Biotechnology: Class 11 — Chapter 3: Biomolecules

Carbohydrates are classified into three major categories based on the number of monomeric units:

1. Monosaccharides: Simple sugars that cannot be further hydrolysed. They contain free aldehyde ($-CHO$) or ketone ($>C=O$) groups and two or more hydroxyl ($-OH$) groups, with the general formula $C_n(H_2O)_n$.
2. Oligosaccharides: Carbohydrates containing 2 to 10 monosaccharide units joined by glycosidic bonds (e.g., maltose, lactose, sucrose).
3. Polysaccharides: High-molecular-weight polymers consisting of more than 10 monosaccharide units linked by glycosidic bonds (e.g., starch, glycogen, cellulose, chitin).

• Asymmetric (Chiral) Carbon: All monosaccharides except dihydroxyacetone contain one or more chiral carbons, making them optically active isomers (enantiomers). A molecule with $n$ chiral centres has $2^n$ stereoisomers (e.g., glyceraldehyde has $2^1 = 2$; glucose has $2^4 = 16$).
• D and L Isomers: Determined by the orientation of the $-OH$ group on the chiral carbon most distant from the carbonyl carbon. If $-OH$ is on the right, it is a D-sugar; if on the left, it is an L-sugar. Most biological sugars are D-sugars.
• Anomers: Isomeric cyclic forms of monosaccharides that differ only in configuration about the hemiacetal or hemiketal carbon (anomeric carbon). In the $\alpha$-anomer, the $-OH$ group is opposite the $CH_2OH$ group; in the $\beta$-anomer, it is on the same side.
• Mutarotation: The spontaneous interconversion of $\alpha$ and $\beta$ anomers in aqueous solution via a brief opening into the linear form.
• Epimers: Isomers differing in configuration at only one specific carbon atom (e.g., mannose is a C-2 epimer of glucose; galactose is a C-4 epimer of glucose).
• Glycoconjugates: Carbohydrates covalently linked to proteins or lipids:
  • Glycoproteins: Predominantly protein component.
  • Proteoglycans: Predominantly carbohydrate component.
  • Glycolipids: Carbohydrate conjugated with lipids.

Peptidoglycan: Rigid component of bacterial cell walls. It is a heteropolysaccharide of alternating $\beta(1\rightarrow4)$ linked N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues, cross-linked by short peptides. Lysozyme (found in human tears) kills bacteria by hydrolysing this $\beta(1\rightarrow4)$ glycosidic linkage.

Agar: Gelatinous heteropolysaccharide from marine red algae (e.g., Gelidium, Gracilaria). Composed of sulphated D-galactose and L-galactose derivatives ether-linked between C3 and C6. Agarose is the purified, minimally charged component used as an inert support for gel electrophoresis.

Fatty acids are long-chain hydrocarbons containing a terminal carboxylic acid group. They are synthesized from two-carbon units, resulting in an even number of carbon atoms.

• Saturated Fatty Acids: Contain no double bonds (e.g., Palmitic acid, Stearic acid).
• Unsaturated Fatty Acids: Contain one or more double bonds. Classified into:
  • Monounsaturated (MUFAs): One double bond (e.g., Oleic acid).
  • Polyunsaturated (PUFAs): More than one double bond (e.g., Linoleic acid, Linolenic acid, Arachidonic acid).
• Nomenclature: Denoted as [Total Carbons]:[Number of Double Bonds] (Δ^positions). For example, linoleic acid is $18:2 (\Delta^{9,12})$.

1. Simple Lipids: Esters of fatty acids with various alcohols.
   • Triacylglycerols (Triglycerides): Esters of glycerol and three fatty acids. Simple triglycerides contain identical fatty acids; mixed triglycerides contain different fatty acids. Primary energy storage in adipose tissue.
   • Waxes: Esters of long-chain fatty acids with high-molecular-weight monohydric alcohols. Serve as protective coatings.
2. Compound Lipids: Esters of fatty acids containing additional hydrophilic groups, making them amphipathic.
   • Phospholipids: Major membrane lipids. Composed of two hydrophobic fatty acid tails and a hydrophilic phosphate head. Divided into glycerophospholipids (glycerol backbone, e.g., phosphatidylcholine) and sphingophospholipids (sphingoid base backbone, e.g., sphingomyelin). Form micelles in water.
   • Steroids: Characterized by a four-fused ring structure. Cholesterol is the key precursor for steroid hormones (testosterone, estradiol), vitamin D, and bile acids. Plant steroids include phytosterols and stigmasterols; fungal steroids include ergosterol.

• Chirality: The $\alpha$-carbon is asymmetric in 19 of the 20 standard amino acids (except glycine), allowing for optically active L and D isomers. Only L-amino acids are found in ribosomal proteins.
• Zwitterion State: At physiological pH (~7.0), both the carboxyl group (deprotonated to $-COO^-$) and the amino group (protonated to $-NH_3^+$) are ionized, forming a dipolar ion with a net charge of zero.

• Non-Standard Amino Acids: Modified after translation in proteins (e.g., 4-hydroxyproline, 5-hydroxylysine, selenocysteine, $\gamma$-carboxyglutamic acid).
• Non-Protein Amino Acids: Occur naturally in cells but are not incorporated into proteins (e.g., L-ornithine, L-citrulline, $\beta$-alanine, creatine, $\gamma$-aminobutyrate).

The linear sequence of amino acids linked by covalent peptide bonds (amide bonds). Peptide bond formation occurs via a condensation reaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another, releasing $H_2O$.

• Polarity: Polypeptides have an amino-terminal (N-terminal) end on the left and a carboxy-terminal (C-terminal) end on the right.
• Naming Convention: Amino acid residues are named by adding the suffix -yl sequentially from the N-terminus, leaving the C-terminal residue unchanged.
• The average molecular weight of an amino acid residue is approximately 110 Da.

Peptide Bond Planarity: The six atoms of the peptide group lie in a single plane. Resonance interactions give the peptide bond ~40% double-bond character, preventing free rotation around the $C-N$ bond.

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Backbone Flexibility: Rotation is permitted only around the pure single bonds adjacent to the peptide group: the $C_\alpha-N$ bond (dihedral angle phi, $\phi$) and the $C_\alpha-C$ bond (dihedral angle psi, $\psi$).

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Ramachandran Plot: A 2D plot mapping the sterically allowed conformations of $\phi$ and $\psi$ angles. It defines distinct regions corresponding to common secondary structures: $\beta$-sheets (parallel/antiparallel), right-handed $\alpha$-helices, and collagen helices.

Local spatial folding of the polypeptide backbone, stabilized by hydrogen bonds between main-chain peptide groups:

• \alpha-Helix: A rod-like helical structure stabilized by intrachain hydrogen bonds between the carbonyl oxygen ($C=O$) of residue $i$ and the amide hydrogen ($N-H$) of residue $i+4$. One turn of the helix spans 5.4 Å. Right-handed helices are sterically more stable. Found in keratin, myosin, and ferritin.
• \beta-Pleated Sheet: Formed by hydrogen bonding between peptide groups of adjacent polypeptide strands. Strands can run in the same direction (parallel) or opposite directions (antiparallel).

• Tertiary Structure: The overall three-dimensional folding of a single polypeptide chain. Stabilized by weak interactions (hydrophobic interactions, hydrogen bonds, ionic/electrostatic bonds) and covalent disulfide bonds (formed by the oxidation of cysteine residues). Hydrophobic residues are packed in the interior, while polar residues remain on the exterior.
• Quaternary Structure: The spatial arrangement of multiple polypeptide subunits (identical or non-identical) in a multi-subunit protein complex. Subunits are held together by non-covalent interactions and disulfide bridges (e.g., homodimers, heterotetramers like hemoglobin).

1. Pentose Sugar: Closed five-membered rings. D-ribose in RNA and 2'-deoxy-D-ribose in DNA (lacking an $-OH$ group at the C-2' position).
2. Nitrogenous Bases: Planar, aromatic ring structures that absorb UV light at 260 nm. Divided into:
   • Purines: Double-ring structures; Adenine (A) and Guanine (G).
   • Pyrimidines: Single-ring structures; Cytosine (C), Thymine (T, unique to DNA), and Uracil (U, unique to RNA).
3. Phosphate Group: Esterified to the pentose sugar.

Nucleoside vs. Nucleotide:
$$\text{Nucleoside} = \text{Base} + \text{Pentose Sugar}$$
$$\text{Nucleotide} = \text{Base} + \text{Pentose Sugar} + \text{Phosphate Group}$$

• Phosphodiester Linkage: Nucleotides are covalently linked by a $3',5'$-phosphodiester bond, where the 3'-hydroxyl group of one sugar is esterified to the 5'-phosphate group of the adjacent sugar. This establishes a distinct $5' \rightarrow 3'$ polarity.
• Watson-Crick Double Helix: DNA consists of two antiparallel polynucleotide chains wound around a central axis in a right-handed double helix. The sugar-phosphate backbones form the outer rails, while the bases stack inside.
• Complementary Base Pairing: Adenine pairs with Thymine via 2 hydrogen bonds ($A = T$); Guanine pairs with Cytosine via 3 hydrogen bonds ($G \equiv C$).
• Structural Variants: B-DNA (most stable, standard physiological form), A-DNA (right-handed, wider, 11 bp/turn), and Z-DNA (left-handed, zigzag backbone, 12 bp/turn).
• Denaturation (Melting): Separation of double-stranded DNA into single strands by heating or chemical treatment, which disrupts hydrogen bonds. The temperature at which 50% of DNA is denatured is the melting temperature ($T_m$). Spontaneous renaturation upon cooling is called annealing.

• Messenger RNA (mRNA): Single-stranded linear molecule that carries genetic information from DNA to ribosomes. Features untranslated regions (UTRs), an initiation codon, a coding region, and a stop codon. Eukaryotic mRNA undergoes 5' capping (7-methylguanylate) and 3' polyadenylation.
• Ribosomal RNA (rRNA): Structural and catalytic component of ribosomes.
  • Prokaryotic (70S) Ribosome: Contains 16S rRNA (30S subunit), 23S and 5S rRNAs (50S subunit).
  • Eukaryotic (80S) Ribosome: Contains 18S rRNA (40S subunit), 28S, 5.8S, and 5S rRNAs (60S subunit).
• Transfer RNA (tRNA): Small adaptor molecules that transfer amino acids to ribosomes during translation. Folds into a clover-leaf secondary structure with an acceptor arm (terminating in a $3'\text{-CCA}$ sequence for amino acid attachment) and an anticodon arm.