Biochemistry MC2 Notes: Modules 1–4

Module 1: INTRODUCTION TO BIOCHEMISTRY

Definition and scope
- Biochemistry deals with the chemical processes occurring in living matter to explain life phenomena such as digestion, absorption, metabolism, respiration, and reproduction.
- It provides the physicochemical basis for understanding life processes in allied health professions.
Short history of biochemistry
- Biochemistry is a relatively young science; term coined in 1930 by Carl Newburg.
- Karl Scheele (1700) is considered the “Father of Biochemistry” for early work on chemical composition of living matter.
Relevance to medical and allied health students
- Explains differentiation of cells and organisms; origin of life; hormone action and its role in diseases at the molecular level; foundational for understanding disease mechanisms.
Branches and scope
- ANIMAL BIOCHEMISTRY (physiological chemistry)
- PLANT BIOCHEMISTRY (phytochemistry; genetic engineering applications)
Biomolecules and the hierarchy of molecular organization
- Biomolecules: proteins, carbohydrates, lipids, nucleoproteins.
- Building blocks (monomers) and precursors give rise to macromolecules (polymers) and supramolecular units (granules, membranes, vesicles, tubules, cisternae, reticuli).
- ORGANELLES are the functional units at the cellular level; the highest level in the molecular hierarchy.
Living vs. non-living matter (biochemical standpoint)
- Living matter is highly organized, with specialized cellular functions; energy extraction and conversion; growth, replication/reproduction; metabolism; motility; irritability.
General properties of organic compounds (vs inorganic)
- I. Covalent bonds; mostly non-electrolytes; few ionize; many are insoluble in water; nonpolar solvents prevail.
- II. Isomerism is common; multiple structural variants with same atoms but different arrangements.
- III. Organic compounds are generally unstable; flammable; may char and decompose at moderate temperatures; lack sharp melting points.
- IV. Organic reactions tend to be slower than inorganic reactions; lab reactions often require longer times or catalysts.
Self-Assessment Self-Assessment Questions (SAQ) and Answers (ASAQ)
- SAQ #1: What are the two branches of biochemistry? (Plant/Phytochemistry and Animal/Physiological chemistry)
- SAQ #1: What are the four important studies yielded in biochemistry? (Differentiation of Cells & Organism; Understanding of Origin of Life; Hormone action and memory; Emergence of diseases at molecular level)
- SAQ #1: Building blocks and biomolecules (Carbohydrates – monosaccharides; Proteins – amino acids; Lipids – fatty acids; Nucleoproteins – nucleic acids)
- SAQ #1: Examples of supramolecular bodies (granules, membranes, vesicles, tubules, cisternae, reticuli)
- SAQ #1: Properties common to living organisms not manifested by non-living matter (metabolism, motility, growth, irritability, reproduction, energy extraction and transformation, etc.)
Connections to foundational principles and real-world relevance
- Links to organic chemistry, physiology, and clinical biochemistry (e.g., metabolism, nutrition, enzymology, hormones).
Numerical references and formulas (examples)
- Biomolecule building blocks and formulas:
- Trioses: $C3H6O_3$
- Tetroses: $C4H8O_4$
- Pentoses: $C5H{10}O_5$
- Hexoses: $C6H{12}O_6$
- Heptoses: $C7H{14}O_7$
- Disaccharides: $C{12}H{22}O_{11}$
Summary of Module 1 takeaways
- Biochemistry bridges chemistry with biology; it explains how molecular interactions translate to cellular, tissue, and organismal function.

Module 2: BIOCHEMISTRY OF THE CELL

Module objective (Intended Learning Outcomes, ILO)
- Explain differences in physico-chemical properties of cells; describe chemical composition and intracellular reactions; differentiate prokaryotic vs. eukaryotic cells; identify biochemical systems in cellular structures; execute lab simulations of diffusion, osmosis, dialysis, surface tension.
Outline of topics
- General physico-chemical properties of cells; differences between prokaryotic and eukaryotic cells; biomolecules in cellular structures; chemical reactions in living cells; biochemical processes in cells.
General physicochemical properties of cells
- Factors influencing cell size/shape: functional adaptation; surface tension; glycolipid content; cytoplasm viscosity; mechanical pressure; intracellular biochemical reactions.
Differences between prokaryotic and eukaryotic cells (biochemical systems view)
- Table: cell wall, membrane, DNA, nucleus, chromosomes, nuclear membrane, Golgi, lysosome, microbodies, endoplasmic reticulum, ribosomes (70S in prokaryotes vs 80S in eukaryotes).
Biochemical systems in the cell (overview of organelles and functions)
- I. Water: ~70-90% of cytoplasm; universal solvent; high specific heat; determinant of cell structures via ions.
- II. Cell membrane and associated structures
- Membrane is lipoprotein with a lipid matrix sandwiched between protein layers (peripheral and integral proteins).
- Function: semi-permeable barrier; passive transport (water, urea, chlorides) and active transport (sodium, potassium, amino acids, glucose, etc.).
- Glycocalyx: mucopolysaccharides, glycolipids, glycoproteins; functions include diffusion barrier, tissue organization, cell recognition, and diffusion/osmosis/surface tension.
- Membrane lipid/protein composition varies by organelle (examples: RBC 40% lipid/60% protein; mitochondria 20-25% lipid/75-80% protein; neurilemma 75% lipid/25% protein).
- III. Cytosol (cytoplasmic matrix): major glycolytic and carbohydrate metabolism processes
- Glycolysis; HMP shunt (pentose phosphate pathway); gluconeogenesis; glycogenesis.
- IV. Nucleus: Perinuclear membrane; DNA; chromosomes (DNA + histones).
- V. Mitochondria: energy production via Respiratory Electron Transport Chain (ETC) and oxidative phosphorylation; beta-oxidation; Knoop's oxidation.
- VI. Endoplasmic Reticulum: lipid synthesis; steroid hormone production.
- VII. Golgi complex: glycosylation; vesicular transport and secretion of proteins/enzymes.
- VIII. Lysosomes: hydrolytic enzymes for intracellular digestion (phosphatases, peptidases, glycosidases, RNase, DNase).
- IX. Microbodies/Peroxisomes: oxidation of nutrients; metabolism of hydrogen peroxide; enzymes like catalase; found in kidney and liver.
Chemical reactions in cells
- Oxidation: loss of electrons; aerobic (oxidation with oxygen) vs anaerobic (loss of hydrogen or electrons without oxygen).
- Reduction: gain of electrons; redox coupling with oxidation.
- Hydrolysis: addition of water leading to fragmentation; condensation is the reverse, forming larger molecules with water release.
- Tautomerism: isomerization via intramolecular rearrangement; enol-keto tautomerism.
Characteristics of cellular reactions
- Mild reactions; enzyme-catalyzed acceleration; ordered processes due to cellular differentiation.
Self-Assessment Questions (SAQ) and answers (ASAQ)
- SAQ #3: List 2 reasons why cells vary in size/shape; 2+ biochemical functions of glycocalyx; etc.
- ASAQ #3 provides enumeration-type answers (e.g., prokaryotic/eukaryotic DNA, nuclear membrane presence, etc.).
Connections to laboratory concepts
- Diffusion, osmosis, dialysis, and surface tension are foundational to understanding transport and membrane physiology.
Summary of Module 2 takeaways
- Cellular life is organized into hierarchies with membranes and organelles performing specialized biochemical functions; transport and energy metabolism are central to cellular homeostasis.

Module 3: CHEMISTRY OF CARBOHYDRATES

Intent and scope
- Carbohydrates are the simplest yet most abundant biomolecules; foundational to energy and structure; form a significant portion of foods and energy metabolism.
Definitions and classifications
- Carbohydrates (saccharides) are polyhydroxyaldehydes or polyhydroxyketones and derivatives.
- Major classes: Monosaccharides, Oligosaccharides, Polysaccharides, Derived carbohydrates.
Monosaccharides (classification by carbon count)
- Trioses: $C3H6O_3$
- Tetroses: $C4H8O_4$
- Pentoses: $C5H{10}O_5$
- Hexoses: $C6H{12}O_6$
- Heptoses: $C7H{14}O_7$
Oligosaccharides and polysaccharides
- Disaccharides: $C{12}H{22}O_{11}$ (e.g., sucrose, lactose, maltose)
- Trisaccharides (e.g., raffinose)
- Polysaccharides: Starch (plant storage), Glycogen (animal storage), Dextrin, Cellulose (structural; indigestible; fiber)
- Homopolysaccharides vs heteropolysaccharides (mucopolysaccharides): Heparin, Hyaluronic acid, Chondroitin sulfate; glycoproteins/glycolipids as membrane components.
Functions of carbohydrates
- Structural (cell wall components, cellulose; chitin in arthropods; alginate/pectin in plant matrices).
- Energy source and storage (glucose as a major energy source; starch in plants; glycogen in animals).
- Other roles: antigen-antibody interactions (glycoproteins), filtration barriers, lubrication of joints, protective cell coats (glycophorins on RBCs), regulatory (glycoproteins as cofactors or signal molecules), transport (secretory proteins), cell membrane components (glycoproteins, mucopolysaccharides), clotting protein components (fibrinogen glycoprotein family), catalytic functions (some enzymes are glycoproteins).
- Carbon source for biosynthesis of other biomolecules.
Structural and chemical properties
- Monosaccharides: cyclic forms via hemiacetal/hemiketal formation; mutarotation (alpha/beta anomers); Haworth projections (pyranose/furanose forms).
- Isomerism: D/L notation; epimers (e.g., glucose vs galactose at C4, glucose vs mannose at C2); anomers (alpha/beta) arising from ring closure at C-1.
- Ring notation: Haworth (cyclic) vs Fisher (open-chain) projection; mutarotation demonstrates interconversion between forms.
Reactions of carbohydrates
- Reducing sugars form osazone crystals with phenylhydrazine (aldehyde/ketone group responsible).
- Reduction: glucose → sorbitol; mannose → mannitol (biologically relevant in diabetes and culture media).
- Oxidation: aldoses → aldonic acids (glucose → gluconic acid); aldaric acids (glucose → saccharic acid); uronic acids (glucose → glucuronic acid).
- Alkaline and acidic reactions show various transformations: Lobry de Bruyn–Alberda van Ekenstein rearrangement; Mutarotation; Molisch test for carbohydrates; Seliwanoff’s test for ketoses; Bial’s orcinol test for pentoses; Benedict’s/Fehling’s tests for reducing sugar.
Laboratory topics and activities
- Formula writing and ring structures (Haworth projections) for pyranose and furanose forms.
- Lab techniques to identify and differentiate carbohydrates using qualitative/quantitative tests.
Self-Assessment and Practice items (SAQ/ASAQ)
- Matching, multiple-choice, and short-answer questions covering: structural forms (Fisher/Haworth), mutarotation, epimers, alkali/acid reactions, tests for reducing sugars, etc.
Laboratory activities
- Formula writing (HD: ring forms like pyranose/furanose; chemical names for acids like gluconic), structural drawings for disaccharides (sucrose/maltose/lactose).
Key carbohydrate formulas and examples (LaTeX-formatted):
- Monosaccharide group formulas: Trioses $C3H6O3$ , Tetroses $C4H8O4$ , Pentoses $C5H{10}O5$ , Hexoses $C6H{12}O6$ , Heptoses $C7H{14}O_7$
- Disaccharides: $C{12}H{22}O_{11}$ (e.g., Sucrose = glucose + fructose; Lactose = glucose + galactose; Maltose = glucose + glucose)
- Carbohydrate ring stereochemistry: Haworth projections and mutarotation concept (alpha/beta anomers)
Relevance and study connections
- Understanding carbohydrate chemistry underpins metabolism, energy pathways, and diagnostic tests (e.g., reducing sugar tests) used in clinical settings.

Module 4: CHEMISTRY OF LIPIDS

Lipids: definition and properties
- Lipids are water-insoluble organic substances; soluble in organic nonpolar solvents (chloroform, ether, acetone, benzene).
- They serve as membrane components, energy storage, transport forms of fuel, regulatory hormones, protective barriers, enzyme cofactors (some vitamins), neurotransmitter transport, receptor functions, and immune determinants.
Classification of lipids
- A. Fatty acids (the building blocks of many lipids)
- B. Lipids containing glycerol (glycerol-containing lipids):
- 1) Neutral fats (triacylglycerols/ triglycerides)
- 2) Phosphoglycerides (glycerol phosphatides; phospholipids)
- C. Lipids not containing glycerol:
- 1) Sphingolipids (ceramide, sphingomyelin, glycosphingolipids)
- 2) Aliphatic alcohols and waxes
- 3) Terpenes
- 4) Steroids
- 5) Prostaglandins
- D. Lipids that combine with other lipids or proteins: lipoproteins; glycolipids
Fatty acids: structure and nomenclature
- Structure: aliphatic monocarboxylic acids; chain length 4–24 C atoms; can be saturated or unsaturated; naturally occurring FAs are usually even-numbered (C16–C18 common).
- Cis configuration predominates in natural fatty acids; trans fats are rare in nature.
- Delta (Δ) nomenclature (counting from carboxyl end): e.g., linoleic acid 18:2(Δ9,12); palmitic acid 16:0; oleic acid 18:1(Δ9).
- N-system nomenclature: counts from methyl end, e.g., linoleic acid 18:2(n-6).
Important fatty acids (examples)
- Lauric (C12:0), Myristic (C14:0), Palmitic (C16:0), Stearic (C18:0), Palmitoleic (C16:1), Oleic (C18:1), Linolenic (C18:3), Linoleic (C18:2), Arachidonic (C20:4).
Glycerol and glycerol-containing lipids
- Glycerol: C3H8O3; by-product in soap manufacture; used in pharmacology and cosmetics; glycerol backbone in triglycerides and phosphoglycerides; hydrolysis yields glycerol and fatty acids.
- Phosphoglycerides (phospholipids): amphipathic; major components of membranes; lecithin, cephalin, and lipositols as examples; lysolecithin (detergent; disruptive to membranes) arises from phosphorylation and removal of middle fatty acid.
- Cardiolipin: diphosphatidylglycerol; important in mitochondrial membranes; unique structure with two phosphatidic acid units connected by glycerol.
- Plasmalogens: phospholipids with ether linkage at the alpha position of glycerol; significant in brain and muscle tissues.
Lipids not containing glycerol
- Sphingolipids: backbone of sphingosine; three components (one sphingosine, one fatty acid, one polar head group); cerebrosides, gangliosides; CNS predominance in white matter; ceramide and sphingomyelin are major sphingolipids; glycosphingolipids (glycolipids) lack phosphate and contain carbohydrates; cerebrosides (galactocerebrosides in adult brain; glucocerebrosides in others); gangliosides contain sialic acid.
- Waxes: long-chain fatty acids esterified to long-chain alcohols; protective coatings (skin, fur, leaves, fruits).
- Terpenes: polymers of isoprene units; vitamins A, E, K are lipid-soluble terpenes; coenzymes and non-saponifiable lipids; carotenoids and ubiquinone are terpenoid lipids.
- Steroids: tetracyclic ring system (perhydrocyclopentanophenanthrene); oxygenated substituents at C3; examples include cholesterol, bile acids, adrenocortical hormones, androgens, estrogens; some steroids (e.g., digitoxigenin) function as cardiac glycosides.
- Prostaglandins: fatty acid derivatives with hormone-like regulatory actions; many subtypes (PGE1, PGF1α, etc.) with roles in vascular tone, labor induction, and inflammation.
Cholesterol and bile acids
- Cholesterol: abundant in membranes; precursor to bile acids, steroid hormones; normal plasma cholesterol ~200 mg/100 mL; amphipathic with cholesterol esters as storage in lipoproteins.
- Bile acids/salts: steroid in nature; emulsifying agents for lipid absorption in the intestine; side chains with COOH groups; glycocholic, cholic, deoxycholic, lithocholic acids as examples.
Lipoproteins
- Lipids transported in the blood bound to proteins; HDL, LDL, VLDL, chylomicrons with distinct compositions and roles in lipid transport and disease risk.
Prostaglandins, vitamins, and enzymes
- Prostaglandins: regulatory lipids with diverse actions (e.g., PGE1, PGE2) and therapeutically exploited in obstetrics and cardiovascular contexts.
Laboratory tests and practical properties of lipids
- Iodine number, saponification number, acid number, Polenske number, Reichert-Meissel number, acetyl number for fats/oils; Liebermann-Burchard test for cholesterol; Salkowski’s test for cholesterol/phospholipids; practical tests to identify fats/oils.
Some key practice items and assessment tools (SAQ/ASAQ/MATCHING/FILL-IN-THE-BLANK)
- True/False and modified multiple-choice questions cover: fatty acid structure, chain length, cis/trans, esterification, saponification, bile acids, and the role of lipids in membranes and transport.
- Laboratory activities and exercises include: diffusion, formula writing for fatty acids, ring structures (Haworth), and lipid reactions (reactions of fats).
Important formulas and examples (LaTeX)
- Fatty acid nomenclature: $ext{e.g., } ext{linoleic acid} = 18:2( ext{n-6}) ext{ or } 18:2( ext{Δ}9,12)$
- Glycerol backbone: $C3H8O_3$
- Cardiolipin: diphosphatidylglycerol (structure described, not a simple formula)
- Phosphoglycerides: major membrane lipids; Lecithin and Cephalin as examples; chemical structure implications on membrane properties (amphipathic,
 glycosyl and phosphate groups).
Connections to health and disease
- Lipid dysregulation relates to cardiovascular disease; cholesterol metabolism links to bile acids and steroid synthesis; peroxisomal and mitochondrial lipid metabolism is central to energy homeostasis and detoxification.
Summary of Module 4 takeaways
- Lipids are diverse, energetically important, and structurally essential components of membranes and signaling; their chemistry is governed by hydrophobic/hydrophilic balance and functional groups; lipid classification informs understanding of nutrition, metabolism, and pathology.