Cell Chemistry & Biomolecules – Comprehensive Study Notes

Chemical Composition of the Cell

Living matter is a complex mixture of chemicals ranging from very small molecules (e.g., $H_2O$ ) to very large polymers (e.g., DNA, polysaccharides).
Water
- Most abundant substance in all known organisms (70–90 % of cell mass).
- Provides the aqueous medium (cytosol) in which organelles and soluble proteins reside.
- Its polarity drives the segregation of non-polar molecules (basis of membrane formation) and the solubility of polar/charged compounds.
Cytoplasm
- Composed of cytosol (water + dissolved proteins, ions, small molecules) and suspended organelles.
- Site of many metabolic pathways and macromolecular assemblies.

Hierarchy of Biological Organization

Atom – smallest unit of an element; building block of matter.
Element – pure substance that cannot be chemically broken down.
Molecule – two or more atoms chemically bonded (smallest unit of a compound).
Organelle – specialized intracellular structure (e.g., nucleus, ribosome).
Cell – smallest unit exhibiting all characteristics of life.
Tissue – group of similar cells performing a common function (muscle, bone, skin, etc.).
Organ – collection of tissues cooperating for a specific task (heart, stomach, brain).
System – group of organs working together (digestive, skeletal, etc.).
Organism – complete living entity; may be unicellular or multicellular (with multiple organ systems).

Three Molecular Levels of Organization

Elements (and simple ions)
- Major: Oxygen, Carbon, Nitrogen, Hydrogen, Phosphorus, Sulfur.
- Ions: Sodium, Potassium, Magnesium, Calcium, Chloride.
- Trace minerals: Manganese, Iron, Cobalt, Copper, Zinc, Aluminum, Iodine, Nickel, Chromium, Selenium, Boron, Vanadium, Molybdenum, Silicon, Tin, Fluorine.
Building Blocks (small bio-organic molecules)
- Amino acids, nucleotides, sugars, fatty acids, glycerol, phosphate, purines, pyrimidines, ribose, deoxyribose, others.
Macromolecules (polymers of building blocks)
- Nucleic Acids.
- Proteins.
- Lipids (technically not always polymers but large assemblies).
- Carbohydrates / Polysaccharides.

Nucleic Acids

Subtypes: DNA and RNA.
General architecture
- Polymer of nucleotides linked via phosphodiester bonds.
- Each nucleotide = nitrogenous base + pentose sugar + phosphate.
DNA (Deoxyribonucleic Acid)
- Bases: Adenine, Guanine, Cytosine, Thymine.
- Sugar: deoxyribose.
- Double-stranded helix; repository of hereditary information; directs macromolecule synthesis and energy production; transmitted to progeny.
RNA (Ribonucleic Acid)
- Bases: Adenine, Guanine, Cytosine, Uracil (replaces thymine).
- Sugar: ribose.
- Generally single-stranded; often folds into hairpins.
- Functional classes
- Messenger RNA (mRNA): conveys genetic code from DNA to ribosome.
- Transfer RNA (tRNA): adaptor between mRNA codon and amino acid during translation.
- Ribosomal RNA (rRNA): structural/enzymatic core of ribosome; catalyzes peptide-bond formation.
- Small stable RNAs / ribozymes: diverse regulatory or catalytic roles; some still unknown.
Additional facts
- Some viruses store genomes as RNA; a few reverse-transcribe RNA → DNA.
- Mitochondria possess their own circular DNA distinct from nuclear genome.
- Nucleotide triphosphates (e.g., $ATP$ ) act as universal energy currency and ancient signalling molecules.

Proteins

Composed of 20 standard amino acids, each with common backbone ((\alpha)-carboxyl, (\alpha)-amino, (\alpha)-hydrogen) and variable side chain ((R)).
Amino acid classification (by side-chain properties)
- Charge: acidic ((\text{Asp}^−, \text{Glu}^−)), basic ((\text{Lys}^+, \text{Arg}^+, \text{His}^+)).
- Polarity: hydrophilic vs. hydrophobic (e.g., (\text{Val}, \text{Leu}, \text{Ile})).
- Special groups: sulfur-containing (Cys, Met), aromatic (Phe, Tyr, Trp).
Sequence of amino acids (primary structure) is dictated by mRNA codon order; determines higher-order folding and function.
Cellular roles
- Structural (cytoskeleton, collagen) and motor (myosin, dynein).
- Enzymatic catalysis (metabolic reactions).
- Signalling (hormones, receptors) and regulation (transcription factors).
- Multifunctionality: some proteins perform several of the above.
Domains: distinct structural/functional modules (e.g., catalytic vs. regulatory), often evolutionarily conserved across species (yeast → human).
Membrane proteins may contain hydrophobic trans-membrane domains enabling insertion into lipid bilayer.

Lipids

Chemically dominated by C–H bonds → nonpolar; water-insoluble.
Fatty acids
- Saturated: only single C–C bonds → straight, pack tightly (solid fats).
- Unsaturated: one or more C=C → kinked, lower packing, increase membrane fluidity.
Major lipid classes
1. Fatty acids (energy storage).
2. Triglycerides (glycerol + 3 fatty acids) – long-term energy reserve.
3. Phospholipids – glycerol + 2 fatty acids + phosphate-containing polar head; amphipathic; self-assemble into bilayers → basis of all cellular membranes.
4. Steroids – four fused carbon rings; membrane components (cholesterol) and signalling molecules (hormones).
Membrane architecture
- Phospholipid bilayer with two leaflets.
- Fluid mosaic: embedded proteins, glycolipids, cholesterol.
- Proper balance of saturated/unsaturated chains maintains fluidity.

Carbohydrates

Chemical formula approximates “carbon + water” ((\text{C}n\text{H}{2n}\text{O}_n)). Highly polar; readily dissolve in water.
Structural hierarchy
- Monosaccharides: glucose, fructose, galactose.
- Disaccharides: lactose (glucose + galactose), sucrose (glucose + fructose).
- Polysaccharides: glycogen (animals), cellulose/chitin (structural in plants/arthropods).
Biological functions
1. Immediate energy source (glycolysis of glucose).
2. Energy storage (glycogen in liver, muscle; limited glycogen in astrocytes of brain).
3. Structural components (cellulose in cell walls; chitin in exoskeletons; bacterial cell wall polysaccharides).
4. Membrane integration (glycolipids) and signalling (glycosaminoglycans in extracellular matrix).
Medical relevance
- ~10 distinct glycogen storage diseases arise from enzyme mutations in glycogen synthesis/breakdown.

Integrated Biomolecular Perspective

Four macromolecule classes (carbohydrates, lipids, proteins, nucleic acids) provide complementary capabilities—no single class suffices for all cellular needs.
Membrane proteins combine hydrophobic (lipid-soluble) and hydrophilic (aqueous) regions enabling function as
- Receptors (signal detection),
- Channels/carriers (regulated or leak pathways),
- Anchors (cytoskeleton/extracellular matrix connections),
- Enzymes.
Principle of solubility partitioning
- Polar/charged molecules dissolve in water.
- Non-polar molecules dissolve in lipid/oil phases.
- Amphipathic molecules (e.g., phospholipids) possess both regions, driving membrane formation and compartmentalization.
Energy & information flow
- $DNA \xrightarrow{\text{transcription}} RNA \xrightarrow{\text{translation}} \text{Protein}$ (central dogma).
- Reverse information flow exists in retroviruses (RNA → DNA).
- $ATP$ couples catabolic (energy-releasing) and anabolic (energy-consuming) reactions.

Condensed Key Points (Exam Checklist)

Water dominates cellular mass and chemistry; polarity underpins molecular interactions.
Carbohydrates: polar; exist as mono-, di-, polysaccharides; energy and structural roles; glucose sole brain fuel; glycogen storage pathology.
Lipids: four main classes; mostly hydrophobic; phospholipids are amphipathic and central to membranes.
Proteins: polymers of amino acids; sequence ⇒ structure ⇒ function; carry out virtually all cellular activities; membrane insertion via hydrophobic domains.
Nucleic Acids: polymers of four nucleotides; DNA stores, RNA transfers information; RNA can be catalytic; mitochondria contain autonomous DNA.
Solubility rule: polar/charged ↔ water; non-polar ↔ lipid; amphipathic ↔ interface (membranes).
Biological organization ascends from atoms → elements → building blocks → macromolecules → organelles → cells → tissues → organs → systems → organisms.