11bio9

Biomolecules

Explore the chemical composition of living organisms and understand the structure and function of biomolecules that make life possible.

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Chapter Overview

Brief Introduction

Biomolecules are the chemical compounds found in living organisms. This chapter explores the diversity of biomolecules, from small molecules like amino acids and sugars to macromolecules like proteins and nucleic acids. We'll examine their structure, classification, and vital functions in biological systems.

Learning Objectives

• Understand the chemical composition of living tissues
• Learn about primary and secondary metabolites
• Study the structure and function of biomacromolecules
• Comprehend protein structure and enzyme action
• Explore the classification and properties of carbohydrates, lipids, and nucleic acids

Key Topics Covered

• Chemical analysis of living tissues
• Primary and secondary metabolites
• Proteins and their structure
• Polysaccharides and carbohydrates
• Nucleic acids
• Enzymes and their action
• Classification of biomolecules
• Composition of cells

Interactive Chapter Index

Chemical Composition

Explore how to analyze the chemical composition of living tissues and compare it with non-living matter.

Primary & Secondary Metabolites

Learn about the different types of metabolites found in living organisms and their functions.

Biomacromolecules

Understand the classification of biomolecules based on their molecular weight and properties.

Proteins

Discover the structure and functions of proteins, the most diverse biomacromolecules.

Polysaccharides

Study the structure and roles of polysaccharides in energy storage and structural support.

Enzymes

Learn about enzyme structure, classification, and how they catalyze biochemical reactions.

Full Chapter Notes

9.1 How to Analyse Chemical Composition?

All living organisms are made up of similar chemical elements, but the relative abundance of carbon and hydrogen is higher in living matter compared to non-living matter like earth's crust.

Chemical Analysis Process:

1. Take living tissue (vegetable, liver, etc.) and grind it in trichloroacetic acid
2. Filter through cheesecloth to obtain two fractions:
   • Acid-soluble pool (filtrate)
   • Acid-insoluble fraction (retentate)
3. For inorganic analysis:
   • Weigh living tissue (wet weight)
   • Dry it to get dry weight
   • Burn it completely to get ash containing inorganic elements

Element	% Weight of Earth's crust	% Weight of Human body
Hydrogen (H)	0.14	0.5
Carbon (C)	0.03	18.5
Oxygen (O)	46.6	65.0
Nitrogen (N)	very little	3.3
Sulphur (S)	0.03	0.3

Q: Why is the relative abundance of carbon and hydrogen higher in living organisms compared to non-living matter?

A: The higher relative abundance of carbon and hydrogen in living organisms is because:

1. Carbon forms the backbone of all organic molecules due to its tetravalency and ability to form stable covalent bonds
2. Most biomolecules are hydrocarbons or their derivatives (proteins, carbohydrates, lipids, nucleic acids)
3. Water (H₂O), which makes up 70-90% of cellular mass, contributes to hydrogen content
4. Carbon's ability to form diverse molecules enables the complexity required for life

9.2 Primary and Secondary Metabolites

Metabolites are biomolecules that can be classified into primary and secondary metabolites based on their functions in the organism.

Primary Metabolites:

• Have identifiable functions in normal physiological processes
• Found in all living organisms
• Examples: Amino acids, sugars, fatty acids, glycerol, nucleotides
• Essential for basic metabolic processes like respiration, digestion

Secondary Metabolites:

• Found mainly in plants, fungi and microbes
• Functions not always clearly understood
• Often useful for human welfare
• Examples: Alkaloids, flavonoids, rubber, essential oils, antibiotics

Type	Examples
Pigments	Carotenoids, Anthocyanins
Alkaloids	Morphine, Codeine
Terpenoides	Monoterpenes, Diterpenes
Essential oils	Lemon grass oil
Toxins	Abrin, Ricin

Q: What is the main difference between primary and secondary metabolites?

A: The main differences are:

Primary Metabolites	Secondary Metabolites
Found in all living organisms	Found mainly in plants, fungi and microbes
Have known physiological functions	Functions not always clearly understood
Essential for basic metabolic processes	Often involved in defense, attraction, or other ecological interactions
Examples: Glucose, amino acids	Examples: Morphine, rubber

9.3 Biomacromolecules

Biomolecules can be classified based on their molecular weight into micromolecules and macromolecules.

Classification of Biomolecules:

• Micromolecules (Biomolecules):
  • Molecular weight less than 1000 Da
  • Found in acid-soluble pool
  • Examples: Amino acids, sugars, nucleotides, fatty acids
• Macromolecules (Biomacromolecules):
  • Molecular weight 10,000 Da and above
  • Found in acid-insoluble fraction
  • Examples: Proteins, nucleic acids, polysaccharides, lipids

Note: Lipids have molecular weight less than 800 Da but are found in acid-insoluble fraction because they are arranged into membrane structures that form vesicles during tissue grinding.

Component	% of the total cellular mass
Water	70-90
Proteins	10-15
Carbohydrates	3
Lipids	2
Nucleic acids	5-7
Ions	1

Q: Why are lipids considered macromolecules even though their molecular weight is less than 800 Da?

A: Lipids are considered macromolecules because:

1. They are arranged into structures like cell membranes and other membranes
2. When tissue is ground, these membrane fragments form vesicles that are not water soluble
3. The vesicles get separated along with the acid-insoluble pool
4. Although individual lipid molecules are small, they function as part of larger structural complexes
5. Their behavior during chemical analysis is similar to other macromolecules

9.4 Proteins and 9.7 Structure of Proteins

Proteins are polypeptides - linear chains of amino acids linked by peptide bonds. They are heteropolymers made of 20 types of amino acids.

Protein Structure Levels:

1. Primary Structure: The sequence of amino acids in a polypeptide chain
2. Secondary Structure: Local folding into structures like α-helix or β-pleated sheet
3. Tertiary Structure: Three-dimensional folding of the entire polypeptide chain
4. Quaternary Structure: Arrangement of multiple polypeptide chains (subunits)

Figure: Four levels of protein structure

Protein	Functions
Collagen	Intercellular ground substance
Trypsin	Enzyme
Insulin	Hormone
Antibody	Fights infectious agents
GLUT-4	Enables glucose transport into cells

Q: What is the difference between essential and non-essential amino acids?

A: The differences are:

• Essential amino acids:
  • Cannot be synthesized by the human body
  • Must be obtained through diet
  • Examples: Valine, leucine, isoleucine, lysine, etc.
• Non-essential amino acids:
  • Can be synthesized by the human body
  • Not required in diet (but still important)
  • Examples: Alanine, glycine, serine, etc.
• There are 9 essential amino acids and 11 non-essential amino acids for humans
• The classification is based on human metabolic capabilities, not the importance of the amino acids

9.5 Polysaccharides

Polysaccharides are long chains of sugars (carbohydrates) and are another class of macromolecules found in the acid-insoluble fraction.

Types of Polysaccharides:

• Cellulose:
  • Polymer of glucose
  • Homopolymer
  • Structural component of plant cell walls
• Starch:
  • Storage form of energy in plants
  • Forms helical structures that can hold I₂ molecules (blue color)
  • Variant of cellulose
• Glycogen:
  • Storage form in animals
  • Highly branched structure
  • Stored in liver and muscles
• Chitin:
  • Complex polysaccharide in exoskeletons of arthropods
  • Contains amino-sugars

Figure: Structures of common polysaccharides

Q: What is the difference between the reducing end and non-reducing end of a polysaccharide chain?

A: The differences are:

• Reducing end:
  • The right end of the polysaccharide chain
  • Has a free anomeric carbon (C1 of glucose)
  • Can reduce certain reagents (hence the name)
  • Can participate in redox reactions
• Non-reducing end:
  • The left end of the polysaccharide chain
  • Does not have a free anomeric carbon
  • Cannot reduce reagents
  • Terminated by a non-reducing sugar
• In glycogen, the non-reducing ends are where glucose units are added or removed during metabolism

9.8 Enzymes

Enzymes are proteins (except ribozymes which are RNA) that catalyze biochemical reactions with high specificity and efficiency.

Enzyme Characteristics:

• Have an active site where substrate binds
• Lower activation energy of reactions
• Highly specific for their substrates
• Not consumed in the reaction
• Work best at optimal temperature and pH
• Can be regulated by inhibitors and activators

Figure: Mechanism of enzyme action

Enzyme Classification:

1. Oxidoreductases/dehydrogenases: Catalyze oxidation-reduction reactions
2. Transferases: Transfer functional groups between molecules
3. Hydrolases: Catalyze hydrolysis reactions (break bonds with water)
4. Lyases: Remove groups to form double bonds or add groups to double bonds
5. Isomerases: Rearrange atoms in a molecule to form isomers
6. Ligases: Join two molecules with covalent bonds using ATP energy

Example: Carbonic anhydrase catalyzes the reaction: CO₂ + H₂O ⇌ H₂CO₃. Without enzyme: ~200 molecules/hour. With enzyme: ~600,000 molecules/second - a 10 million-fold increase in rate!

Q: How do enzymes lower the activation energy of a reaction?

A: Enzymes lower activation energy through several mechanisms:

1. Orienting substrates: Properly positioning substrates for reaction
2. Straining bonds: Distorting substrate bonds to make them easier to break
3. Providing alternative pathways: Creating different transition states with lower energy requirements
4. Microenvironment: Active site provides optimal conditions (pH, charge distribution)
5. Covalent catalysis: Temporary covalent bonds between enzyme and substrate
6. Acid-base catalysis: Donating or accepting protons at the active site

This reduction in activation energy allows reactions to proceed much faster at biological temperatures.

Chapter Summary

Key Takeaways:

• Living organisms have higher relative abundance of carbon and hydrogen compared to non-living matter
• Biomolecules can be classified as micromolecules (small) and macromolecules (large)
• Primary metabolites have known functions while secondary metabolites are often specialized compounds
• Proteins have four levels of structure and perform diverse functions
• Polysaccharides serve as energy stores (starch, glycogen) and structural components (cellulose, chitin)
• Enzymes are biological catalysts that lower activation energy and increase reaction rates dramatically
• Water is the most abundant component of living cells (70-90% of cellular mass)

NCERT Solutions

Question 1: What are macromolecules? Give examples.

Macromolecules are large complex molecules with molecular weights of 10,000 daltons or more that are found in the acid-insoluble fraction of living tissues. They are typically polymers made of repeating subunits.

Examples:

• Proteins: Polymers of amino acids (e.g., hemoglobin, collagen)
• Nucleic acids: Polymers of nucleotides (DNA, RNA)
• Polysaccharides: Polymers of monosaccharides (starch, cellulose, glycogen)
• Lipids: Although not strictly macromolecules (MW < 800 Da), they are included due to their membrane organization

Question 2: What is meant by tertiary structure of proteins?

The tertiary structure of a protein refers to the overall three-dimensional shape of a single polypeptide chain, formed by further folding of the secondary structures (α-helices and β-pleated sheets).

Key features:

• Results from interactions between R groups of amino acids
• Stabilized by various bonds:
  • Hydrogen bonds
  • Disulfide bridges (between cysteine residues)
  • Ionic interactions
  • Hydrophobic interactions
  • Van der Waals forces
• Gives the protein its functional shape
• Essential for biological activity of the protein
• Example: Myoglobin has a compact tertiary structure with a heme group pocket

Question 5: Explain the composition of triglyceride.

A triglyceride (also called triacylglycerol) is composed of:

1. Glycerol backbone: A 3-carbon alcohol with a hydroxyl group (-OH) on each carbon
2. Three fatty acids: Long hydrocarbon chains with a carboxyl group (-COOH) at one end

Formation:

• Each of glycerol's three hydroxyl groups forms an ester bond with the carboxyl group of a fatty acid
• This is a condensation reaction (releases three water molecules)

Types:

• Simple triglycerides: All three fatty acids are identical
• Mixed triglycerides: Two or three different fatty acids
• Saturated: All fatty acids have no double bonds (solid at room temp)
• Unsaturated: One or more fatty acids have double bonds (liquid at room temp)

Function: Main storage form of fat in adipose tissue, providing energy and insulation.

Question 7: Draw the structure of the amino acid, alanine.

The structure of alanine (an α-amino acid) is:

Figure: Structure of alanine

Key features:

• Central α-carbon (chiral center)
• Amino group (-NH₂) and carboxyl group (-COOH) attached to α-carbon
• R group (side chain) for alanine is -CH₃ (methyl group)
• At physiological pH, exists as zwitterion (NH₃⁺ and COO⁻)
• Non-polar, aliphatic amino acid
• Non-essential amino acid (can be synthesized by human body)

Question 11: Describe the important properties of enzymes.

Important properties of enzymes:

1. Catalytic efficiency: Enzymes greatly increase reaction rates (typically 10⁶ to 10¹² times faster than uncatalyzed reactions)
2. Specificity: Each enzyme typically catalyzes only one specific reaction or type of reaction
3. Active site: Contains a specific region where substrate binds and reaction occurs
4. Optimum conditions: Each enzyme works best at specific temperature and pH
5. Regulation: Enzyme activity can be regulated by:
   • Inhibitors (competitive, non-competitive)
   • Activators
   • Feedback inhibition
   • Allosteric regulation
6. Reusability: Enzymes are not consumed in reactions
7. Lower activation energy: Enzymes reduce the energy barrier for reactions
8. Protein nature: Most enzymes are proteins (except ribozymes which are RNA)
9. Formation of enzyme-substrate complex: Temporary ES complex forms during catalysis
10. Denaturation: Lose activity at high temperatures or extreme pH due to loss of tertiary structure

Practice Questions

1. Which of the following is not a macromolecule?

a) Protein b) Nucleic acid c) Polysaccharide d) Amino acid

Correct Answer: d) Amino acid

Explanation: Amino acids are the monomeric units of proteins (which are macromolecules) but are themselves small molecules with molecular weights less than 1000 Da. The other options - proteins, nucleic acids, and polysaccharides - are all macromolecules with molecular weights typically above 10,000 Da.

2. The most abundant protein in the biosphere is:

a) Collagen b) Hemoglobin c) RuBisCO d) Insulin

Correct Answer: c) RuBisCO

Explanation: Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO) is the most abundant protein in the biosphere because it catalyzes the first major step of carbon fixation in photosynthesis, a process occurring in all green plants. While collagen is the most abundant protein in animals, RuBisCO's universal presence in photosynthetic organisms makes it the most abundant overall.

3. Which level of protein structure is stabilized by disulfide bonds?

a) Primary b) Secondary c) Tertiary d) Quaternary

Correct Answer: c) Tertiary

Explanation: Disulfide bonds (between cysteine residues) are covalent bonds that help stabilize the tertiary structure of proteins. While they can also occur between different polypeptide chains in quaternary structure, the primary stabilization is at the tertiary level. Primary structure is the amino acid sequence (peptide bonds), and secondary structure involves hydrogen bonds forming α-helices and β-sheets.

1. What are the differences between primary and secondary metabolites?

Answer:

Primary Metabolites	Secondary Metabolites
Involved in normal growth, development and reproduction	Not directly involved in normal growth and development
Found in all living organisms	Found mainly in plants, fungi and microbes
Have identifiable metabolic functions	Functions often not clearly understood
Examples: Amino acids, sugars, nucleotides	Examples: Alkaloids, flavonoids, rubber

2. Explain why lipids are found in the acid-insoluble fraction despite having molecular weight less than 800 Da.

Answer:

Lipids are found in the acid-insoluble fraction because:

1. They are arranged into membrane structures in cells (cell membrane, organelle membranes)
2. When tissue is ground, these membranes break into vesicles that are not water-soluble
3. The membrane fragments form part of the acid-insoluble pellet during centrifugation
4. Although individual lipid molecules are small (MW < 800 Da), they are organized into larger macromolecular complexes
5. Their hydrophobic nature makes them insoluble in the aqueous acid solution

Thus, lipids behave like macromolecules in the fractionation process even though their individual molecular weights are below the typical macromolecule range.

1. Describe the four levels of protein structure with examples.

Answer:

Proteins have four levels of structural organization:

1. Primary Structure:

• The linear sequence of amino acids in a polypeptide chain
• Determined by peptide bonds between carboxyl and amino groups
• Example: The specific sequence of 574 amino acids in hemoglobin β-chain

2. Secondary Structure:

• Local folding of polypeptide chain into regular structures
• Main types:
  • α-helix: Right-handed coil stabilized by hydrogen bonds between every 4th amino acid (e.g., keratin)
  • β-pleated sheet: Zigzag structure with hydrogen bonds between adjacent strands (e.g., silk fibroin)

3. Tertiary Structure:

• Three-dimensional folding of the entire polypeptide chain
• Stabilized by interactions between R groups:
  • Hydrogen bonds
  • Ionic bonds
  • Hydrophobic interactions
  • Disulfide bridges (covalent S-S bonds)
• Example: Myoglobin's compact globular structure with heme pocket

4. Quaternary Structure:

• Arrangement of multiple polypeptide chains (subunits)
• Stabilized by same interactions as tertiary structure
• Example: Hemoglobin with 4 subunits (2 α and 2 β chains)

2. Explain the mechanism of enzyme action with reference to activation energy.

Answer:

Enzymes catalyze reactions by lowering the activation energy required for the reaction to proceed:

1. Activation Energy Concept:

• Activation energy is the energy barrier that must be overcome for reactants to convert to products
• Even exergonic (energy-releasing) reactions require some initial energy input
• Enzymes provide an alternative pathway with lower activation energy

2. Mechanism of Enzyme Action:

1. Substrate Binding: Substrate binds to enzyme's active site, forming enzyme-substrate (ES) complex
2. Induced Fit: Enzyme changes shape to better fit substrate, stressing critical bonds
3. Transition State Stabilization: Enzyme stabilizes the high-energy transition state, lowering its energy
4. Product Formation: Reaction occurs, converting substrate to product
5. Product Release: Products are released, enzyme returns to original state

3. Ways Enzymes Lower Activation Energy:

• Orienting substrates: Proper positioning increases likelihood of effective collisions
• Straining bonds: Distorting substrate bonds makes them easier to break
• Providing favorable microenvironment: Active site may have different pH or charge distribution
• Covalent catalysis: Temporary covalent bonds between enzyme and substrate
• Acid-base catalysis: Donating or accepting protons

Example: Carbonic anhydrase increases the rate of CO₂ + H₂O ⇌ H₂CO₃ reaction by 10 million times by lowering the activation energy barrier.

Interactive Flashcards

What are the four levels of protein structure?

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1. Primary: Amino acid sequence
2. Secondary: Local folding (α-helix, β-sheet)
3. Tertiary: 3D structure of entire polypeptide
4. Quaternary: Arrangement of multiple subunits

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