Cell Structure

1. Microscopy & Magnification

Microscopy: a technical field that uses a microscope to view specimens (samples/objects) that are otherwise not visible to the naked eye — the science of investigating small objects and structures. A small object is "magnified" for viewing and analysis.

Why can't we see cells? The smallest structure visible to our eye is 50–100 µm. Most cells are only 5–40 µm, so they fall outside our visible range — even skin (the largest organ) shows no cells to the naked eye. Hospital blood/urine tests = microscopy of specimens on slides.

Magnification

Definition: magnification is the ratio of the image size (I) to the actual size (A).

• Magnification = enlarging the apparent size, not the physical size (like zooming a photo — the object itself stays the same).
• It only makes the image bigger, not clearer → clarity is resolution (section 3).
• No unit for magnification — it is "times" (×). Units in numerator and denominator cancel.
• Image size and actual size must be in the SAME unit → convert first if they differ (e.g. 5 µm vs 1 mm).

Unit conversions

Unit	cm	mm	µm	nm
in metres	10⁻² m	10⁻³ m	10⁻⁶ m	10⁻⁹ m

2. Types of Microscopy

Two types — they differ in the source of radiation (what is projected on the specimen): light or an electron beam.

3. Light Microscope

Parts and their jobs

1. Lamp — source of light.
2. Diaphragm — controls the amount of light projected onto the slide (may hold a filter).
3. Condenser lens (convex) — focuses the light rays onto the slide by converging the divergent rays. It does not magnify.
4. Objective lens — 1st magnifying lens (×4, ×10, ×40; ×100 oil immersion) on a revolving nosepiece.
5. Eyepiece lens — 2nd magnifying lens (usually ×10).
6. Coarse adjustment knob — achieves the optimal distance between slide & objective lens.
7. Fine adjustment knob — achieves optimal sharpness / clarity.

Other labelled parts on the diagram: head (turret), nosepiece, arm, stage (holds slide; stage clips hold it in place), stage stop, illumination, base, light-intensity control.

Main features of a light microscope

1. Source of radiation: light
2. Maximum useful magnification: ×1500 (beyond this the image is not clearer)
3. Can view live and dead specimens (does not harm living cells)
4. Produces coloured images — (a) light is a combination of colours (VIBGYOR); (b) organic dyes are used for staining
5. Magnifying lenses are made of optical glass
6. Portable, inexpensive, easy to operate, does not need a skilled professional (even school students use it)

Limit: shows only cell outline and nucleus — organelles like mitochondria are not clearly visible (see cheek-cell picture below).

4. Electron Microscope

	Transmission EM (TEM)	Scanning EM (SEM)
e⁻ beam	transmits through the specimen	reflected from the surface; reflected beams are captured to form the image
image	2D	3D
specimen	must be extremely thin	does not have to be thin
preparation	relatively harder	relatively easier

5. Resolution

Definition: the minimum distance between 2 points before they can be seen as separate points — the ability to distinguish between 2 distinct points.

• Resolution depends on the wavelength (λ) of the radiation (light or e⁻ beam).
• Shorter wavelength ⇒ higher resolution.
• Resolution is "generally" half the λ of the radiation.

Resolution of a LIGHT microscope	Resolution of an ELECTRON microscope
λ of light taken as 400 nm (visible light 400 nm violet – 700 nm red; violet is shortest)	λ of the electron beam taken as 1 nm
⇒ resolution = 200 nm (½ × 400)	⇒ resolution = 0.5 nm (½ × 1)
2 points must be ≥ 200 nm apart to be seen as separate; can view specimens as small as ~200 nm	2 points must be ≥ 0.5 nm apart to be seen as separate

Micrograph examples on the board: cheek cells under a LM (pink outlines + a dark nucleus only) · TEM of a mitochondrion from a liver cell (flat 2D, cristae visible) · mitochondrion under SEM (3-D, coloured by computer).

6. Classification of Living Organisms

5 kingdoms (earlier 3): Prokaryota (bacteria), Protoctista, Fungi, Plantae, Animalia. The big dividing factor is the cell: bacteria = prokaryotes; the other four = eukaryotes.

Prokaryotes (bacteria)	Eukaryotes
strictly unicellular (a colony = many separate cells, not one organism) NO true nucleus NO membrane-bound organelles DNA coiled & concentrated in a region called the nucleoid	have a TRUE nucleus often multicellular (plants & animals strictly; yeast is the only unicellular fungus; protoctista = mixed "dumping ground" kingdom) have membrane-bound organelles

Q: What is a "true nucleus"? A nucleus contains genetic material; if it is enclosed by a (double) membrane it is a true nucleus. Genetic material with no membrane around it = naked DNA (still has genetic material — it just has no nucleus).

7. The Cell — Basic Unit of Life

Cell = basic unit of life. Robert Hooke saw plant cork cells under a microscope; each tiny box had a boundary, so he called it a "cell" (like a jail cell — a small enclosed space).

• Structural unit: structure = shape/framework (like a building or phone). Cells → tissue → organ → organ system → organism, so every organism's structure traces back to cells.
• Functional unit: all vital processes (respiration → ATP, protein synthesis, lipid & enzyme synthesis, DNA replication) happen inside cells (cytoplasm / nucleus). ATP is the only energy form the body can use.
• A cell can be thought of as a "bag" in which the chemistry of life occurs.

8. Animal Cell & Plant Cell (cartoon diagrams)

Real cells are never perfect circles — these are cartoon diagrams. Animal cells are irregular (jelly-like, no fixed shape); plant cells have a regular, definite shape because of the cell wall.

Only in PLANT cells (the 4 differences — memorise!)
cell wall	cellulose, outermost, fully permeable (cell membrane = semi-permeable)
chloroplast	site of photosynthesis
large permanent central vacuole	membrane = tonoplast; contents = cell sap (animal cells: only small temporary vacuoles)
plasmodesmata	cytoplasmic channels between neighbouring cells

Common to both: nucleus (+nucleolus, double membrane, pores), RER, SER, Golgi, mitochondria, ribosomes, cytoplasm, cell membrane, cytoskeleton. Animal only: centrioles (in the centrosome / MTOC), lysosomes (a special Golgi vesicle).

9. Structures & Functions of Cellular Organelles

(i) Cell membrane

• Semi-permeable — does not allow all substances to pass through. Letting everything in → cell swells & lyses (or toxins enter); letting everything out → loses vital substances.
• Made of a phospholipid bilayer = 2 layers (bi = two); each phospholipid = phosphate head + fatty-acid (lipid) tails — 2 different materials joined.

Functions: (i) protects the cytoplasm (and organelles) from harmful/toxic substances; (ii) regulation of material in & out of the cell through its permeability (permeable to a substance → lets it in; impermeable → blocks it). Also separates the cell's internal environment from the external. Full detail: Chapter 4.

Nucleic acids (quick intro)

(ii) Nucleus, nuclear membrane, nucleolus

• Nucleus = control centre of the cell (like brain / CPU) — contains genetic information as DNA; DNA is made of genes; each gene codes for a polypeptide (amino acids → polypeptide → protein).
• Each gene = its own specific "passcode" → its own mRNA → its own polypeptide.
• ① The nucleus is the site of TRANSCRIPTION (DNA → mRNA). Whole chain below = protein synthesis.

Why a messenger? DNA can't leave the nucleus and amino acids can't enter it → mRNA is the "WhatsApp" courier. Nucleus also holds rRNA (made in the nucleolus). Mitochondria have DNA but no nucleus.

• Nuclear membrane (envelope): a double membrane — a protective boundary controlling what enters/leaves; if everything entered the nucleus it could burst. The membrane itself is impermeable; substances move only through nuclear pores.
• Nucleolus: a dense body within the nucleus, not membrane-bound, a dense network of RNA and DNA (contains rRNA) — responsible for synthesising ribosomes, which take part in protein synthesis.

(iii) Ribosomes

Definition: small, dense, rounded and granular particles of ribosomal RNA + protein (≈65 % rRNA, 35 % protein — values not required). Made in the nucleolus. Not surrounded by a membrane.

• Made of 2 subunits — large + small.
• 70S (smaller): prokaryotic cells, mitochondria, chloroplasts.
• 80S (larger): eukaryotic cells — attached to RER and freely suspended in cytoplasm (same type, same job).
• Only difference at AS level = size (S = Svedberg unit).
• Ribosome = site of TRANSLATION (mRNA → polypeptide; tRNA brings amino acids — Chapter 6).

(iv) Rough endoplasmic reticulum (RER)

• Usually continuous with the nuclear membrane — mRNA leaving the nuclear pore finds ribosomes faster ("the nearer college" analogy: both colleges offer the same, but the closer is easier).
• Surface carries 80S ribosomes → rough, grainy look under the microscope.
• Definition (3 keywords): system of INTERCONNECTED, FLATTENED, MEMBRANOUS SACS (called cisternae; one = cisterna).

Functions of RER:

1. Involved in protein synthesis via translation (because of ribosomes).
2. Protein folding (= post-translational modification) — many polypeptide chains fold together in the correct orientation to give a protein.
3. Packages the protein into vesicles and transports it to the Golgi body (like gift-wrapping before handing over — it can't just eject it).

(v) Golgi apparatus / Golgi body

• A stack of flattened membranous sacs (cisternae); each sac has a swelling at its end where a vesicle pinches off (like flaky skin peeling) — the swollen end forms the vesicle, which then pinches off and repeats.
• Unlike ER the sacs are not interconnected (stacked like books) and have no ribosomes.

Functions of Golgi body: (1) protein modification (2) packages proteins into vesicles for secretion (3) production of lysosomes.

When folding is complete in the RER, a fully folded protein molecule (made of polypeptide chains) is formed → it goes to the Golgi, where other biological molecules are attached to form conjugated molecule(s) = molecules created when 2 distinct molecules from different categories combine.

protein +	=	conjugated protein
lipids (short chain attached)	→	lipoprotein
sugars (carbohydrates)	→	glycoprotein

Naming trick: the main molecule is the last word (the "surname"); the short chain attached is the prefix. Same logic: peptidoglycan = carbohydrate (glycan) main + peptide chain attached.

Pathway: final modified protein is packaged in vesicles → used inside the cell, or moved to the cell membrane and secreted out (e.g. enzymes, peptide hormones like insulin / glucagon).

(vi) Lysosomes

• Spherical, single-membrane-enclosed organelle; a specialised Golgi vesicle (released into the cytoplasm).
• Contains an array of hydrolytic (digestive) enzymes at a low (acidic) pH — each enzyme has an optimum pH; these work best in acid.
• Hydrolytic enzymes are proteins → made in RER, modified & packaged by Golgi (recall!).

Functions of lysosome:

1. Autophagy — ordered and purposeful digestion of cell organelles (auto = self, phagy = digestion). Happens automatically when an organelle is worn out → beneficial to the cell.
2. Autolysis — self-destruction of cells: digestive enzymes leak out of the lysosome and start destroying the cell (acid is toxic) = "lysosomal cell death".
3. Phagocytosis — digestion of foreign particles that got into the cell, e.g. bacteria.

(vii) Smooth endoplasmic reticulum (SER)

• Responsible for synthesis of lipids — e.g. steroids (steroidal hormones: oestrogen, progesterone, testosterone). (Peptide hormones such as insulin & glucagon are protein-based → RER/Golgi, not SER.)
• System of interconnected flattened membranous sacs (cisternae) — same structure as RER but no ribosomes → smooth; also called "agranular ER".
• Detoxification (e.g. alcohol, toxins) — liver cells have a lot of SER.
• No ribosomes ⇒ no translation / no protein synthesis or modification in the SER.

(viii) Mitochondria

• Double membrane: smooth outer membrane + folded inner membrane. Folds = cristae (singular crista). Plural mitochondria / singular mitochondrion.
• 2 compartments: intermembrane space (IMS) (gap between membranes) and matrix (inner medium).
• Stalked particles (lollipop-shaped) on the cristae; head = enzyme ATP synthase → makes ATP.
• Has its own circular (naked) DNA — no membrane round it, so not a nucleus — and 70S ribosomes.
• DNA + ribosomes ⇒ can do transcription & translation ⇒ protein synthesis ⇒ a self-replicating organelle.
• Production of ATP via aerobic respiration ("powerhouse"). ATP = energy currency; the only form of energy cells can use for active processes.

Matrix contains soluble enzymes for respiration. Cristae give a large surface area for enzyme reactions. Cells use ATP from respiration for energy-requiring processes.

(ix) Chloroplast (plants — self-replicating organelle)

• Only in autotrophic cells (auto = self; they make their own food); green pigment = chlorophyll (gives leaves their green colour).
• Double membrane (outer + inner) with an intermembrane space; own circular DNA and 70S ribosomes ⇒ self-replicating (protein synthesis possible).
• Thylakoid = one flattened disc (coin-like); granum (plural grana) = stack of thylakoids; grana joined by inter-granal lamellae. (Granum = singular, grana = plural.)
• Stalked particles on the thylakoid membranes (head = ATP synthase) → ATP is made.
• Chlorophyll in the thylakoid/grana → light energy is absorbed / trapped there.
• Stroma = the surrounding medium → site of the light-independent reaction.

Chloroplasts convert solar (light) energy into chemical (food) energy by photosynthesis.

10. Mitochondria vs Chloroplast

Mitochondria	Chloroplast
2 compartments: IMS + matrix	3 compartments: IMS + stroma + thylakoid (space)
Cristae (folds of inner membrane) give large surface area for enzyme reactions	Thylakoid membrane gives large surface area for enzyme reactions
Sausage-shaped	Oval / spherical
Matrix has soluble enzymes for respiration	Stroma has soluble enzymes for photosynthesis
Inner membrane is folded (cristae)	Inner membrane is not folded

Tip: the folds (cristae) are why mitochondria look "sausage-like"; a chloroplast's membranes are smooth and round.

11. Plant-only Structures

(x) Cellulose cell wall

• Outermost covering of a plant cell; made of the polysaccharide cellulose (poly = many; built from cellulose fibres in a criss-cross mesh).
• The gaps in the mesh are pores → anything small enough passes → fully permeable (no filtering). Cellulose fibres are highly tensile (can bear huge pressure — like a PVC pipe vs a thread).

Functions:

1. Mechanical strength → prevents cell lysis (animal cells burst if too much water enters; the wall resists swelling — turgor).
2. Protects the protoplasm from invading micro-organisms (pores too small for bacteria/viruses).
3. Maintains shape — structural framework, mechanical support (like a building's framework) → definite regular shape.
4. Permeable for diffusion; helps absorption of minerals & solutes with water in root-hair cells.
5. May also serve as a reservoir for food.

(xi) Large permanent vacuole & tonoplast (only in plant cells)

• Contents of the vacuole = cell sap (glucose, sucrose, amino acids, water, nutrients, metabolic waste).
• Cell sap is enclosed by a membrane called the tonoplast — selectively permeable, regulates entry/exit of substances into/out of the cell sap, so waste/nutrients don't leak into the cytoplasm and disturb enzymes.

Functions of the large permanent vacuole:

• Storage site for useful substances (glucose, amino acids, water) and waste (metabolic waste products).
• Vacuolar turgidity pushes the chloroplasts to the edge of the cell ⇒ maximises light absorption ⇒ increases efficiency of photosynthesis (light travels a shorter distance).
• Turgidity supports the plant cell and maintains its shape.

(xii) Plasmodesmata

Definition: made up of cytoplasmic strands which run transversely across the walls of a plant cell — channels where the cell wall & membrane boundary is absent between 2 adjacent plant cells (singular plasmodesma).

Functions: (1) transport of water, sugars, amino acids, proteins, hormones etc. between adjacent cells; (2) rapid communication between adjacent cells because substances do not have to cross the cell boundary (cell wall & membrane). Cytoplasm is a semi-fluid (sol-gel).

12. Cytoskeleton & Microtubules

(xiii) Cytoskeleton — "skeleton of the cell" (structural framework)

Component	Diameter	Note
① Microtubules	10–25 nm (largest)	tubulin protein; hollow
② Intermediate filaments	7–10 nm
③ Microfilaments	3–7 nm (smallest)	actin filament, myosin, tropomyosin

Functions of cytoskeleton:

1. Structural support and gives shape to a particular cell.
2. Intracellular movement of organelles.
3. Plays a part in cell division through centrioles.
4. Muscle cell contraction (via actin & myosin microfilaments).
5. Movement of an entire cell via flagellum (e.g. sperm cell).

(1) Microtubule structure & assembly

• Microtubules are made of tubulin protein, 2 types: α-tubulin and β-tubulin.
• 1 α + 1 β = tubulin dimer (heterodimer, since the two units differ).
• Numerous dimers polymerise into a long chain = protofilament — no fixed number of dimers (board example: 4 or 8).
• 13 protofilaments join into a hollow cylinder = microtubule — here the number 13 is fixed. Cross-section ≈ 25 nm.

13. Centrioles, Cilia, Flagella, Microvilli

★ Centrioles (near the nucleus)

• Only in animal cells (absent in plants; usually absent in fungi). Made up of microtubules.
• Always exist as a pair at right angles to each other, close to the nucleus — never a single one.
• Arise from MTOCs (microtubule organising centres) — regions where microtubules assemble. The most common MTOC = centrosome (the region holding the 2 centrioles).
• Arrangement: "9 + 0" = 9 microtubule triplets around a hollow centre (triplets linked by connecting fibrils).
• 3 microtubules = 1 triplet; 9 × 3 = 27 microtubules (each microtubule = 13 protofilaments).

★ Cilium (plural cilia)

• Small, slender, hair-like projections on the surface of some cells (e.g. lungs/airways, oviduct/fallopian tubes — wave to move mucus / the ovum).
• A centriole moves to the cell surface membrane and is modified into a basal body (the part beneath the membrane) which templates the formation of the cilium. The cilium = outgrowth of microtubules enclosed by the cell membrane.
• Cross-section (axoneme): "9 + 2" = 9 doublets around 2 central singlets.
• Each doublet: A microtubule (complete circle, 13 filaments) + B microtubule (incomplete, 11 filaments). A carries dynein arms (outer + inner) pointing toward the neighbouring B.
• Dynein = motor protein: converts the chemical energy of ATP into mechanical energy → arms grip the adjacent doublet, push/slide it, release, grip again (rhythmic wave). If the doublets were not attached they would just slide past each other.

	Centriole	Cilium / eukaryotic flagellum
arrangement	9 + 0 (triplets)	9 + 2 (doublets + 2 singlets)
location	inside cell, no membrane covering	outgrowth beyond the cell; covered by cell membrane
job	spindle fibres in cell division	movement (dynein + ATP)

★ Eukaryotic flagellum

Long tail-like projection used for locomotion of the whole cell (e.g. sperm cell); structure, dynein arms and movement are identical to cilia: 9 + 2, with a basal body (BB) and enclosed by the cell membrane. Not the same as the bacterial flagellum (made of flagellin protein; see prokaryotes).

★ Microvilli (brush border)

Finger-like membrane protrusions (projections) supported by the actin cytoskeleton. Function: increases the surface area for faster absorption via diffusion, osmosis and/or active transport (e.g. epithelial cells lining the small intestine; cells have many mitochondria, ER, Golgi, lysosomes).

14. Structure of a Prokaryotic Cell (Bacteria)

Always unicellular; oldest and simplest living cells; ubiquitous (found everywhere), huge numbers. Size 1–5 µm.

Structure	Details / function
Peptidoglycan cell wall (murein)	peptide chain attached to carbohydrate (glycan = main molecule). Bacteria need water/moisture → wall gives mechanical support and prevents osmotic lysis (osmosis = passive movement of water); (ii) protection against phagocytes. With the membrane = cell boundary.
Cell membrane	regulates entry & exit of substances; semi-permeable (filter).
Circular DNA	genes code for bacterial proteins; no free ends; naked (no histones), free in cytoplasm, no nuclear membrane → no true nucleus. Does transcription.
70S ribosomes	protein synthesis via translation. DNA + ribosomes ⇒ bacteria make their own proteins/enzymes.
Cytoplasm	contains soluble enzymes for vital life processes (e.g. respiration — no mitochondria, enzymes do it in cytoplasm/membrane).
Plasmid	small fragment of extra genetic material (double-stranded ring DNA). Serves as a vector in genetic engineering (cut the ring with a restriction enzyme, insert the desired gene → bacterium makes a new protein; Ch. 8).
Slimy capsule	protective layer of polysaccharides + protein (sticky). (i) gives pathogenicity (disease-causing ability — only capsulate bacteria are virulent); (ii) protects against phagocytosis (and bacteriophage attachment); helps stick to surfaces.
Flagellum	made of the protein flagellin; locomotion (whip-like movement).
Pili / sex pili	hollow tubular external structures of pilin protein; transfer of DNA between prokaryotic cells by conjugation ("Bluetooth / AirDrop" of genes).

15. Modes of Transmission of Bacterial Genes

• Transformation: random uptake of bacterial gene/DNA present in the surroundings through the cell boundary.
• Transduction: a virus (bacteriophage) transfers genetic material from one bacterium to another (viral vector — phage picks up donor DNA in A, injects it into B). Bacteriophage = virus that "eats" (phage) bacteria.
• Conjugation: bacterial genes are transferred from one bacterium to another through the conjugation tube (mating-pair formation) built by the sex pili.

16. Comparison: Prokaryote · Animal · Plant

Property	Bacteria / prokaryotes	Animal	Plant
Cellular organisation	unicellular	multicellular	multicellular
★ Cell wall	peptidoglycan	absent	cellulose
DNA	circular / naked DNA (no histones)	linear, wrapped around histones	linear, wrapped around histones
Nucleus	absent	present	present
Membrane-bound organelles	absent (no RER, SER, mitochondria, Golgi, chloroplast)	present	present
Reproduction	asexual only — binary fission	both sexual & asexual observed	both sexual & asexual observed
Cell division	binary fission (no mitosis/meiosis)	mitosis & meiosis	mitosis & meiosis
Ribosomes	70S	80S (mitochondria: 70S)	80S (mito & chloroplast: 70S)
Flagella	present (some)	absent (except sperm — cell-type specific)	absent
Average size	1–5 µm	10 µm – 100 µm

★ Fungi (eukaryotes) have a chitin cell wall. Eukaryotic DNA: helical DNA wrapped around histone protein. Why no mitosis/meiosis in bacteria? Both are nuclear divisions and there is no true nucleus. Prokaryotes are ~10× smaller than eukaryotic cells and evolved first.

17. Viruses (average size 20–300 nm)

• A cell needs cell membrane + genetic material + protoplasm. A virus has only genetic material (cell membrane? ✗ · genetic material ✓ · protoplasm ✗) → acellular particle/species.
• Why non-living? no cytoplasm · no ribosomes · no metabolism (no enzymes, no ATP, no respiration). Outside a host cell they are inactive particles that use no energy; they only become active inside a host.
• They hijack the protein-synthesis machinery of the host cell to make viral proteins. All viruses are parasitic.

Part	Details
Genome — compulsory	genetic information, either DNA or RNA, never both; 4 types: ss DNA, ds DNA, ss RNA, ds RNA
Capsid — compulsory	protein coat made of protein sub-units capsomeres. Roles: ① protects the genetic material ② helps attachment to host cells
Envelope — some only	phospholipid membrane taken from the host cell's membrane when the virus leaves. With envelope = enveloped (e.g. HIV); without = non-enveloped / naked (e.g. polio, rhino virus)

How a virus replicates (e.g. a DNA virus)

1. Virus attaches to the host cell (via capsid) and enters; capsid breaks up, releasing the genome into the host cytoplasm.
2. Viral DNA is transcribed into viral mRNA using the host's DNA polymerase (in host nucleus) — the virus has no enzymes of its own.
3. Viral mRNA attaches to host ribosomes → translation → viral proteins (capsomeres).
4. Viral genomes + capsids assemble into many new viruses (replication).
5. Host cell fills up, bursts (lysis) and dies — hence all viruses are parasitic (a parasite harms its host, like a malarial mosquito).

18. Organelle Sizes & Quick Recap

Organelle (largest → smallest)	Size
Nucleus	5–10 µm
Chloroplast	5–7 µm
Mitochondria	0.5 to 3 µm
Nucleolus	0.2 to 3.5 µm
Lysosomes	0.1 to 1.2 µm
Golgi body	1 µm
SER	50 nm
RER	20–30 nm
Ribosomes	20–30 nm