Biochemistry Notes for IBPS AFO NABARD

These Biochemistry Notes are essential for IBPS AFO, NABARD, RRB SO, and other agriculture exams. In this post, we have thoroughly covered all the different topics related to biochemistry.

Introduction, Carbohydrates – Importance & Classification

Biochemistry

• Definition: The chemistry of living organisms.
• Living organisms (microorganisms, plants, animals) share the same chemical components.
• Focus: Study of synthesis and utilization of these components in life processes.
• Bridges the gap between conventional chemistry and biology.
• Life: A series of thousands of ordered chemical reactions; chemistry underpins all biological phenomena.

History of Biochemistry

• 17th and 18th centuries: Foundations laid in various fields of biology.
• 19th century:
  • Cell theory: Schleiden and Schwann.
  • Inheritance: Mendel.
  • Evolution: Darwin.
• 1828: Wohler’s synthesis of urea from lead cyanate and ammonia.
• 1857: Louis Pasteur’s work on fermentations; highlighted enzyme importance.
• 1897: Edward Buchner’s enzyme extraction from yeast cells; fermenting sugar into alcohol.
• 1903: Term “biochemistry” introduced by Neuberg.

Advances in the 20th Century

• Early 20th century: Rapid growth in chemical analysis, separation methods, and electronic instrumentation.
• 1926: James Sumner established the protein nature of enzymes; isolated and crystallized urease.
• Glycolytic pathway: Elucidated by Embden and Meyerhof, with contributions from Otto Warburg, Cori, and Parnas.
• 1930-40: Krebs established the citric acid and urea cycles.
• 1940: Lipmann described the central role of ATP in biological systems.
• 1953: Structure of DNA established by Watson and Crick.
• 1956: DNA polymerase discovered by Kornberg.
• 1953: Frederick Sanger’s protein sequencing.
• 1977: Sanger’s nucleic acid sequencing.
• 1980: Development of recombinant DNA research by Snell and coworkers.

Carbohydrates

• Definition: Compounds with the empirical formula (CH2O)n, though variations exist.
• Chemically defined as polyhydroxy aldehydes or ketones, their derivatives, and polymers.

Occurrence and Importance

• Major group of naturally occurring biomolecules.
• Light energy is converted to chemical energy in plants and stored in sugars and carbohydrate derivatives.
• Plant dry substance: 50-80% carbohydrates.
• Structural materials in plants: Cellulose and hemicelluloses.
• Storage polysaccharide in plants: Starch.
• Plant constituents: Pectins and sugars (sucrose, glucose).
• Sugars conjugated with other molecules: Glycosides.
• Animal carbohydrates: Mainly in combination with proteins as glycoproteins.
• Storage form in animals: Glycogen (in liver and muscles).
• Other roles: Blood group substances, mucins, mucopolysaccharides (ground substance between cells).
• Chitin: Found in the exo-skeleton of lower animals; polymer of N-acetyl glucosamine.
• Carbohydrates in polymeric substances: Fats (fatty acid esters of glycerol), ribose, and deoxyribose (nucleic acids).
• Energy sources: Adenosine triphosphate (ATP) and related substances.
• Carbon skeletons: Derived from carbohydrates.
• Industrial importance: Basic raw material for industries like sugar, starch, paper, wood pulp, textiles, plastics, food processing, and fermentation.

Classification of Carbohydrates

1. Monosaccharides
2. Oligosaccharides
3. Polysaccharides

Classification of Carbohydrates

Overview Table

Category	Definition	Properties	Classification	Reducing Nature
Monosaccharides (Simple Sugars)	Low molecular weight carbohydrates that cannot be hydrolyzed further	Crystalline, soluble in water, sweet in taste	Based on number of carbon atoms (triose, tetrose, pentose, hexose, heptose), based on functional group (aldose, ketose)	All are reducing
Oligosaccharides	Contain 2-10 monosaccharides joined by glycosidic bonds	Powdery or crystalline, soluble in water, sweet in taste	Disaccharide, trisaccharide, tetrasaccharide, pentasaccharide	Some are reducing, some are non-reducing
Polysaccharides (Glycans)	Contain many monosaccharides joined by glycosidic bonds	Insoluble in water, tasteless, linear or branched	Based on monosaccharides (homoglycans, heteroglycans), based on function (storage, structural)	Non-reducing; give deep blue (amylose) or red color (amylopectin) with iodine

Detailed Classification of Monosaccharides

Type	Number of Carbon Atoms	Aldose	Ketose	Occurrence
Simple Monosaccharides
Triose	3	D-Glycerose	Dihydroxyacetone	Intermediary metabolites in glucose metabolism
Tetrose	4	D-Erythrose	D-Erythrulose
Pentose	5	D-Ribose, L-Arabinose, D-Xylose	D-Ribulose, D-Xylulose	Ribose (nucleic acids), L-Arabinose (oligosaccharides), D-Xylose (gum arabic, cherry gums, wood gums, proteoglycans)
Hexose	6	D-Glucose, D-Galactose, D-Mannose	D-Fructose	D-Glucose (fruit juices, cane sugar), D-Galactose (lactose, lipids), D-Mannose (plant mannosans, glycoproteins)
Heptose	7	–	D-Sedoheptulose	Intermediate in carbohydrate metabolism
Derived Monosaccharides
Deoxysugar	5	2-Deoxyribose	–	DNA
Deoxysugar	6	L-Rhamnose	–	Component of cell wall
Aminosugar	6	D-Glucosamine	–	Major component of polysaccharide (chitin)
Polyol	6	Sorbitol	–	Berries
Polyol	6	Mannitol	–	Commercially prepared from mannose and fructose
Aldonic acid	6	Gluconic acid	–
Uronic acid	6	Glucuronic acid	–	Constituent of chondroitin sulfate
Uronic acid	6	Galacturonic acid	–	Constituent of pectin
Aldaric acid (Saccharic acid)	6	Glucaric acid	–	Oxidation product of glucose
Aldaric acid (Saccharic acid)	6	Mucic acid	–	Oxidation product of galactose

Classification of Polysaccharides

Category	Type	Examples
Homopolysaccharides	Made from a single kind of monosaccharide	Starch, cellulose, inulin, glycogen, chitin
Heteropolysaccharides	Made from more than one type of monosaccharide	Hemicellulose, Mucopolysaccharides (Chondroitin sulfate, Hyaluronic acid, Heparin, Keratan sulfate)
Storage Polysaccharides	–	Starch, glycogen, inulin, galactomannan
Structural Polysaccharides	–	Cellulose, chitin, hemicellulose

 

Plant Fatty Acids

 

Fatty Acids Overview:

• Fatty acids are carboxylic acids with hydrocarbon chains ranging from 2 to 36 carbons.
• Over 200 fatty acids have been isolated from plants, with a few present in large quantities termed as major fatty acids.
• Fatty acids present in smaller amounts are called minor fatty acids, and those unique to certain species are unusual fatty acids.

 

Major Fatty Acids:

• Saturated: Lauric (12:0), myristic (14:0), palmitic (16:0), and stearic (18:0).
• Unsaturated: Oleic (18:1Δ9), linoleic (18:2Δ9,12), and α-linolenic (18:3Δ9,12,15).
• Common in all plant lipids, they have unbranched carbon chains and naturally occurring double bonds in the cis configuration.

Minor Fatty Acids:

• Include short and medium-chain saturated fatty acids like butyric (4:0), caproic (6:0), caprylic (8:0), and capric (10:0).

 

Unusual Fatty Acids:

• Found in specific species:
  • Ricinoleic acid: 12-hydroxy oleic acid in castor bean.
  • Erucic acid: In rape seed.
  • Hydnocarpic and chaulmoogric acids: In chaulmoogra oil used for treating leprosy.

 

Essential Fatty Acids:

• Not synthesized by the human body, must be obtained through diet.
• Linoleic acid (n-6): Precursor for arachidonic acid.
• α-Linolenic acid (n-3): Found in fish oils and spirulina, important for nervous tissue and retina.

 

Simple Lipids

Fats and Oils:

• Triacylglycerols (Triglycerides): Glycerol esterified with three fatty acids.
• Solid fats (rich in saturated fatty acids) vs. liquid oils (rich in unsaturated fatty acids).
• Stored in plant seeds, fruits (e.g., avocado), and mesocarp (e.g., oil palm).

 

Storage and Structural Fats:

• Stored in endosperm as oil bodies surrounded by phospholipid membranes.
• Leaves contain up to 7% of their dry weight as fats, mainly in chloroplast membranes.

 

Compound Lipids

Phospholipids:

• Key component of cell membranes, containing glycerol, fatty acids, phosphoric acid, and a nitrogenous base.
  • Phosphatidyl choline (lecithin): Important for lung function.
  • Phosphatidyl ethanolamine (cephalin), serine, inositol, glycerol: Diverse functions in cellular processes.

 

Sphingophospholipids:

• Have sphingosine instead of glycerol, forming ceramides which are structural components in seeds of certain plants.

Glycolipids and Sulpholipids:

• Glycolipids have monosaccharide residues attached, found in plant tissues.
• Sulpholipids, like those in chloroplast thylakoid membranes, contain sulphated glucose.

 

Waxes

Types and Functions:

• Esters of long-chain fatty acids and alcohols.
• Found in beeswax, carnauba wax, and jojoba oil, used in various industries.
• Cuticular wax: Covers plant epidermal cells, reducing water loss and protecting against environmental damage.

Sterols

Characteristics and Functions:

• Steroid nucleus structure, classified based on side chains and functional groups.
• Cholesterol: Major animal sterol, precursor to hormones and vitamins.
• Plant Sterols: Stigmasterol and β-sitosterol, function in membrane stability and hormone synthesis (e.g., brassinosteroids).

Brassinosteroids

Plant Growth Regulators:

• Promote elongation, enhance resistance to stress, and have hormonal effects.
• Widely distributed in various plant parts, with brassinolide and castasterone being significant.

Properties of Fats

Physical:

• Greasy, insoluble in water, soluble in organic solvents.
• Emulsification necessary for digestion, as seen in milk and egg yolk.

Chemical:

• Hydrolysis yields glycerol and fatty acids, with saponification producing soaps.
• Rancidity due to hydrolysis or oxidation results in spoilage.

Proteins

General Overview:

• Origin of the Term: Coined by J.J. Berzelius in 1838, derived from the Greek word “Proteios” meaning “first rank”.
• Composition: Macromolecular polymers composed of amino acids linked by peptide bonds, containing carbon, hydrogen, oxygen, nitrogen, and sulfur.

Elementary Composition:

• Typical percentages: Carbon (50-55%), Hydrogen (6-8%), Oxygen (20-23%), Nitrogen (15-18%), Sulfur (Traces).

Occurrence:

• Found in all living cells, forming essential constituents of protoplasm, cell membrane, and nuclear material.
• Present as simple proteins or complexes with lipids or nucleic acids.
• Tissue-specific protein composition varies (e.g., muscle, bone, brain, blood).
• Seeds of cereal and leguminous plants have higher protein content compared to stems, leaves, and flowers.
• Tuber crops have lower protein content.

Functions:

• Enzymes: Specialized proteins with catalytic activities present in all organisms.
• Regulation: Proteins regulate metabolic reactions, both directly as enzymes and indirectly as hormones and hormone receptors.
• Biological Processes: Central to numerous physiological and metabolic processes.

Amino Acids

General Overview:

• 20 different amino acids form all proteins, each with trivial names based on their source or properties (e.g., Asparagine from asparagus, Glycine named for its sweet taste).
• All except proline have an amino group and a carboxyl group attached to the alpha carbon, differing in their side chains (R groups).
• Referred to as standard or protein amino acids.

Classification of Protein Amino Acids:

1. Non-Polar or Hydrophobic, Aliphatic R Groups:
   • Includes Glycine, Alanine, Valine, Leucine, Isoleucine, and Proline.
   • Promote hydrophobic interactions within protein structures.
   • Glycine offers flexibility, Proline reduces flexibility.
2. Non-Polar Aromatic R Groups:
   • Includes Phenylalanine, Tyrosine, and Tryptophan.
   • Participate in hydrophobic interactions and absorb UV light at 280 nm.
   • Tyrosine and Tryptophan are more polar than Phenylalanine.
3. Polar, Uncharged R Groups:
   • Includes Serine, Threonine, Cysteine, Methionine, Asparagine, and Glutamine.
   • More hydrophilic due to hydroxyl, sulfur, and amide groups.
4. Charged R Groups:
   • Acidic: Aspartic and Glutamic acids (net negative charge at pH 7.0).
   • Basic: Lysine, Arginine, and Histidine (net positive charge at pH 7.0).

Properties of Amino Acids:

Physical:

• White crystalline substances, soluble in water, and insoluble in non-polar solvents.
• High melting points (200-300°C), tasteless, sweet, or bitter.
• Used as flavoring agents (e.g., sodium glutamate).

Amphoteric Nature:

• Contain both acidic (COOH) and basic (NH2) groups.
• React with both acids and bases, exist as zwitterions (inner salts) in water.
• Isoeletric pH: pH at which the amino acid has no net charge.

Isomerism:

• All amino acids except glycine have an asymmetric carbon atom (alpha position).
• Exist in optically active forms: L (common) and D configurations.
• Optical rotation indicated by symbols + or -.

Chemical Properties:

1. Reactions Due to Amino Group:
   • Formaldehyde Reaction: Amino group forms complex with formaldehyde, titrated against alkali to measure total free amino acids.
   • Nitrous Acid Reaction: Forms hydroxyacids and releases nitrogen gas.
   • Ninhydrin Reaction: Oxidatively deaminates amino acids, producing Ruhemann’s purple, used for quantitative determination of amino acids.
2. Reactions Due to Carboxyl Group:
   • Decarboxylation: Produces corresponding amines, e.g., histamine from histidine, involved in physiological responses.

Essential Amino Acids:

• Cannot be synthesized by higher animals, must be obtained from diet.
• Essential amino acids: Methionine, Arginine, Threonine, Tryptophan, Valine, Isoleucine, Leucine, Phenylalanine, Histidine, Lysine (Remember MATTVILPHLy).

Peptides

Formation:

• Amino acids linked by peptide bonds between alpha-carboxyl and alpha-amino groups.
• Peptides vary in length: dipeptides, tripeptides, oligopeptides, and polypeptides.

Peptides of Physiological Interest:

• Glutathione: Tripeptide (gamma-glutamyl cysteinyl glycine), involved in detoxification.
• Oxytocin and Vasopressin: Nonapeptides, function as hormones.
• Aspartame: Dipeptide (L-aspartyl-L-phenylalanine), used as an artificial sweetener.

Organization of Plant Cells

Plant cells have unique structures and organelles, each performing specific functions vital for the plant’s survival and growth. Key organelles include:

• Cell Wall: A rigid outer layer made of cellulose, providing structural support and protection.
• Chloroplast: Contains chlorophyll and is the site of photosynthesis where light energy is converted into chemical energy.
• Mitochondria: The powerhouse of the cell, generating ATP through cellular respiration.
• Ribosomes: Sites of protein synthesis, found free-floating in the cytoplasm or attached to the endoplasmic reticulum.
• Vacuole: A large central sac storing nutrients, waste products, and helps maintain turgor pressure.
• Nucleus: Contains genetic material (DNA) and controls cellular activities.

Photosynthesis

Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy stored in glucose. This process sustains the existence of most life on Earth.

Photosynthesis Equation:

6CO2+6H2O+solar energy→C6H12O6+6O26CO_2 + 6H_2O + \text{solar energy} \rightarrow C_6H_{12}O_6 + 6O_26CO2​+6H2​O+solar energy→C6​H12​O6​+6O2​

Light Reactions

Occurs in the thylakoid membranes of the chloroplast and involves:

1. Photochemical Excitation of Chlorophyll: Chlorophyll absorbs light energy, exciting electrons.
2. Photooxidation: Splitting of water molecules to release oxygen, protons, and electrons.
3. Photoreduction: Formation of NADPH by transferring excited electrons through electron transport chains.
4. Photophosphorylation: Generation of ATP using the proton gradient created by electron flow.

Dark Reactions (Calvin Cycle)

Takes place in the stroma of the chloroplast and uses ATP and NADPH to convert CO2 into glucose. Key steps include:

1. Carbon Fixation: CO2 combines with ribulose-1,5-bisphosphate (RuBP) to form 3-phosphoglycerate (3PG).
2. Reduction: 3PG is converted into glyceraldehyde-3-phosphate (G3P) using ATP and NADPH.
3. Regeneration of RuBP: G3P is used to regenerate RuBP, allowing the cycle to continue.

Flavonoids and Alkaloids

Flavonoids and alkaloids are secondary metabolites with significant roles in plant coloration, defense, and human health benefits.

Flavonoids:

• Types: Anthocyanins, Flavonones, Flavanol, Flavones.
• Functions: Provide color to fruits and flowers, act as antioxidants, and protect against UV radiation.

Alkaloids:

• Examples: Caffeine, morphine, quinine.
• Functions: Serve as defense compounds against herbivores and pathogens, have medicinal properties.

Plant Hormones

Plant hormones regulate growth, development, and responses to environmental stimuli. Major hormones include:

1. Auxins (e.g., Indole-3-acetic acid): Promote cell elongation, root growth, and differentiation.
2. Gibberellins: Stimulate stem elongation, seed germination, and flowering.
3. Cytokinins: Promote cell division and delay aging of leaves.
4. Abscisic Acid (ABA): Induces dormancy, closes stomata during water stress.
5. Ethylene: Promotes fruit ripening and leaf abscission.
6. Phenolics: Include compounds like caffeic acid, which protect against pathogens.

Carotenoids

Carotenoids are pigments involved in photosynthesis and protection against oxidative damage. They are precursors to vitamin A.

Herbicides

Herbicides are chemicals used to control unwanted plants. They interfere with plant growth processes, often targeting specific enzymes or pathways unique to plants.

Plant Pigments: Structure and Function of Chlorophyll and  Carotenoids

Chlorophylls

Chlorophylls are essential pigments in photosynthetic organisms, functioning within chromoproteins (pigment-protein complexes). They are predominantly found in the chloroplasts of higher plants, algae, and cyanobacteria. The main chlorophylls in plants are chlorophyll a and chlorophyll b. Additionally, chlorophylls c1, c2, and d are found in various algae.

Structure:

• Chlorophylls are tetrapyrroles with four pyrrole rings coordinated to a central magnesium (Mg) atom, forming a magnesium-porphyrin structure.
• Chlorophyll a (C55H72MgN4O5) and chlorophyll b (C55H70MgN4O6) differ slightly in their molecular structure, particularly in their side chains.

Function:

• Chlorophylls absorb light primarily in the blue-violet and red regions of the electromagnetic spectrum.
• Chlorophyll a absorbs maximally at 430 nm and 662 nm, while chlorophyll b absorbs at 453 nm and 642 nm.
• This complementary absorption allows plants to utilize a broader range of the light spectrum for photosynthesis.

Carotenoids

Carotenoids are accessory pigments found in the chloroplasts of plants. They play a crucial role in photosynthesis by absorbing light energy and protecting chlorophyll from photo-damage.

Structure:

• Carotenoids are long polyisoprenoid molecules with conjugated double bonds.
• There are two main types: carotenes (hydrocarbons without oxygen, e.g., β-carotene) and xanthophylls (oxygenated, e.g., violaxanthin).

Function:

• Carotenoids absorb light in the 400-500 nm range, covering parts of the spectrum not efficiently absorbed by chlorophylls.
• They protect the photosynthetic apparatus by quenching triplet chlorophyll and singlet oxygen, preventing oxidative damage.

Phycobilins

Phycobilins are linear tetrapyrroles found in red algae and cyanobacteria. Unlike chlorophylls, they do not have a central magnesium ion.

Structure:

• Phycobilins are water-soluble and covalently bonded to proteins, forming phycobiliproteins.
• Major phycobilins include phycoerythrobilin (red pigment) and phycocyanobilin (blue pigment).

Function:

• They capture light energy and transfer it to chlorophylls for photosynthesis, extending the range of light wavelengths that can be utilized.

Sterols: Basic Structure and Role of Brassinosterols in Plants

Basic Structure of Sterols

Sterols are essential components of cell membranes, providing structural integrity and fluidity.

Structure:

• Sterols have a steroid nucleus consisting of four fused rings: three cyclohexane rings and one cyclopentane ring.
• The basic structure is known as perhydrocyclopentano phenanthrene.
• They have a hydroxyl group at position 3, a double bond between carbons 5 and 6, and variable side chains at position 17.

Examples:

• Cholesterol: Most abundant in animal membranes.
• Stigmasterol and β-sitosterol: Common in plant membranes, differing from cholesterol in their side chains.
• Ergosterol: Found in fungi, with a double bond between C7 and C8.

Brassinosterols

Brassinosterols are a class of plant steroids, with brassinolide being the most studied. They are involved in various physiological processes and are considered a distinct class of plant hormones.

Discovery and Sources:

• Brassinolide was first isolated from Brassica napus pollen in 1979.
• Brassinosterols are present in various plant parts, including pollen, leaves, flowers, seeds, and stems.

Function:

• Brassinosterols are active at very low concentrations (nM to pM range).
• They promote stem elongation, enhance stress tolerance, and modulate gene expression.
• They are essential for plant growth and development, affecting processes like cell expansion, division, and differentiation.

Evidence of Hormonal Role:

1. Distribution: Found across a wide range of plant species and tissues.
2. Low Concentration Effectiveness: Active at extremely low concentrations.
3. Range of Effects: Influence numerous physiological processes distinct from other hormones.
4. Transport and Response: Can be applied to one part of a plant and transported to another, eliciting responses even in small amounts.

Overall, chlorophylls and carotenoids are vital for capturing light energy for photosynthesis, while sterols, particularly brassinosterols, play crucial roles in maintaining cellular structure and regulating plant growth and development.

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