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Biomolecules: A Detailed Guide

1. Carbohydrates
2. Proteins
3. Lipids
4. Nucleic Acids

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1. Carbohydrates

Definition and General Formula

Classification

• Glucose - the predominant sugar in human blood; the brain's primary fuel
• Fructose - found in fruits; metabolized in the liver
• Galactose - from lactose digestion; found in milk

• Starch - plant storage form (amylose + amylopectin)
• Glycogen - animal/human storage form found in liver and muscle; a highly branched polysaccharide made of glucose units linked by α(1→4) bonds with α(1→6) branch points
• Cellulose - structural polysaccharide in plants; β(1→4) linkages make it indigestible by humans

Structure of Starch and Glycogen

Functions

• Primary energy source: oxidation yields 4 kcal/g
• Structural role (cellulose in plants, chitin in insects)
• Cell recognition and signaling (glycoproteins, glycolipids)
• Energy storage (glycogen in liver and muscle)

Digestion

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2. Proteins

Building Blocks: Amino Acids

• A central alpha-carbon (Cα)
• A carboxyl group (-COOH; ionized to -COO⁻ at physiologic pH)
• An amino group (-NH₂; protonated to -NH₃⁺ at physiologic pH)
• A distinctive side chain (R group) that determines properties

Classification of Amino Acids (by R group)

Levels of Protein Structure

• α-Helix: coiled structure; carbonyl group forms H-bond with the nitrogen 4 amino acids farther along the chain
• β-Sheet: extended parallel/antiparallel strands held by H-bonds
• Proline disrupts α-helices because its ring structure restricts backbone rotation

Key Points

• Proteins containing only one polypeptide do not have quaternary structure
• Disulfide bonds (-S-S-) form between two cysteine residues; stabilize extracellular proteins (e.g., albumin, fibrinogen)
• Hydrophobic side chains cluster in the protein interior (hydrophobic effect)
• Polar/charged side chains face outward toward the aqueous environment

Energy from Proteins

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3. Lipids

Definition

Major Classes

a) Fatty Acids

• Saturated: no double bonds (e.g., Palmitate C16:0, Stearate C18:0) - solid at room temperature
• Monounsaturated: one double bond (e.g., Oleate C18:1) - liquid at room temperature
• Polyunsaturated: multiple double bonds (e.g., linoleate, arachidonate)

b) Triacylglycerols (Fats/Triglycerides)

c) Phospholipids

• A glycerol backbone
• Two fatty acid tails (hydrophobic)
• A phosphate group linked to a polar head group (hydrophilic)
• This amphipathic nature drives spontaneous bilayer formation

d) Sterols

• Cholesterol: present in animal cell membranes; precursor for steroid hormones (cortisol, estrogen, testosterone, aldosterone), bile acids, and Vitamin D
• Steroid hormones: derived from cholesterol; act as intracellular receptors

e) Glycolipids and Sphingolipids

• Found in cell membranes, especially the nervous system (myelin sheath)
• Sphingomyelin is abundant in nerve cell membranes

Energy from Lipids

Body Fuel Stores Summary

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4. Nucleic Acids

Definition

Nucleotide Structure

1. A pentose sugar (deoxyribose in DNA; ribose in RNA)
2. A nitrogenous base (purine or pyrimidine)
3. A phosphate group

DNA - Deoxyribonucleic Acid

Key Features of DNA

• Double helix: two antiparallel polynucleotide strands wound around each other
• Sugar-phosphate backbone forms the outside; bases point inward
• Watson-Crick base pairing via hydrogen bonds:
  • A pairs with T (2 hydrogen bonds)
  • G pairs with C (3 hydrogen bonds)
• Individual strands are held by covalent bonds; the two strands are held together by noncovalent forces (H-bonds + van der Waals stacking interactions)
• The double helix buries hydrophobic bases in its interior; charged phosphates and polar hydroxyl groups face the aqueous environment

Functions of DNA

• Carries the complete genetic information (genome)
• Template for replication and transcription
• Mutations in DNA → changes in protein structure → disease

RNA - Ribonucleic Acid

• Contains ribose (has -OH at 2' carbon) instead of deoxyribose
• Single-stranded (mostly)
• Contains uracil instead of thymine

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Bonds That Stabilize Biomolecules

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Summary Table

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📚 B.Pharm 2nd Semester — Biochemistry (BP203T)

UNIT I: BIOMOLECULES

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INTRODUCTION TO BIOMOLECULES

1. Carbohydrates
2. Lipids
3. Proteins (Amino Acids)
4. Nucleic Acids

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SECTION 1: CARBOHYDRATES

1.1 Definition

1.2 Classification

• Aldoses - contain an aldehyde group (-CHO) e.g., Glucose, Galactose
• Ketoses - contain a keto group (>C=O) e.g., Fructose

• Trioses (C3): Glyceraldehyde, Dihydroxyacetone
• Pentoses (C5): Ribose, Deoxyribose, Ribulose
• Hexoses (C6): Glucose, Fructose, Galactose

1.3 Important Monosaccharides

• Most important monosaccharide; blood sugar in humans (normal fasting: 70-100 mg/dL)
• Exists mainly in ring (pyranose) form in solution
• Aldohexose; the brain depends almost exclusively on glucose for energy
• Linear (Fischer) form: aldehyde at C1, hydroxyl groups at C2-C6

• Ketohexose; sweeter than glucose
• Found in fruits and honey
• Metabolized in the liver; does not require insulin for cellular uptake

• Ribose (C5): found in RNA, ATP, NAD⁺, FAD
• Deoxyribose (C5): found in DNA (lacks -OH at C2)

1.4 Disaccharides

1.5 Polysaccharides

• Made of glucose units; two components:
  • Amylose - unbranched; α(1→4) linkages; ~20-25% of starch
  • Amylopectin - branched; α(1→4) chain with α(1→6) branch points every 24-30 residues; ~75-80% of starch

• Stored in liver (~100g) and muscle (~400g)
• Highly branched: α(1→4) chain with α(1→6) branches every 8-12 residues (more branches than amylopectin)
• Released rapidly as glucose when blood glucose falls

• β(1→4) linkages between glucose units - humans cannot digest it
• Acts as dietary fiber; important for gut motility

1.6 Biological Roles of Carbohydrates

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SECTION 2: LIPIDS

2.1 Definition

2.2 Classification

• Fats (Triacylglycerols / Triglycerides): 3 fatty acids + 1 glycerol
• Waxes: fatty acid + long-chain alcohol

• Phospholipids: glycerol + 2 fatty acids + phosphate + polar head group
  • Phosphatidylcholine (lecithin), Phosphatidylethanolamine (cephalin), Phosphatidylserine, Phosphatidylinositol
• Glycolipids: ceramide + sugar; e.g., cerebrosides, gangliosides
• Sphingolipids: sphingosine backbone; e.g., sphingomyelin (major in myelin sheath)
• Lipoproteins: lipid + protein complexes for transport in blood (LDL, HDL, VLDL)

• Fatty acids, sterols, cholesterol, bile acids, steroid hormones, fat-soluble vitamins (A, D, E, K)

2.3 Fatty Acids

2.4 Triacylglycerols (TAGs)

• Stored mainly in adipose tissue
• Hydrophobic → compact storage (unlike glycogen which is hydrated)
• Mobilized during fasting by hormone-sensitive lipase

2.5 Phospholipids

• Phosphatidylcholine (lecithin): most abundant; forms bilayer; component of lung surfactant
• Phosphatidylethanolamine: inner leaflet of plasma membrane
• Phosphatidylserine: inner membrane; important in apoptosis signaling
• Phosphatidylinositol: precursor of second messenger IP₃/DAG

2.6 Cholesterol

• A sterol (steroid + alcohol)
• Has a characteristic 4-ring (steroid nucleus) structure
• Present in all animal cell membranes; modulates membrane fluidity
• Precursor for:
  • Steroid hormones: cortisol, aldosterone, estrogen, testosterone, progesterone
  • Bile acids: emulsify dietary fats for absorption
  • Vitamin D: after UV-B skin exposure
  • Cholesterol esters: storage/transport form

2.7 Biological Roles of Lipids

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SECTION 3: AMINO ACIDS AND PROTEINS

3.1 Amino Acids — Definition and General Structure

• An alpha-carbon (Cα)
• A carboxyl group (-COOH) → ionized as -COO⁻ at physiologic pH
• An amino group (-NH₂) → protonated as -NH₃⁺ at physiologic pH
• A side chain (R group) — unique to each amino acid

3.2 Classification of Amino Acids

• Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Proline (Pro, P), Phenylalanine (Phe, F), Tryptophan (Trp, W), Methionine (Met, M)
• Side chains are "oily" — cluster inside folded proteins (hydrophobic effect)
• Proline is unique: its R group forms a ring with its own nitrogen → secondary amino group → breaks α-helices

• Serine (Ser, S), Threonine (Thr, T), Tyrosine (Tyr, Y), Asparagine (Asn, N), Glutamine (Gln, Q), Cysteine (Cys, C)
• Participate in hydrogen bonds
• Cys: -SH group → forms disulfide bonds (-S-S-) between cysteines → stabilize protein structure
• Ser, Thr, Tyr: phosphorylated by kinases → signal transduction

• Aspartate (Asp, D), Glutamate (Glu, E)
• Lose protons at physiologic pH → negative charge (-COO⁻)

• Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)
• Accept protons → positive charge
• Histidine: only amino acid that ionizes within the physiologic pH range (7.35-7.45) → important buffer in hemoglobin and other proteins

• Essential amino acids (cannot be synthesized; must come from diet): Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Leucine, Lysine
  • Mnemonic: PVT TIM HaLL
• Non-essential amino acids: Synthesized by the body (e.g., Alanine, Glycine, Serine)
• Conditionally essential: Required only in disease states or rapid growth (e.g., Arginine, Glutamine)

3.3 Peptide Bond

• Has partial double bond character (resonance) → rigid, planar
• Trans configuration is preferred
• The backbone of a polypeptide is -[NH-CHR-CO]n-

• 2 AAs → dipeptide
• 3 AAs → tripeptide
• Up to ~50 AAs → polypeptide (or oligopeptide)

• 50 AAs → protein

3.4 Levels of Protein Structure

• The linear sequence of amino acids from N-terminus to C-terminus
• Held by covalent peptide bonds
• Determines all higher levels of structure
• Example: The specific sequence of 574 amino acids in hemoglobin β-chain

• Local regular folding of the polypeptide backbone
• Held by hydrogen bonds between backbone C=O and N-H groups
• Two major types:
  • α-Helix: right-handed coil; C=O of residue n hydrogen bonds to N-H of residue n+4; 3.6 residues per turn; Proline breaks it
  • β-Sheet: extended strands linked by H-bonds; can be parallel or antiparallel

• Overall 3D shape of a single polypeptide chain
• Stabilized by multiple noncovalent forces + disulfide bonds:
  • Hydrophobic interactions (nonpolar R groups buried inside)
  • Ionic (electrostatic) bonds (salt bridges)
  • Hydrogen bonds (polar side chains)
  • Van der Waals forces
  • Disulfide bonds (-S-S-) between Cys residues (covalent)

• Assembly of two or more polypeptide subunits (chains)
• Held by the same noncovalent forces as tertiary structure
• Example: Hemoglobin = 2α + 2β subunits; Insulin = A chain + B chain (linked by disulfide bonds)

3.5 Biological Roles of Proteins

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SECTION 4: NUCLEIC ACIDS

4.1 Definition and Types

• DNA (Deoxyribonucleic acid): stores genetic information
• RNA (Ribonucleic acid): involved in expressing genetic information (transcription, translation)

4.2 Structure of a Nucleotide

1. Pentose sugar: Deoxyribose (in DNA) or Ribose (in RNA)
2. Nitrogenous base: Purine or Pyrimidine
3. Phosphate group (one to three; monophosphate, diphosphate, triphosphate)

Memory Aid: PuRines have double rings (think: pURe gold = more valuable, more rings). Pyrimidines = CUT (Cytosine, Uracil, Thymine)

4.3 Structure of DNA

• Two antiparallel polynucleotide strands wound around each other in a right-handed double helix
• Sugar-phosphate backbone forms the outer (hydrophilic) part
• Nitrogenous bases are inside (hydrophobic), stacked perpendicular to the helix axis
• Strands are held together by hydrogen bonds between complementary base pairs:
  • A — T (Adenine-Thymine): 2 hydrogen bonds
  • G ≡ C (Guanine-Cytosine): 3 hydrogen bonds
• Chargaff's Rule: In any DNA, %A = %T and %G = %C
• Helix parameters: ~10 base pairs per turn; 3.4 Å between base pairs; 34 Å per turn
• Backbone: nucleotides linked by phosphodiester bonds (between 3'-OH of one sugar and 5'-phosphate of next)

4.4 Structure of RNA

4.5 Types of RNA

4.6 Biological Roles of Nucleic Acids

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QUICK COMPARISON TABLE

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HIGH-YIELD EXAM POINTS

1. Reducing sugars: All monosaccharides; maltose, lactose are reducing disaccharides. Sucrose is NON-reducing (anomeric carbons of both monomers are involved in the bond).
2. Chargaff's Rule: A=T, G≡C in DNA; (A+G)/(T+C) = 1 always.
3. Essential amino acids: PVT TIM HaLL (9 essential AAs).
4. Proline — breaks alpha helices; has secondary amino group (imino group).
5. Histidine — only amino acid that ionizes within physiologic pH range; key buffer in hemoglobin.
6. Disulfide bonds — covalent; between cysteine residues; stabilize extracellular proteins.
7. Phospholipids are amphipathic → form bilayers → basis of all biological membranes.
8. Glycogen has more branch points than starch (branch every 8-12 residues vs. 24-30 in amylopectin) → allows faster glucose mobilization.
9. Insulin glargine (pharmaceutical application): created by substituting Asn→Gly at A21 and adding Arg residues to C-terminus of B chain → shifts isoelectric point, slower absorption → long-acting insulin.
10. Fat-soluble vitamins (A, D, E, K) are lipid biomolecules; absorbed with dietary fat.

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PHARMACEUTICAL RELEVANCE

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📝 BIOMOLECULES — SHORT NOTES

B.Pharm 2nd Sem | BP203T Biochemistry | Unit I

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1. CARBOHYDRATES

Classification:

Types of Monosaccharides:

• Aldose = aldehyde group → Glucose, Galactose
• Ketose = keto group → Fructose
• Pentose (C5): Ribose (RNA), Deoxyribose (DNA)
• Hexose (C6): Glucose (blood sugar), Fructose, Galactose

Key Disaccharides:

Key Polysaccharides:

Functions:

• Energy (4 kcal/g) → Glycogen in liver & muscle
• Structure → Cellulose, Chitin
• Cell recognition → Glycoproteins, Blood groups (ABO)
• Nucleic acid backbone → Ribose, Deoxyribose
• Coenzyme component → Ribose in ATP, NAD⁺

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2. LIPIDS

Classification:

Fatty Acids:

• Saturated (no double bonds): Palmitic (C16:0), Stearic (C18:0) — solid
• Monounsaturated (1 double bond): Oleic (C18:1) — olive oil
• Polyunsaturated: Linoleic (C18:2), Linolenic (C18:3) — Essential (must come from diet)
• Arachidonic acid → precursor of eicosanoids (prostaglandins, thromboxanes, leukotrienes)

Triacylglycerols (TAGs):

• 3 fatty acids + glycerol (ester bonds)
• Major energy store in adipose tissue
• 9 kcal/g; mobilized by hormone-sensitive lipase

Phospholipids:

• Glycerol + 2 FA + phosphate + polar head group
• Amphipathic → form cell membrane bilayers
• Types: Phosphatidylcholine (lecithin), Phosphatidylethanolamine, Phosphatidylserine, Phosphatidylinositol
• Lecithin → lung surfactant; liposome drug delivery

Cholesterol:

• Sterol with 4-ring steroid nucleus
• Modulates membrane fluidity
• Precursor → steroid hormones, bile acids, Vitamin D

Functions of Lipids:

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3. AMINO ACIDS & PROTEINS

Amino Acids:

Classification by R group:

Essential Amino Acids (9):

Special Points:

Peptide Bond:

• Formed between -COOH of one AA and -NH₂ of another → releases H₂O (condensation)
• Has partial double bond character → rigid, planar, usually trans

Protein Structure — 4 Levels:

• α-Helix: C=O of residue n H-bonds to N-H of residue n+4; 3.6 residues/turn
• β-Sheet: Extended strands, H-bonds between strands; parallel or antiparallel
• Proline breaks α-helices
• Hydrophobic R groups face inside; polar/charged face outside

Functions of Proteins:

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4. NUCLEIC ACIDS

Nucleotide = Pentose sugar + Nitrogenous base + Phosphate group

Bases:

Memory: "CUT the Py" → Cytosine, Uracil, Thymine = Pyrimidines

DNA vs RNA:

DNA Double Helix (Watson & Crick, 1953):

• Two antiparallel strands; right-handed helix
• Backbone: Sugar-phosphate (outside, hydrophilic)
• Bases: inside (hydrophobic), stacked
• Base pairing:
  • A = T (2 H-bonds)
  • G ≡ C (3 H-bonds)
• Strands linked by phosphodiester bonds
• Chargaff's Rule: %A = %T, %G = %C

Types of RNA:

Functions of Nucleic Acids:

• DNA → stores and replicates genetic info
• mRNA/rRNA/tRNA → protein synthesis
• ATP → universal energy currency
• cAMP, cGMP → second messengers
• NAD⁺, FAD, CoA → coenzymes (contain nucleotide portion)

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MASTER SUMMARY TABLE

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HIGH-YIELD EXAM POINTS (One-liners)

1. Sucrose = non-reducing sugar (both anomeric carbons locked)
2. Glycogen branches every 8-12 residues; Amylopectin every 24-30
3. Cellulose has β(1→4) bonds → not digested by humans → dietary fiber
4. Lipids yield 9 kcal/g (double that of carbs/proteins)
5. Essential fatty acids: Linoleic (ω-6) and α-Linolenic acid (ω-3)
6. Essential amino acids: 9 (PVT TIM HaLL)
7. Proline → breaks α-helix (secondary amino group, ring structure)
8. Histidine → ionizes at physiological pH → acts as buffer in hemoglobin
9. Cysteine → disulfide bonds → stabilize protein 3D structure
10. Chargaff's rule: A=T, G≡C in DNA
11. Thymine only in DNA; Uracil only in RNA
12. 3 H-bonds in G≡C; 2 H-bonds in A=T
13. Phospholipids are amphipathic → form bilayers → basis of all membranes
14. Cholesterol precursor → steroid hormones + bile acids + Vitamin D
15. tRNA has cloverleaf secondary structure + anticodon loop

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PHARMACEUTICAL APPLICATIONS (Short)

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