Plus One Zoology Notes Chapter 4 Biomolecules is part of Plus One Zoology Notes. Here we have given Kerala Plus One Zoology Notes Chapter 4 Biomolecules.
|Text Book||NCERT Based|
|Category||Kerala Plus One|
Kerala Plus One Zoology Notes Chapter 4 Biomolecules
The cell is composed of a variety of organic and inorganic compounds, which performs various functions. The organic or biological molecules are small and simple molecules which often assemble to form large and complex macromolecules.
Analysis of the chemical composition
- The chemical composition of living organisms can find out by performing chemical analysis.
- The living tissue which is to be analyzed is ground in trichloroacetic acid (CI3C COOH) to obtain a slurry.
- A slurry is filtered to get:
- The filtrate (acid-soluble fraction contain biomolecules)
- Retentate( acid insoluble fraction).
- Thousands of organic compounds are found in the filtrate.
- Separation techniques are used for separating one compound from another.
- Molecular formula and probable structure can be found by using analytical techniques.
- All carbon-containing compounds that we get from living tissues are called biomolecules.
Analysis of inorganic compounds
♦ Ash analysis
- This is a destructive technique to analyze inorganic compounds in a living organism.
- Living tissue is taken. It is dried to evaporate all water, and the remaining material gives its dry weight.
- The dried material is burnt.
- All organic gaseous compounds will be removed to leave “ash”.This technique is ash analysis.
- Ash contains many inorganic elements like Ca, Mg, S, P etc.and also inorganic compounds .
♦ Element analysis
It gives elemental a composition of living tissue in the form of hydrogen, oxygen, chlorine, carbon.
♦ Analysis of compounds
- It gives an idea of the kind of organic and inorganic constituents.
- List of representative inorganic constituents of living tissues.
♦ Analysis from the chemistry point of view
Functional groups of compounds like aldehydes, ketones, and aromatic compounds, etc. can be identified.
♦ Analysis from the biological point of view
From the biological point of view, we can classify them into amino acids, fatty acids, nucleotide bases etc.
- Amino acids are organic compounds, which are building blocks of proteins.
- They are compounds containing an amino group (NH2) and acidic group (-COOH) on the same α – carbon. So, they are called α – amino acids.
Structure of amino acid
- An amino acid consists of a carbon atom with four constituent groups occupying: the four valency positions.
- The four substituent groups are, a hydrogen atom (H), an amino group (-NH2), a carboxyl group (-COOH) and a side chain (R group)
- Amino acids are amphoteric compounds because they contain both a basic group and an acidic group.
- The chemical and physical properties of amino acids depending upon the amino group, carboxyl group, and R group.
- Acidic amino acid more carboxyl group
Eg., Glutamic acid
- Basic amino acid more amino group
- Neutral amino acid equal amino and a carboxyl group.
- Aromatic amino acids
Eg., tyrosine, phenylalanine, tryptophan.
- Acidic amino acid more carboxyl group
- Some amino acids have ionizable nature of amino groups and carboxyl groups. Hence, in solutions of different pH, the structure of amino acid changes.
- They are water-insoluble compounds.
- Lipids are esters of fatty acids with various alcohol.
- Based on the melting point, lipids are of two types fats and oils.
- Fats: Solid form of lipids at room temperature.
- Oils: Lipids that are in liquid form in room temperature are called oils. Oils have a low melting point. So it remains as oil in winters,
eg., gingelly oil.
- Fats are esters of fatty acids with glycerols.
- Fatty acids are organic acids having hydrocarbon chains that end in a COOH group attached to an R group.
- The R group could be methyl (CH3), or ethyl (C2H5), or higher number of CH2 groups ( 1 to 19 carbons).
- Palmitic acid has 16 carbons.
- Arachidonic acid has 20 carbons.
- Fatty acids are of two types, including carboxyl carbon.
- Saturated fatty acids (without double or single bonds)
- Unsaturated fatty acids (with one or more double bonds in their carbon chain).
- Some lipids have phosphorous and phosphorylated organic compounds in them.
- These lipids are called phospholipids. They are seen in a cell membrane
Nucleotide and Nucleoside
- Living organisms have a number of carbon compound in which heterocyclic rings can be found are called nucleotides.
Eg., adenine, guanine, cytosine, uracil, and thymine.
When these nitrogen bases are formed attached to a sugar, they are called nucleoside. Eg; Adenosine, guanosine etc.
Adenine + Sugar = Adenosine
If a phosphate group is esterified to the sugar of a nucleoside, it is called nucleotide.
Eg., Adenylic acid, thymidylic acid etc.
Adenine + Phosphate = Adenylic acid
Nucleotides are the structural unit of nucleic acids. They function as genetic material in living organisms.
Primary and secondary metabolites
All chemical compounds present in the living tissues are called biomolecules. These are also called metabolites.
♦ Primary metabolites
- Biomolecules which involve directly in the normal growth, development, and reproduction of an organism are called primary metabolites.
- Eg., sugars, amino acids, fatty acids, and glycerol etc.
♦ Secondary metabolites
- Biomolecules which are not directly involved in the normal growth, development, and reproduction of an organism are called secondary metabolites.
- Eg., Pigments, alkaloids, essential oils, toxins, drugs etc.
- Many of the secondary metabolites are useful to human welfare.
Eg., Rubber, spices etc.
- Some secondary metabolites have ecological importance.
|Essential oils||Lemongrass oil|
|Polymeric substances||Rubber, gums, cellulose|
- Largely sized biomolecules having molecular weight more than 10,000 daltons are called biomacromolecules.
- They are found in an acid-insoluble fraction.
- Acid-insoluble fraction includes
- Nucleic acids
- A molecular weight of lipids does not exceed 800 daltons. But it comes under insoluble fraction because lipids are arranged into structures like cell membranes are broken and form vesicles which are water-insoluble, ie lipids are not strictly macromolecules.
- Acid-insoluble fraction includes macromolecules from cytoplasm and organelles.
- Proteins are polypeptides, composed of many chains of amino acids.
- In protein molecules, amino acids are linked together by a peptide bond.
- Protein is a heteropolymer protein molecule is formed of different types of monomers) and not a homopolymer.
- Homopolymer has only one type of monomer repeating ‘ n’ number of times.
- Amino acids are necessary for our health. They are supplied through diet. So the dietary proteins are the source of essential amino acids.
- Amino acids can be essential or non-essential.
♦ Essential amino acids
These amino acids are not synthesized in our body and must be supplied with the food.
♦ Non-essential amino acids
These amino acids can be synthesized in our body and they need not be supplied in the diet.
Functions of protein in living organisms
- Transport of nutrients across the cell membrane.
- Some are hormones,
- They act as antibodies to fight infectious organisms.
- Some proteins act as enzymes. Collagen is the most abundant protein in the animal world and Ribulose biphosphate Carboxylase Oxygenase (RuBisCO) is the most abundant protein in the whole of the biosphere.
|Collagen||Intercellular ground substance|
|Antibody||Fights infectious agents|
|Receptor||Sensory reception (smell, taste, hormone)|
|GLUT4||Enables glucose transport into cells.|
Structure of proteins
- Proteins are heteropolymers containing strings of amino acids.
- Structure of molecules means different things in different context.
- In inorganic chemistry, the molecular formulae represent the structure of a molecule eg., NaCI, MgCl2 etc.
- In Organic chemistry, two-dimensional view of a molecule represents the structure. Eg..benzene, naphthalene, etc.
- Physicists consider three-dimensional views of molecular structures. In Biology, the different levels of the molecule represent the structure.
Eg., proteins have four levels of structural organization Primary structure, secondary structure, tertiary structure, and quaternary structure.
♦ Primary structure
- It is the linear sequence of amino acids in a polypeptide chain, describes the sequence of amino acids, ie. the positional informational in a protein.
- A left end of the chain has first amino acid (N terminal amino acid).
- Right end has last amino acid (C terminal amino acid).
♦ Secondary structure
- The polypeptide chain is coiled to form a three-dimensional structure.
- Hydrogen bonds are formed between amino acids giving the chain a helical shape. It has only right-handed helices.
a. A Secondary structure
b. A Tertiary structure of a protein
♦ Tertiary structure
The long protein chain is also folded upon itself like a hollow swollen ball giving rise to the tertiary structure.
- It gives a three-dimensional view of a protein.
- The structure is necessary for many biological activities of the protein.
♦ Quaternary structure.
- The structure contains more than one polypeptide chain.
- In quaternary structure, polypeptide subunits are arranged in a linear string of spheres or spheres are arranged one upon each other in the form of a cube or plate,
eg., Haemoglobin has 4 subunits, of these 2 are identical to each other, 2 subunits are a type and 2 subunits are p-type.
- They are long chains of sugars.
- Building blocks of polysaccharides are monosaccharides.
- Polysaccharides are condensation polymers in which monosaccharides are held together through glycosidic linkage.
- They are colorless, tasteless. So they are called non-sugars.
Eg., Cellulose, starch, glycogen, insulin. Polysaccharides are of two types based on their composition:
They are composed of only one type of monosaccharide.ie.glucose
They are composed of two or more monosaccharides.eg., chitin
Examples of polysaccharides
- It is a homopolymer.
- Composed of only one type of mono charade, glucose.
- Plant cell walls are made of cellulose.
- Paper made from plant pulp is cellulose.
- Cotton fiber is cellulose, they cannot hold l2 because cellulose does not contain complex helices.
- It is the storehouse of energy in plant tissues.
- Starch forms a helical secondary structures.
- It can hold the iodine molecule (l2) in the secondary structure.
- The starch l2 is blue in color.
- It is the storage polysaccharide in animals.
- It is a mono-polymer and is made up of a large number of glucose units.
- It is particularly called animal starch.
- It is a highly branched chain of a glucose molecule.
- The right end of a polysaccharide is reducing end while the left end is known as a non-reducing end.
4. Insulin: It is a polymer of fructose.
5. Chitin: It is a heteropolymer.
- It is formed of amino sugars and chemically modified sugars (eg., glucosamine, N acetylgalactosamine.)
- It is found in the exoskeletons of arthropods (eg..insects).
- These are macromolecules found in an acid-insoluble fraction.
- Nucleic acids are polymers of nucleotides.
- A nucleotide contains a monosaccharide and heterocyclic nitrogenous bases along with phosphate group.
- Nitrogenous bases are of two types:
- Purines Adenine and Guanine
- PyrimidinesThymine, Cytosine, Uracil. Uracil is present in RNA at the place of thymine.
- Monosaccharides present in a nucleic acid is a pentose sugar.
- The pentose sugar present in DNA is deoxyribose sugar and in RNA is ribose sugar.
- It occurs in the form of phosphoric acid.
- A phosphate group is also found to esterified to the sugars they are called nucleotide.
- A nucleotide without a phosphate is said to be nucleoside,
- There are two types of nucleic acids :
i. DNA (Deoxyribonucleic acid)
ii. RNA (Ribonucleic acid)
Refer section 4.4
Nature of Bond linking Monomers in a Polymer
- In a protein or a polypeptide, the amino acids are linked by a peptide bond.
- The peptide bond is formed when the carboxyl group (-COOH) of one amino acid reacts with the amino group (NH2) of the next amino acid with the elimination of water.
- In a polysaccharide, the individual monosaccharides are linked by a glycosidic bond.
- This bond is also formed by dehydration.
- A glycosidic bond is formed between two carbon atoms of two adjacent monosaccharides.
♦ Nucleic acids
- In a nucleic acid, a phosphate molecule links the 3′ carbon of one sugar of one nucleotide to the 5′ carbon of the sugar of the succeeding nucleotide.
- The bond between the phosphate and hydroxyl group of sugar is called ester bond. ! One ester bond is seen on either side, it is I called phosphodiester bond.
♦ The secondary structure of DNA (Watson-Crick Model)
- Nucleic acid exhibit a variety of secondary I structures.eg., Watson Crick model.
- This model was proposed by James Watson and Francis Crick.
- DNA exists as a double helix.
- It consists of two polynucleotide strands.
- Two strands are arranged antiparallel.
- The backbone is formed by the sugar phosphate-sugar chain.
- The nitrogen bases are projected perpendicular to this backbone but face inside.
- Nitrogen bases include Adenine (A), Guanine (G), Thymine (T) and Cytosine (C).
- Adenine pairs with Thymine (A=T) by two hydrogen bonds.
- Guanine pairs with Cytosine by three hydrogen bonds.
- Nitrogen base pairs form the steps of DNA.
- At each step of ascent, the strand turns 36°.
- Length of one full turn is 34 A0 (ie. 3.4° for each step). This form of DNA with above-mentioned features is called BDNA
The dynamic state of body constituents Concepts of Metabolism
- All living organisms contain thousands of biomolecules are present in a certain concentration.
- All the biochemical reactions taking place inside a living system together constitute metabolism.
- The organic molecule taking part in metabolism are called metabolites.
- Each metabolic reactions results in the transformation of biomolecule:
- Removal of C02 from amino acids to
- Removal of an amino group in a nucleotide base.
- Hydrolysis of a glycosidic bond in a disaccharide.
- Majority of these metabolic reactions do not occur in isolation but are always linked to some other reactions.
- In metabolism, there is a series of linked reactions called metabolic pathways,
- A flow of metabolites through the metabolic pathways has definite rate and direction like automobile traffic. This metabolite flow is called the dynamic state of body constituents.
- Every chemical reaction of the metabolic
- a pathway is a catalyzed reaction,
- The interlinked metabolic traffic is very smooth and without a single mishap under healthy conditions, The catalysts which hasten the rate of a given metabolic conversation are also protein with catalytic power are named enzyme.
Metabolic basis for living
- Metabolic pathways are of 2 types
i. Anabolic pathway
ii. Catabolic pathway
♦ Anabolic pathway
- It is a biosynthetic pathway.
- The pathway in which more complex structure is formed from the simple structures, it is called the anabolic pathway.
- Eg., The conversion of acetic acid into cholesterol.
- Anabolic pathway consumes energy.
Eg., Synthesis of protein from amino acids require energy input.
♦ Catabolic pathway
- It is a degradation pathway.
- A metabolic pathway in which the simple structures are formed from a complex structure, it is called a catabolic pathway.
- It involves the release of energy eg., a formation of lactic acid from glucose (glycolysis), respiration
- The energy released through catabolism is stored in the form of chemical bonds.
- The energy present in the chemical bond is called bond energy.
- The most important” energy currency” in a living system is the bond energy in adenosine triphosphate (ATP).
The Living State
- All living organisms exist in a steady state characterized by a concentration of biomolecules or metabolites.
- There is a continuous flow of biomolecules in the metabolic pathways is called metabolic flux.
- In terms of physics, the system at equilibrium cannot perform work.
- The living state is a non-equilibrium steady state to be able to perform work.
- Metabolism provides energy, Hence the living and metabolism are synonymous.
- Without metabolism, there cannot be a living state.
- All enzymes are proteins but all proteins are not enzymes.
- Ribozymes are nucleic acids (RNA) that behave like enzymes.
- Like all proteins, enzymes have primary, secondary and tertiary structure.
- The tertiary structure of an enzyme has some crevices or pockets called ‘active site’ into which the substrate fits.
- A small molecule which catalyzes chemical reactions is called a catalyst.
- Inorganic catalysts work at high temperature and pressure. But enzymes get damaged at a high temperature above 40°C.
- Thermophilic organisms have enzymes which are stable at high temperatures (up to 8090° C).
- Thermal stability is the important quality of these enzymes, Isolated from thermophilic organisms.
Chemical compounds undergo two types of changes,
- Physical change is the change in shape or change in state without breaking of bonds. Eg., melting of ice into water
- A breaking of bonds and the formation of new bonds are in the chemical changes or chemical reactions.
- The reaction is of two types: inorganic and organic.
♦ Inorganic chemical reaction
- It is the chemical reaction of inorganic compounds.
♦ Organic chemical reaction
It is the chemical reaction of organic compounds.
Eg., Hydrolysis of starch into glucose.
- The rate of the physical or chemical process is the amount of product formed per unit time expressed as,
Here, δ P (delta P)is the amount of the product formed and δt (delta t) is the time.
- If the direction of the process is specified, the rate can be called as velocity.
- The rate of physical and chemical processes are influenced by temperature and other factors.
- Catalyzed reactions proceed at higher rates than that of uncatalyzed reactions.
- A chemical reaction is very slow in the absence of an enzyme and only 200 molecules of carbonic acid (H2CO3) are formed per hour.
- In the presence of carbonic anhydrase enzyme within the cytoplasm, 6,00,000 molecules of H2CO3 are formed per second.
- The enzyme-catalyzed reaction is about 10 million times faster than the non catalyzed reaction.
- A multistep chemical reaction in which each of the steps is catalyzed by the same enzyme.
- Glycolysis is a metabolic pathway in which glucose is converted into pyruvic acid through ten different enzyme-catalyzed metabolic reactions.
The same pathway results in different products in different conditions.
- In skeletal muscle, glucose is converted to lactic acid.
- In yeast during fermentation, glucose is converted to ethanol (alcohol).
the process of Enzyme action
- A metabolic conversion is called reaction, The substance formed after a reaction is called end product.
- The substance which is converted into a product is called a substrate.
- The part of the enzyme that takes part in catalyzing reaction is called “active site” of the enzyme.
- The enzyme converts a substrate (S) into a product (P).
- The substrate ‘ S’ binds to the enzyme ‘ E’ at it’s” active site”. This leads to the formation of Enzyme Substrate complex (ES complex).
- This ES complex formation is the transition state structure (structure of substrate being formed during when the substrate is bound to an enzyme).
- The structure of the substrate (S) gets converted into the structure of the product. The transition state is the state of higher energy and lesser stability as compared to the product.
- The difference in the average energy content of ‘S’ from its transition state is called activation energy.
- In the graph, the Y-axis represents the potential energy content.X axis represents the progression of the structural transformation.
- There is an energy level difference between ‘S’and ‘P’.
- If the P is at a lower energy level than ‘ S’ the reaction is an exothermic reaction. There is no need to supply energy for the formation of the product.
- However in a reaction, whether it is an exothermic (spontaneous) or endothermic (energy-requiring reaction), ‘S’ has to go through much higher energy state or transition state.
Nature of Enzyme action.
The catalytic cycle of enzyme action
- First, the substrate binds to the active site of the enzyme, E+S.
- This induces some changes in enzymes so that the substrate is tightly bound with the active site of the enzyme (ES).
- The active site breaks chemical bonds of the substrate (EP).
- The enzyme releases the products and the free enzyme is ready to bind to other molecules of the substrate (E+S).
- The pathway of this transformation must go through the so-called transition state structure.
Factors Affecting Enzyme Activity
- The activity of an enzyme can be affected by a change in the conditions which alter the tertiary structure of the protein.
- These include temperature, pH and change in substrate concentration.
- Each enzyme shows it’s the highest activity at a particular temperature called optimum temperature.
- Low temperature preserves the enzyme in a temporarily inactive state.
- High temperature destroys enzymes. Because proteins are denatured by heat.
- Enzymes are very sensitive to pH
- Each enzyme shows it’s the highest activity at optimum pH.
- Activity declines both below and above the optimum value.
♦ Concentration of Substrate
- Increase in substrate concentration increases the rate of the reaction.
- The reaction reaches maximum velocity
- It is not exceeded by any further rise in substrate concentration.
- At this stage, the enzyme molecules are fully saturated. No active site is left free to bind with additional substrate molecule.
Inhibition of Enzyme action
- The activity of an enzyme is also sensitive to the presence of specific chemicals that bind to the enzyme. When the binding of the chemicals shuts of enzyme activity, the process is called inhibition.
- The chemicals which inhibit the enzyme action are called inhibitor.
- When the inhibitor closely resembles the substrate in its molecular structure and inhibits the activity of the enzyme, it is known as a competitive inhibitor.
- The inhibitor competes with the substrate for the active site of the enzyme.
- The substrate cannot bind and the enzyme action declines.
eg., Inhibition of succinic dehydrogenase by malonate.
- Competitive inhibitors are used in the control of bacterial pathogens.
Classification of enzymes
Enzymes are divided into six classes
♦ Oxidoreductases / dehydrogenases
Enzymes which catalyse oxidoreduction between two substrates S and S’.
Enzymes catalyzing a transfer of a group, G (other than hydrogen) between a pair of substrate S and S’.
Enzymes catalyzing the hydrolysis of ester, ether, peptide, glycosidic, CC, C halide bonds or PN bonds.
Enzymes that catalyze the removal of groups from substrates by mechanisms other than hydrolysis leaving double bonds.
Includes all enzymes catalyzing the interconversion of optical, geometric or positional isomers.
Enzymes catalyzing the linking together of 2 compounds, e.g., enzymes which catalyze joining of CO, CS bonds.
- Enzymes are composed of several polypeptide chains.
- Cofactors are non-protein constituents bound to the enzyme to make the enzyme catalytically active.
- The protein portion of the enzyme is called apoenzyme.
- Cofactors are of three types:
♦ Prosthetic group
The organic compounds which are tightly bound to the apoenzyme.
Eg., Peroxidase, and catalase, which catalyze the break down of hydrogen peroxide to water and oxygen. Haem is the prosthetic group.
• The organic compounds which are loosely attached to the apoenzyme.
• Their association with coenzyme is only transient, usually occurs during the time of catalysis.
Eg., NAD, and NADP contain vitamin niacin.
Importance of Coenzyme
i. It is essential for bringing the substrate in contact with an enzyme.
ii. It picks up a product of the reaction and transfers it to another reactant.
♦ Metal ions
- They form coordination bonds with side chains at active site and the same time form one or more coordination bonds with the substrate.
Eg., Zn is a cofactor for Carboxypeptidase.
- The catalytic activity of the enzyme is lost when the cofactor is removed.
- This proves that cofactor plays a crucial role in the catalytic activity of the enzyme.
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