of light. Polymerase

enzymes catalyze reactions associated with the synthesis of polymers (DNA




and RNA). Isomerase enzymes convert molecules into their chemical isomers,

and aminoacyl-t-RNA-synthase enzymes catalyze reactions resulting in the

formation of aminoacyl-t-RNA.

Enzyme complexes may have multiple functions, and be named for only one of

these. For example, the pyruvate dehydrogenase complex catalyzes a reaction

removing a carboxyl group from pyruvate, but also catalyzes a reaction

removing electrons and hydrogen protons from pyruvate and passing them to

NAD (pyruvate is oxidized and NAD is reduced). The complex also binds a two

-carbon acetyl group to coenzyme A forming acetyl-CoA. This enzyme should

not be confused with the pyruvate decarboxylase complex associated with

fermentation. It removes a carboxyl group from pyruvate and in the process

forms carbon dioxide and acetaldehyde.

Documents

UNIT-I Biomolecules