Reductionist Biology: Physico-Chemical Approach

• Biology focuses on the study of living organisms
• Cell theory emphasizes the unity through cellular organization in all life forms
• Understanding physiological and behavioral processes involves a physico-chemical approach using cell-free systems
• This approach describes various processes in molecular terms, using analysis of living tissues
• 'Reductionist Biology' applies physics and chemistry to understand biology

G.N. Ramachandran

• G.N. Ramachandran (1922-2001) founded the 'Madras school' of biopolymer conformational analysis
• He discovered the triple helical structure of collagen, published in Nature in 1954
• Ramachandran created an analysis of protein conformations called the 'Ramachandran plot'
• He graduated top of his class in B.Sc. Physics from the University of Madras in 1942
• He earned a Ph.D. from Cambridge University in 1949
• Linus Pauling's work deeply influenced Ramachandran to solve the structure of collagen

What is a Cell?

• The cell represents the basic unit of life in all living organisms, distinguishing them from non-living things
• Unicellular organisms can exist independently and perform all essential life functions within a single cell
• A complete cell structure is essential for independent living
• Anton Von Leeuwenhoek was the first to observe and describe a live cell
• Robert Brown discovered the nucleus
• Electron microscope revealed the detailed structural components of cells

Cell Theory

• In 1838, Matthias Schleiden, a German botanist, found that plants consist of different kinds of cells forming plant tissues
• Theodor Schwann (1839), a British Zoologist, reported that animal cells have a thin outer layer, known as the plasma membrane
• Based on plant tissue studies, Schwann recognized the cell wall as a unique feature of plant cells
• Schleiden and Schwann collectively developed the cell theory
• Rudolf Virchow (1855) explained that cells divide, forming new cells from pre-existing cells (Omnis cellula-e cellula)

Overview of the Cell

• Cell theory's modern interpretation maintains that all living organisms are composed of cells, which includes their products and that all cells originate from pre-existing cells
• Onion cells feature a cell wall as the outer boundary and a cell membrane within
• Human cheek cells have only an outer membrane
• Inside cells is a dense, membrane-bound nucleus containing chromosomes and DNA
• Eukaryotic cells possess a nucleus
• Prokaryotic cells lack a membrane-bound nucleus
• Cytoplasm, a semi-fluid matrix, fills the cell volume in both cell types, and is where all cellular activities happen
• Eukaryotic cells contain membrane-bound organelles like the endoplasmic reticulum (ER), Golgi complex, lysosomes, mitochondria, microbodies, and vacuoles
• Prokaryotic cells do not have membrane-bound organelles.
• Ribosomes, which are not membrane-bound, exist in all cells (eukaryotic and prokaryotic)
• Ribosomes are found in cytoplasm, chloroplasts (in plants), mitochondria, and on rough ER
• Animal cells have centrosomes, helping in cell division and are not membrane bound
• Mycoplasmas, the smallest cells, measure only 0.3 µm in length
• Bacteria have sizes between 3 to 5 µm
• The egg of an ostrich is the largest isolated single cell
• Human red blood cells are about 7.0 µm in diameter
• Nerve cells can be classified as some of the longest cells
• Cell shapes include disc-like, polygonal, columnar, cuboid, thread-like, and irregular

Prokaryotic Cells

• Prokaryotic cells include bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms)
• Prokaryotic cells generally are smaller and multiply more quickly than eukaryotic cells
• The four basic shapes of bacteria include bacillus (rod-like), coccus (spherical), vibrio (comma-shaped), and spirillum (spiral)

Organization of Prokaryotic Cells

• Prokaryotic cell organization is fundamentally similar, with diverse shapes and functions
• Most prokaryotes feature a cell wall surrounding the cell membrane, except for mycoplasma
• The cytoplasm is the fluid matrix that fills the cell
• There is no defined nucleus
• Genetic material is not enveloped by a nuclear membrane
• Many bacteria have small circular DNA called plasmids, outside the genomic DNA
• Plasmids give bacteria unique characteristics, like antibiotic resistance
• Eukaryotes have nuclear membranes
• Prokaryotes do not have organelles except ribosomes
• Prokaryotes have unique inclusions
• Mesosome is the characteristic of prokaryotes and infoldings of the cell membrane

Cell Envelope and Modifications

• Most prokaryotic cells, especially bacterial cells, contain a chemically complex cell envelope
• The cell envelope has a tightly bound three-layered structure: an outermost glycocalyx, a cell wall, and a plasma membrane
• Each envelope layer has a distinct function, acting together as a single protective unit
• Gram-positive bacteria take up Gram stain
• Gram-negative bacteria do not take up Gram stain
• Glycocalyx varies in composition and thickness among different bacteria
• Slime layer is a loose sheath
• Capsule is a thick and tough layer
• The cell wall determines the cell shape and provides strong support, preventing collapse
• The plasma membrane is selectively permeable and interacts with the outside environment
• Plasma membrane structure is similar to that of eukaryotes
• Mesosome helps in cell wall and DNA replication, distributing to daughter cells, respiration, secretion, increases in surface area, and contributes to enzymatic content
• Cyanobacteria have cytoplasm extensions called chromatophores which contain pigments
• Bacterial cells can be motile or non-motile
• Motile cells have thin filamentous extensions from cell walls called flagella
• A bacterial flagellum consists of three parts: a filament, hook, and basal body
• The filament is the longest portion, extending from the cell surface
• Pili and fimbriae are surface structures that do not aid in motility
• Pili are elongated tubular structures made of a special protein
• Fimbriae are small bristle-like fibers that sprout from the cell, helping the bacteria attach

Ribosomes and Inclusion Bodies

• Ribosomes in prokaryotes associate with the plasma membrane of the cell
• They measure about 15 nm by 20 nm in size
• Ribosomes consist of two subunits - 50S and 30S units
• 50S and 30S units together form 70S prokaryotic ribosomes and are the site of protein synthesis
• Polysomes translate mRNA into proteins
• Inclusion bodies store reserve material and lie freely in the cytoplasm (e.g., 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 compartmentalize their cytoplasm via membrane-bound organelles
• Eukaryotic cells have an organized nucleus with a nuclear envelope
• Eukaryotic cells have locomotory and cytoskeletal structures
• Eukaryotic genetic material is organized into chromosomes
• Plant and animal cells differ
• Plant cells have cell walls, plastids, and a large central vacuole
• Animal cells feature centrioles

Cell Membrane

• Detailed study of the cell membrane became possible after the invention of the electron microscope in the 1950s
• Cell membranes are mainly lipids and proteins
• Phospholipids are major lipids arranged in a bilayer, with polar heads facing outward and hydrophobic tails inward
• This arrangement protects the nonpolar tail of saturated hydrocarbons from the aqueous environment
• In addition to phospholipids, membranes also contain cholesterol
• Cell membranes also contain proteins and carbohydrates
• The ratio of protein and lipid varies considerably in different cell types
• In human erythrocytes, 52% of the membrane is protein, and 40% is lipid
• Membrane proteins may be integral or peripheral
• Peripheral proteins are surface proteins
• Integral proteins are partially or fully buried in the membrane
• According to the fluid mosaic model proposed by Singer and Nicolson (1972), lipids enable lateral movement of proteins within the bilayer and this ability to move is measured as fluidity of the membrane
• Membrane fluidity is important for cell growth, intercellular junctions, secretion, endocytosis, and cell division
• Molecules are transported across the plasma membrane
• Passive transport does not need any enery
• Selective permeability only allows certain molecules to transported across the membrane
• Neutral solutes move via simple diffusion from high to low concentration
• Water moves via osmosis from high to low concentration
• Polar molecules require carrier proteins to transport across the membrane
• Active transport transports molecules against their gradient, from low to high concentration, using ATP energy, e.g., Na+/K+ Pump.

Cell Wall

• The cell wall is a non-living rigid structure enclosing the plasma membrane of fungi and plants
• The cell wall gives shape, protects from mechanical damage and infection, helps in cell-to-cell interaction, and blocks undesirable macromolecules
• Algae cell walls consist of cellulose, galactans, mannans, and mineral such as calcium carbonate
• Plant cell walls consist of cellulose, hemicellulose, pectins, and proteins
• The primary wall of a young plant cell can grow
• As the cell matures and the secondary wall forms on the inner side, growth stops
• The middle lamella, made of calcium pectate, holds neighboring cells together
• Plasmodesmata connect the cytoplasm of neighboring cells through the cell wall and middle lamellae

Endomembrane System

• The functions of membranous organelles such as the endoplasmic reticulum (ER), Golgi complex, lysosomes, and vacuoles are coordinated
• Mitochondria, chloroplasts, and peroxisomes are not part of the endomembrane system
• Electron microscopic studies reveal that the endoplasmic reticulum (ER) is a network of tiny tubular structures scattered in the cytoplasm
• The ER divides the intracellular space into luminal (inside ER) and extra luminal (cytoplasm) compartments
• Rough endoplasmic reticulum (RER) has ribosomes on its outer surface and is continuous with the outer membrane of the nucleus
• Smooth endoplasmic reticulum (SER) lacks ribosomes and is the site of lipid synthesis
• In animal cells, SER is where lipid-like steroidal hormones are synthesized

Golgi Apparatus

• Camillo Golgi (1898) saw and named the Golgi bodies
• The Golgi consists of flat, disc-shaped sacs called cisternae (0.5µm to 1.0µm diameter)
• Cisternae are stacked parallel to each other
• The cisternae are concentrically arranged near the nucleus
• The convex cis face is the forming face
• The concave trans face is the maturing face
• The cis and trans faces are interconnected but different
• Golgi apparatus packages materials to be delivered to intracellular targets or secreted outside the cell
• Vesicles from the ER fuse with the cis face and move toward the maturing trans face
• Proteins synthesized by ribosomes modify in the Golgi, and are released from its trans face
• Golgi apparatus provides glycoproteins and glycolipids

Lysosomes

Lysosomes have hydrolytic enzymes (hydrolases – lipases, proteases, carbohydrases)

• Lysosomes are optimally active at an acidic pH
• Lysosomes digest carbohydrates, proteins, lipids, and nucleic acids

Vacuoles

• Vacuoles are membrane-bound spaces in the cytoplasm containing water, sap, excretory products, and other materials
• Vacuoles are bound by a single membrane called the tonoplast
• Plant cells feature vacuoles occupying up to 90% of the cell volume
• Tonoplasts facilitate the transport of ions and other materials against concentration gradients into the vacuole
• Osmoregulation and excretion occurs through contractile vacuoles In Amoeba
• Food vacuoles form by engulfing particles from outside

Mitochondria

• Mitochondria are not visible unless stained
• Mitochondria number varies per cell depending on the cell's physiological activity
• Typically mitochondria are sausage-shaped or cylindrical, 0.2-1.0µm diameter (average 0.5µm) and length 1.0-4.1µm
• Each mitochondrion is a double membrane-bound structure
• The outer and inner membranes separates the lumen into two aqueous compartments
• The inner compartment has a dense substance called the matrix
• The outer membrane defines the organelle
• The inner membrane forms infoldings called cristae which increase the surface area
• The two membranes have their own specific enzymes
• Mitochondria are the sites of aerobic respiration
• The produce cellular energy via ATP, giving them the nickname 'power houses'
• The matrix includes a single circular DNA molecule, some RNA molecules, ribosomes (70S), and protein synthesis components
• Mitochondria divide by fission

Plastids

• Plastids are found in plant cells and euglenoids
• Plastids bear specific pigments for coloration
• Plastids can be classified as chloroplasts, chromoplasts, and leucoplasts, based on pigment type
• Chloroplasts contain chlorophyll and carotenoid pigments that trap light energy for photosynthesis
• Chromoplasts possess fat-soluble carotenoid pigments like carotene, xanthophylls
• Chromoplasts give pants a yellow, orange, or red color
• Leucoplasts are colorless
• Amyloplasts store carbohydrates (starch), e.g., potato
• Elaioplasts store oils and fats
• Aleuroplasts store proteins
• Chloroplasts of green plants are found in the mesophyll cells of the leaves
• Chloroplasts are lens-shaped, oval, spherical, discoid, or ribbon-like in shape, having a variable length (5-10µm) and width (2-4µm)
• Number of chloroplasts vary from single chloroplast per cell of Chlamydomonas to 20-40 chloroplasts per mesophyll cell
• Chloroplasts are also double membrane bound
• The inner chloroplast membrane is relatively less permeable
• Stroma is the space limited by the inner membrane of the chloroplast.
• Stroma includes organized flattened membranous sacs called thylakoids
• Thylakoids are in piles called grana
• Stroma lamellae: flat membranous tubules connecting thylakoids of different grana
• The thylakoid membrane is the space called a lumen
• The stroma contains enzymes for carbohydrate and protein synthesis
• Chloroplasts contain small, double-stranded circular DNA molecules and ribosomes
• Chlorophyll pigments are in the thylakoids
• Chloroplast ribosomes are smaller (70S) than cytoplasmic ribosomes (80S)

Ribosomes

• George Palade (1953) first observed ribosomes under the electron microscope as dense particles
• Ribosomes contain ribonucleic acid (RNA) and proteins and are not surrounded by any membrane
• Eukaryotic ribosomes are 80S
• Prokaryotic ribosomes are 70S
• ‘S’ (Svedberg’s Unit) stands for the sedimentation coefficient as a measure of density and size
• Each ribosome has a larger and smaller subunit
• 80S ribosomes have 60S and 40S subunits
• 70S ribosomes have 50S and 30S subunits

Cytoskeleton

• The cytoskeleton is an elaborate network of proteinaceous structures consisting of microtubules, microfilaments and intermediate filaments present in the cytoplasm
• The cytoskeleton contributes to 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 structures function like oars, moving either the cell or surrounding fluid
• Flagella are comparatively longer and responsible for cell movement
• Prokaryotic bacteria also possess flagella that are structurally different from eukaryotic
• Cilia and flagella are covered with plasma membrane
• The axoneme (core) contains microtubules running parallel to the long axis
• Axonemes have doublet peripheral microtubules radially arranged, and there is a pair of microtubules centrally located and this arrangement is referred to as the 9+2 array
• Central tubules connect via bridges, are enclosed by a central sheath and are connected by radial spokes to the tubules of each peripheral doublet
• Peripheral doublets are also interconnected by linkers
• Both the cilium and flagellum emerge from centriole-like basal bodies

Centrosome and Centrioles

• The centrosome contains two perpendicular cylindrical structures called centrioles
• Centrioles are surrounded by pericentriolar materials
• Centrioles are organized in a cartwheel fashion
• Centrioles are made up of nine evenly spaced peripheral fibrils of tubulin protein, with each fibril being a triplet and the peripheral triplets are linked
• Hub: the proteinaceous central part of the proximal region connected with peripheral triplet tubules via radial spokes
• The centrioles form the basal body of cilia or flagella, and the spindle fibres give rise to spindle apparatus during cell division in animal cells

Nucleus

• Robert Brown first described the nucleus as a cell organelle in 1831
• Flemming gave the name chromatin to the material of the nucleus later stained by basic dyes
• The space between the two membranes in the nuclear envelope (10 to 50 nm in width) is called the perinuclear space
• The nuclear envelope separates the materials inside the nucleus from the cytoplasm
• Outer membrane is continuous with the endoplasmic reticulum
• There are nuclear pores, formed by fusions of both membranes
• Nuclear pores: passages through which RNA and protein molecules move between the nucleus and cytoplasm
• There is normally only one nucleus per cell
• Nuclear matrix / nucleoplasm includes the nucleolus and chromatin
• The nucleolus is spherical
• Nucleous contains no membranes and contains continous nucleoplasm
• Active ribosomal RNA synthesis occurs in the nucleolus
• Larger nucleoli are present in cells actively synthesizing protein

Chromosomes

• The interphase nucleus has nucleoprotein fibers called chromatin(DNA + Histones+non Histones)
• Chromatin structures are visible during certain stages of cell division
• A single human cell contains approximately 2 meters of DNA, distributed among forty-six (twenty three pairs) chromosomes
• Every dividing chromosome has a primary constriction / centromere
• Disc-shaped kinetochores are on the sides of chromosomes to hold the two chromatids during division
• Chromosomes are classified into four types on the position of the centromere
• Middle centromere of the metacentric chromosome forms two equal arms
• Sub-metacentric chromosome- Centromere slightly away from the middle of the chromosome giving off one shorter and longer arm
• Acrocentric chromosome has centromere near the end forming one extremely short and one very long arm
• The telocentric chromosome features a terminal centromere
• Secondary constrictions are present at a constant location
• Satellite is a fragment that some chromosomes display

Microbodies

• Plant and animal cells contain microbodies, minute membrane bound vesicles filled with enzymes