Cell Biology Notes
Biology: The Study of Living Organisms
Biology focuses on living organisms.
Early studies emphasized diversity in form and appearance.
Cell theory highlights the unity of life through cellular organization.
Cell structure and growth via division are key concepts.
Living phenomena require intact cellular organization.
Physico-chemical approach uses cell-free systems to study physiological and behavioral processes. This allows description in molecular terms.
Analysis of living tissues reveals elements and compounds present.
Questions arise about the function of these compounds within cells, relating to processes like digestion, excretion, memory, defense, recognition, etc.
The goal is to understand the molecular basis of physiological processes and abnormal processes in disease.
Reductionist Biology: Applying physics and chemistry to understand biology.
G.N. Ramachandran
G.N. Ramachandran: Founder of the 'Madras school' of conformational analysis of biopolymers.
Discovered the triple helical structure of collagen (published in Nature, 1954).
Developed the 'Ramachandran plot' for analyzing allowed protein conformations.
Born October 8, 1922, near Cochin, India.
His father was a mathematics professor and influenced his interest in mathematics.
Graduated top of his class in B.Sc. (Honors) Physics at the University of Madras in 1942.
Received a Ph.D. from Cambridge University in 1949.
Inspired by Linus Pauling's work on α-helix and β-sheet structures, which directed his focus to collagen structure.
Passed away on April 7, 2001, at age 78.
Cell: The Unit of Life
Living organisms are distinguished from non-living things by the presence of cells.
All organisms are composed of cells.
Unicellular organisms: single cell.
Multicellular organisms: many cells.
What is a Cell?
Unicellular organisms have:
Independent existence.
Ability to perform essential life functions.
A complete cell structure is necessary for independent living.
Cell: fundamental structural and functional unit of all living organisms.
Antonie Von Leeuwenhoek: first saw and described a live cell.
Robert Brown: discovered the nucleus.
Microscope and electron microscope advancements revealed cell structural details.
Cell Theory
1838: Matthias Schleiden (German botanist) observed that plants are composed of different kinds of cells forming plant tissues.
1839: Theodore Schwann (German zoologist) reported that animal cells have a thin outer layer (plasma membrane).
Schwann concluded cell wall is unique to plant cells.
Schwann proposed animals and plants are composed of cells and cell products.
Schleiden and Schwann formulated the cell theory, but it didn't explain new cell formation.
1855: Rudolf Virchow explained that cells divide and new cells are formed from pre-existing cells (Omnis cellula-e cellula).
Virchow modified Schleiden and Schwann's hypothesis, giving the cell theory its final shape.
Modern Cell Theory:
All living organisms are composed of cells and cell products.
All cells arise from pre-existing cells.
Overview of Cell
Onion cells (plant cells) have a distinct cell wall and cell membrane.
Human cheek cells have an outer membrane.
Nucleus: dense membrane-bound structure containing chromosomes and DNA.
Eukaryotic cells: have membrane-bound nuclei.
Prokaryotic cells: lack a membrane-bound nucleus.
Cytoplasm: semi-fluid matrix occupying cell volume, site of cellular activities.
Eukaryotic cells contain membrane-bound organelles:
Endoplasmic reticulum (ER).
Golgi complex.
Lysosomes.
Mitochondria.
Microbodies.
Vacuoles.
Prokaryotic cells lack membrane-bound organelles.
Ribosomes: non-membrane bound organelles in all cells (eukaryotic and prokaryotic); found in cytoplasm, chloroplasts (plants), mitochondria, and on rough ER.
Animal cells contain centrosomes (non-membrane bound) for cell division.
Cells vary greatly in size, shape, and activities.
Mycoplasmas: smallest cells, 0.3 \, \mu m in length.
Bacteria: 3 to 5 \, \mu m.
Largest isolated single cell: ostrich egg.
Human red blood cells: about 7.0 \, \mu m in diameter.
Nerve cells: some of the longest cells.
Cell shapes: disc-like, polygonal, columnar, cuboid, thread-like, or irregular, depending on function.
Prokaryotic Cells
Prokaryotic cells: bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
Generally smaller and multiply more rapidly than eukaryotic cells.
Vary greatly in shape and size.
Basic shapes of bacteria:
Bacillus (rod-like).
Coccus (spherical).
Vibrio (comma-shaped).
Spirillum (spiral).
Prokaryotic cell organization is fundamentally similar despite diverse shapes/functions.
All prokaryotes have a cell wall surrounding the cell membrane (except mycoplasma).
Cytoplasm: semi-fluid matrix filling the cell.
No well-defined nucleus; genetic material is naked (not enveloped by a nuclear membrane).
Genomic DNA: single chromosome/circular DNA.
Plasmids: small circular DNA outside genomic DNA, conferring unique phenotypic characters (e.g., antibiotic resistance).
Nuclear membrane: found in eukaryotes, not prokaryotes.
No organelles (like eukaryotes) in prokaryotic cells, except ribosomes.
Inclusions: unique to prokaryotes.
Mesosome: specialized differentiated form of cell membrane (infoldings of cell membrane), characteristic of prokaryotes.
Cell Envelope and its Modifications
Most prokaryotic cells (especially bacteria) have a chemically complex cell envelope: a tightly bound three-layered structure.
Outermost glycocalyx.
Cell wall.
Plasma membrane.
Each layer performs distinct functions but acts as a single protective unit.
Bacteria classified into two groups based on cell envelopes and Gram staining:
Gram positive: take up Gram stain.
Gram negative: do not take up Gram stain.
Glycocalyx: differs in composition and thickness among bacteria.
Slime layer: loose sheath.
Capsule: thick and tough.
Cell wall: determines cell shape, provides structural support to prevent bursting or collapsing.
Plasma membrane: selectively permeable, interacts with the outside world; structurally similar to eukaryotes.
Mesosome: formed by extensions of plasma membrane into the cell (vesicles, tubules, and lamellae); helps in:
Cell wall formation.
DNA replication and distribution to daughter cells.
Respiration.
Secretion processes.
Increasing surface area of the plasma membrane.
Enzymatic content.
Chromatophores: membranous extensions into the cytoplasm that contain pigments (e.g., in cyanobacteria).
Bacterial cells: motile or non-motile.
Motile cells have flagella: thin filamentous extensions from cell wall.
Bacterial flagellum: filament (longest portion extending from cell surface), hook, and basal body.
Pili and Fimbriae: surface structures of bacteria (but do not play a role in motility).
Pili: elongated tubular structures made of special protein.
Fimbriae: small bristle-like fibers sprouting out of the cell; help attach bacteria to rocks in streams and host tissues.
Ribosomes and Inclusion Bodies
Ribosomes in prokaryotes are associated with the plasma membrane.
Size: 15 \, nm \times 20 \, nm.
Made of two subunits: 50S and 30S.
Together they form 70S prokaryotic ribosomes.
Ribosomes: site of protein synthesis.
Polyribosomes/polysomes: several ribosomes attached to a single mRNA.
Ribosomes of a polysome translate the mRNA into proteins.
Inclusion bodies: reserve material in prokaryotic cells stored in the cytoplasm, not bound by any membrane system.
Examples: phosphate granules, cyanophycean granules, and glycogen granules.
Gas vacuoles: found in blue-green, purple, and green photosynthetic bacteria.
Eukaryotic Cells
Eukaryotes: protists, plants, animals, and fungi.
Eukaryotic cells: extensive compartmentalization of cytoplasm through membrane-bound organelles.
Possess an organized nucleus with a nuclear envelope.
Have complex locomotory and cytoskeletal structures.
Genetic material is organized into chromosomes.
Not all eukaryotic cells are identical.
Plant cells:
Cell walls.
Plastids.
Large central vacuole.
Animal cells:
Centrioles (absent in almost all plant cells).
Cell Membrane
Detailed structure of the membrane was studied after the advent of the electron microscope in the 1950s.
Chemical studies showed that the cell membrane is mainly composed of lipids and proteins.
Major lipids are phospholipids, arranged in a bilayer.
Polar head toward the outer sides.
Hydrophobic tails toward the inner part.
This ensures that the nonpolar tail of saturated hydrocarbons is protected from the aqueous environment.
Membrane also contains cholesterol.
Biochemical investigation revealed that the cell membranes also possess protein and carbohydrate.
Ratio of protein and lipid varies considerably in different cell types.
In human beings, the membrane of the erythrocyte has approximately 52% protein and 40% lipids.
Depending on the ease of extraction, membrane proteins can be classified as integral and peripheral.
Peripheral proteins lie on the surface of the membrane.
Integral proteins are partially or totally buried in the membrane.
Fluid Mosaic Model
An improved model of the structure of cell membrane was proposed by Singer and Nicolson (1972) widely accepted as fluid mosaic model.
According to this, the quasi-fluid nature of lipid enables lateral movement of proteins within the overall bilayer.
This ability to move within the membrane is measured as its fluidity.
The fluid nature of the membrane is also important from the point of view of functions like cell growth, formation of intercellular junctions, secretion, endocytosis, cell division etc.
One of the most important functions of the plasma membrane is the transport of the molecules across it.
The membrane is selectively permeable to some molecules present on either side of it.
Transport Across Membranes
Passive transport: Many molecules can move briefly across the membrane without any requirement of energy.
Neutral solutes may move across the membrane by the process of simple diffusion along the concentration gradient (from higher concentration to lower concentration).
Movement of water by diffusion is called osmosis.
As the polar molecules cannot pass through the nonpolar lipid bilayer, they require a carrier protein of the membrane to facilitate their transport across the membrane.
Active transport: A few ions or molecules are transported across the membrane against their concentration gradient (i.e., from lower to the higher concentration).
Such a transport is an energy-dependent process, in which ATP is utilized.
Example: Na^+/K^+ Pump.
Cell Wall
Non-living rigid structure called the cell wall forms an outer covering for the plasma membrane of fungi and plants.
Cell wall not only gives shape to the cell and protects the cell from mechanical damage and infection, it also helps in cell-to-cell interaction and provides barrier to undesirable macromolecules.
Algae have cell wall, made of cellulose, galactans, mannans and minerals like calcium carbonate, while in other plants it consists of cellulose, hemicellulose, pectins and proteins.
The cell wall of a young plant cell, the primary wall is capable of growth, which gradually diminishes as the cell matures and the secondary wall is formed on the inner (towards membrane) side of the cell.
The middle lamella is a layer mainly of calcium pectate which holds or glues the different neighboring cells together.
The cell wall and middle lamellae may be traversed by plasmodesmata which connect the cytoplasm of neighboring cells.
Endomembrane System
While each of the membranous organelles is distinct in terms of its structure and function, many of these are considered together as an endomembrane system because their functions are coordinated.
The endomembrane system includes endoplasmic reticulum (ER), golgi complex, lysosomes and vacuoles.
Since the functions of the mitochondria, chloroplast and peroxisomes are not coordinated with the above components, these are not considered as part of the endomembrane system.
The Endoplasmic Reticulum (ER)
Electron microscopic studies of eukaryotic cells reveal the presence of a network or reticulum of tiny tubular structures scattered in the cytoplasm that is called the endoplasmic reticulum (ER).
Hence, ER divides the intracellular space into two distinct compartments, i.e., luminal (inside ER) and extra luminal (cytoplasm) compartments.
The ER often shows ribosomes attached to their outer surface.
The endoplasmic reticulum bearing ribosomes on their surface is called rough endoplasmic reticulum (RER).
In the absence of ribosomes they appear smooth and are called smooth endoplasmic reticulum (SER).
RER is frequently observed in the cells actively involved in protein synthesis and secretion.
They are extensive and continuous with the outer membrane of the nucleus.
The smooth endoplasmic reticulum is the major site for synthesis of lipid.
In animal cells lipid-like steroidal hormones are synthesised in SER.
Golgi Apparatus
Camillo Golgi (1898) first observed densely stained reticular structures near the nucleus.
These were later named Golgi bodies after him.
They consist of many flat, disc-shaped sacs or cisternae of 0.5 \,\mu m to 1.0 \, \mu m diameter.
These are stacked parallel to each other.
Varied number of cisternae are present in a Golgi complex.
The Golgi cisternae are concentrically arranged near the nucleus with distinct convex cis or the forming face and concave trans or the maturing face.
The cis and the trans faces of the organelle are entirely different, but interconnected.
The golgi apparatus principally performs the function of packaging materials, to be delivered either to the intra-cellular targets or secreted outside the cell.
Materials to be packaged in the form of vesicles from the ER fuse with the cis face of the golgi apparatus and move towards the maturing face.
This explains, why the golgi apparatus remains in close association with the endoplasmic reticulum.
A number of proteins synthesised by ribosomes on the endoplasmic reticulum are modified in the cisternae of the golgi apparatus before they are released from its trans face.
Golgi apparatus is the important site of formation of glycoproteins and glycolipids.
Lysosomes
These are membrane-bound vesicular structures formed by the process of packaging in the golgi apparatus.
The isolated lysosomal vesicles have been found to be very rich in almost all types of hydrolytic enzymes (hydrolases – lipases, proteases, carbohydrases) optimally active at the acidic pH.
These enzymes are capable of digesting carbohydrates, proteins, lipids and nucleic acids.
Vacuoles
The vacuole is the membrane-bound space found in the cytoplasm.
It contains water, sap, excretory product and other materials not useful for the cell.
The vacuole is bound by a single membrane called tonoplast.
In plant cells the vacuoles can occupy up to 90 per cent of the volume of the cell.
In plants, the tonoplast facilitates the transport of a number of ions and other materials against concentration gradients into the vacuole, hence their concentration is significantly higher in the vacuole than in the cytoplasm.
In Amoeba, the contractile vacuole is important for osmoregulation and excretion.
In many cells, as in protists, food vacuoles are formed by engulfing the food particles.
Mitochondria
Mitochondria (sing.: mitochondrion), unless specifically stained, are not easily visible under the microscope.
The number of mitochondria per cell is variable depending on the physiological activity of the cells.
In terms of shape and size also, considerable degree of variability is observed.
Typically it is sausage-shaped or cylindrical having a diameter of 0.2-1.0 \, \mu m (average 0.5 \, \mu m) and length 1.0-4.1µm.
Each mitochondrion is a double membrane-bound structure with the outer membrane and the inner membrane dividing its lumen distinctly into two aqueous compartments, i.e., the outer compartment and the inner compartment.
The inner compartment is filled with a dense homogeneous substance called the matrix.
The outer membrane forms the continuous limiting boundary of the organelle.
The inner membrane forms a number of infoldings called the cristae (sing.: crista) towards the matrix.
The cristae increase the surface area.
The two membranes have their own specific enzymes associated with the mitochondrial function.
Mitochondria are the sites of aerobic respiration.
They produce cellular energy in the form of ATP, hence they are called ‘power houses’ of the cell.
The matrix also possesses single circular DNA molecule, a few RNA molecules, ribosomes (70S) and the components required for the synthesis of proteins.
The mitochondria divide by fission.
Plastids
Plastids are found in all plant cells and in euglenoides.
These are easily observed under the microscope as they are large.
They bear some specific pigments, thus imparting specific colours to the plants.
Based on the type of pigments plastids can be classified into chloroplasts, chromoplasts and leucoplasts.
The chloroplasts contain chlorophyll and carotenoid pigments which are responsible for trapping light energy essential for photosynthesis.
In the chromoplasts, fat soluble carotenoid pigments like carotene, xanthophylls and others are present.
This gives the part of the plant a yellow, orange or red colour.
The leucoplasts are the colourless plastids of varied shapes and sizes with stored nutrients:
Amyloplasts store carbohydrates (starch), e.g., potato.
Elaioplasts store oils and fats.
Aleuroplasts store proteins.
Majority of the chloroplasts of the green plants are found in the mesophyll cells of the leaves.
These are lens-shaped, oval, spherical, discoid or even ribbon-like organelles having variable length (5-10µm) and width (2-4µm).
Their number varies from 1 per cell of the Chlamydomonas, a green alga to 20-40 per cell in the mesophyll.
Like mitochondria, the chloroplasts are also double membrane bound.
Of the two, the inner chloroplast membrane is relatively less permeable.
The space limited by the inner membrane of the chloroplast is called the stroma.
A number of organised flattened membranous sacs called the thylakoids, are present in the stroma.
Thylakoids are arranged in stacks like the piles of coins called grana (singular: granum) or the intergranal thylakoids.
In addition, there are flat membranous tubules called the stroma lamellae connecting the thylakoids of the different grana.
The membrane of the thylakoids enclose a space called a lumen.
The stroma of the chloroplast contains enzymes required for the synthesis of carbohydrates and proteins.
It also contains small, double-stranded circular DNA molecules and ribosomes.
Chlorophyll pigments are present in the thylakoids.
The ribosomes of the chloroplasts are smaller (70S) than the cytoplasmic ribosomes (80S).
Ribosomes
Ribosomes are the granular structures first observed under the electron microscope as dense particles by George Palade (1953).
They are composed of ribonucleic acid (RNA) and proteins and are not surrounded by any membrane.
The eukaryotic ribosomes are 80S while the prokaryotic ribosomes are 70S.
Each ribosome has two subunits, larger and smaller subunits.
The two subunits of 80S ribosomes are 60S and 40S while that of 70S ribosomes are 50S and 30S.
Here ‘S’ (Svedberg’s Unit) stands for the sedimentation coefficient; it is indirectly a measure of density and size.
Both 70S and 80S ribosomes are composed of two subunits.
Cytoskeleton
An elaborate network of filamentous proteinaceous structures consisting of microtubules, microfilaments and intermediate filaments present in the cytoplasm is collectively referred to as the cytoskeleton.
The cytoskeleton in a cell are involved in many functions such as mechanical support, motility, maintenance of the shape of the cell.
Cilia and Flagella
Cilia (sing.: cilium) and flagella (sing.: flagellum) are hair-like outgrowths of the cell membrane.
Cilia are small structures which work like oars, causing the movement of either the cell or the surrounding fluid.
Flagella are comparatively longer and responsible for cell movement.
The prokaryotic bacteria also possess flagella but these are structurally different from that of the eukaryotic flagella.
The electron microscopic study of a cilium or the flagellum show that they are covered with plasma membrane.
Their core called the axoneme, possesses a number of microtubules running parallel to the long axis.
The axoneme usually has nine doublets of radially arranged peripheral microtubules, and a pair of centrally located microtubules.
Such an arrangement of axonemal microtubules is referred to as the 9+2 array.
The central tubules are connected by bridges and is also enclosed by a central sheath, which is connected to one of the tubules of each peripheral doublets by a radial spoke.
Thus, there are nine radial spokes.
The peripheral doublets are also interconnected by linkers.
Both the cilium and flagellum emerge from centriole-like structure called the basal bodies.
Centrosome and Centrioles
Centrosome is an organelle usually containing two cylindrical structures called centrioles.
They are surrounded by amorphous pericentriolar materials.
Both the centrioles in a centrosome lie perpendicular to each other in which each has an organisation like the cartwheel.
They are made up of nine evenly spaced peripheral fibrils of tubulin protein.
Each of the peripheral fibril is a triplet.
The adjacent triplets are also linked.
The central part of the proximal region of the centriole is also proteinaceous and called the hub, which is connected with tubules of the peripheral triplets by radial spokes made of protein.
The centrioles form the basal body of cilia or flagella, and spindle fibres that give rise to spindle apparatus during cell division in animal cells.
Nucleus
Nucleus as a cell organelle was first described by Robert Brown as early as 1831.
Later the material of the nucleus stained by the basic dyes was given the name chromatin by Flemming.
The interphase nucleus (nucleus of a cell when it is not dividing) has highly extended and elaborate nucleoprotein fibres called chromatin, nuclear matrix and one or more spherical bodies called nucleoli (sing.: nucleolus).
Electron microscopy has revealed that the nuclear envelope, which consists of two parallel membranes with a space between (10 to 50 nm) called the perinuclear space, forms a barrier between the materials present inside the nucleus and that of the cytoplasm.
The outer membrane usually remains continuous with the endoplasmic reticulum and also bears ribosomes on it.
At a number of places the nuclear envelope is interrupted by minute pores, which are formed by the fusion of its two membranes.
These nuclear pores are the passages through which movement of RNA and protein molecules takes place in both directions between the nucleus and the cytoplasm.
Normally, there is only one nucleus per cell, variations in the number of nuclei are also frequently observed.
Some mature cells even lack nucleus, e.g., erythrocytes of many mammals and sieve tube cells of vascular plants.
The nuclear matrix or the nucleoplasm contains nucleolus and chromatin.
The nucleoli are spherical structures present in the nucleoplasm.
The content of nucleolus is continuous with the rest of the nucleoplasm as it is not a membrane bound structure.
It is a site for active ribosomal RNA synthesis.
Larger and more numerous nucleoli are present in cells actively carrying out protein synthesis.
Chromosome Structure
The interphase nucleus has a loose and indistinct network of nucleoprotein fibres called chromatin.
During cell division, cells show structured chromosomes in place of the nucleus.
Chromatin contains DNA and some basic proteins called histones, some non-histone proteins and also RNA.
A single human cell has approximately two metre long thread of DNA distributed among its forty six (twenty three pairs) chromosomes.
Every chromosome (visible only in dividing cells) essentially has a primary constriction or the centromere on the sides of which disc shaped structures called kinetochores are present.
Centromere holds two chromatids of a chromosome.
Based on the position of the centromere, the chromosomes can be classified into four types.
The metacentric chromosome has middle centromere forming two equal arms of the chromosome.
The sub-metacentric chromosome has centromere slightly away from the middle of the chromosome resulting into one shorter arm and one longer arm.
In case of acrocentric chromosome the centromere is situated close to its end forming one extremely short and one very long arm, whereas the telocentric chromosome has a terminal centromere.
Sometimes a few chromosomes have non-staining secondary constrictions at a constant location. This gives the appearance of a small fragment called the satellite.
Microbodies
Many membrane bound minute vesicles called microbodies that contain various enzymes, are present in both plant and animal cells.