Biomolecules: Organic Molecules to Nucleic Acids (Module -3)

3.1 Organic Molecules

• Organic molecules contain both carbon and hydrogen atoms.

• Four classes of organic molecules (biomolecules) in living organisms: Carbohydrates, Lipids, Proteins, Nucleic acids.

• Functions of biomolecules in the cell are diverse.

• Carbon and Life context: Carbon is the basis of life; carbon forms versatile covalent bonds enabling complex structures such as lipids (energy storage), carbohydrates (structure), proteins (hemoglobin), and genetic material (DNA) (refer to Figure 3.1 in the source).

• The Carbon Atom

  • Can form four covalent bonds.

  • Bonds with carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur.

  • C—C bonds are very stable.

  • Can form long carbon chains (hydrocarbons).

  • Can form single, double, or triple bonds and ring structures.

  • Branching at carbon atoms leads to complex carbon skeletons.

• The Carbon Skeleton and Functional Groups

  • The carbon chain of an organic molecule is called its skeleton or backbone.

  • Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structures and functions.

• Functional Groups (Table 3.1 summary)

  • Hydroxyl: R–OH

  • Alcohol (e.g., ethanol)

  • Polar; forms hydrogen bonds

  • Present in sugars and some amino acids

  • Carbonyl: includes Aldehyde (R–CHO) and Ketone (R–CO–R')

  • Polar

  • Present in sugars

  • Carboxyl (carboxylic acid): R–COOH

  • Polar, acidic

  • Amine: R–NH2

  • Polar, basic; present in amino acids

  • Sulfhydryl: R–SH

  • Thiol (e.g., ethanethiol)

  • Phosphate: R–O–P(=O)(OH)2

  • Organic phosphate; present in nucleotides, phospholipids

  • Functional groups determine chemical reactivity and polarity of organic molecules.

• Isomers

  • Isomers have identical molecular formulas but different atomic arrangements.

  • Example: C3H6O3 compounds like glyceraldehyde and dihydroxyacetone have the same formula but different structures (one has O= on end carbon, the other on middle carbon).

3.2 Carbohydrates

• Characteristics: contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.

• Monomers are monosaccharides.

• Functions: energy source; building material (structural role).

• Varieties: Monosaccharides, Disaccharides, Polysaccharides.

• Structural materials and examples

  • Structural carbohydrates in nature include cellulose (plants), chitin (exoskeletons of some animals and fungal cell walls).

  • Peptidoglycan found in bacterial cell walls.

  • Plants store energy as starch; animals store energy as glycogen; cellulose is the most abundant organic molecule on Earth and is indigestible by many animals.

• Monosaccharides

  • Monosaccharide = single sugar molecule; simple sugar.

  • Backbone length: 3 to 7 carbon atoms.

  • Hexoses (6 carbons): glucose (blood sugar), fructose (fruit sugar), galactose.

  • Pentoses (5 carbons): ribose, deoxyribose (sugars in nucleotides of DNA).

• Disaccharides

  • Formed by two monosaccharides joined via dehydration synthesis.

  • Examples: lactose, sucrose, maltose.

  • Hydrolysis breaks disaccharides into monosaccharides.

• Synthesis and Degradation (example: maltose)

  • Dehydration synthesis: two glucose molecules combine to form maltose with release of water.

  • Reaction: ext{glucose} + ext{glucose}
    ightarrow ext{maltose} + ext{H}_2 ext{O}

  • Hydrolysis: maltose + H2O yields two glucose molecules.

  • Reaction: ext{maltose} + ext{H}_2 ext{O}
    ightarrow 2 ext{glucose}

• Polysaccharides: energy-storage and structural roles

  • Polysaccharide = polymer of monosaccharides.

  • Starch (plants) and glycogen (animals) are energy-storage polysaccharides.

  • Cellulose (plant cell walls) provides structural support; chitin in fungi and some animal exoskeletons; peptidoglycan in bacteria cell walls.

  • Most monosaccharides in these polymers form polymers without amino acid subunits (contrast to proteins).

• Starch and Glycogen (structure and function)

  • Starch: plant energy storage; can be branched or unbranched.

  • Glycogen: highly branched energy storage in animals.

  • Electron micrographs show location of starch in plant cells and glycogen in liver cells.

• Cellulose, Microfibrils, and Hydrogen Bonding

  • Cellulose fibers criss-cross plant cell walls for strength.

  • Each cellulose fiber contains microfibrils; glucose units linked with a distinct bond pattern that allows hydrogen bonding between microfibrils.

  • The alternating orientation of glucose units increases strength.

3.3 Lipids

• Characteristics: highly varied structure; large, nonpolar, insoluble in water.

• Functions: long-term energy storage; structural components of membranes; heat retention; cell signaling/regulation; protection.

• Varieties: fats, oils, phospholipids, steroids, waxes.

• Types of Lipids (Table 3.3 summary)

  • Fats: long-term energy storage and insulation; animal sources (butter, lard).

  • Oils: long-term energy storage in plants and seeds; cooking oils.

  • Phospholipids: major component of plasma membranes; food additive.

  • Steroids: component of cell membranes; hormonal regulation; e.g., cholesterol, testosterone, estrogen; cholesterol is a precursor to other steroids.

  • Waxes: protection and water loss prevention (e.g., plant cuticle, earwax, beeswax).

  • Candles and polishes: other uses of some lipids.

• Triglycerides: long-term energy storage

  • Formed by one glycerol molecule linked to three fatty acids via dehydration synthesis.

  • Functions: long-term energy storage and insulation.

  • Structure: glycerol + 3 fatty acids → triglyceride + 3 H2O.

  • Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds).

  • Unsaturated fats tend to be liquid at room temperature; common in plant oils.

  • Saturated fats tend to be solid at room temperature; examples include butter and lard.

  • Trans fats: triglycerides with at least one trans double bond; associated with health concerns.

• Phospholipids: membrane components

  • Structure: glycerol linked to two fatty acids (nonpolar tails) and a modified phosphate group (polar head).

  • Heads are polar and hydrophilic; tails are nonpolar and hydrophobic.

  • Function: form phospholipid bilayer in cell membranes; dual polarity drives bilayer formation in aqueous environments.

  • Tail kinks (due to unsaturations) affect membrane fluidity.

  • Visual: bilayer arrangement with hydrophilic heads facing water and hydrophobic tails away from water.

• Steroids

  • Structure: four fused carbon rings; different functional groups determine specific steroids.

  • Functions: membrane components; hormonal regulation.

  • Examples: Cholesterol, Testosterone, Estrogen.

  • Note: Testosterone and estrogen differ by attached functional groups on the same carbon skeleton; cholesterol is a precursor to several steroids.

• Waxes

  • Long-chain fatty acids linked to alcohols.

  • Properties: solid at room temperature; waterproof; resistant to degradation.

  • Functions: protection; barrier against water loss.

  • Examples: earwax, plant cuticle, beeswax.

3.4 Proteins

• Proteins are polymers of amino acids linked by peptide bonds.

  • A peptide bond is a covalent bond between amino acids.

  • Two or more amino acids form a peptide; long chains form a polypeptide.

  • A protein is a folded polypeptide that has a specific three-dimensional shape essential for function.

• Functions of Proteins

  • Metabolism: many enzymes catalyze chemical reactions.

  • Support: structural proteins like keratin and collagen.

  • Transport: membrane channels and carrier proteins regulate movement of substances.

  • Defense: antibodies bind to antigens to protect from pathogens.

  • Regulation: regulatory proteins such as hormones.

  • Motion: actin and myosin drive muscle contraction; microtubules move cell components.

• Amino Acids: protein monomers

  • There are 20 common amino acids.

  • Amino acids differ by their R (side) groups, which vary in complexity.

  • Classes of R groups include nonpolar (hydrophobic), polar (hydrophilic), and ionized (charged).

  • Examples provided include valine, leucine, proline, methionine, phenylalanine (nonpolar);
    cysteine, serine, glutamine, tyrosine, asparagine, threonine (polar);
    lysine, arginine, aspartic acid, glutamic acid, histidine (ionized).

• Protein structure: four levels

  • Primary structure: linear sequence of amino acids; encoded by genes in DNA.

  • Secondary structure: alpha helices and beta pleated sheets stabilized by hydrogen bonds.

  • Tertiary structure: three-dimensional folding driven by interactions among side chains and water, covalent bonds, and other chemical contacts.

  • Quaternary structure: two or more folded polypeptides interact to perform a biological function.

• Protein folding and diseases

  • Chaperone proteins assist in proper folding and correction of misfolded proteins.

  • Defects in chaperones can contribute to diseases such as Alzheimer disease and cystic fibrosis.

  • Prions are misfolded proteins that can induce misfolding in other proteins; implicated in fatal brain diseases (e.g., Mad Cow Disease).

3.5 Nucleic Acids

• Nucleic acids are polymers of nucleotides.

• Two main varieties: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

  • DNA stores genetic information for replication and for amino acid sequence in proteins.

  • RNA performs a wide range of cellular functions, including protein synthesis and gene expression regulation.

• Structure of a nucleotide

  • Composed of three parts: a phosphate group, a pentose sugar, and a nitrogen-containing base.

  • Five types of nucleotides exist in nucleic acids.

  • DNA bases: adenine (A), guanine (G), cytosine (C), thymine (T).

  • RNA bases: adenine (A), guanine (G), cytosine (C), uracil (U).

• Nucleotides: DNA vs RNA bases

  • Pyrimidines: cytosine (C) and thymine (T) in DNA; cytosine (C) and uracil (U) in RNA.

  • Purines: adenine (A) and guanine (G) in both DNA and RNA.

• Structure of DNA and RNA

  • Backbone: alternating sugar-phosphate sugar-phosphate in the strand.

  • RNA: typically single-stranded; DNA: usually double-stranded.

  • DNA forms a double helix; strands are held together by hydrogen bonds between complementary bases.

  • Complementary base pairing: A pairs with T (DNA) or with U (RNA); C pairs with G in both.

  • The order of nucleotides within a strand is variable; the pairing between strands follows base-pair rules.

• Comparing DNA and RNA structures

  • DNA: sugar = deoxyribose; bases = A, G, C, T; double-stranded; features a helix.

  • RNA: sugar = ribose; bases = A, G, C, U; usually single-stranded; no canonical double helix.

  • Table summary: DNA contains deoxyribose; RNA contains ribose; bases differ as above; strands/disposition differ; helix presence differs.

• ATP: adenosine triphosphate

  • ATP is a nucleotide (adenine + ribose + three phosphates).

  • High-energy molecule due to the last two unstable phosphate bonds.

  • Hydrolysis of the terminal phosphate yields ADP (adenosine diphosphate) and inorganic phosphate P_i, releasing energy for cellular work.

  • ATP is the energy currency of the cell.

  • Reaction (illustrative): ext{ATP}
    ightarrow ext{ADP} + ext{P_i} + ext{energy}