Introduction to Cell Biology

Introduction to Cell Biology

• Biology studies living organisms and their diversity.
• Cell theory highlights the fundamental unity among diverse life forms via cellular organization.
• Cell structure and division explain the base of biological structures.
• Living phenomena need intact cellular organization.
• Physiological and behavioral processes are studied using a physico-chemical approach with cell-free systems for molecular-level descriptions.
• Living tissues are analyzed for their elemental and compound composition, identifying organic compounds in organisms.
• Reductionist Biology studies living organisms using physics and chemistry concepts and techniques.
• This encompasses studying the molecular basis of physiological processes like digestion, excretion, memory, defense, and recognition, and the approach is also vital in understanding the molecular basis of diseased conditions
• A description of biomolecules is provided in Chapter 9.

G.N. Ramachandran

• G.N. Ramachandran (1922-2001) founded the 'Madras school' of conformational analysis of biopolymers.
• He discovered the triple helical structure of collagen in 1954, published in Nature.
• Introduced the 'Ramachandran plot' for analyzing allowed protein conformations.
• Graduated top of his class in B.Sc. Physics from the University of Madras in 1942.
• Earned a Ph.D. from Cambridge University in 1949.
• Linus Pauling's models of α-helix and β-sheet structures influenced Ramachandran so that he was directed to solving the structure of collagen.

What is a cell?

• The presence of cells differentiates living organisms from non-living things.
• Unicellular organisms can exist independently and perform all essential life functions.
• A complete cell structure is required for independent living.
• A cell is the fundamental structural and functional unit of life.
• Anton Von Leeuwenhoek was the first to observe and describe a live cell.
• Robert Brown discovered the nucleus.
• Microscopes led to the discovery of the cell's structural details.

Cell Theory

• Matthias Schleiden (1838) found that plants consist of different kinds of cells which form plant tissues.
• Theodore Schwann (1839) reported that animal cells have a plasma membrane and concluded that animal and plant bodies are composed of cells and cell products.
• Schleiden and Schwann together formulated the cell theory.
• Rudolf Virchow (1855) stated that cells divide, and new cells are formed from pre-existing cells ("Omnis cellula-e cellula").
• Modern Cell Theory states that all living organisms are composed of cells and cell products and all cells arise from pre-existing cells.

Overview of a Cell

• The onion cell (a plant cell) has a cell wall as its outer boundary and a cell membrane.
• Human check cells have an outer membrane.
• Eukaryotic cells possess a membrane-bound nucleus, while prokaryotic cells lack one.
• The nucleus contains chromosomes with genetic material, DNA.
• Cytoplasm, a semi-fluid matrix, occupies the cell's volume in both cell types.
• The cytoplasm is where cellular activities and chemical reactions occur, maintaining the cell's living state.
• Eukaryotic cells contain membrane-bound organelles like the endoplasmic reticulum (ER), Golgi complex, lysosomes, mitochondria, microbodies, and vacuoles, which are absent in prokaryotic cells.
• Ribosomes, non-membrane-bound organelles, are present in both prokaryotic and eukaryotic cells, within the cytoplasm, chloroplasts (plants), mitochondria, and rough ER.
• Animal cells have a centrosome, a non-membrane bound organelle, that functions in cell division.
• Mycoplasmas, the smallest cells, measure only 0.3µm in length, while bacteria range from 3 to 5µm.
• The egg of an ostrich is the largest isolated single cell.
• Human red blood cells have a diameter of about 7.0 µm.
• Nerve cells are among the longest cells.
• Cells come in various shapes: disc-like, polygonal, columnar, cuboid, thread-like, or irregular, which correlate with their function.

Prokaryotic Cells

• Prokaryotic cells include bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
• Prokaryotes are generally smaller and multiply faster than eukaryotic cells.
• Basic bacterial shapes are bacillus (rod), coccus (spherical), vibrio (comma), and spirillum (spiral).
• Fundamental prokaryotic cell organization is similar despite diverse shapes and functions.
• All prokaryotes have a cell wall around the cell membrane, except mycoplasma.
• The cytoplasm is the fluid matrix filling the cell.
• Prokaryotes lack a well-defined nucleus; instead, they have naked genetic material not enveloped by a nuclear membrane.
• Plasmids (small circular DNA outside the genomic DNA) are present in many bacteria and provide unique phenotypic characters, such as antibiotic resistance.
• Eukaryotes contain a nuclear membrane, which is absent in prokaryotes.
• Eukaryotic organelles are absent in prokaryotic cells.
• Mesosome, a specialized differentiated form of the cell membrane, is characteristic of prokaryotes and is essential infoldings of the cell membrane

Cell Envelope and its Modifications

• Bacterial cells contain a complex cell envelope that comprises three layers: glycocalyx, cell wall, and plasma membrane which form a protective unit.
• Gram-positive bacteria take up Gram stain, while Gram-negative bacteria do not.
• Glycocalyx composition and thickness vary; it can be a slime layer or a tough capsule.
• The cell wall determines cell shape and provides support against bursting or collapsing.
• The plasma membrane, structurally similar to that of eukaryotes, is selectively permeable and interacts with the external environment.
• Mesosomes, formed by plasma membrane extensions (vesicles, tubules, and lamellae), aid in cell wall formation, DNA replication, respiration, secretion, increasing surface area, and enzymatic content.
• Cyanobacteria have membranous extensions called chromatophores containing pigments.
• Motile bacterial cells possess flagella.
• A bacterial flagellum consists of three parts: filament, hook, and basal body.
• Pili and fimbriae are surface structures that do not contribute to motility; pili are tubular structures, and fimbriae are bristle-like fibers that aid in attachment.

Ribosomes and Inclusion Bodies

• Prokaryotic ribosomes attach to the plasma membrane of the cell.
• Prokaryotic Ribosomes measure approximately 15 nm x 20 nm
• Prokaryotic ribosomes are composed of two subunits (50S and 30S), forming 70S ribosomes.
• Ribosomes function as the site of protein synthesis.
• A polysome is formed when several ribosomes attach to a single mRNA.
• Genetic Code: The information within the mRNA is translated by the polysome ribosomes into proteins.
• Inclusion bodies are reserve materials in prokaryotic cells stored in the cytoplasm, not bound by any membrane, including phosphate, cyanophycean, and glycogen granules.
• Gas vacuoles are present in blue-green, purple, and green photosynthetic bacteria.

Eukaryotic Cells

• Eukaryotes include protists, plants, animals, and fungi.
• Eukaryotic cells compartmentalize the cytoplasm extensively with membrane-bound organelles.
• Eukaryotic cells possess an organized nucleus with a nuclear envelope.
• Eukaryotic cells exhibit complex locomotory and cytoskeletal structures.
• Eukaryotic Genetic material is organized into chromosomes.
• Plant cells differ from animal cells by having cell walls, plastids, and a large central vacuole, while animal cells have centrioles.

Cell Membrane

• Cell: the detailed structure was studied after the advent of the electron microscope in the 1950s.
• Chemical studies show the cell membrane consists mainly of lipids and proteins.
• Phospholipids arrange into a bilayer with polar heads outwards and hydrophobic tails inwards, protecting the nonpolar tails.
• The membrane contains cholesterol.
• Cell membrane contains protein and carbohydrate.
• Erythrocyte membrane: Protein-Lipid Ratio is approximately 52% to 40% respectively in human erythrocyte.
• Membrane proteins include integral and peripheral proteins.
• Peripheral proteins are on the membrane surface, while integral proteins are partially or wholly embedded.
• Singer and Nicolson proposed the Fluid Mosaic Model in 1972.
• Lipid fluidity allows lateral protein movement within the bilayer.
• Membrane fluidity is important for functions like cell growth, intercellular junctions, secretion, endocytosis, and cell division.
• Plasma Membrane Function: Transport of molecules across the membrane.
• Selective Permeablility: The membrane is selectively permeable to molecules.
• Passive transport enables certain molecules to move without energy.
• Simple diffusion enables neutral solutes to move along the concentration gradient passively.
• Osmosis enables water to move from higher to lower concentration passively.
• Polar molecules use carrier proteins to cross the nonpolar lipid bilayer.
• Active transport: A few ions/molecules are transported against their concentration gradient using ATP.
• Sodium-potassium (Na+/K+) pump exemplify active transport.

Cell Wall

• Non-living rigid cell wall structure is the outer covering for fungi and plants.
• Cell Wall Functions: Providing shape, protect from mechanical damage and infection, helps in cell-to-cell interaction and acting as a barrier to macromolecules.
• Algae cell wall composition: Cellulose, galactans, mannans, minerals like calcium carbonate.
• Other plants cell wall composition consists of cellulose, hemicellulose, pectins, and proteins.
• A young plant cell's primary wall is capable of growth that diminishes when the secondary wall is formed.
• Middle lamella primarily consists of calcium pectate, gluing neighboring cells together.
• Plasmodesmata traverse the cell wall and middle lamellae: Connecting cytoplasm of neighboring cells.

Endomembrane System

• Membranous organelles which coordinate in function are collectively called endomembrane system.
• The endomembrane system includes the endoplasmic reticulum (ER), Golgi complex, lysosomes, and vacuoles.
• Mitochondria, chloroplasts, and peroxisomes aren't associated with the endomembrane system as they're functions are not coordinated with it.

Endoplasmic Reticulum (ER)

• Network of tubular structures scattered in the cytoplasm.
• ER divides the intracellular space into luminal (inside ER) and extra luminal (cytoplasm) compartments.
• Rough Endoplasmic Reticulum (RER) shows ribosomes on its outer surface.
• Smooth Endoplasmic Reticulum (SER) has no ribosomes.
• RER is present in cells involved in protein synthesis and secretion and is continuous with the nuclear membrane.
• The smooth endoplasmic reticulum is the major site for synthesis of lipid.
• Animal cells synthesize steric hormones in the smooth endoplasmic reticulum.

Golgi Apparatus

• Camillo Golgi first observed densely stained reticular structures near the nucleus in 1898 and they were later named Golgi bodies.
• Consists of cisternae (flat, disc-shaped sacs), measure approximately 0.5µm to 1.0µm diameter, which are stacked parallel to each other.
• Cisternae number vary in a Golgi complex.
• Golgi cisternae are concentrically arranged near the nucleus with distinct convex cis (forming) and concave trans (maturing) faces; both faces remain interconnected.
• Golgi Apparatus Function: packaging materials for intracellular delivery or for secretion.
• Vesicles from the ER fuse with the cis face of the Golgi apparatus and move towards the maturing face.
• Golgi Apparatus Location in The Cell: in close association with the endoplasmic reticulum.
• Golgi apparatus' cisternae helps: modifies proteins synthesized by ribosomes on the ER.
• Glycoproteins and glycolipids formation happens in the golgi apparatus.

Lysosomes

• Membrane-bound vesicular structures formed by packaging in the Golgi apparatus.
• Lysosomal vesicles are rich in hydrolytic enzymes (hydrolases – lipases, proteases, carbohydrases).
• Enzymes are active at the acidic pH.
• The enzyme has the capability to digest carbohydrates, proteins, lipids, and nucleic acids.

Vacuoles

• A membrane-bound space in the cytoplasm that contains water, sap, excretory products, etc
• A single membrane called tonoplast, the vacuole is bound to it.
• A plant cell's vacuole occupies approximately 90% of the cell's volume.
• Tonoplast helps the transport of ions and materials against concentration gradients, so their concentration is significantly higher in the vacuole than in the cytoplasm.
• Contractile vacuole helps with osmoregulation and excretion in Amoeba.
• Food vacuoles are formed by engulfing food particles.

Mitochondria

• Not easily visible unless specifically stained.
• Mitochondria number varies depending on the physiological activity of the cells.
• The shape can be Sausage-shaped or cylindrical in shape.
• Mitochondria measure approximately 0.2-1.0µm in diameter (average 0.5µm) and length between 1.0-4.1µm.
• Mitochondria contain a double membrane structure which has both outer and inner membranes dividing its lumen into two aqueous compartments.
• The inner compartment contains the matrix.
• The outer membrane is the limiting boundary of the organelle.
• The inner membrane forms infoldings called cristae towards the matrix, increasing the surface area.
• Membranes have specific enzymes linked with the function of the mitochondria.
• Mitochondria are the sites of aerobic respiration which: produces ATP, and is known as the power houses of the cell.
• The matrix contains a single circular DNA molecule, RNA molecules, ribosomes (70S), and the components needed for protein synthesis.
• Mitochondria divide by fission.

Plastids

• Found in plant cells and euglenoides.
• Plastids are categorized as chloroplasts, chromoplasts, and leucoplasts based on their pigments.
• Contain chlorophyll and carotenoid pigments which capture light energy for photosynthesis.
• Contains fat soluble carotenoid pigments.
• Chromoplasts give plants yellow, orange, or red colors.
• Leucoplasts are colorless plastids that store nutrients: Amyloplasts (carbohydrates/starch), e.g., potato; elaioplasts (oils and fats); aleuroplasts (proteins).
• Majority of chloroplasts: in the mesophyll cells of leaves.
• They Measure approximately 5-10µm long and 2-4µm wide.
• A green alga has 1 chloroplast, while mesophyll has 20-40.
• The inner chloroplast membrane, of the two membranes, is relatively less permeable.
• Stroma = the space limited by the inner membrane of the chloroplast.
• Numerous flattened membranous sacs called thylakoids are in the stroma.
• Thylakoids are stacked up which are called grana (singular: granum) that are intergranal thylakoids.
• Stroma lamellae: are flat membrane tubules that connect the thylakoids of the different grana.
• Lumen: the thylakoids enclose this space
• The stroma contains the enzymes need to synthesize carbohydrates and proteins, double-stranded circular DNA molecules, and ribosomes.
• Thylakoids: chlorophyll pigments are present in this structure
• Chloroplasts Ribosomes measure 70S which is smaller than the cytoplasmic ribosomes, that measure 80S.

Ribosomes

• Granular structures: George Palade (1953) was the first to observe ribosomes under the electron microscope.
• Composed of RNA and proteins.
• Not surrounded by any membrane = non-membrane bound.
• Eukaryotic ribosomes measure 80S, while prokaryotic ribosome measure 70S
• Each ribosome contains two subunits: larger and smaller.
• 80S ribosomes subunits measure 60S and 40S
• 70S ribosomes subunits measure 50S and 30S
• S stands for Svedberg's Unit referring to sedimentation coefficient; and indirectly a measure of density and size.
• Both 70S and 80S ribosomes are composed of two subunits.

Cytoskeleton

• Elaborate network of filamentous proteinaceous structures consists of microtubules, microfilaments and intermediate filaments that are present in the cytoplasm.
• Play a critical role in mechanical support, motility, and maintenance of the cell's shape.

Cilia and Flagella

• Cilia and flagella: hairlike outgrowths of the cell membrane.
• Cilia: small structures that functions similar to oars to promote movement.
• Flagella: comparatively longer and responsible for movement in the cell.
• Prokaryotic flagella: structurally different that eukaryotic, despite both cell types having flagella
• Cilia/flagella are covered with plasma membrane.
• Axoneme core: possess multiple microtubules running parallel to the long axis.
• Axoneme exhibits nine doublets of radially arranged peripheral microtubules, and a pair of is centrally located microtubules = referred to as the 9+2 array.
• Central tubules: Connected by bridges and is also enclosed by a central sheath.
• Radial spoke: Central sheath is connected to each of peripheral doublets; there are nine radial spokes.
• Peripheral doublets: interconnected by linkers.
• The cilium and flagellum emerge from a centriole-like stricture called the basal bodies

Centrosome and Centrioles

• Centrosome: an organelle generally contains two cylindrical structures called centrioles
• Amorphous pericentriolar materials: surrounds the centrioles.
• Cartwheel: both centrioles in a centrosome lie perpendicular to each each other with organization like this.
• Composition of centrioles made of nine evenly spaced peripheral fibrils of tubulin proteins where each of the peripheral fibril is a triplet with adjacent triplets linked
• Hub: The central part of the proximal region of the centriole Is proteinaceous
• Radial spokes: connect to tubules of the peripheral triplets made of protein
• Centrioles form basal body of cilia or flagella Spindle fibers give rise to apparatus during cell division in animal cells.

Nucleus

• Nucleus as a cell organelle was first described by Robert Brown as early.
• Chromatin: the material of the nucleus stained by basic dyes was given this name.
• Nuclear matrix
• Nucleoli (sing.: nucleolus)
• Nuclear Envelope: has a barrier between the materials in and out of the cytoplasm
• Minute pores: formed by fusion of the two membranes.
• Nuclear pores: the passages which allow for RNA and proteins between both spaces. Normally, one-nucleus per cell is present.
• Mature cells lack a nucleus. e.g., erythrocytes of many mammals and sieve tube cells of vascular plants
• Nucleolus and Chromatin are in the nuclear matrix or the nucleoplasm
• Nucleoli are are spherical structures present the nucleoplasm
• The content of nucleolus is continuous with the rest of the nucleoplasm as it not membrane bound
• It is a site for Active ribosomal RNA synthesis
• Larger and more numerous nucleoli are present in cells actively carrying out protein synthesis.

Chromosome

• Interphase nucleus= consists of nucleoproteins
• Structured chromosomes is the result of cell division Chromatin contains DNA and histones and RNA,
• Each cell contains to metres of DNA.
• Visible only in dividing cells has a primary constriction on each site.
• Kinetochores present in the center, holds the chromatids from each other
• Metacentric: Middle centromere forming two arms,
• Sub-metacentric: one shorter, longer and results from centromere are in the middle of the chromosome resulting into.
• Acrocentric: Centromere close at the end,
• Telocentric; Terminal centromere

Microbodies

• Membrane-bound vesicles containing various enzymes, present in both plant and animal cells.