Biomolecules: Chapter 9

• Biology studies living organisms, revealing their diversity through detailed descriptions of form and appearance.
• Cell theory highlights the unity of life through the cellular organization in all life forms.
• Cell structure and division are described, creating a mystery around living phenomena relating to cellular organization.
• Physiological and behavioral processes can be studied using a physico-chemical approach with cell-free systems.
• This approach enables the description of processes in molecular terms through the analysis of living tissues.
• Studying compounds inside a cell helps understand how they carry out physiological processes like digestion and excretion.
• Understanding molecular basis helps explain abnormal processes during disease.
• Reductionist Biology applies physics and chemistry concepts to study living organisms.
• Chapter 9 provides a description of biomolecules.

G.N. Ramachandran

• G.N. Ramachandran was the founder of the 'Madras school' of conformational analysis of biopolymers.
• He discovered the triple helical structure of collagen, published in Nature in 1954.
• Ramachandran's analysis of allowed protein conformations using the 'Ramachandran plot' is a major contribution to structural biology.
• Ramachandran graduated top of his class in B.Sc. (Honors) Physics from the University of Madras in 1942.
• He received a Ph.D. from Cambridge University in 1949.
• Linus Pauling's work on α-helix and β-sheet structures influenced Ramachandran to solve the structure of collagen.
• He was born on October 8, 1922, and passed away on April 7, 2001, at the age of 78.

Cell

• The presence of the cell distinguishes living organisms from non-living things.
• All organisms consist of cells, either single (unicellular) or multiple (multicellular).
• Unicellular organisms independently exist and carry out essential life functions.
• A complete cell structure is necessary for independent living.
• A cell is the fundamental structural and functional unit of all living organisms.
• Anton Von Leeuwenhoek first observed and described a live cell.
• Robert Brown discovered the nucleus.
• Microscopes, including the electron microscope, revealed the structural details of the cell.

Cell Theory

• Matthias Schleiden (1838) found that plants are made of different kinds of cells forming plant tissues.
• Theodore Schwann (1839) reported that animal cells have a thin outer layer, the plasma membrane.
• Schwann noted that plant cells uniquely possess a cell wall.
• Schleiden and Schwann proposed that animal and plant bodies are composed of cells and their products.
• Rudolf Virchow (1855) explained that cells divide and form from pre-existing cells.
• The modern cell theory includes:
  • All living organisms are composed of cells and cell products.
  • All cells arise from pre-existing cells.

Cell Overview

• Plant cells have a distinct cell wall and a cell membrane, while animal cells have an outer membrane.
• Inside each cell is a nucleus, which contains chromosomes with DNA.
• Eukaryotic cells have a membrane-bound nucleus, while prokaryotic cells do not.
• Cytoplasm, a semi-fluid matrix, fills the cell and is the site of cellular activities.
• Eukaryotic cells have membrane-bound organelles like the ER, Golgi complex, lysosomes, mitochondria, microbodies, and vacuoles.
• Prokaryotic cells lack membrane-bound organelles.
• Ribosomes, which are non-membrane bound, are in all cells and within chloroplasts, mitochondria, and on rough ER.
• Animal cells have a centrosome, a non-membrane bound organelle that aids in cell division.
• Cells vary greatly in size, shape, and activities.
• Mycoplasmas are the smallest cells, measuring 0.3 µm in length.
• Bacteria range from 3 to 5 µm in size.
• The egg of an ostrich is the largest isolated single cell.
• Human red blood cells are about 7.0 µm in diameter.
• Nerve cells are some of the longest cells and cells may be disc-like, polygonal, columnar, cuboid, thread-like, or irregular in shape.
• A cell's shape is related to its function.

Prokaryotic Cells

• Prokaryotic cells include bacteria, blue-green algae, mycoplasma, and PPLO which are small and fast multiplying.
• Basic bacterial shapes:
  • Bacillus (rod-like)
  • Coccus (spherical)
  • Vibrio (comma-shaped)
  • Spirillum (spiral)
• Prokaryotic cell organization remains similar despite varying functions and shapes.
• Most prokaryotes have a cell wall around the cell membrane, except mycoplasma.
• Cytoplasm fills the cell, lacking a defined nucleus and not enveloped by a nuclear membrane.
• Many bacteria contain small circular DNA called plasmids, outside the genomic DNA which provide unique characteristics like antibiotic resistance.
• Nuclear membranes are present in eukaryotes.
• Prokaryotes have inclusions and mesosomes.
• Mesosomes are infoldings of the cell membrane and a characteristic of prokaryotes.

Cell Envelope & Modifications

• Bacterial cells have a complex cell envelope with three layers:
  • Glycocalyx (outermost)
  • Cell wall
  • Plasma membrane
• The layers offer protection as a single unit.
• Cell envelopes differentiate bacteria into Gram-positive (take up gram stain) and Gram-negative (do not take up gram stain).
• Glycocalyx varies in composition and thickness to either a slime layer or a tough capsule.
• Cell wall determines cell shape and prevents bursting or collapsing.
• Plasma membrane is selectively permeable and interacts with the outside world, and is similar in structure to eukaryotes.
• Mesosomes are formed by extensions of the plasma membrane into vesicles, tubules, and lamellae.
• Mesosomes facilitate cell wall formation, DNA replication, distribution to daughter cells, respiration, secretion, surface area increase, and enzymatic content.
• Cyanobacteria contain chromatophores, which are extensions into the cytoplasm that contain pigments.
• Bacterial cells can be motile or non-motile, and motile cells have flagella.
• Bacterial flagellum has three parts:
  • Filament (longest portion)
  • Hook
  • Basal body
• Pili and Fimbriae are surface structures that do not aid in motility.
• Pili are tubular, made of special protein.
• Fimbriae are small bristle-like fibers that help attach bacteria to rocks and host tissues.

Ribosomes and Inclusion Bodies

• Ribosomes attach to the plasma membrane in prokaryotes.
• Prokaryotic ribosomes are 15 nm by 20 nm, consisting of 50S and 30S subunits forming 70S ribosomes.
• Ribosomes are responsible for protein synthesis.
• Several ribosomes bind to an mRNA to form a polyribosome or polysome, which translates the mRNA into proteins.
• Reserve materials are stored as inclusion bodies within the cytoplasm and are not bound by membrane.
• Examples include phosphate granules, cyanophycean granules, and glycogen granules.
• Gas vacuoles are in blue green, purple, and green photosynthetic bacteria.

Eukaryotic Cells

• Eukaryotes include protists, plants, animals, and fungi.
• Eukaryotic cells feature extensive compartmentalization of the cytoplasm through membrane-bound organelles.
• They possess a nucleus with a nuclear envelope, locomotory structures, and cytoskeletal structures.
• Genetic material is organized into chromosomes.
• Plant cells differ from animal cells by possessing cell walls, plastids, and a large central vacuole.
• Animal cells have centrioles, which are absent in almost all plant cells.

Cell Membrane

• The structure of the cell membrane was studied in detail after the advent of the electron microscope in the 1950s.
• Chemical studies showed that the cell membrane mainly comprises lipids and proteins.
• Major lipids are phospholipids arranged in a bilayer with polar heads outward and hydrophobic tails inward.
• Nonpolar tails of saturated hydrocarbons are protected from the aqueous environment.
• Cholesterol and carbohydrates are also found in the cell membrane.
• Erythrocyte membranes consist of 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 proposed the fluid mosaic model in 1972 and the quasi-fluid nature of lipid enables lateral movement of proteins.
• Membrane fluidity is important for cell growth, intercellular junctions, secretion, endocytosis, and cell division.
• The plasma membrane transports molecules through passive and active transport.
• Passive transport allows molecules to move across the membrane without energy and neutral solutes diffuse along the concentration gradient.
• Water moves by osmosis from higher to lower concentration.
• Polar molecules use carrier proteins to cross the nonpolar lipid bilayer.
• Active transport moves ions or molecules against the concentration gradient, requiring energy (ATP), e.g., Na+/K+ Pump.

Cell Wall

• The cell wall is a non-living rigid structure outside the plasma membrane in fungi and plants which gives shape, protects against mechanical damage and infection and allows cell-to-cell interaction.
• Algae cell walls are made of cellulose, galactans, mannans, and minerals (calcium carbonate).
• Plant cell walls consist of cellulose, hemicellulose, pectins, and proteins.
• A young plant cell has a primary wall that grows and matures, while the secondary wall forms on the inner side.
• The middle lamella, primarily of calcium pectate, holds neighboring cells together.
• Plasmodesmata traverse the cell wall and middle lamellae, connecting the cytoplasm of neighboring cells.

Endomembrane System

• The endomembrane system coordinates organelle functions (endoplasmic reticulum, Golgi complex, lysosomes, vacuoles).
• Mitochondria, chloroplasts, and peroxisomes are not part of this system.

Endoplasmic Reticulum (ER)

• Electron microscopy reveals a network of tubular structures in cytoplasm called the ER which divides the intracellular space into luminal and extra luminal.
• Rough Endoplasmic Reticulum (RER) has ribosomes, is involved in protein synthesis and secretion, and is continuous with the nucleus's outer membrane.
• In the absence of ribosomes, the ER is smooth (SER) and it's the major site for lipid synthesis.
• Steroidal hormones are synthesized in SER of animal cells.

Golgi Apparatus

• Camillo Golgi (1898) discovered reticular structures near the nucleus, known as Golgi bodies.
• The Golgi apparatus consists of disc-shaped sacs or cisternae, stacked parallel to each other.
• Cisternae are concentrically arranged near the nucleus, with a convex cis (forming) face and a concave trans (maturing) face.
• The Golgi apparatus packages materials for intracellular or extracellular delivery, and ER vesicles fuse with the cis face to move towards the maturing face.
• The Golgi apparatus modifies proteins synthesized by ribosomes on the ER and forms glycoproteins and glycolipids.

Lysosomes

• Lysosomes are vesicular structures formed by the Golgi apparatus.
• They contain hydrolytic enzymes (hydrolases), which are most active at acidic pH.
• These enzymes digest carbohydrates, proteins, lipids, and nucleic acids.

Vacuoles

• Vacuoles are membrane-bound spaces in the cytoplasm, containing water, sap, excretory products, and other non-useful materials and bound by a single membrane called tonoplast.
• Tonoplast facilitates the movement of ions and materials against concentration gradients, resulting in higher vacuole concentration.
• Contractile vacuoles in Amoeba are important for osmoregulation and excretion.
• In protists, food vacuoles are formed by engulfing food particles.

Mitochondria

• The number of mitochondria per cell depend on physiological activities and are sausage-shaped, cylindrical structures.
• Each mitochondrion is a double membrane-bound structure dividing its lumen into two aqueous compartments: outer and inner.
• The inner compartment contains a dense matrix, while the outer membrane forms the boundary of the organelle.
• The inner membrane forms infoldings called cristae, increasing the surface area and have enzymes associated with mitochondrial function.
• Mitochondria are the site of aerobic respiration, producing ATP and are thus known as the 'power houses' of the cell.
• The matrix contains a single circular DNA molecule, RNA molecules, ribosomes (70S), and components for protein synthesis which divides by fission.

Plastids

• Plastids are found in all plant cells and euglenoids and have specific pigments for specific colors.
• Plastids are classified into Chloroplasts, Chromoplasts and Leucoplasts.
• Chloroplasts have chlorophyll and carotenoid pigments for trapping light energy essential for photosynthesis.
• Chromoplasts have fat soluble carotenoid pigments like carotene and xanthophylls and provide yellow, orange, or red color.
• Leucoplasts are colorless plastids with stored nutrients.
  • Amyloplasts store carbohydrates (starch).
  • Elaioplasts store oils and fats.
  • Aleuroplasts store proteins.
• Most chloroplasts in green plants are in the mesophyll cells of leaves, lentil in shape having variable length and width.
• Their number varies from 1 per cell of Chlamydomonas to 20-40 per cell in the mesophyll.
• Like mitochondria, chloroplasts are double membrane bound organelles where the space limited by the inner membrane inside is called the stroma.
• Organized flattened membranous sacs called thylakoids are present in the stroma as arranged stacks called grana.
• Flat membranous tubules, called stroma lamellae, connect the thylakoids of different grana.
• The thylakoid membrane encloses a space called a lumen.
• The stroma contains enzymes for the synthesis of carbohydrates and proteins, double-stranded circular DNA molecules, and ribosomes.
• Chlorophyll pigments are in the thylakoids.
• The ribosomes of chloroplasts are smaller (70S) than cytoplasmic ribosomes (80S).

Ribosomes

• Ribosomes are granular structures observed by George Palade (1953), composed of RNA and proteins and not surrounded by a membrane.
• Eukaryotic ribosomes are 80S, while prokaryotic ribosomes are 70S.
• Each ribosome has larger and smaller subunits.
• 80S ribosomes have 60S and 40S subunits.
• 70S ribosomes have 50S and 30S subunits.
• Here ‘S’ (Svedberg’s Unit) stands for the sedimentation coefficient, indirectly a measure of density and size.

Cytoskeleton

• The cytoskeleton is a network of filamentous proteinaceous structures including microtubules, microfilaments, and intermediate filaments.
• The cytoskeleton provides mechanical support, motility, and maintains cell shape.

Cilia and Flagella

• Cilia and flagella are hair-like outgrowths of the cell membrane and are responsible for cell movement.
• Cilia are small which work like oars, causing the movement of either the cell or the surrounding fluid.
• Flagella are longer and responsible for cell movement.
• Prokaryotic bacteria also possess flagella but these are structurally different from that of the eukaryotic flagella.
• The core of a cilium or flagellum, the axoneme, has microtubules running parallel to the long axis having nine doublets of radially arranged peripheral microtubules and a pair of centrally located microtubules known as the 9+2 array.
• The central tubules are connected by bridges and enclosed by a central sheath, connected to one of the tubules of each peripheral doublets by radial spokes.
• The peripheral doublets are interconnected by linkers.
• Both the cilium and flagellum emerge from centriole-like structure called the basal bodies.

Centrosome and Centrioles

• The centrosome has two cylindrical structures called centrioles, surrounded by pericentriolar materials.
• The centrioles are perpendicular to each other, organized like a cartwheel and made up of nine evenly spaced peripheral fibrils of tubulin protein.
• Each peripheral fibril is a triplet connected to adjacent triplets.
• The central part is the hub with radial spokes.
• Centrioles form the basal body of cilia or flagella, and spindle fibers in animal cells during cell division.

Nucleus

• Robert Brown first described the nucleus as a cell organelle in 1831. Flemming then defines chromatin as the material of the nucleus stained by basic dyes.
• The interphase nucleus consisting of chromatin, nuclear matrix, and nucleoli.
• The nuclear envelope consists of two membranes and a perinuclear space and forms a barrier to materials from the cytoplasm.
• The outer membrane connects to the ER and has ribosomes.
• Nuclear pores are passages for RNA and protein molecules that occurs between the nucleus and the cytoplasm.
• Cells normally have only one nucleus, variations are also observed.
• Some mature cells lacking nucleus (e.g, erythrocytes of many mammals and sieve tube cells of vascular plants.)
• The nuclear matrix contains nucleolus and chromatin, nucleoli are spherical and are a site for active ribosomal RNA synthesis.
• Larger and more numerous nucleoli are also present in cells that actively carry out protein synthesis.

Chromosomes

• The interphase nucleus consist of a network of nucleoprotein fibers called chromatin. During cell division cells show structured chromosomes.
• Chromatin contains DNA, histones, non-histone proteins, and RNA.
• A single human cell contains two meters long thread of DNA distributed among its forty six chromosomes.
• Every chromosome has a primary constriction or the centromere on the sides of which disc shaped structures called kinetochores are present.
• Based on the position of the centromere, the chromosomes can be classified into four types
  • Metacentric chromosome has middle centromere forming two equal arms
  • Sub-metacentric chromosome has centromere slightly away from the middle resulting into one shorter arm and one longer arm.
  • Acrocentric chromosome the centromere is situated close to its end, forming one extremely short and one very long arm i.e. near to its end.
  • Telocentric chromosome has a terminal centromere.

Microbodies

• Microbodies are membrane-bound vesicles that contain various enzymes, in both plant and animal cells.