Biomolecules

How to Analyse Chemical Composition?

Biomolecules in Living Organisms & their Analysis

• Living organisms are made of various elements and compounds.
• Elements in living organisms include carbon, hydrogen, and oxygen.
• These elements are also found in non-living things like the earth’s crust.
• Carbon and hydrogen are more abundant in living organisms than in the earth’s crust.
• To find out what organic compounds are in living organisms, we do a chemical analysis.

Steps for Chemical Analysis:

1. Take a living tissue (like a vegetable or liver).
2. Grind it with trichloroacetic acid (Cl₃CCOOH) using a mortar and pestle.
3. Strain the mixture through cheesecloth or cotton to get two parts:
   • Filtrate (acid-soluble pool)
   • Retentate (acid-insoluble fraction)
4. Scientists find thousands of organic compounds in the filtrate.

Identifying Compounds:

• Extract compounds from the tissue.
• Use separation techniques to isolate and purify the compounds.
• Analytical techniques help determine the molecular formula and structure.

Biomolecules:

• Organic compounds from living tissues are called ‘biomolecules.’
• Living organisms also have inorganic elements and compounds.

Finding Inorganic Elements:

1. Weigh a small amount of living tissue (wet weight).
2. Dry it to remove all water (dry weight).
3. Burn it to oxidize all carbon compounds to gas.
4. The remaining material (ash) contains inorganic elements like calcium and magnesium.

Organic and Inorganic Compounds:

• Elemental analysis shows the composition of living tissues (hydrogen, oxygen, chlorine, carbon, etc.).
• Compound analysis shows organic (like amino acids, nucleotide bases, fatty acids) and inorganic constituents.

Examples:

• Organic Compounds: Amino acids, nucleotide bases, fatty acids.
• Inorganic Elements: Calcium, magnesium.
• Inorganic Compounds: Sulphate, phosphate.

1. Amino Acids

• Organic compounds with an amino group and an acidic group on the same carbon (α-carbon).
• Called α-amino acids; they are substituted methanes.
• Four groups attached to α-carbon: hydrogen, carboxyl group, amino group, and a variable R group.
• 20 types of amino acids in proteins.
• Examples:
  • Glycine: R group is hydrogen.
  • Alanine: R group is a methyl group.
  • Serine: R group is hydroxy methyl.
• Properties depend on amino, carboxyl, and R groups.
• Types:
  • Acidic: e.g., Glutamic acid.
  • Basic: e.g., Lysine.
  • Neutral: e.g., Valine.
  • Aromatic: e.g., Tyrosine, Phenylalanine, Tryptophan.
• Amino acids can ionize in solutions of different pH levels.

2. Lipids

• Generally water-insoluble.
• Can be simple fatty acids or glycerol-based.
• Fatty acids have a carboxyl group and an R group (1 to 19 carbons).
  • Examples:
    • Palmitic acid: 16 carbons.
    • Arachidonic acid: 20 carbons.
• Saturated (no double bonds) or unsaturated (one or more double bonds).
• Glycerol is trihydroxy propane.
• Fatty acids esterified with glycerol form monoglycerides, diglycerides, and triglycerides (fats and oils).
• Oils have lower melting points (e.g., gingelly oil).
• Phospholipids contain phosphorus and are found in cell membranes (e.g., Lecithin).
• Complex lipids found in neural tissues.

3. Nucleotides and Nucleic Acids

• Carbon compounds with heterocyclic rings include nitrogen bases.
  • Examples: Adenine, Guanine, Cytosine, Uracil, Thymine.
• Nitrogen bases attached to sugar are nucleosides.
  • Examples: Adenosine, Guanosine, Thymidine, Uridine, Cytidine.
• Nucleosides with a phosphate group become nucleotides.
  • Examples: Adenylic acid, Thymidylic acid, Guanylic acid, Uridylic acid, Cytidylic acid.
• DNA and RNA are nucleic acids made of nucleotides.
• DNA and RNA function as genetic material.

Primary and Secondary Metabolites

Metabolites

• Biomolecules in living organisms are called metabolites.
• Thousands of organic compounds like amino acids and sugars are metabolites.

Primary Metabolites

• Found in animal tissues.
• Include amino acids, sugars, and other essential compounds.
• Have identifiable functions in normal physiological processes.

Secondary Metabolites

• Found in plant, fungal, and microbial cells.
• Include alkaloids, flavonoids, rubber, essential oils, antibiotics, colored pigments, scents, gums, and spices.
• Roles in host organisms are not fully understood.
• Many are useful to humans (e.g., rubber, drugs, spices, scents, pigments).
• Some have ecological importance.

Examples of Secondary Metabolites:

• Alkaloids: Used in medicine.
• Flavonoids: Found in fruits and vegetables.
• Rubber: Used in tires and other products.
• Essential Oils: Used in perfumes and aromatherapy.
• Antibiotics: Used to treat infections.
• Colored Pigments: Found in flowers and fruits.
• Scents: Found in flowers.
• Gums and Spices: Used in cooking and industry.

Key Points

• Primary metabolites are essential for normal physiological functions.
• Secondary metabolites have varied uses and ecological roles.

Biomacromolecules

Types of Compounds

• Compounds in the acid-soluble pool have molecular weights of 18 to 800 daltons (Da).
• Acid-insoluble fraction contains four types of organic compounds:
  • Proteins
  • Nucleic acids
  • Polysaccharides
  • Lipids
• Except for lipids, these compounds have molecular weights over 10,000 Da.

Micromolecules vs. Macromolecules

• Micromolecules:
  • Molecular weight less than 1,000 Da.
  • Found in the acid-soluble pool.
• Macromolecules (Biomacromolecules):
  • Found in the acid-insoluble fraction.
  • Include proteins, nucleic acids, and polysaccharides.

Lipids

• Lipids have molecular weights under 800 Da.
• Present in the acid-insoluble fraction because they form structures like cell membranes.
• When cells are ground, membranes break into vesicles, which are not water-soluble.
• These vesicles get separated with the acid-insoluble pool.

Chemical Composition of Living Tissues

• Acid-soluble pool represents the cytoplasmic composition.
• Macromolecules from cytoplasm and organelles form the acid-insoluble fraction.
• Together, they represent the entire chemical composition of living tissues.

Abundance in Living Organisms

• Water is the most abundant chemical in living organisms.

Key Points

• Biomolecules are either micromolecules (small) or macromolecules (large).
• Proteins, nucleic acids, and polysaccharides are macromolecules.
• Lipids, although small, form part of the macromolecular fraction due to their structural roles.
• Water is the most common chemical in living organisms.

Proteins

• Polypeptides: Proteins are long chains of amino acids linked by peptide bonds.
• Amino Acids: There are 20 types, such as alanine, cysteine, proline, tryptophan, and lysine.
• Heteropolymer: Proteins are heteropolymers with different amino acids, unlike homopolymers with one repeating monomer.
• Essential vs. Non-essential Amino Acids:
  • Essential amino acids must be obtained from the diet.
  • Non-essential amino acids are made by the body.
• Functions: Proteins transport nutrients, fight infections, act as hormones and enzymes.
• Examples:
  • Collagen: Most abundant in animals.
  • RuBisCO: Most abundant in the biosphere.

Polysaccharides

• Macromolecules: Long chains of sugars, also known as carbohydrates.
• Structure: Resemble threads, made of monosaccharide building blocks.
• Examples:
  • Cellulose: Made of glucose, a homopolymer, found in plant cell walls.
  • Starch: Energy storage in plants, forms helical structures.
  • Glycogen: Energy storage in animals, has branches.
  • Inulin: Polymer of fructose.
• Reducing and Non-reducing Ends: The right end of a polysaccharide chain is the reducing end, and the left is the non-reducing end.
• Complex Polysaccharides: Include amino-sugars and modified sugars.
  • Chitin: Found in the exoskeletons of arthropods.

Nucleic Acids

• A Macromolecules: Found in the acid-insoluble fraction.
• Polynucleotides: Nucleic acids are long chains of nucleotides.
• Nucleotide Components:
  • Heterocyclic Compound: Nitrogenous bases (adenine, guanine, uracil, cytosine, thymine).
  • Monosaccharide: Ribose or deoxyribose.
  • Phosphoric Acid/Phosphate
• Types:
  • DNA (Deoxyribonucleic Acid): Contains deoxyribose.
  • RNA (Ribonucleic Acid): Contains ribose.

Structure of Proteins

• Heteropolymers: Proteins are made of different amino acids.
• Primary Structure:
  • Sequence: Order of amino acids in a protein chain.
  • Ends: N-terminal (first amino acid) and C-terminal (last amino acid).
• Secondary Structure:
  • Helix: Some parts of the protein chain form a helix (like a spiral staircase).
  • Other Forms: Other parts of the protein chain fold differently.
• Tertiary Structure:
  • 3D Shape: Protein chain folds into a 3D shape, essential for function.
• Quaternary Structure:
  • Subunits: Some proteins have multiple polypeptide subunits.
  • Example: Hemoglobin has 4 subunits (2 α and 2 β).

Key Points

• Proteins are essential for many functions in the body and are made of different amino acids.
• Polysaccharides are important for energy storage and structure in plants and animals.
• Nucleic acids are essential macromolecules made of nucleotides.
• Proteins have complex structures that determine their function.
• Protein structure levels: primary (sequence), secondary (helices and folds), tertiary (3D shape), quaternary (subunits).
• Hemoglobin is an example of a protein with quaternary structure.

Nature of Bonds Linking Monomers in a Polymer

• Polypeptides/Proteins:
  • Peptide Bond: Links amino acids.
  • Formation: Carboxyl group (-COOH) of one amino acid reacts with amino group (-NH2) of the next, releasing water (dehydration).
• Polysaccharides:
  • Glycosidic Bond: Links monosaccharides.
  • Formation: Dehydration between two carbon atoms of adjacent monosaccharides.
• Nucleic Acids:
  • Phosphodiester Bond: Links nucleotides.
  • Formation: Phosphate group links 3’-carbon of one sugar to 5’-carbon of the next sugar.
• DNA Structure (Watson-Crick Model):
  • Double Helix: Two strands of polynucleotides run in opposite directions.
  • Backbone: Sugar-phosphate-sugar chain.
  • Base Pairing: Adenine (A) pairs with Thymine (T) (2 hydrogen bonds), Guanine (G) pairs with Cytosine (C) (3 hydrogen bonds).
  • Helix Details:
    • Each step: Pair of bases.
    • 36° turn per step.
    • 10 steps/base pairs per full turn.
    • Pitch: 34Å.
    • Rise per base pair: 3.4Å.
  • Form: B-DNA (most common).

Key Points

• Monomers in polymers (proteins, polysaccharides, nucleic acids) are linked by specific bonds formed through dehydration.
• DNA structure is a double helix with specific base pairing (A-T, G-C).

Dynamic State of Body Constituents – Concept of Metabolism

• Biomolecules: Thousands of organic compounds present in living organisms.
• Turnover: Biomolecules are constantly being transformed into other biomolecules and made from others.
• Metabolism:
  • All chemical reactions occurring in living organisms.
  • Examples:
    • Removal of CO2 from amino acids.
    • Removal of amino group from nucleotide base.
    • Hydrolysis of glycosidic bond in disaccharides.
• Metabolic Pathways:
  • Series of Linked Reactions: Metabolites are converted in sequences (linear or circular).
  • Flow of Metabolites: Definite rate and direction, like traffic.
  • Dynamic State: Smooth and efficient interlinked metabolic traffic.
• Catalysis:
  • All metabolic reactions are catalysed.
  • Catalysts are proteins called enzymes.
  • Even simple processes like CO2 dissolving in water are catalysed.

Key Points

• Metabolism involves continuous transformation of biomolecules via catalysed reactions.
• Metabolic pathways ensure efficient and smooth flow of metabolites.

Metabolic Basis for Living

Metabolic Pathways

• Anabolic Pathways (Biosynthetic)
  • Build complex structures from simpler ones.
  • Example: Acetic acid becomes cholesterol.
  • Consume energy.
  • Example: Building proteins from amino acids needs energy.
• Catabolic Pathways (Degradation)
  • Break down complex structures into simpler ones.
  • Example: Glucose becomes lactic acid in muscles.
  • Release energy.
  • Example: Energy is released when glucose breaks down into lactic acid through glycolysis (10 steps).

Energy in Living Organisms

• Energy is stored in chemical bonds, especially in ATP (Adenosine Triphosphate).
• This stored energy is used for:
  • Biosynthetic work (making new compounds).
  • Osmotic work (controlling fluid balance).
  • Mechanical work (movement and other physical activities).

Bioenergetics

• The study of how living organisms get, store, and use energy.
• You will learn more about this in higher classes.

The Living State

Biomolecules and Metabolites

• Living organisms have many chemical compounds called metabolites or biomolecules.
• Each biomolecule has a specific concentration:
  • Example: Blood glucose level is 4.5-5.0 mM.
  • Hormones are present in tiny amounts (nanograms/mL).

Steady-State vs. Equilibrium

• Living organisms exist in a steady-state, not at equilibrium.
• Equilibrium means no work can be done, but living things must always work.
• To stay in a steady-state and do work, energy input is required.
• Metabolism provides the energy needed.
• Key point: Metabolism is essential for the living state; without it, life wouldn’t exist.

Enzymes

What Are Enzymes?

• Almost all enzymes are proteins.
• Some nucleic acids act as enzymes, called ribozymes.
• Enzymes have a complex structure:
  • Primary Structure: Sequence of amino acids.
  • Secondary and Tertiary Structure: Protein chain folds and creates pockets.

Active Site

• A pocket in the enzyme where the substrate fits.
• Enzymes use their active sites to speed up reactions.

Enzymes vs. Inorganic Catalysts

• Inorganic catalysts work well at high temperatures and pressures.
• Enzymes can be damaged at high temperatures (above 40°C).
• Enzymes from organisms in hot environments (like hot springs) are stable at high temperatures (up to 80°-90°C).

Chemical Reactions

Types of Changes in Chemical Compounds

• Physical Change: Shape changes without breaking bonds (e.g., ice melting).
• Chemical Reaction: Bonds are broken and new ones are formed (e.g., Ba(OH)₂ + H₂SO₄ → BaSO₄ + 2H₂O).

Reaction Rate

• The amount of product formed per unit time.
• Affected by temperature (rate doubles or halves with every 10°C change).
• Enzyme-catalyzed reactions are much faster than uncatalyzed ones.

Example of Enzyme Action

• Without enzyme: CO₂ + H₂O → H₂CO₃ (slow, 200 molecules/hour).
• With enzyme (carbonic anhydrase): Reaction speeds up to 600,000 molecules/second.

Metabolic Pathways

• Multi-step reactions where each step is catalyzed by enzymes.
• Example: Glucose → 2 Pyruvic acid through ten enzyme-catalyzed steps.
• Different conditions produce different products:
  • Anaerobic (no oxygen) in muscles: Lactic acid.
  • Aerobic (with oxygen): Pyruvic acid.
  • In yeast (fermentation): Ethanol (alcohol).

How Do Enzymes Speed Up Chemical Reactions?

• Active Site: The part of the enzyme where the substrate fits.
• Substrate (S): The chemical that is converted into a product (P) by the enzyme.
• Enzyme-Substrate Complex (ES): When the substrate binds to the enzyme.
  • This binding is temporary and forms a new structure called the transition state.
  • After the reaction, the product is released from the active site.

Transition State and Activation Energy

• Transition State: A high-energy state that the substrate must go through to become the product.
• Activation Energy: The energy needed to reach the transition state.
• Enzymes lower the activation energy, making it easier for the reaction to happen.

Nature of Enzyme Action

Catalytic Cycle of Enzyme Action

1. Binding: Substrate binds to the enzyme’s active site.
2. Induced Fit: The enzyme changes shape to fit the substrate more tightly.
3. Reaction: The enzyme breaks the substrate’s bonds and forms the enzyme-product complex (EP).
4. Release: The enzyme releases the product and is ready to start the cycle again with a new substrate.

Key Points

• Enzymes are proteins with specific three-dimensional structures.
• They speed up reactions by lowering the activation energy.
• The enzyme’s active site is crucial for binding substrates and catalyzing reactions.
• Enzymes are reusable; they are not changed by the reactions they catalyze.

Factors Affecting Enzyme Activity

Temperature and pH

• Enzymes work best at a specific temperature and pH (optimum).
• Activity decreases if the temperature or pH is too high or too low.
  • Low temperatures make enzymes inactive temporarily.
  • High temperatures can denature (destroy) enzymes.

Substrate Concentration

• Increasing substrate concentration initially increases reaction speed.
• Maximum velocity (Vmax) is reached when all enzyme molecules are occupied.
• No further increase in reaction speed after Vmax, even if more substrate is added.

Inhibitors

• Inhibitors: Chemicals that decrease enzyme activity.
  • Competitive Inhibitors: Resemble the substrate and compete for the active site.
  • Example: Malonate inhibits succinic dehydrogenase by resembling succinate.

Classification and Nomenclature of Enzymes

Enzyme Classes

• Enzymes are grouped based on the reactions they catalyze. There are six main classes:

1. Oxidoreductases (Dehydrogenases)
   • Catalyze oxidation-reduction reactions.
   • Example: S reduced + S’ oxidized → S oxidized + S’ reduced.
2. Transferases
   • Transfer a group (not hydrogen) between molecules.
   • Example: S – G + S’ → S + S’ – G.
3. Hydrolases
   • Catalyze hydrolysis (breaking bonds with water).
   • Example: Breaking ester, ether, peptide, or glycosidic bonds.
4. Lyases
   • Remove groups from molecules without hydrolysis, forming double bonds.
5. Isomerases
   • Catalyze the conversion of isomers (same formula, different structure).
6. Ligases
   • Join two molecules together.
   • Example: Catalyze the formation of bonds like C-O, C-S, C-N, P-O.

Each enzyme class has subclasses and is named with a four-digit number for specific identification.

Co-factors

• Enzymes sometimes need non-protein helpers called co-factors to be active.
• The protein part of an enzyme is called the apoenzyme.

Types of Co-factors

1. Prosthetic Groups
   • Tightly bound to the apoenzyme.
   • Example: Haem in peroxidase and catalase helps break down hydrogen peroxide.
2. Co-enzymes
   • Temporarily bind to the apoenzyme during catalysis.
   • Can assist in various enzyme reactions.
   • Often made from vitamins.
   • Example: NAD and NADP contain the vitamin niacin.
3. Metal Ions
   • Form bonds with the enzyme’s active site and the substrate.
   • Example: Zinc is a co-factor for the enzyme carboxypeptidase.

• Enzymes lose their catalytic activity if the co-factor is removed, showing how essential co-factors are for enzyme function.

Chapter Summary:

• Living organisms have diverse forms but similar chemical composition and metabolic reactions.
• Living tissues and non-living matter have similar elemental composition qualitatively.
• Carbon, hydrogen, and oxygen are more abundant in living systems.
• Water is the most abundant chemical in living organisms.
• Living organisms have many small biomolecules (<1000 Da).
  • Examples: Amino acids, sugars, fatty acids, glycerol, nucleotides, nucleosides, and nitrogen bases.
  • 20 types of amino acids and 5 types of nucleotides exist.
• Fats and oils are glycerides, with fatty acids esterified to glycerol.
• Phospholipids have a phosphorylated nitrogenous compound.
• Three types of macromolecules in living systems:
  1. Proteins
  2. Nucleic acids (RNA and DNA)
  3. Polysaccharides
• Lipids are associated with membranes and separate in the macromolecular fraction.
• Biomacromolecules are polymers made of different building blocks:
  • Proteins: Heteropolymers of amino acids.
  • Nucleic acids: Composed of nucleotides.
  • Polysaccharides: Cell wall components, exoskeleton of arthropods, and energy storage (starch, glycogen).
• Biomacromolecules have hierarchical structures:
  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Functions of biomacromolecules:
  • Nucleic acids: Genetic material.
  • Polysaccharides: Structural components and energy storage.
  • Proteins: Cellular functions (enzymes, antibodies, receptors, hormones, structural proteins).
• Collagen: Most abundant protein in animals.
• RuBisCO: Most abundant protein in the biosphere.
• Enzymes: Proteins that catalyze biochemical reactions.
  • Ribozymes: Nucleic acids with catalytic power.
  • Enzymes have substrate specificity, optimal temperature, and pH.
  • High temperatures denature enzymes.
  • Enzymes lower activation energy and speed up reactions.
• Nucleic acids: Carry hereditary information, passed from parents to offspring.