Biomolecules

Given/Concept: Carbohydrates are polyhydroxy aldehydes or ketones. They are classified on the basis of the number of sugar units they contain.

Classification of Carbohydrates:

1. Monosaccharides (Simple sugars):
- Cannot be hydrolysed further into simpler sugars.
- General formula: $(CH_2O)_n$ where $n = 3$ to $7$.
- Classified by number of carbon atoms:
- Trioses ($n=3$): e.g., Glyceraldehyde, Dihydroxyacetone
- Tetroses ($n=4$): e.g., Erythrose
- Pentoses ($n=5$): e.g., Ribose, Deoxyribose
- Hexoses ($n=6$): e.g., Glucose, Fructose, Galactose
- Heptoses ($n=7$): e.g., Sedoheptulose
- Further classified as aldoses (contain aldehyde group, $-CHO$) or ketoses (contain ketone group, $C=O$).

2. Oligosaccharides:
- Contain 2–10 monosaccharide units joined by glycosidic bonds.
- Sub-classified as:
- Disaccharides (2 units): e.g., Sucrose (glucose + fructose), Maltose (glucose + glucose), Lactose (glucose + galactose)
- Trisaccharides (3 units): e.g., Raffinose
- Tetrasaccharides (4 units): e.g., Stachyose

3. Polysaccharides:
- Contain more than 10 (often hundreds to thousands) monosaccharide units.
- Two types:
- Homopolysaccharides: Made of one type of monosaccharide. e.g., Starch, Glycogen, Cellulose (all made of glucose)
- Heteropolysaccharides: Made of two or more types of monosaccharides. e.g., Hyaluronic acid, Heparin

Conclusion: Carbohydrates are broadly classified into monosaccharides, oligosaccharides, and polysaccharides based on the degree of polymerisation.

Concept: The D- and L- designation of glucose is based on the configuration of the asymmetric carbon atom farthest from the carbonyl (aldehyde) group, i.e., C-5 in glucose. This is compared to the reference molecule glyceraldehyde.

| Feature | D-Glucose | L-Glucose |
|---|---|---|
| Configuration at C-5 | The $-OH$ group on C-5 is on the right side (same as D-glyceraldehyde) | The $-OH$ group on C-5 is on the left side (same as L-glyceraldehyde) |
| Reference | Based on D-glyceraldehyde | Based on L-glyceraldehyde |
| Occurrence in nature | Naturally occurring form; found in plants and animals | Rarely found in nature |
| Biological activity | Metabolically active; can be utilised by cells | Not metabolised by most organisms |
| Optical rotation | Dextrorotatory (+) — rotates plane-polarised light to the right | Levorotatory (−) — rotates plane-polarised light to the left |
| Mirror image | D and L forms are mirror images (enantiomers) of each other | Mirror image of D-glucose |

Note: The D/L designation refers to the spatial configuration at the reference carbon, not to the direction of optical rotation.

Conclusion: D- and L-glucose are enantiomers differing in the orientation of the $-OH$ group at C-5. D-glucose is the biologically important form.

Given: The disaccharide made up of glucose and fructose is Sucrose.

Concept: Sucrose is formed by a glycosidic bond between C-1 of $\alpha$-D-glucose and C-2 of $\beta$-D-fructose. This is an $\alpha$-1,2-glycosidic bond (also written as $\alpha,\beta$-1,2 linkage). Since both anomeric carbons are involved in the bond, sucrose is a non-reducing sugar.

Structure of Sucrose:

The Haworth projection of sucrose is represented as:

$$\underbrace{\alpha\text{-D-Glucose}}_{\text{(pyranose ring)}} \xrightarrow{\alpha(1\to2)\beta\text{-glycosidic bond}} \underbrace{\beta\text{-D-Fructose}}_{\text{(furanose ring)}}$$

The structural formula can be described as:
- $\alpha$-D-Glucopyranose ring (6-membered) linked at its C-1 anomeric carbon
- to $\beta$-D-Fructofuranose ring (5-membered) at its C-2 anomeric carbon
- via an $\alpha$-1,2-glycosidic bond with elimination of one water molecule ($H_2O$).

Molecular formula of sucrose: $C_{12}H_{22}O_{11}$

Reaction:
$$\text{Glucose } (C_6H_{12}O_6) + \text{Fructose } (C_6H_{12}O_6) \xrightarrow{-H_2O} \text{Sucrose } (C_{12}H_{22}O_{11})$$

Key feature: Both anomeric $-OH$ groups are involved in the glycosidic bond, so sucrose has no free anomeric carbon and is a non-reducing disaccharide.

Concept: Both starch and glycogen are homopolysaccharides made of $\alpha$-D-glucose units. They differ in the degree of branching.

---
Partial Structure of Starch:

Starch has two components:
- Amylose (~20%): Unbranched chain of $\alpha$-D-glucose units linked by $\alpha$(1→4) glycosidic bonds. Forms a helical structure.
- Amylopectin (~80%): Branched chain with $\alpha$(1→4) linkages in the main chain and $\alpha$(1→6) linkages at branch points (branching every 24–30 glucose units).

Partial structure of amylose (linear portion):
$$\ldots -[\alpha\text{-D-Glc}]\xrightarrow{\alpha(1\to4)}-[\alpha\text{-D-Glc}]\xrightarrow{\alpha(1\to4)}-[\alpha\text{-D-Glc}]-\ldots$$

At branch point in amylopectin:
$$\ldots -[\text{Glc}]\xrightarrow{\alpha(1\to4)}-[\text{Glc}]\xrightarrow{\alpha(1\to4)}-[\text{Glc}]-\ldots$$
$$\hspace{5.5cm}\downarrow \alpha(1\to6)$$
$$\hspace{5.5cm}[\text{Glc}]\xrightarrow{\alpha(1\to4)}-[\text{Glc}]-\ldots$$

---
Partial Structure of Glycogen:

- Glycogen is the animal storage polysaccharide (found in liver and muscle).
- Structure is similar to amylopectin but more highly branched — branching occurs every 8–12 glucose units (compared to 24–30 in amylopectin).
- Main chain: $\alpha$(1→4) glycosidic bonds.
- Branch points: $\alpha$(1→6) glycosidic bonds.

Partial structure:
$$\ldots -[\text{Glc}]\xrightarrow{\alpha(1\to4)}-[\text{Glc}]\xrightarrow{\alpha(1\to4)}-[\text{Glc}]-\ldots$$
$$\hspace{3.5cm}\downarrow \alpha(1\to6) \hspace{1.5cm}\downarrow \alpha(1\to6)$$
$$\hspace{3.5cm}[\text{Glc}]-\ldots \hspace{1.5cm}[\text{Glc}]-\ldots$$

Key difference: Glycogen is more extensively branched than starch (amylopectin), allowing faster mobilisation of glucose.

Major Functions of Carbohydrates:

1. Energy Source:
- Carbohydrates are the primary source of energy for living organisms.
- Glucose is completely oxidised to release energy: $$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{Energy (ATP)}$$
- 1 gram of carbohydrate yields approximately 4 kcal of energy.

2. Energy Storage:
- Starch (in plants) and glycogen (in animals) serve as stored forms of energy.
- Glycogen is stored in liver and muscle cells and mobilised when energy is needed.

3. Structural Role:
- Cellulose provides structural rigidity to plant cell walls.
- Chitin (a polysaccharide) forms the exoskeleton of arthropods and cell walls of fungi.
- Peptidoglycans (contain carbohydrate components) form bacterial cell walls.

4. Component of Nucleic Acids:
- Ribose (in RNA) and deoxyribose (in DNA) are pentose sugars that form the backbone of nucleic acids.

5. Cell Recognition and Signalling:
- Oligosaccharides on cell surfaces (as glycoproteins and glycolipids) act as cell recognition markers and are involved in cell–cell communication.
- Blood group antigens (A, B, O) are determined by oligosaccharide chains.

6. Lubrication:
- Mucopolysaccharides (e.g., hyaluronic acid) act as lubricants in joints and connective tissues.

7. Protein Sparing:
- Adequate carbohydrate intake prevents the use of proteins as an energy source, thus sparing proteins for their structural and functional roles.

Conclusion: Carbohydrates serve as energy sources, structural components, informational molecules, and metabolic intermediates in living systems.

Concept: Isomers are compounds that have the same molecular formula but differ in the arrangement of atoms. In monosaccharides, several types of isomerism are observed.

Types of Isomerism in Monosaccharides:

1. Structural Isomers (Constitutional Isomers):
- Compounds with the same molecular formula but different structural arrangements.
- e.g., Glucose ($C_6H_{12}O_6$) is an aldohexose; Fructose ($C_6H_{12}O_6$) is a ketohexose — they are structural isomers.

2. Stereoisomers:
Compounds with the same structural formula but different spatial arrangement of atoms.

(a) D- and L-Isomers (Enantiomers):
- Based on the configuration at the reference asymmetric carbon (farthest from carbonyl group).
- D-glucose has $-OH$ on the right at C-5; L-glucose has $-OH$ on the left at C-5.
- They are non-superimposable mirror images.

(b) Epimers:
- Stereoisomers that differ in configuration at only one asymmetric carbon (other than the anomeric carbon).
- e.g., D-Glucose and D-Galactose differ at C-4 → they are C-4 epimers.
- e.g., D-Glucose and D-Mannose differ at C-2 → they are C-2 epimers.

(c) Anomers:
- Stereoisomers that differ in configuration at the anomeric carbon (C-1 in aldoses, C-2 in ketoses) formed during ring closure.
- $\alpha$-D-Glucose: $-OH$ at C-1 is on the same side as the ring oxygen (axial/below in Haworth).
- $\beta$-D-Glucose: $-OH$ at C-1 is on the opposite side from the ring oxygen (equatorial/above in Haworth).
- Interconversion between $\alpha$ and $\beta$ forms in solution is called mutarotation.

3. Mutarotation:
- The spontaneous interconversion of $\alpha$ and $\beta$ anomers in aqueous solution through the open-chain form.
- At equilibrium: ~36% $\alpha$-D-glucose, ~64% $\beta$-D-glucose.

Conclusion: Isomerisation in monosaccharides includes structural isomerism, D/L isomerism, epimerism, and anomerism, all arising from the presence of multiple asymmetric carbon atoms.

Concept: Both sphingolipids and glycerolipids are complex lipids found in biological membranes, but they differ in their backbone structure and composition.

| Feature | Glycerolipids | Sphingolipids |
|---|---|---|
| Backbone | Glycerol (3-carbon alcohol) | Sphingosine (long-chain amino alcohol, 18 carbons) |
| Fatty acid linkage | Fatty acids are linked to glycerol via ester bonds ($-COO-$) | One fatty acid is linked to the amino group of sphingosine via an amide bond ($-CO-NH-$) |
| Number of fatty acids | Two fatty acids (in phospholipids) or three (in triacylglycerols) | One fatty acid |
| Head group | Phosphate + alcohol (e.g., choline, ethanolamine, serine) in phosphoglycerides | Phosphocholine (in sphingomyelin) or sugar residues (in glycosphingolipids) |
| Examples | Phosphatidylcholine, Phosphatidylethanolamine, Phosphatidylserine, Triacylglycerol | Sphingomyelin, Cerebrosides, Gangliosides |
| Location | Major component of all biological membranes | Abundant in nervous tissue (myelin sheath), brain |
| Hydrolysis products | Glycerol + fatty acids + phosphate + alcohol | Sphingosine + fatty acid + phosphate/sugar |

Conclusion: The key difference is the backbone: glycerolipids use glycerol while sphingolipids use sphingosine as the backbone molecule.

Given: Membrane lipids include phospholipids (glycerophospholipids and sphingomyelin) and glycolipids.

Concept: The term amphipathic (also called amphiphilic) refers to molecules that possess both a hydrophilic (water-loving) region and a hydrophobic (water-fearing) region within the same molecule.

Explanation:

Membrane lipids (e.g., phosphatidylcholine) have two distinct structural regions:

1. Hydrophilic Head (Polar region):
- Consists of the phosphate group and the attached polar alcohol (e.g., choline, ethanolamine, serine).
- This region is charged/polar and interacts favourably with water molecules.
- It faces the aqueous environment (cytoplasm or extracellular fluid).

2. Hydrophobic Tail (Non-polar region):
- Consists of two long fatty acid chains (hydrocarbon tails).
- These are non-polar and do not interact with water.
- They face the interior of the membrane, away from water.

Structural representation:
$$\underbrace{\text{Polar head (phosphate + alcohol)}}_{\text{Hydrophilic}} - \text{Glycerol} - \underbrace{\text{Two fatty acid tails}}_{\text{Hydrophobic}}$$

Significance:
- This amphipathic nature drives the spontaneous formation of lipid bilayers in aqueous environments.
- In a bilayer, hydrophobic tails face inward (away from water) and hydrophilic heads face outward (toward water), forming a stable membrane structure.

Conclusion: Membrane lipids are called amphipathic because they contain both a polar hydrophilic head group and non-polar hydrophobic fatty acid tails in the same molecule.

Concept: Fatty acids are long-chain carboxylic acids. They are classified as saturated or unsaturated based on the presence of double bonds in the hydrocarbon chain.

| Feature | Saturated Fatty Acids | Unsaturated Fatty Acids |
|---|---|---|
| Double bonds | No carbon–carbon double bonds; all carbons are saturated with hydrogen | Contain one or more carbon–carbon double bonds ($C=C$) |
| General formula | $CH_3-(CH_2)_n-COOH$ | Contain $-CH=CH-$ in the chain |
| Types | — | Monounsaturated (one double bond); Polyunsaturated (two or more double bonds) |
| Physical state | Solid at room temperature (due to tight packing of straight chains) | Liquid at room temperature (due to kinks/bends at double bonds preventing tight packing) |
| Melting point | Higher melting point | Lower melting point |
| Chain geometry | Straight, linear chain | Kinked/bent chain at the site of double bond (usually *cis* configuration) |
| Examples | Palmitic acid ($C_{16:0}$), Stearic acid ($C_{18:0}$) | Oleic acid ($C_{18:1}$, one double bond), Linoleic acid ($C_{18:2}$), Arachidonic acid ($C_{20:4}$) |
| Sources | Animal fats (butter, lard), coconut oil | Vegetable oils (olive, sunflower), fish oils |
| Health effects | Excess intake associated with cardiovascular disease | Essential fatty acids (linoleic, linolenic) are required in diet |

Notation: Fatty acids are written as $C_{\text{chain length}:\text{number of double bonds}}$.
- e.g., Palmitic acid = $C_{16:0}$; Oleic acid = $C_{18:1}$

Conclusion: The key difference is the presence of $C=C$ double bonds: saturated fatty acids have none (solid, high melting point) while unsaturated fatty acids have one or more (liquid, low melting point).

Concept: Amino acids are the building blocks of proteins. They contain an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain (R group) attached to the $\alpha$-carbon. They are classified based on the chemical nature of the R group.

Categories of Amino Acids:

1. Non-polar (Hydrophobic) Amino Acids:
- R group is non-polar/aliphatic or aromatic.
- Tend to be located in the interior of proteins (away from water).
- Examples: Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp), Methionine (Met).

2. Polar, Uncharged Amino Acids:
- R group is polar but carries no net charge at physiological pH (7.0).
- Can form hydrogen bonds with water.
- Examples: Serine (Ser), Threonine (Thr), Cysteine (Cys), Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln).

3. Positively Charged (Basic) Amino Acids:
- R group carries a positive charge at physiological pH.
- Examples: Lysine (Lys) — $\varepsilon$-amino group; Arginine (Arg) — guanidinium group; Histidine (His) — imidazole group.

4. Negatively Charged (Acidic) Amino Acids:
- R group carries a negative charge at physiological pH.
- Examples: Aspartic acid/Aspartate (Asp), Glutamic acid/Glutamate (Glu).

5. Classification based on nutritional requirement:
- Essential amino acids: Cannot be synthesised by the human body; must be obtained from diet. (9 in humans): His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val.
- Non-essential amino acids: Can be synthesised by the body. e.g., Ala, Gly, Ser, Asp, Glu.

6. Classification based on R group structure:
- Aliphatic: Gly, Ala, Val, Leu, Ile
- Aromatic: Phe, Tyr, Trp
- Sulphur-containing: Cys, Met
- Hydroxyl-containing: Ser, Thr
- Amide-containing: Asn, Gln
- Imino acid: Pro (contains imino group, $-NH-$, not $-NH_2$)

Conclusion: Amino acids are categorised based on the polarity, charge, and chemical nature of their R groups into non-polar, polar uncharged, acidic, and basic types.

Definition of Zwitterion:

A zwitterion (from German *Zwitter* = hybrid) is a molecule that carries both a positive charge and a negative charge simultaneously on different atoms, resulting in an overall net charge of zero. It is also called a dipolar ion or inner salt.

Concept in Amino Acids:

Amino acids contain both an acidic carboxyl group ($-COOH$) and a basic amino group ($-NH_2$). At physiological pH (around 7.0, i.e., at the isoelectric point), the carboxyl group loses a proton (becomes $-COO^-$) and the amino group gains a proton (becomes $-NH_3^+$). This doubly charged form is the zwitterion.

Reaction:
$$\underbrace{H_2N-CH(R)-COOH}_{\text{Uncharged form}} \rightleftharpoons \underbrace{^+H_3N-CH(R)-COO^-}_{\text{Zwitterion (dipolar ion)}}$$

Structure of Zwitterion (using Alanine as example):

$$\begin{array}{c} H \\ | \\ ^+H_3N - C - COO^- \\ | \\ CH_3 \end{array}$$

Or in a more explicit representation:
$$^+H_3N-\underset{|}{\overset{|}{C}}(R)(H)-COO^-$$

Where:
- $^+H_3N-$ = protonated amino group (positively charged)
- $-COO^-$ = deprotonated carboxyl group (negatively charged)
- $R$ = side chain
- Net charge = $+1 + (-1) = 0$

Key point: In aqueous solution at the isoelectric point (pI), amino acids predominantly exist as zwitterions, not as uncharged molecules. This is the most stable form of an amino acid in solution.

1. Non-Standard Amino Acids:

- The 20 amino acids commonly found in proteins are called standard or canonical amino acids.
- Non-standard amino acids are amino acids that are derived from the 20 standard amino acids by post-translational modifications (chemical modifications after the protein is synthesised).
- They are found within proteins but are not directly encoded by the genetic code.
- They arise by enzymatic modification of standard amino acids after incorporation into the polypeptide chain.

Examples of non-standard amino acids:
- 4-Hydroxyproline: Derived from proline by hydroxylation; found in collagen.
- 5-Hydroxylysine: Derived from lysine by hydroxylation; found in collagen.
- $\varepsilon$-N-Methyllysine: Found in histone proteins.
- $\gamma$-Carboxyglutamate: Found in blood clotting proteins (e.g., prothrombin).
- Selenocysteine: Sometimes called the 21st amino acid; contains selenium instead of sulphur.
- Desmosine: Found in elastin (cross-linking amino acid).

2. Non-Protein Amino Acids:

- These are amino acids that are NOT incorporated into proteins at all.
- They are found as free molecules in cells and serve important metabolic or physiological functions.
- They may be D-amino acids or $\beta$-, $\gamma$-amino acids (not $\alpha$-amino acids).

Examples of non-protein amino acids:
- $\beta$-Alanine: Found in coenzyme A and carnosine.
- $\gamma$-Aminobutyric acid (GABA): A neurotransmitter in the brain.
- Ornithine and Citrulline: Intermediates in the urea cycle.
- Homocysteine: Intermediate in methionine metabolism.
- D-Amino acids: Found in bacterial cell walls (e.g., D-glutamate, D-alanine in peptidoglycan).
- Canavanine: Found in jack beans; toxic analogue of arginine.

Conclusion: Non-standard amino acids are modified forms of standard amino acids found in proteins, while non-protein amino acids are amino acids not incorporated into proteins but serve other biological roles.

Concept: A peptide bond is a covalent amide bond formed between the $\alpha$-carboxyl group ($-COOH$) of one amino acid and the $\alpha$-amino group ($-NH_2$) of another amino acid, with the elimination of a water molecule ($H_2O$). This reaction is called a condensation reaction (or dehydration synthesis).

Mechanism of Peptide Bond Formation:

Step 1: The carboxyl group of amino acid 1 reacts with the amino group of amino acid 2.

Step 2: A water molecule is eliminated.

Step 3: A peptide ($-CO-NH-$) bond is formed.

Reaction:
$$H_2N-\underset{R_1}{\underset{|}{CH}}-COOH \;+\; H_2N-\underset{R_2}{\underset{|}{CH}}-COOH \xrightarrow{-H_2O} H_2N-\underset{R_1}{\underset{|}{CH}}-\underbrace{CO-NH}_{\text{Peptide bond}}-\underset{R_2}{\underset{|}{CH}}-COOH$$

General equation:
$$\text{Amino acid}_1 + \text{Amino acid}_2 \xrightarrow{\text{condensation}} \text{Dipeptide} + H_2O$$

Properties of the Peptide Bond:
1. It has partial double bond character due to resonance between the $C=O$ and $C-N$ bonds.
2. The peptide bond is planar (all four atoms $C_\alpha$, $C$, $O$, $N$, $H$, $C_\alpha$ lie in the same plane).
3. It is rigid and does not allow free rotation.
4. It is predominantly in the trans configuration (R groups on opposite sides).
5. The bond length of $C-N$ in peptide bond is 0.133 nm (shorter than a typical $C-N$ single bond of 0.149 nm).

Polypeptide chain: Multiple amino acids joined by peptide bonds form a polypeptide. The chain has a free $-NH_2$ at the N-terminus and a free $-COOH$ at the C-terminus.

Conclusion: Peptide bonds are formed by condensation reactions between the carboxyl group of one amino acid and the amino group of the next, releasing water.

Given: A tripeptide: Lys-Glu-Lys (Lysine–Glutamic acid–Lysine)

Concept: In a peptide, amino acids are joined by peptide bonds ($-CO-NH-$). The sequence is written from N-terminus (left) to C-terminus (right).

Side chains (R groups):
- Lysine (Lys, K): R = $-(CH_2)_4-NH_2$ (positively charged at physiological pH: $-(CH_2)_4-NH_3^+$)
- Glutamic acid (Glu, E): R = $-(CH_2)_2-COOH$ (negatively charged at physiological pH: $-(CH_2)_2-COO^-$)

Structure of Lys-Glu-Lys:

$$\underbrace{H_2N-\overset{\displaystyle|(CH_2)_4NH_2}{\underset{|}{CH}}-CO}_{\text{Lys (N-terminus)}}-\underbrace{NH-\overset{\displaystyle|(CH_2)_2COOH}{\underset{|}{CH}}-CO}_{\text{Glu}}-\underbrace{NH-\overset{\displaystyle|(CH_2)_4NH_2}{\underset{|}{CH}}-COOH}_{\text{Lys (C-terminus)}}$$

Expanded structural representation:

$$H_2N-\underset{\displaystyle(CH_2)_4-NH_2}{\underset{|}{CH}}-\overset{\text{peptide bond}}{\underbrace{CO-NH}}-\underset{\displaystyle(CH_2)_2-COOH}{\underset{|}{CH}}-\overset{\text{peptide bond}}{\underbrace{CO-NH}}-\underset{\displaystyle(CH_2)_4-NH_2}{\underset{|}{CH}}-COOH$$

Key features:
- N-terminus: Free $-NH_2$ of the first Lys
- C-terminus: Free $-COOH$ of the second Lys
- Two peptide bonds ($-CO-NH-$) connecting the three amino acids
- Net charge at physiological pH: $+1$ (Lys) $-1$ (Glu) $+1$ (Lys) $= +1$ (overall positive)

Molecular formula: $C_{16}H_{32}N_4O_6$ (after loss of 2 water molecules from condensation)

Concept: The secondary structure of a protein refers to the local, regular, repeating folding patterns of the polypeptide backbone, stabilised primarily by hydrogen bonds between the carbonyl oxygen ($C=O$) and the amide hydrogen ($N-H$) of the peptide backbone.

Major Secondary Structures:

---
1. $\alpha$-Helix (Alpha Helix):

- Proposed by Linus Pauling and Robert Corey (1951).
- The polypeptide backbone coils into a right-handed helix (clockwise when viewed from the N-terminus).
- Stabilisation: Hydrogen bonds form between the $C=O$ of residue $n$ and the $N-H$ of residue $n+4$ (i.e., every 4th amino acid).
- Parameters:
- 3.6 amino acid residues per turn
- Pitch (rise per turn) = 0.54 nm
- Rise per residue = 0.15 nm
- Diameter ≈ 0.5 nm
- R groups project outward from the helix axis.
- Helix breakers: Proline (Pro) disrupts the $\alpha$-helix due to its rigid ring structure.
- Example: Found abundantly in $\alpha$-keratin (hair, nails), myoglobin.

---
2. $\beta$-Pleated Sheet (Beta Sheet):

- Also proposed by Pauling and Corey.
- The polypeptide chain is almost fully extended and arranged side by side.
- Stabilisation: Hydrogen bonds form between adjacent polypeptide strands (inter-strand H-bonds between $C=O$ and $N-H$).
- The backbone has a pleated/zigzag appearance; R groups alternate above and below the plane.
- Types:
- Parallel $\beta$-sheet: Adjacent strands run in the same direction (N→C); H-bonds are slightly bent.
- Antiparallel $\beta$-sheet: Adjacent strands run in opposite directions (N→C and C→N); H-bonds are straight and stronger.
- Example: Found in $\beta$-keratin (silk fibroin), immunoglobulins.

---
3. $\beta$-Turn (Beta Turn / Reverse Turn):

- A short loop structure that allows the polypeptide chain to reverse direction (180°).
- Involves 4 amino acid residues.
- Stabilised by a hydrogen bond between the $C=O$ of residue 1 and the $N-H$ of residue 4.
- Proline and Glycine are commonly found in $\beta$-turns.
- Important in connecting $\beta$-strands in antiparallel $\beta$-sheets.

---
4. Random Coil:

- Regions of the polypeptide that do not have a regular, repeating secondary structure.
- Flexible and irregular regions.

---
Conclusion: The major secondary structures are the $\alpha$-helix and $\beta$-pleated sheet, both stabilised by hydrogen bonds between backbone atoms. The $\beta$-turn helps in chain reversal.

Concept: Protein structure is described at four levels of organisation. Tertiary and quaternary structures represent the third and fourth levels respectively.

| Feature | Tertiary Structure | Quaternary Structure |
|---|---|---|
| Definition | The overall three-dimensional folding of a single polypeptide chain, including all secondary structural elements and the loops connecting them | The arrangement and association of two or more polypeptide chains (subunits) to form a functional protein complex |
| Level | Third level of protein structure | Fourth level of protein structure |
| Number of chains | Involves a single polypeptide chain | Involves two or more polypeptide chains (subunits) |
| Interactions involved | Hydrophobic interactions, hydrogen bonds, ionic (electrostatic) bonds, disulphide bonds ($-S-S-$), van der Waals forces between R groups | Same types of non-covalent interactions (hydrophobic, hydrogen bonds, ionic bonds) between subunits; sometimes disulphide bonds between chains |
| Result | Gives the protein its specific 3D shape (globular or fibrous) | Gives the oligomeric protein its final functional form |
| Examples | Myoglobin (single chain, globular protein), Ribonuclease A | Haemoglobin ($\alpha_2\beta_2$ — 4 subunits), Collagen (3 chains), Insulin (2 chains: A and B linked by disulphide bonds) |
| Prerequisite | Requires primary and secondary structure | Requires tertiary structure of individual subunits |
| Functional significance | Creates the active site of enzymes; determines protein function | Allows cooperative interactions between subunits (e.g., cooperative O$_2$ binding in haemoglobin); allows allosteric regulation |

Conclusion: Tertiary structure describes the 3D folding of a single polypeptide chain, while quaternary structure describes the association of multiple polypeptide subunits into a multi-subunit complex.

Concept: Nucleosides and nucleotides are the building blocks of nucleic acids (DNA and RNA). They differ in the presence of a phosphate group.

| Feature | Nucleoside | Nucleotide |
|---|---|---|
| Definition | A compound consisting of a nitrogenous base linked to a pentose sugar (ribose or deoxyribose) via an N-glycosidic bond | A compound consisting of a nitrogenous base + pentose sugar + one or more phosphate groups; i.e., a nucleoside with a phosphate group |
| Components | Nitrogenous base + Pentose sugar | Nitrogenous base + Pentose sugar + Phosphate group(s) |
| Phosphate group | Absent | Present (at 5' carbon of sugar) |
| Bond type | N-glycosidic bond between base and sugar | N-glycosidic bond (base–sugar) + Phosphoester bond (sugar–phosphate) |
| Formula | Base + Sugar | Base + Sugar + Phosphate |
| Examples (RNA bases) | Adenosine, Guanosine, Cytidine, Uridine | AMP, GMP, CMP, UMP (monophosphates); ATP, GTP (triphosphates) |
| Examples (DNA bases) | Deoxyadenosine, Deoxyguanosine, Deoxycytidine, Thymidine | dAMP, dGMP, dCMP, dTMP |
| Charge | Neutral (no phosphate) | Negatively charged (due to phosphate group) |
| Role | Precursor to nucleotides; found in some coenzymes | Monomeric units of DNA and RNA; energy currency (ATP); signalling molecules (cAMP) |

Relationship:
$$\text{Nucleoside} + \text{Phosphate} \rightarrow \text{Nucleotide}$$
$$\text{Nucleotide} - \text{Phosphate} \rightarrow \text{Nucleoside}$$

Conclusion: A nucleotide is a phosphorylated nucleoside. The presence of the phosphate group is the key difference between a nucleotide and a nucleoside.

Concept: The primary structure of DNA refers to the linear sequence of deoxyribonucleotides in a polynucleotide chain, connected by 3',5'-phosphodiester bonds.

Components of DNA:
Each deoxyribonucleotide consists of:
1. A nitrogenous base — Adenine (A), Guanine (G), Cytosine (C), or Thymine (T)
2. 2'-Deoxyribose sugar (pentose sugar lacking $-OH$ at C-2')
3. A phosphate group ($-PO_4^{3-}$)

Formation of the Primary Structure:

- Nucleotides are joined by 3',5'-phosphodiester bonds.
- The phosphate group of one nucleotide is esterified to the 3'-OH of the preceding sugar and the 5'-OH of the following sugar.
- This creates the sugar-phosphate backbone of DNA.

Directionality:
- The DNA strand has a defined polarity: a free 5'-phosphate end (5' terminus) and a free 3'-hydroxyl end (3' terminus).
- By convention, the sequence is written from 5' → 3' direction.
- e.g., 5'-ATCG-3'

Representation:
$$5'-\underbrace{pA}_{\text{dAMP}}-\underbrace{pT}_{\text{dTMP}}-\underbrace{pC}_{\text{dCMP}}-\underbrace{pG}_{\text{dGMP}}-3'$$

Where $p$ represents the phosphodiester linkage.

Phosphodiester bond:
$$\ldots-\text{Sugar}_1-\underbrace{O-PO_2^{-}-O}_{\text{Phosphodiester bond}}-\text{Sugar}_2-\ldots$$

The bond is formed between:
- The 3'-OH of one deoxyribose and
- The 5'-phosphate of the next deoxyribose.

Key features of primary structure:
1. The sequence of bases encodes genetic information.
2. The backbone (sugar-phosphate) is uniform; only the bases vary.
3. The backbone is negatively charged due to phosphate groups.
4. The primary structure determines all higher-order structures.

Conclusion: The primary structure of DNA is the specific linear sequence of deoxyribonucleotides linked by 3',5'-phosphodiester bonds, read from the 5' to 3' direction.

Given: A tetranucleotide with sequence 5'-A-T-C-G-3' (DNA oligonucleotide)

Concept: In a DNA oligonucleotide, deoxyribonucleotides are joined by 3',5'-phosphodiester bonds. The sequence is written from 5' end (free phosphate) to 3' end (free hydroxyl).

Bases:
- A = Adenine (purine)
- T = Thymine (pyrimidine)
- C = Cytosine (pyrimidine)
- G = Guanine (purine)

Structure of 5'-A-T-C-G-3' oligonucleotide:

$$\begin{array}{l}$$
5'-\text{end} \\
|\quad \text{(Free phosphate at 5' carbon)} \\
\text{Phosphate} - 5'\text{-Deoxyribose}-3' \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad\quad \text{Adenine (A)} \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad \text{Phosphodiester bond} \\
\quad\quad\quad\quad\quad\quad | \\
\text{Phosphate} - 5'\text{-Deoxyribose}-3' \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad\quad \text{Thymine (T)} \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad \text{Phosphodiester bond} \\
\quad\quad\quad\quad\quad\quad | \\
\text{Phosphate} - 5'\text{-Deoxyribose}-3' \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad\quad \text{Cytosine (C)} \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad \text{Phosphodiester bond} \\
\quad\quad\quad\quad\quad\quad | \\
\text{Phosphate} - 5'\text{-Deoxyribose}-3'-OH \\
\quad\quad\quad\quad\quad\quad | \\
\quad\quad\quad\quad\quad \text{Guanine (G)} \\
3'-\text{end (Free 3'-OH)}
\end{array}

Simplified linear representation:
$$5'\text{-}p\text{A}-p\text{T}-p\text{C}-p\text{G-}3'\text{-OH}$$

Where:
- $p$ = phosphate group
- Each nucleotide is connected via a 3',5'-phosphodiester bond
- The 5' end has a free phosphate group
- The 3' end has a free hydroxyl ($-OH$) group

Note: The nitrogenous bases project sideways from the sugar-phosphate backbone. In the double helix, these bases would pair with complementary bases on the opposite strand (A pairs with T; C pairs with G).

Background: In 1953, James D. Watson and Francis H.C. Crick proposed the double helical model of DNA, based on X-ray diffraction data by Rosalind Franklin and Maurice Wilkins, and Chargaff's rules. They were awarded the Nobel Prize in Physiology or Medicine in 1962.

Key Features of the Watson-Crick Model (B-DNA):

1. Double-stranded structure:
- DNA consists of two polynucleotide strands wound around a common central axis.
- The two strands are antiparallel — one runs 5'→3' and the other runs 3'→5'.

2. Right-handed helix:
- The double helix is right-handed (coils clockwise when viewed from above).

3. Sugar-phosphate backbone:
- The sugar-phosphate backbone is on the outside of the helix.
- The nitrogenous bases are on the inside, stacked perpendicular to the helix axis.

4. Base pairing (Chargaff's rules):
- The two strands are held together by hydrogen bonds between complementary base pairs:
- Adenine (A) pairs with Thymine (T): 2 hydrogen bonds ($A=T$)
- Cytosine (C) pairs with Guanine (G): 3 hydrogen bonds ($C\equiv G$)
- This is called Watson-Crick base pairing or complementary base pairing.
- Purines always pair with pyrimidines (A-T and G-C).

5. Dimensions of B-DNA:
- Diameter: 2.0 nm (20 Å)
- Pitch (rise per complete turn): 3.4 nm (34 Å)
- Number of base pairs per turn: 10
- Rise per base pair: 0.34 nm (3.4 Å)
- Angle of rotation per base pair: 36°

6. Major and Minor grooves:
- The double helix has two grooves:
- Major groove: Wider groove (2.2 nm wide)
- Minor groove: Narrower groove (1.2 nm wide)
- Proteins (transcription factors, restriction enzymes) interact with DNA through these grooves.

7. Base stacking:
- Adjacent base pairs are stabilised by hydrophobic stacking interactions (van der Waals forces) between the flat aromatic rings of the bases.

8. Complementarity:
- The two strands are complementary to each other.
- If one strand is 5'-ATCG-3', the complementary strand is 3'-TAGC-5' (or 5'-CGAT-3').

Significance:
- The model immediately suggested the mechanism of DNA replication (each strand serves as a template).
- It explained how genetic information is stored and transmitted.

Conclusion: The Watson-Crick model describes DNA as a right-handed antiparallel double helix with complementary base pairing (A=T and C≡G), a sugar-phosphate backbone on the outside, and bases stacked on the inside.

Concept: DNA can adopt different helical conformations depending on the hydration level, base sequence, and ionic conditions. The three major forms are A-DNA, B-DNA, and Z-DNA.

---
1. B-DNA (Watson-Crick form):
- The most common physiological form; found under high humidity (92% relative humidity) and normal physiological conditions.
- Right-handed double helix.
- 10 base pairs per turn.
- Pitch: 3.4 nm; Rise per bp: 0.34 nm; Diameter: 2.0 nm.
- Bases are nearly perpendicular to the helix axis.
- Has distinct major groove (wide, deep) and minor groove (narrow, shallow).
- This is the form described by Watson and Crick.

---
2. A-DNA:
- Found under low humidity conditions (75% relative humidity) or in DNA-RNA hybrid duplexes.
- Right-handed double helix.
- 11 base pairs per turn (more compact).
- Pitch: 2.8 nm; Rise per bp: 0.26 nm; Diameter: 2.3 nm (wider and shorter than B-DNA).
- Bases are tilted (~20°) with respect to the helix axis.
- Has a deep, narrow major groove and a shallow, wide minor groove.
- The helix is shorter and wider than B-DNA.

---
3. Z-DNA:
- Discovered by Alexander Rich (1979).
- Found in sequences with alternating purine-pyrimidine residues (e.g., alternating GC sequences) under high salt conditions.
- Left-handed double helix (coils counter-clockwise) — the key distinguishing feature.
- 12 base pairs per turn.
- Pitch: 4.5 nm; Rise per bp: 0.38 nm; Diameter: 1.8 nm (narrowest).
- The backbone has a zigzag appearance (hence 'Z').
- Has only one groove (equivalent to the minor groove of B-DNA).
- Biological role: may be involved in gene regulation.

---
Comparison Table:

| Feature | A-DNA | B-DNA | Z-DNA |
|---|---|---|---|
| Helix direction | Right-handed | Right-handed | Left-handed |
| bp per turn | 11 | 10 | 12 |
| Pitch | 2.8 nm | 3.4 nm | 4.5 nm |
| Rise per bp | 0.26 nm | 0.34 nm | 0.38 nm |
| Diameter | 2.3 nm | 2.0 nm | 1.8 nm |
| Base tilt | ~20° | ~0° | ~9° |
| Conditions | Low humidity | Physiological | High salt, alternating GC |

Conclusion: DNA exists in three major forms — A, B, and Z — differing in handedness, dimensions, and conditions of formation. B-DNA is the biologically predominant form.

Concept: Transfer RNA (tRNA) is an adaptor molecule that carries amino acids to the ribosome during protein synthesis. Its secondary structure resembles a cloverleaf when drawn in two dimensions, proposed based on the work of Robert Holley (1965, Nobel Prize 1968).

General features of tRNA:
- Single-stranded RNA molecule (~73–93 nucleotides long).
- Contains unusual/modified bases (e.g., pseudouridine $\Psi$, dihydrouridine D, inosine I, ribothymidine T).
- Folds back on itself to form intramolecular base pairs, creating the cloverleaf structure.

Structure of the Cloverleaf Model:

The cloverleaf has four arms (stems) and three loops (plus one variable loop):

1. Acceptor Stem (Amino Acid Arm):
- Located at the 3' end of the tRNA.
- Consists of 7 base pairs formed between the 5' and 3' ends of the molecule.
- The 3' end always has the sequence 5'-CCA-3' (CCA tail), which is the site of amino acid attachment (amino acid is esterified to the 3'-OH of the terminal adenosine).
- The 5' end usually has a phosphate group.

2. D-Loop (Dihydrouridine Loop):
- Located on the left side of the cloverleaf.
- Contains dihydrouridine (D) residues (unusual base).
- Involved in recognition by aminoacyl-tRNA synthetase (the enzyme that charges tRNA with the correct amino acid).
- The stem has ~3–4 base pairs.

3. Anticodon Loop:
- Located at the bottom of the cloverleaf (opposite to the acceptor stem).
- Contains the anticodon — a sequence of 3 nucleotides that is complementary to the codon on mRNA.
- The anticodon loop has 7 nucleotides (the middle 3 form the anticodon).
- This loop is critical for codon–anticodon recognition during translation.

4. TΨC Loop (T-Loop or Ribothymidine Loop):
- Located on the right side of the cloverleaf.
- Contains the sequence TΨC (ribothymidine-pseudouridine-cytidine).
- Involved in interaction with the ribosome (specifically with 5S rRNA).
- The stem has ~5 base pairs.

5. Variable Loop:
- Located between the anticodon loop and the TΨC loop.
- Size varies from 3–21 nucleotides depending on the tRNA species.
- Used to classify tRNAs into Class I (small variable loop, 3–5 nt) and Class II (large variable loop, 13–21 nt).

Three-dimensional (L-shaped) structure:
- In 3D, the cloverleaf folds into an L-shaped tertiary structure.
- The acceptor stem and TΨC arm form one arm of the L.
- The D-arm and anticodon arm form the other arm of the L.
- The anticodon is at one end and the CCA-3' amino acid attachment site is at the other end (~7.5 nm apart).

Summary of cloverleaf features:

| Component | Location | Function |
|---|---|---|
| Acceptor stem | 3' end | Amino acid attachment (CCA-3') |
| D-loop | Left arm | Aminoacyl-tRNA synthetase recognition |
| Anticodon loop | Bottom | Codon recognition on mRNA |
| TΨC loop | Right arm | Ribosome interaction |
| Variable loop | Between anticodon and TΨC | Classification of tRNA |

Conclusion: The cloverleaf model of tRNA shows four base-paired stems and three major loops (D-loop, anticodon loop, TΨC loop) plus a variable loop, with the CCA-3' acceptor end for amino acid attachment and the anticodon loop for mRNA codon recognition.

Correct Answer: (b) Aldehyde and ketone groups

Justification:
Carbohydrates are defined as polyhydroxy aldehydes (aldoses) or polyhydroxy ketones (ketoses). For example, glucose is an aldohexose (contains an aldehyde group $-CHO$ at C-1) and fructose is a ketohexose (contains a ketone group $C=O$ at C-2). Both types also contain multiple hydroxyl ($-OH$) groups, but the defining functional groups that classify a sugar as an aldose or ketose are the aldehyde and ketone groups respectively.

Correct Answer: (c) Sucrose

Justification:
Sucrose is a non-reducing disaccharide because the glycosidic bond is formed between the anomeric carbon (C-1) of $\alpha$-D-glucose and the anomeric carbon (C-2) of $\beta$-D-fructose ($\alpha$-1,2-glycosidic bond). Since both anomeric carbons are involved in the bond, there is no free anomeric $-OH$ group available to open the ring and act as a reducing agent. In contrast, maltose, lactose, and cellobiose all have one free anomeric carbon and are therefore reducing disaccharides.

Correct Answer: (b) Amino acids

Justification:
Proteins are polymers of amino acids. The amino acids are joined together by peptide bonds ($-CO-NH-$) formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of the next. The resulting chain is called a polypeptide. There are 20 standard amino acids that serve as the building blocks (repeating units) of all proteins.

Correct Answer: (a) $\alpha$-helix

Justification:
The $\alpha$-helix is the most common and most stable secondary structure found in proteins. It is a right-handed helical coil stabilised by intramolecular hydrogen bonds between the $C=O$ of residue $n$ and the $N-H$ of residue $n+4$. It is found abundantly in many proteins such as myoglobin, haemoglobin, and $\alpha$-keratin. While $\beta$-pleated sheets are also important, the $\alpha$-helix is considered the most prevalent secondary structural element.

Correct Answer: (a) Nitrogenous base, sugar and phosphate

Justification:
A nucleotide is composed of three components: (1) a nitrogenous base (purine or pyrimidine), (2) a pentose sugar (ribose in RNA; deoxyribose in DNA), and (3) one or more phosphate groups. The base is attached to the sugar via an N-glycosidic bond, and the phosphate is attached to the 5' carbon of the sugar via a phosphoester bond. A nucleoside (option c) contains only the base and sugar without the phosphate.

Correct Answer: (b) Hydrogen bond

Justification:
The two complementary strands of the DNA double helix are held together by hydrogen bonds between the complementary nitrogenous bases: Adenine (A) forms 2 hydrogen bonds with Thymine (T) ($A=T$) and Cytosine (C) forms 3 hydrogen bonds with Guanine (G) ($C\equiv G$). These are non-covalent interactions. Note: Phosphodiester bonds connect nucleotides within the same strand (backbone), not between the two strands.

Correct Answer: (b) Triacylglycerol

Justification:
Triacylglycerol (also called triglyceride) is the primary storage form of lipids in animals. It consists of a glycerol backbone esterified with three fatty acid molecules. Triacylglycerols are stored in adipose tissue and serve as a concentrated energy reserve (yielding ~9 kcal/g). Sphingolipids are structural membrane lipids, eicosanoids are signalling molecules, and fatty acids are the building blocks of lipids, not storage forms per se.

Correct Answer: (d) Ester bond

Justification:
In glycerolipids, fatty acids are attached to the hydroxyl groups ($-OH$) of the glycerol backbone through ester bonds ($-COO-$, also called acyl ester bonds). The reaction involves the carboxyl group ($-COOH$) of the fatty acid condensing with the hydroxyl group ($-OH$) of glycerol with the elimination of water: $$\text{Glycerol}-OH + HOOC-\text{Fatty acid} \rightarrow \text{Glycerol}-O-CO-\text{Fatty acid} + H_2O$$ This ester linkage is the defining bond in triacylglycerols and glycerophospholipids.