Cell Biology Notes
Biology: The Study of Living Organisms
Biology focuses on living organisms, initially emphasizing their diversity through detailed descriptions of form and appearance.
Cell theory highlights the unity underlying this diversity, emphasizing the cellular organization of all life forms.
Cell structure and growth via division are key aspects of study.
Cell theory introduces a mystery concerning living phenomena (physiological and behavioral processes), emphasizing the necessity of cellular organization integrity for these phenomena to be observed.
A physico-chemical approach, involving cell-free systems, can be used to study these processes at a molecular level.
Analysis of living tissues reveals elements and compounds, indicating organic compounds present in living organisms.
Key questions include:
What are these compounds doing inside a cell?
How do they carry out physiological processes (digestion, excretion, memory, defense, recognition)?
The goal is to understand the molecular basis of all physiological processes and explain abnormalities during disease.
This approach is termed ‘Reductionist Biology,’ applying physics and chemistry concepts to understand biology.
G.N. Ramachandran
G.N. Ramachandran was a prominent figure in protein structure, founding the 'Madras school' of conformational analysis of biopolymers.
His notable contributions include:
Discovery of the triple helical structure of collagen (published in Nature, 1954).
Analysis of allowed protein conformations using the ‘Ramachandran plot’.
Born on October 8, 1922, near Cochin, India.
His father, a mathematics professor, influenced his interest in mathematics.
He graduated top of his class in B.Sc. (Honors) Physics from the University of Madras in 1942.
Received a Ph.D. from Cambridge University in 1949.
Met Linus Pauling at Cambridge, who influenced him to solve the structure of collagen after Pauling's publications on α-helix and β-sheet structures.
Passed away on April 7, 2001, at age 78.
Cell: The Basic Unit of Life
Living organisms possess something that inanimate things lack: the cell, which is the basic unit of life.
Organisms can be unicellular (single-celled) or multicellular (composed of many cells).
What is a Cell?
Unicellular organisms can:
Exist independently.
Perform essential life functions.
A complete cell structure is necessary for independent living.
The cell is the fundamental structural and functional unit of all living organisms.
Antonie Von Leeuwenhoek was the first to observe and describe a live cell.
Robert Brown discovered the nucleus.
Microscopes, including the electron microscope, have enabled the detailed study of cell structures.
Cell Theory
In 1838, Matthias Schleiden, a German botanist, observed that plants are composed of different kinds of cells forming plant tissues.
In 1839, Theodore Schwann, a German zoologist, reported that animal cells have a thin outer layer (plasma membrane).
Schwann also concluded that the cell wall is a unique feature of plant cells.
Schleiden and Schwann jointly formulated the cell theory, which initially lacked an explanation of how new cells form.
In 1855, Rudolf Virchow explained that cells divide and new cells are formed from pre-existing cells (Omnis cellula-e cellula).
The modern cell theory states:
All living organisms are composed of cells and cell products.
All cells arise from pre-existing cells.
Overview of a Cell
Onion cells (plant cells) have a distinct cell wall and a cell membrane.
Human cheek cells have an outer cell membrane.
Inside each cell is a dense, membrane-bound nucleus containing chromosomes and DNA.
Eukaryotic cells have a membrane-bound nucleus.
Prokaryotic cells lack a membrane-bound nucleus.
The cytoplasm, a semi-fluid matrix, fills the cell and is the site of cellular activities.
Eukaryotic cells contain membrane-bound organelles like the endoplasmic reticulum (ER), Golgi complex, lysosomes, mitochondria, microbodies, and vacuoles.
Prokaryotic cells lack membrane-bound organelles.
Ribosomes (non-membrane bound organelles) are found in all cells.
Ribosomes are present in the cytoplasm, chloroplasts (in plants), mitochondria, and on rough ER.
Animal cells have centrosomes (non-membrane bound organelles) that help in cell division.
Cells vary in size, shape, and activities.
Mycoplasmas, the smallest cells, are approximately 0.3 \, \mu m in length.
Bacteria range from 3 to 5 \, \mu m .
The largest isolated single cell is an ostrich egg.
Human red blood cells are about 7.0 \, \mu m in diameter.
Nerve cells are among the longest cells.
Cell shapes vary (disc-like, polygonal, columnar, cuboid, thread-like, or irregular) depending on their function.
Prokaryotic Cells
Prokaryotic cells include bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
They are generally smaller and multiply faster than eukaryotic cells.
They vary in shape and size.
Basic shapes of bacteria:
Bacillus (rod-like)
Coccus (spherical)
Vibrio (comma-shaped)
Spirillum (spiral)
Prokaryotic cell organization is similar despite diverse shapes and functions.
Most prokaryotes have a cell wall around the cell membrane, except for mycoplasma.
The cytoplasm is a semi-fluid matrix.
There is no well-defined nucleus; the genetic material (DNA) is naked and not enveloped by a nuclear membrane.
Many bacteria contain plasmids (small circular DNA) outside the genomic DNA, which confer unique phenotypic characters like antibiotic resistance.
Nuclear membranes are exclusive to eukaryotes.
Prokaryotic cells lack organelles found in eukaryotes, except for ribosomes.
Prokaryotes possess unique inclusions and mesosomes (specialized differentiated forms of the cell membrane).
Mesosomes are infoldings of the cell membrane.
Cell Envelope and its Modifications
Most prokaryotic cells, especially bacterial cells, have a chemically complex cell envelope (glycocalyx, cell wall, and plasma membrane).
The cell envelope layers perform distinct functions but act as a single protective unit.
Bacteria are classified into Gram-positive (take up Gram stain) and Gram-negative (do not take up Gram stain) based on cell envelope differences.
Glycocalyx composition and thickness vary among bacteria.
It can be a loose sheath (slime layer) or a thick, tough capsule.
The cell wall determines cell shape and provides structural support to prevent bursting or collapsing.
The plasma membrane is selectively permeable and interacts with the external environment; it is structurally similar to eukaryotic membranes.
Mesosomes are extensions of the plasma membrane (vesicles, tubules, and lamellae) that help in cell wall formation, DNA replication, and distribution to daughter cells.
Mesosomes also aid respiration, se
creation, increasing surface area, and enzymatic content.
Cyanobacteria have chromatophores (membranous extensions into the cytoplasm) containing pigments.
Bacterial cells may be motile or non-motile; motile cells have flagella (thin filamentous extensions).
Bacterial flagella consist of a filament, hook, and basal body.
The filament is the longest part extending from the cell surface.
Pili and Fimbriae are surface structures that do not aid in motility.
Pili are elongated tubular structures made of special proteins.
Fimbriae are small bristle-like fibers that help bacteria attach to surfaces and host tissues.
Ribosomes and Inclusion Bodies
In prokaryotes, ribosomes are associated with the plasma membrane.
Prokaryotic Ribosomes are about 15 \, nm by 20 \, nm and are composed of two subunits: 50S and 30S, forming a 70S ribosome.
Ribosomes are the sites of protein synthesis.
Several ribosomes can attach to a single mRNA, forming a polyribosome or polysome.
Polysomes translate mRNA into proteins.
Inclusion bodies store reserve material in prokaryotic cells.
They are not membrane-bound and lie free in the cytoplasm.
Examples: phosphate granules, cyanophycean granules, and glycogen granules.
Gas vacuoles are found in blue-green, purple, and green photosynthetic bacteria.
Eukaryotic Cells
Eukaryotes include protists, plants, animals, and fungi.
Eukaryotic cells have extensive compartmentalization of the cytoplasm via membrane-bound organelles.
They possess an organized nucleus with a nuclear envelope.
Eukaryotic cells have complex locomotory and cytoskeletal structures.
Their genetic material is organized into chromosomes.
All eukaryotic cells are not identical; plant and animal cells differ.
Plant cells have cell walls, plastids, and a large central vacuole, which are absent in animal cells.
Animal cells have centrioles, which are absent in almost all plant cells.
Cell Membrane
Detailed membrane structure was studied after the advent of the electron microscope in the 1950s.
Chemical studies of red blood cells (RBCs) helped deduce plasma membrane structure.
Cell membranes are mainly composed of lipids and proteins.
Lipids are arranged in a bilayer, mainly phospholipids.
Polar heads face outwards; hydrophobic tails face inwards, protecting the nonpolar tails from the aqueous environment.
Membranes also contain cholesterol.
Biochemical investigations revealed the presence of proteins and carbohydrates.
The protein-to-lipid ratio varies in different cell types.
Erythrocyte membranes are approximately 52% protein and 40% lipids.
Membrane proteins are classified as integral (partially or totally buried) and peripheral (lie on the surface).
Singer and Nicolson (1972) proposed the fluid mosaic model.
The quasi-fluid nature of lipid allows lateral movement of proteins within the bilayer.
Fluidity is important for cell growth, intercellular junctions, secretion, endocytosis, and cell division.
The plasma membrane is selectively permeable.
Passive transport allows molecules to move across the membrane without energy.
Neutral solutes move via simple diffusion along the concentration gradient.
Water moves via osmosis.
Polar molecules require carrier proteins for transport across the nonpolar lipid bilayer.
Active transport moves ions or molecules against their concentration gradient, requiring energy (ATP).
Example: \, Na^+/K^+ Pump.
Cell Wall
A non-living rigid cell wall covers the plasma membrane in fungi and plants.
The cell wall provides shape, protects from mechanical damage and infection, aids in cell-to-cell interaction, and acts as a barrier to undesirable macromolecules.
Algae cell walls are made of cellulose, galactans, mannans, and minerals like calcium carbonate.
Plant cell walls consist of cellulose, hemicellulose, pectins, and proteins.
The primary cell wall in young plant cells is capable of growth, which diminishes as the cell matures.
The secondary cell wall forms on the inner side of the cell.
The middle lamella, made of calcium pectate, glues neighboring cells together.
Plasmodesmata traverse the cell wall and middle lamellae, connecting the cytoplasm of neighboring cells.
Endomembrane System
The endomembrane system includes the endoplasmic reticulum (ER), Golgi complex, lysosomes, and vacuoles.
Mitochondria, chloroplasts, and peroxisomes are not part of the endomembrane system because their functions are not coordinated with the other components.
Endoplasmic Reticulum (ER)
Eukaryotic cells contain a network of tiny tubular structures called the endoplasmic reticulum (ER).
The ER divides the intracellular space into luminal (inside ER) and extra-luminal (cytoplasm) compartments.
Rough endoplasmic reticulum (RER) has ribosomes attached to its outer surface; smooth endoplasmic reticulum (SER) lacks ribosomes.
RER is prominent in cells involved in protein synthesis and secretion; it is extensive and continuous with the outer nuclear membrane.
SER is the major site for lipid synthesis; lipid-like steroidal hormones are synthesized in SER of animal cells.
Golgi Apparatus
Camillo Golgi (1898) first observed densely stained reticular structures near the nucleus, later named Golgi bodies.
The Golgi apparatus consists of flat, disc-shaped sacs or cisternae (0.5µm to 1.0µm diameter).
Cisternae are stacked parallel to each other in a Golgi complex.
The Golgi cisternae are concentrically arranged near the nucleus with distinct convex cis (forming) and concave trans (maturing) faces.
The cis and trans faces are different but interconnected.
The Golgi apparatus functions in packaging materials for intracellular delivery or secretion.
Vesicles from the ER fuse with the cis face and move toward the maturing trans face, explaining its association with the ER.
Proteins synthesized by ribosomes on the ER are modified in the Golgi cisternae before release from the trans face.
The Golgi apparatus is important for glycoprotein and glycolipid formation.
Lysosomes
Lysosomes are membrane-bound vesicular structures formed by packaging in the Golgi apparatus.
They contain hydrolytic enzymes (hydrolases – lipases, proteases, carbohydrases) that are optimally active at acidic pH.
These enzymes digest carbohydrates, proteins, lipids, and nucleic acids.
Vacuoles
The vacuole is a membrane-bound space in the cytoplasm, containing water, sap, excretory products, and other materials not useful for the cell.
The vacuole is bound by a single membrane called the tonoplast.
In plant cells, vacuoles can occupy up to 90% of the cell's volume.
The tonoplast facilitates the transport of ions and materials against concentration gradients into the vacuole.
In Amoeba, the contractile vacuole is important for osmoregulation and excretion.
In protists, food vacuoles are formed by engulfing food particles.
Mitochondria
Mitochondria are not easily visible without specific staining.
The number of mitochondria per cell varies based on physiological activity.
They are typically sausage-shaped or cylindrical with a diameter of 0.2-1.0 \, \mu m (average 0.5 \, \mu m) and a length of 1.0-4.1 \, \mu m.
Each mitochondrion is double membrane-bound, dividing its lumen into the outer and inner compartments.
The inner compartment is filled with the matrix.
The outer membrane forms the boundary; the inner membrane forms infoldings called cristae that increase surface area.
The two membranes have specific enzymes for mitochondrial function.
Mitochondria are the sites of aerobic respiration and produce cellular energy in the form of ATP, and are thus known as the ‘power houses’ of the cell.
The matrix contains a single circular DNA molecule, RNA molecules, 70S ribosomes, and components for protein synthesis.
Mitochondria divide by fission.
Plastids
Plastids are found in all plant cells and euglenoids.
They contain specific pigments, imparting specific colors to plants.
Plastids are classified into chloroplasts, chromoplasts, and leucoplasts based on the type of pigments they contain.
Chloroplasts contain chlorophyll and carotenoid pigments, which trap light energy for photosynthesis.
Chromoplasts contain fat-soluble carotenoid pigments (carotene, xanthophylls), giving plant parts yellow, orange, or red colors.
Leucoplasts are colorless plastids that store nutrients.
Amyloplasts store carbohydrates (starch), e.g., potato.
Elaioplasts store oils and fats.
Aleuroplasts store proteins.
Chloroplasts are mostly found in mesophyll cells of leaves.
They are lens-shaped, oval, spherical, discoid, or ribbon-like, with a length of 5-10 \, \mu m and width of 2-4 \, \mu m.
Their number varies from 1 per cell in Chlamydomonas to 20-40 per cell in mesophyll cells.
Like mitochondria, chloroplasts are double membrane-bound.
The inner chloroplast membrane is less permeable.
The space limited by the inner membrane is called the stroma.
Thylakoids (organized flattened membranous sacs) are present in the stroma and arranged in stacks called grana.
Stroma lamellae connect the thylakoids of different grana.
The thylakoid membrane encloses the lumen.
The stroma contains enzymes for carbohydrate and protein synthesis, small double-stranded circular DNA molecules, and ribosomes.
Chlorophyll pigments are present in the thylakoids.
Chloroplast ribosomes are smaller (70S) than cytoplasmic ribosomes (80S).
Ribosomes
Ribosomes are granular structures observed under the electron microscope by George Palade (1953).
They are composed of ribonucleic acid (RNA) and proteins and are not surrounded by a membrane.
Eukaryotic ribosomes are 80S, while prokaryotic ribosomes are 70S.
Each ribosome has two subunits: a larger and a smaller subunit.
The 80S ribosomes have 60S and 40S subunits, while the 70S ribosomes have 50S and 30S subunits.
'S' (Svedberg’s Unit) is the sedimentation coefficient, measuring density and size indirectly.
Cytoskeleton
The cytoskeleton is an elaborate network of filamentous proteinaceous structures (microtubules, microfilaments, and intermediate filaments) in the cytoplasm.
It provides mechanical support, motility, and maintenance of cell shape.
Cilia and Flagella
Cilia and flagella are hair-like outgrowths of the cell membrane.
Cilia are small and work like oars, causing movement of cells or surrounding fluid.
Flagella are longer and responsible for cell movement.
Prokaryotic bacteria also possess flagella, but they differ structurally from eukaryotic flagella.
Cilia and flagella are covered with plasma membrane; their core, the axoneme, possesses microtubules running parallel to the long axis.
The axoneme has nine doublets of radially arranged peripheral microtubules and a pair of centrally located microtubules (9+2 array).
Central tubules are connected by bridges and enclosed by a central sheath, connected to peripheral doublets by radial spokes.
Peripheral doublets are interconnected by linkers.
Cilia and flagella emerge from centriole-like structures called basal bodies.
Centrosome and Centrioles
The centrosome contains two cylindrical structures called centrioles, surrounded by amorphous pericentriolar materials.
Centrioles lie perpendicular to each other and have a cartwheel-like organization.
They are made of nine evenly spaced peripheral fibrils of tubulin protein, each a triplet linked to adjacent triplets.
The central part of the proximal region of the centriole is proteinaceous and called the hub, connected to peripheral triplets by radial spokes.
Centrioles form the basal body of cilia or flagella, and spindle fibers that give rise to the spindle apparatus during cell division in animal cells.
Nucleus
Robert Brown first described the nucleus as a cell organelle in 1831.
Flemming named the material of the nucleus stained by basic dyes as chromatin.
The interphase nucleus (non-dividing cell's nucleus) has nucleoprotein fibers (chromatin), nuclear matrix, and one or more spherical bodies (nucleoli).
The nuclear envelope consists of two parallel membranes separated by a perinuclear space (10 to 50 \, nm), forming a barrier between the nucleus and the cytoplasm.
The outer membrane is continuous with the endoplasmic reticulum and bears ribosomes.
Nuclear pores, formed by the fusion of the two membranes, interrupt the nuclear envelope.
These pores allow the movement of RNA and protein molecules between the nucleus and the cytoplasm.
Normally, there is one nucleus per cell, but variations occur.
Some mature cells lack a nucleus (e.g., erythrocytes of mammals and sieve tube cells of vascular plants).
The nuclear matrix (nucleoplasm) contains the nucleolus and chromatin.
The nucleolus is a spherical structure in the nucleoplasm, continuous with the nucleoplasm without a membrane; it is the site for active ribosomal RNA synthesis.
Larger and more numerous nucleoli are present in cells actively carrying out protein synthesis.
Chromatin consists of DNA and basic proteins called histones, non-histone proteins, and RNA.
A single human cell has approximately two meters of DNA distributed among 46 chromosomes.
Chromosomes (visible only in dividing cells) have a primary constriction or centromere with disc-shaped structures called kinetochores on the sides.
The centromere holds two chromatids of a chromosome.
Based on the position of the centromere, chromosomes are classified into four types:
Metacentric: middle centromere forming two equal arms.
Sub-metacentric: centromere slightly away from the middle, resulting in one shorter and one longer arm.
Acrocentric: centromere is situated close to its end, forming one extremely short and one very long arm.
Telocentric: terminal centromere.
Some chromosomes have non-staining secondary constrictions, giving the appearance of a small fragment called the satellite.
Microbodies
Microbodies are membrane-bound minute vesicles containing various enzymes, present in both plant and animal cells.
Summary
Organisms are made of cells or aggregates of cells.
Cells vary in shape, size, and function.
Cells are eukaryotic or prokaryotic based on the presence or absence of a membrane-bound nucleus and organelles.
A typical eukaryotic cell consists of a cell membrane, nucleus, and cytoplasm; plant cells have a cell wall outside the cell membrane.
The plasma membrane is selectively permeable and facilitates transport of several molecules.
The endomembrane system includes the ER, Golgi complex, lysosomes, and vacuoles.
Cell organelles perform different but specific functions.
The centrosome and centrioles form the basal body of cilia and flagella, which facilitate locomotion; in animal cells, centrioles also form the spindle apparatus during cell division.
The nucleus contains nucleoli and chromatin network, controls organelle activities, and plays a major role in heredity.
The endoplasmic reticulum (ER) contains tubules or cisternae and is of two types: rough and smooth.
ER helps in the transport of substances and the synthesis of proteins, lipoproteins, and glycogen.
The Golgi body is a membranous organelle composed of flattened sacs involved in packaging and transporting cell secretions.
Lysosomes are single-membrane structures containing enzymes for digesting macromolecules.
Ribosomes are involved in protein synthesis, occurring freely in the cytoplasm or associated with the ER.
Mitochondria help in oxidative phosphorylation and generate adenosine triphosphate (ATP); they are bound by a double membrane, with the inner membrane folded into cristae.
Plastids are pigment-containing organelles found only in plant cells.
Chloroplasts are responsible for trapping light energy for photosynthesis; the grana is the site of light reactions, and the stroma is the site of dark reactions.
Green plastids (chloroplasts) contain chlorophyll, while other colored plastids (chromoplasts) may contain pigments like carotene and xanthophyll.
The nucleus is enclosed by the nuclear envelope, a double-membrane structure with nuclear pores.
The inner membrane encloses the nucleoplasm and the chromatin material.
Therefore, the cell is the structural and functional unit of life.