Notes-Part-2-Class-11-Science-Biology-Chapter-6-Biomolecules-Maharashtra Board

Structure of DNA :

DNA is a long chain made up of alternate sugar and phosphate groups. The sugar present in DNA is always a deoxyribose attached to a phosphate group. So, it forms a regular, repeating phosphate sugar sequence.

• A base is attached to sugar -phosphate chain. Together this unit which consist of sugar, phosphate and a base is called nucleotide.
• The nitrogenous base and a sugar of a nucleotide form a molecule called nucleoside. It lacks phosphate group. Four types of nucleoside are found in DNA molecule.
• In a nucleoside, nitrogenous base is attached to the first carbon atom (C-1) of the sugar and when a phosphate group gets attached with that of the carbon (C-5) atom of the sugar molecule a nucleotide molecule is formed.
• A single strand of DNA consists of several thousands of nucleotides one above the other.
• The phosphate group of the lower nucleotide attached with the 5^th carbon atom of the deoxyribose sugar forms phospho-di-ester bond with that of the 3^rd  carbon atom of the deoxyribose sugar of the nucleotide placed just above it.
• Single long chain of polynucleotides of DNA consists of one end with sugar molecules not connected with another nucleotide having C-3 carbon which is not connected with phosphate group.
• The single polynucleotide strand of DNA is not straight but helical in shape.
• The DNA molecule consists of such two helical polynucleotide chains which are complementary to each other.
• The two complementary polynucleotide chains of DNA are held together by the weak hydrogen bonds.
• Adenine always pairs with thymine, and guanine with cytosine (a pyrimidine with a purine).
• Adenine-thymine pair consists of two hydrogen bonds and guanine-cytosine pair consists of three hydrogen bonds (Thus, if the sequence of bases of a polynucleotide chain is known, that of the other can be determined).

Structure of RNA :

• The other nucleic acid found in living organisms is Ribose nucleic acid.
• In most of the organisms it is not found to be hereditary material but in certain organisms like tobacco mosaic virus, it is the hereditary material.
• Like DNA, ribose nucleic acid also consists of polynucleotide chain with the difference that it consists of single ‘strand. Exceptions are Reovirus and wound tumor virus where RNA is double stranded.
• The nucleotides of RNA have ribose sugar instead of the deoxyribose sugar as in the case of DNA.
• In case of RNA; Uracil substitutes thymine of DNA.
• Purine, pyrimidine equality is not found in RNA molecule because of its single stranded structure.
• RNA strand is usually found folded upon itself in certain regions or entirely. These folding helps in stability of the RNA molecule.
• Most of the RNA polynucleotide chains start either with adenine or guanine.

Messenger RNA (mRNA):

• It is a linear polynucleotide.
• It accounts 3% of cellular RNA.
• Its molecular weight is several million.
• mRNA molecule carrying information to form a complete polypeptide chain is called cistron
• Size of mRNA is related to the size of message it contains.
• Synthesis of mRNA begins at 5’ end of DNA strand and terminates at 3’ end.

Role of messenger RNA:

It carries genetic information from DNA to ribosomes, which are the sites of protein synthesis.

Ribosomal RNA (rRNA):

• rRNA was discovered by Kurland in 1960.
• It forms 50-60% part of ribosomes.
• It accounts 80-90% of the cellular RNA.
• It is synthesized in nucleus.
• It gets coiled at various places due to intrachain complementary base pairing.

Role of ribosomal RNA: It provides proper binding site for m-RNA during protein synthesis.

Transfer RNA (tRNA):

• These molecules are much smaller consisting of 70-80 nucleotides.
• Due to presence of complementary base pairing at various places, it is shaped like clover-leaf.
• Each tRNA can pick up particular amino acid.
• In the anticodon loop of tRNA, three unpaired nucleotides are present called as anticodon which pair with codon present on mRNA.
• The specific amino acids are attached at the 3' end in acceptor stem of clover leaf of tRNA.

Following four parts can be recognized on tRNA

• (i) DHU arm (Dihydroxyuracil loop/ amino acid recognition site)
• (ii) Amino acid binding site.
• (iii) Anticodon loop / codon recognition site
• (iv) Ribosome recognition site.

Role of transfer RNA: It helps in elongation of polypeptide chain during the process called translation.

Properties of enzyme :

Proteinaceous Nature:

• All enzymes are basically made up of protein.

Three-Dimensional conformation:

• All enzymes have specific 3-dimensional conformation.
• They have one or more active sites to which substrate (reactant) combines.
• The points of active site where the substrate joins with the enzyme is called substrate binding site.

Catalytic property:

• Enzymes are like inorganic catalysts and influence the speed of biochemical reactions but themselves remain unchanged.
• After completion of the reaction and release of the product they remain active to catalyze again.
• A small quantity of enzymes can catalyze the transformation of a very large quantity of the substrate into an end product.
• For example, sucrase can hydrolyze 100000 times of sucrose as compared with its own weight.

Specificity of action:

• The ability of an enzyme to catalyze one specific reaction and essentially no other is perhaps its most significant property. Each enzyme acts upon a specific substrate or a specific group of substrates.

Reversibility of action:

• Enzymes are very sensitive to temperature and pH.
• Each enzyme exhibits its highest activity at a specific pH i.e. optimum pH.
• Any increase or decrease in pH causes decline in enzyme activity e.g. enzyme pepsin (secreted in stomach) shows highest activity at an optimum pH of 2 (acidic).
• Trypsin (in duodenum) is most active at an optimum pH of 9.5 (alkaline).
• Both these enzymes viz. pepsin and trypsin are protein digesting enzymes.

Temperature:

• Enzymes are destroyed at higher temperature of 60-70°C or below, they are not destroyed but become inactive.
• This inactive state is temporary and the enzyme can become active at suitable temperature.
• Most of the enzymes work at an optimum temperature between 20°C and 35°C.

Nomenclature of Enzymes :

• Enzymes are named by adding the suffix- ‘ase’ to the name of the substrate on which they act e.g. protease, sucrase nuclease etc. which break up proteins, sucrose and nucleic acids respectively.
• The enzymes can be named according to the type of function they perform. For e.g., dehydrogenase remove hydrogen, carboxylase add CO; decarboxylases remove CO₂, oxidases helping in oxidation.
• Some enzymes are named according to the source from which they are obtained. For e.g., papain from papaya, bromelain from the member of Bromeliaceae family, pineapple.
• According to international code of enzyme nomenclature, the name of each enzyme ends with an -ase an consists of double name.
• The first name indicates the nature of substrate upon which the enzyme acts and the second name indicates the reaction catalyzed. For e.g., pyruvic decarboxylase catalyses the removal of CO₂ from the substrate pyruvic acid.
• Similarly, the enzyme glutamate pyruvate transaminase catalyses the transfer of an amino group from the substrate glutamate to another substrate pyruvate.

Classification of Enzymes :

Enzymes are classified into six classes:

(i) Oxidoreductases: These enzymes catalyze oxidation and reduction reaction by the transger of hydrogen and/or oxygen. e. g. alcohol dehydrogenase

Alcohol + NAD⁺ \(\frac {alocohole}{dehydogenase}\)>  Aldehyde + NADH₂

(ii) Transferases : These enzymes catalyse the transfer of certain groups between two molecules. e.g. glucokinase

Glucose + ATP \(\underrightarrow {Glucokinase}\) Glu-6-Phosphate + ADP

(iii) Hydrolases: These are enzymes catalyse hydrolytic reactions. This class includes amylases, proteases, lipases etc. eg. Sucrase

Sucrose  \(\underrightarrow {Sucrase}\)  Glucose + Fructose + H₂O

(iv) Lyases : These enzymes are involved in elimination reactions resulting in the removal of a group of atoms from substrate molecule to leave a double bond.

It includes aldolases, decarboxylases, and dehydratases, e.g fumarate hydratase.

Histidine \(\frac {histidine}{decarboxylase}\)> Histamine + CO₂

(v) Isomerases : These enzymes catalyze structural rearrangements within a molecule.

Their nomenclature is based on the type of isomerism. Thus these enzymes are identified as racemases, epimerases, isomerases, mutases, e.g. xylose isomerase.

Glu-6-Phosphate \(\underrightarrow {isomarase}\) Fructose-6-Phosphate

(vi) Ligases or Synthetases : These are the enzymes which catalyse the covalent linkage of the molecules utilizing the energy obtained from hydrolysis of an energy-rich compound like ATP, GTP e.g. glutathione synthetase, Pyruvate carboxylase.

Pyruvate + CO₂ + ATP \(\frac {pyruvate}{carboxylase}\)> Oxaloacetate + ADP + Pi

Lock and Key model:

• Lock and Key model was first postulated in 1894 by Emil Fischer.
• This model explains the specific action of an enzyme with a single substrate.
• In this model, lock is the enzyme and key is the substrate.
• The correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme).

Induced Fit model (Flexible Model):

• Induced Fit model was first proposed in 1959 by Koshland.
• This model states that approach of a substrate induces a conformational change in the enzyme.
• It is the more accepted model to understand mode of action of enzyme. '
• The induced fit model shows that enzymes are rather flexible structures in which the active site continually reshapes by its interactions with the substrate until the time the substrate is completely bound to it.
• It is also the point at which the final form and shape of the enzyme is determined.

Concentration of substrate:

• Increase in the substrate concentration gradually increases the velocity of enzyme activity within the limited range of substrate levels.
• A rectangular hyperbola is obtained when velocity is plotted against the substrate concentration.
• Three distinct phases (A, B and C) of the reaction are observed in the graph.
• Where V = Measured velocity, V_max = Maximum velocity, S = Substrate concentration, K_m = Michaelis-Menten constant.
• K_m or the Michaelis-Menten constant is defined as the substrate concentration (expressed in moles/lit) to produce half of maximum velocity in an enzyme catalyzed reaction.

• It indicates that half of the enzyme molecules (i.e. 50%) are bound with the substrate molecules when the substrate concentration equals the Km value.
• Km value is a constant and a characteristic feature of a given enzyme.
• It is a representative for measuring the strength of ES complex.
• A low K_m value indicates a strong affinity between enzyme and substrate, whereas a high Km value reflects a weak affinity between them.
• For majority of enzymes, the Km values are in the range of 10^-5 to 10^-2 moles.

Enzyme Concentration:

• The rate of an enzymatic reaction is directly proportional to the concentration of the substrate.
• The rate of reaction is also directly proportional to the square root of the concentration of enzymes.
• It means that the rate of reaction also increases with the increasing concentration of enzyme and the rate of reaction can also decrease by decreasing the concentration of enzyme.

Temperature:

• The temperature at which the enzymes show maximum activity is called Optimum temperature.
• The rate of chemical reaction is increased by a rise in temperature but this is true only over a limited range of temperature.
• Enzymes rapidly denature at temperature above 40°C.
• The activity of enzymes is reduced at low temperature.
• The enzymatic reaction occurs best at or around 37°C which is the average normal body temperature in homeotherms(Organisms which can maintain their body temperature at constant level are known as homeotherms).

Effect of pH:

• The pH at which an enzyme catalyzes the reaction at the maximum rate is known as optimum pH.
• The enzyme cannot perform its' function beyond the range of its pH value.

Other substances:

• The enzyme action is also increased or decreased in the presence of some other substances such as coenzymes, activators and inhibitors.
• Most of the enzymes are combination of a co-enzyme and an apo-enzyme
• Activators are the inorganic substances which increase the enzyme activity.
• Inhibitor is the substance which reduces the enzyme activity.

(i) Catabolic pathways :

This involves formation of simpler structure from a complex biomolecule.

For e.g. when we eat wheat, bread or chapati, our gastrointestinal tract digests (hydrolyses) the starch to glucose units with help of enzymes and releases energy in form of ATP (Adenosine triphosphate).

(ii) Anabolic pathway

It is also called as biosynthetic pathway that involves formation of a more complex biomolecules from a simpler structure.

For e.g., synthesis of glycogen from glucose and protein from amino acids. These pathways consume energy.

Secondary metabolites (SMs) :

• Biomolecules (organic compounds) like amino acids, proteins, lipids, sugars, etc. can also be called as metabolites.
• The above compounds are present in animal tissues and are called primary metabolites and their functions in normal biological processes are well known.
• The compounds other than primary metabolites found in plants, fungi and microbes are called as secondary metabolites.

Secondary metabolites are small organic molecules produced by organisms that are not essential for their growth, development and reproduction.

Secondary metabolites can be pigments (carotenoids, anthocyanins), alkaloids (morphine, codeine), terpenoides (Monoterpenes Diterpenes), toxins (Abrin, Ricin), drugs (vinblastin, curcumin), Lectins (concanavalin A), essential oils (lemon grass oil), polymeric substances (rubber, gums, cellulose), scents, Spices, antibiotics etc.

• Several types of bacteria, fungi and plants produce secondary metabolites.
• Secondary metabolites can be classified on the basis of chemical structure (e g SMs containing rings, sugar), composition (with or without nitrogen), their solubility in various solvents, or the pathway by which they are synthesized (e.g. phenylpropanoid produces tannins).

Importance of secondary metabolites :

• Drugs developed from secondary metabolites have been used to treat infectious diseases, cancer, hypertension and inflammation.
• Morphine, the first alkaloid isolated from Papaver somniferum is used as pain reliver and cough suppressant.
• Secondary metabolites like alkaloids, nicotine, cocaine and the terpenes, cannabinol are widely used for recreation and stimulation.
• Flavours of secondary metabolites improve our food preferences.
• Tannins are added to Wines and chocolate for improving astringency.
• Since most secondary metabolites have antibiotic property, they are also used as food preservatives.
• Glucosinolates is a secondary metabolite which is naturally present in cabbage imparts a characteristic flavour and aroma because of nitrogen and sulphur containing chemicals. It also offers protection to these plants from many pests.