Detailed Notes 2-Chapter 9-Biomolecules

9.4 PROTEINS

1. Structure and Composition:

   • Proteins are polypeptides, consisting of linear chains of amino acids.
   • Amino acids are linked together by peptide bonds.
   • Each protein is a polymer of amino acids, making it a heteropolymer due to the presence of 20 different types of amino acids.
   • Examples of amino acids include alanine, cysteine, proline, tryptophan, and lysine.

2. Importance of Amino Acid Composition:

   • Knowledge of the amino acid content of proteins is essential, especially in nutrition.
   • Certain amino acids are essential for human health and must be obtained through the diet, as the body cannot synthesize them.

3. Essential vs. Non-Essential Amino Acids:

   • Amino acids can be essential (must be obtained from the diet) or non-essential (can be synthesized by the body).
   • Dietary proteins serve as the source of essential amino acids.

4. Functions of Proteins:

   • Proteins carry out numerous functions in living organisms.
   • They transport nutrients across cell membranes, fight infectious organisms, act as hormones, enzymes, etc.

5. Abundance and Examples:

   • Collagen is cited as the most abundant protein in the animal world.
   • Ribulose bisphosphate carboxylase-oxygenase (RuBisCO) is highlighted as the most abundant protein in the biosphere.

9.5 POLYSACCHARIDES

1. Composition and Structure:

   • Polysaccharides are macromolecules composed of long chains of sugars.
   • These chains are like threads, with different monosaccharides serving as building blocks.

2. Examples:

   • Cellulose is a common polysaccharide consisting of glucose monomers. It is a homopolymer.
   • Starch, found in plants, and glycogen, found in animals, are variants of cellulose and serve as energy storage compounds.
   • Inulin is another polysaccharide made of fructose monomers.

3. Structure and Properties:

   • Polysaccharide chains, such as glycogen, have a reducing end and a non-reducing end, with branches.
   • Starch forms helical secondary structures capable of holding I2 molecules, resulting in a blue color. Cellulose lacks these complex helices and cannot hold I2.
   • Cellulose is a major component of plant cell walls, and materials like paper and cotton fiber are cellulosic.

4. Complex Polysaccharides:

   • Some polysaccharides have more complex structures, with amino-sugars and chemically modified sugars (e.g., glucosamine, N-acetyl galactosamine) as building blocks.
   • Chitin, found in the exoskeletons of arthropods, is an example of a complex polysaccharide and is mostly a homopolymer.

9.6 NUCLEIC ACIDS

1. Composition and Classification:

   • Nucleic acids are macromolecules found in the acid-insoluble fraction of living tissues.
   • They are polynucleotides, along with polysaccharides and polypeptides, constituting the true macromolecular fraction of cells.

2. Structure of Nucleotides:

   • Nucleotides are the building blocks of nucleic acids.
   • Each nucleotide consists of three chemically distinct components: a heterocyclic compound (nitrogenous base), a monosaccharide, and a phosphate group.

3. Components of Nucleotides:

   • Heterocyclic compounds in nucleotides include adenine, guanine, uracil, cytosine, and thymine.
   • Adenine and guanine are purines, while uracil, cytosine, and thymine are pyrimidines.

4. Sugar Component:

   • The sugar found in polynucleotides can be either ribose (a pentose monosaccharide) or 2’ deoxyribose.
   • DNA contains deoxyribose and is called deoxyribonucleic acid.
   • RNA contains ribose and is called ribonucleic acid.

9.7 STRUCTURE OF PROTEINS

1. Primary Structure:

   • The primary structure of a protein refers to the sequence of amino acids, representing the positional information along the protein chain.
   • It is depicted as a linear sequence, starting from the N-terminal amino acid to the C-terminal amino acid.

2. Secondary Structure:

   • Proteins fold into secondary structures, such as helices or sheets, along certain regions of the protein chain.
   • Helices resemble a revolving staircase, typically right-handed, while other regions adopt different folded forms.

3. Tertiary Structure:

   • The long protein chain further folds upon itself, resembling a hollow woolen ball, to form the tertiary structure.
   • Tertiary structure provides a 3-dimensional view of the protein and is crucial for its biological activities.

4. Quaternary Structure:

   • Some proteins consist of multiple polypeptides or subunits.
   • The arrangement of these folded polypeptides or subunits with respect to each other constitutes the quaternary structure.
   • Examples include adult human hemoglobin, which consists of four subunits, two each of a and b types.

9.8 ENZYMES

1. Composition and Behavior:

   • Enzymes are predominantly proteins, although some nucleic acids, known as ribozymes, also exhibit enzymatic activity.

2. Structure of Enzymes:

   • Enzymes, like proteins, possess a primary structure (amino acid sequence), secondary structure, and tertiary structure.
   • The tertiary structure of enzymes forms crevices or pockets, one of which is known as the active site.

3. Active Site and Catalysis:

   • The active site of an enzyme is a specific region where the substrate molecule binds.
   • Enzymes catalyze reactions by binding substrates at their active sites, facilitating the conversion of substrates into products.

4. Comparison with Inorganic Catalysts:

   • Enzyme catalysts exhibit differences from inorganic catalysts.
   • Inorganic catalysts can function efficiently at high temperatures and pressures, whereas enzymes are typically sensitive to high temperatures (above 40°C) and may become damaged.
   • However, enzymes isolated from organisms living in extreme conditions, such as high temperatures in hot vents and sulfur springs, are stable and retain their catalytic activity even at elevated temperatures (up to 80°-90°C).

5. Thermal Stability:

   • Enzymes derived from thermophilic organisms possess thermal stability, an important quality that allows them to maintain catalytic activity at high temperatures.

9.8.1 Chemical Reactions

1. Types of Changes:

   • Physical changes involve alterations in shape or state of matter without breaking bonds.
   • Chemical reactions involve the breaking and formation of bonds, resulting in the transformation of chemical compounds.

2. Examples of Chemical Reactions:

   • Inorganic chemical reaction: Ba(OH)2 + H2SO4 → BaSO4 + 2H2O
   • Organic chemical reaction: Hydrolysis of starch into glucose

3. Rate of Reactions:

   • Rate or velocity of a chemical process is the amount of product formed per unit time.
   • Temperature influences the rate of physical and chemical processes, with a general rule of thumb that rate doubles or halves for every 10°C change.

4. Role of Enzymes:

   • Enzymes catalyze chemical reactions, significantly accelerating their rates.
   • Enzyme-catalyzed reactions proceed much faster compared to uncatalyzed reactions.
   • Example: Carbonic anhydrase catalyzes the conversion of carbon dioxide and water into carbonic acid, increasing the reaction rate by about 10 million times.

5. Variety and Specificity of Enzymes:

   • There are thousands of types of enzymes, each catalyzing a unique chemical or metabolic reaction.
   • Multistep chemical reactions catalyzed by the same or different enzymes are called metabolic pathways.
   • Example: Glucose metabolism, where glucose is converted into pyruvic acid through ten different enzyme-catalyzed reactions.

6. Metabolic Pathway and End Products:

   • Metabolic pathways can lead to different end products under different conditions.
   • Example: Glucose metabolism can produce lactic acid under anaerobic conditions, pyruvic acid under aerobic conditions, and ethanol in yeast fermentation.

9.8.2 How do Enzymes bring about such High Rates of Chemical Conversions?

1. Active Site and Substrate Binding:

   • Enzymes have active sites where substrates bind, forming an enzyme-substrate (ES) complex.
   • The substrate must diffuse towards the active site to form the ES complex.

2. Transition State Formation:

   • The ES complex leads to the formation of a transition state structure of the substrate.
   • This transition state structure represents a high-energy intermediate state between the stable substrate and the product.

3. Structural Transformation and Product Release:

   • The substrate undergoes structural transformation within the active site, eventually forming the product(s).
   • The pathway of transformation must pass through the unstable transition state structure.
   • Multiple intermediate structural states may exist between the substrate and the product.

4. Energy Changes and Activation Energy:

   • The potential energy content is represented on the y-axis of a graph, while the progression of structural transformation is represented on the x-axis.
   • The energy level difference between the substrate (S) and the product (P) determines if the reaction is exothermic (P lower than S) or endothermic (P higher than S).
   • Regardless of whether the reaction is exothermic or endothermic, the substrate must overcome a higher energy state known as the transition state.
   • The difference in average energy content between the substrate and the transition state is termed as the activation energy.

5. Role of Enzymes in Lowering Activation Energy:

   • Enzymes facilitate chemical reactions by lowering the activation energy barrier.
   • By lowering the activation energy, enzymes make the transition from substrate to product more favorable and easier.

9.8.3 Nature of Enzyme Action

1. Formation of Enzyme-Substrate Complex (ES):

   • Each enzyme molecule (E) has a specific binding site for its substrate (S), forming an enzyme-substrate complex (ES).
   • The ES complex is highly reactive but short-lived.

2. Catalytic Cycle:

   • The catalytic cycle of enzyme action involves the following steps:
     1. Substrate Binding: The substrate (S) binds to the active site of the enzyme (E), fitting into it.
     2. Induced Fit: The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.
     3. Chemical Bond Cleavage: The active site of the enzyme, now in close proximity to the substrate, catalyzes the breaking of chemical bonds in the substrate, forming an enzyme-product complex (EP).
     4. Product Release: The enzyme releases the products of the reaction, and the free enzyme is ready to bind to another molecule of the substrate and repeat the catalytic cycle.

9.8.4 Factors Affecting Enzyme Activity

1. Temperature and pH:

   • Enzymes operate optimally within a narrow range of temperature and pH.
   • Each enzyme has an optimum temperature and pH at which it exhibits the highest activity.
   • Activity decreases both below and above the optimum values.
   • Low temperatures can temporarily inhibit enzyme activity, while high temperatures can denature enzymes, rendering them inactive.

2. Concentration of Substrate:

   • Initially, as substrate concentration increases, the velocity of enzymatic reaction rises.
   • Eventually, the reaction reaches a maximum velocity (Vmax), which is not surpassed by further increases in substrate concentration.
   • This occurs because enzyme molecules become saturated with substrate, leaving no free enzyme molecules to bind with additional substrate molecules.

3. Chemical Inhibitors:

   • Enzyme activity can be affected by specific chemicals that bind to the enzyme.
   • Inhibition occurs when a chemical binds to the enzyme and shuts off its activity.
   • Competitive inhibitors closely resemble the substrate in molecular structure and compete with the substrate for the enzyme’s active site.
   • As a result, the substrate cannot bind, and enzyme activity declines.
   • An example is malonate, which inhibits succinic dehydrogenase by resembling its substrate, succinate.

9.8.5 Classification and Nomenclature of Enzymes

1. Oxidoreductases/Dehydrogenases:

   • These enzymes catalyze oxidoreduction reactions between two substrates, S and S’.
   • Example reaction: S reduced + S’ oxidized → S oxidized + S’ reduced.

2. Transferases:

   • Transferases catalyze the transfer of a functional group (other than hydrogen) between a pair of substrates, S and S’.
   • Example reaction: S – G + S’ → S + S’ – G (where G represents the transferred group).

3. Hydrolases:

   • Hydrolases catalyze the hydrolysis of various types of chemical bonds, including ester, ether, peptide, glycosidic, C-C, C-halide, or P-N bonds.

4. Lyases:

   • Lyases catalyze the removal of groups from substrates, resulting in the formation of double bonds, by mechanisms other than hydrolysis.

5. Isomerases:

   • Isomerases catalyze the interconversion of optical, geometric, or positional isomers.

6. Ligases:

   • Ligases catalyze the linking together of two compounds by forming new bonds, such as C-O, C-S, C-N, P-O, etc.

9.8.6 Co-factors

1. Prosthetic Groups:

   • Prosthetic groups are organic compounds that are tightly bound to the apoenzyme (the protein portion of the enzyme) and are essential for the enzyme’s catalytic activity.
   • Examples include heme, which is a prosthetic group in enzymes like peroxidase and catalase. It is a part of the active site of the enzyme and plays a crucial role in the breakdown of hydrogen peroxide to water and oxygen.

2. Co-enzymes:

   • Co-enzymes are also organic compounds, but their association with the apoenzyme is transient, occurring during the course of catalysis.
   • Co-enzymes serve as cofactors in various enzyme-catalyzed reactions and are often involved in carrying or transferring chemical groups.
   • Many coenzymes are derived from vitamins. For example, coenzyme nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin.

3. Metal Ions:

   • Some enzymes require metal ions for their activity. These metal ions form coordination bonds with side chains at the enzyme’s active site and may also interact with the substrate.
   • For example, zinc serves as a cofactor for the proteolytic enzyme carboxypeptidase.