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The Three Domains of Life
Biological diversity (Biodiversity): -Biological diversity, or biodiversity refers to all the variety of life that exists in Earth -The science of classifying organisms is called taxonomy .The classification is an important step in understanding the present diversity and past evolutionary history of life on Earth.
- Linnaean Classification
- All modern classification systems have their roots in the Linnaean classification system. -It consists of a hierarchy of groupings, called taxa Unity in the Diversity of Life: A striking city underline the diversity of life; -Cell is the basic structural and functional unit to all organisms -DNA is the universal genetic language common to all organisms -Unity is evident in many features of cell structure The Biological Species Concept:
- Species is a latin word meaning “kind” of “appearance”
- The biological species is a group of population whose members have the potential to interbreed in nature and produce viable, fertile offspring; they do not breed successfully with members of such groups -Gene flow between populations holds a species together genetically -The biological species concept is based on the potential to interbreed, not on physical similarity Linking Classification and Phylogeny: -Phylogeny is the evolutionary history of a species or group of related species -A phylogenetic tree represents a hypothesis about evolutionary relationships -Each branch point represents the divergence of two evolutionary linages from a common ancestor -Sister taxa are groups that share an immediate common ancestor that is not shared by any other group An organism’s evolutionary history is documented in its genome -Comparing nucleic acids (DNA/RNA) or other molecules to infer relatedness is a valuable approach for tracing organisms’ evolutionary history -DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points that diverge hundreds of millions of years ago -Examination of the sequences of the ribosomal ribonucleic acid (rRNA) (the 16s RNA) form the different organisms and other characteristics concluded they comprised three phylogenetic domains
The three Domains of Life: -Differences in the structures of the cell and their molecules allow all organisms to be divided into three domains, named Bacteria, Archaea, and Eukarya -The prokaryotes include the domains Bacteria and Archaea Prokaryotes: -Most are unicellular, although some species form colonies -Most prokaryotic cells are 0.5-5 much smaller than the 10-100 of many eukaryotic cells -Prokaryotic cells have a variety of shapes -The three most common shapes are spheres (cocci), rods (bacilli), and spirals Archaea -Archaea share certain traits with bacteria and other traits with eukaryotes -Archaea contain polysaccharides and proteins but lack peptidoglycan -Some archaea live in extreme environments and are extremophiles -Extreme halophiles live in highly saline environments -Extreme thermophiles thrive in very hot environments Bacteria: Most bacterial cell walls contain peptidoglycan, a network of sugar polymers cross- linked by polypeptides Domain Eukarya: -Includes protists and three kingdoms -Plants, which produce their own food by photosynthesis -Fungi, which absorb nutrients -Animals, which ingest their food Protists: -Exhibits more structural and functional diversity than any other group of eukaryotes -These are mostly single celled organisms -Some protists are less closely related to other protists than they are to plants, animal, or fungi -Some protists reproduce asexually, while others reproduce sexually, or by the sexual processes of meiosis and fertilisation Genome Size: -Genomes of most bacteria and archaea range from 16 million base pairs (Mb) -Genomes or archaea are mostly within this size range -Eukaryotic genomes tend to be larger -Most plants and animals have genomes greater than 100 Mb; humans have 3,000 Mb -Wishing each domain there is no systematic relationship between genome size and phenotype Number of Genes -Free-living bacteria and archaea have 1,500 to 7,500 genes -Unicellular fungi have about 5,000 genes and multicellular eukaryotes up to at least 40,000 genes -Number of genes is not correlated to genome size
- Muscle cells consist of filaments of the proteins actin and myosin, which together enable muscles to contract => Muscle tissue in the vertebrate body is divided into three types: -Skeletal muscle, or striated muscle, is responsible for voluntary movement -Smooth muscle is responsible for involuntary body activities -Cardiac muscle is responsible for contraction of the heart => Nervous tissue is the groups of organised cells in the nervous system -Nervous tissue is grouped in two main groups: neutrons, or nerves that transmit electrical impulses, Glia, or neuroglia, form myelin, support and protect neutrons The Eukaryotic Cell Cycle Cell Cycle: or cell division cycle, is a series of events that take place in eukaryotic cells leading to its reproduction. -Most cell division (via Mitosis) results in two daughter cells with identical genetic information, DNA -Meiosis yields no-identical daughter cells that have half as many chromosomes as the parent cells The phases of the cell cycle: -Interphase; G1 (gap1 phase), S (DNA synthesis phase), G2 (gap2 phase) -Mitotic (M) phase; prophase, metaphase, anaphase, and telophase In unicellular organisms, division of one cell reproduces the entire organism Multicellular eukaryotes depend on cell division for development from a fertilized egg growth repair Cell division (a) Asexual reproduction (b) Growth and development The continuity of life is based on the reproduction of cells, or cell division The events of mitosis: The Mitotic Spindle: -The mitotic spindle is a structure made of microtubules that controls chromosomes movement during mitosis -In animal cells, assembly of spindle microtubules begins in the centrosom, the microtubule organising centre -The centromere replicates during interphase, forming two centrosomes that migrate to opposite ends of the cell during prophase and proetaphase
Cytokinesis is the process of cytoplasm separation Cytokinesis: cleavage furrow formation in the egg of the green sea urchin The sequential events of the cell cycle are directed by a distinct cell cycle control system, which is similar to a clock The cell cycle control system is regulated by both internal and external signals The clock has specific checkpoints where the cell cycle stops until a go-ahead signal is received Cell cycle and Cancer: -Dysregulation of the cell cycle is common during tumorigenesis (cancer display uncontrolled growth) -Increased levels of CDK molecules and cyclins are sometimes found in human tumours, such breast cancer and brain tumours -Inhibition of certain CDKs has been shown to inhibit tumour cell growth, induce apoptosis and cause tumour regressions in animal models Cyclins are proteins formed and degraded during each cell cycle. The cyclins bind to the CDK molecules, therefore regulating the CDK activity and selecting the proteins to be phosphorylated. Pairing of cyclins with CDKs (CDK1) (CDK1) cyclin- dependent kinases (CDKs) remain fairly stable in the cell , but each must bind the appropriate cyclin in order to be activated. Cell cycle inhibitor Cyclin Kinase Inhibitors (CKI), block the actions of CDKs Fibrous network - to which organelles are tethered, provides structure & organisation, cytosol~ 55% total cell volume and 20% of the cytosine is protein Cytoskeleton proteins including; -Microfilaments (actin) -Myosin (types I & II) -Microtubules (tubular) -Intermediate filaments (cytokeratins) -Intermediate filaments anchor organelle in cells Role of Cytoskeleton:
•Vary degrees of severity •Primarily affects bone •Increased fractures •Secondary features in the eyes, joints, lungs & teeth => Properties of the ECM •Structural support •Regulation •polarity •cell division •adhesion •motility •Development •migration •differentiation •growth factors Fibroectin: binds cells to the ECM -Elastics: provide flexibility to skin, arteries and lungs (not glycosylated) Proteoglycans -Proteoglycans are glycoproteins but consists of much more carbohydrates than protein -The protein backbone of proteoglycans is synthesised, like other secreted proteins, in the endoplasmic reticulum -Several sugars are incorporated in proteoglycans. The most abundant one is N- acetylglucosamine (NAG) -This glycosylation occurs in the Golgi apparatus => Properties of ECM and stem cells -ECM anchors stem cells niches -Anchoring importants for mitotic spindle orientation -Essential in stem cells self-renewal → Properties of the ECM - stiffness, may play a role in cell-fate determination The Endo-membrane System -Compilation of membranous organelles located within the cytoplasm, structural divide, functional diversity and evolved from mitochondria => Plasma Membrane -The plasma membrane is the boundary that separates the living cell from its surroundings -The plasma membrane exhibits selective permeability, allowing some substances to cross it more easily than others
- Compartmentalisation
- Transport
- Signal transduction
- Intracellular junctions Phospholipid Bilayer: -Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions -A phospholipid bilayer can exist as a stable boundary between two aqueous compartments, overall a diameter of 2. -Mosaic
- collecting/clustering of proteins, membrane proteins specific to cell type. Receptor can often infer cell/organ function and key roles in homeostasis Plasma/Organelle Membranes: Membrane fluidity, hydrophobic interactions weaker than covalent bonds, shift of lipids/proteins laterally its is also a rapid process => Why do cells have compartments? -Organelles are dynamic (active) structures that have specific functions and specialised membranes -Organelles form compartments for specific processes Compartments enable divisions of labour within animal cells: -Necessary because they are larger than bacteria and undertake thousands more biochemical reactions,their membrane increase surface area for process, allows cells to vary within tissues according to functions => Nucleus: the central hub for information
- Nuclear envelope - double membrane (bi-layer), envelope contains perforations or pores -Pores contain pore complexes - regulate entry and exit of RNA and proteins -Inner surface of the envelope has a lining - mechanical stability of nucleic structure -Membrane Proteins & Functions -Transport Enzyme activity -Signal transduction Factors which influence membrane fluidity
- Fluidity affected by temperature •Steroids(cholesterol) •Impaired fluidity –loss of membrane function/integrity •Influence cell/organelle function DNA is organised into chromosomes -Chromatin -structure for DNA coiling -Nucleolus - rRNA synthesis - ribosome subunit assembly and export Nucleus provides appropriate environment for transcription and replication of DNA according to the phase of the cell cycle
-Lower diagram shows such a vesicle fusing with a lysosome and digestion taking place Lysosome dysfunction: -Lysosomal storage diseases -Stems from a loss in hydrolytic enzyme function -Enlarged lysosomes - indigestible components -Lipid/protein accumulation in cells End-membrane is a collection of functionally diverse organelles Centrioles and the Centrosome: -Microtubules grow out from a centrosome near the nucleus -The centrosome is a “microtubule-organising centre” -In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring => Microtubules - role in cell cycle:
- Mitosis
- partition of replicated chromosomes -Involves the assembly and disassembly of a key microtubule structure
- mitotic apparatus or mitotic spindle Centrioles: -Centrioles have 27 stable microtubules organised into 9+0 triplets surrounded by a protein matrix -Centriole pairs are organising centres that form microtubule spindles during mitosis The mitotic spindle is an apparatus of microtubules that controls chromosome movement during mitosis -During prophase, assembly of spindle microtubule begins in the centrosome, the microtubule organising centre -The centrosome replicates, forming two centrosomes that migrate to opposite ends of the cell, as spindle microtubules grow out from them -An aster(a radial array of short microtubules) extends from each centrosome -The spindle includes the centrosomes, the spindle microtubules, and the asters -During prometaphase, some spindle microtubules attach to the kineto chores of chromosomes and begin to move the chromosomes -In metaphase, the chromosomes are all lined up at the metaphase plate, the midway point between the spindle’s two poles -In Anaphase, sister chromatids separate and move along the kinetochore microtubules towards opposite ends of the cell -The microtubules shorten by depolymerising at their kinetochore ends -Microtubules are dismantled by kinetochore to release tubulinsubunits Microtubules - organelles movement -Axonal transport of vesicles along microtubules in nerve axons involves kinesis and cytosolic dynein motor proteins: vesicles can be transported 250 - 400 mm/day
-Kinesin/dynein head proteins have ATPase activity and tails that bind to vesicles: kinesis mediates anterograde movement of vesicles towards synapses along singlet microtubules, cytosolic dynein mediates retrograde movement to the cell body for recycling along singlet microtubules -In synaptic endings motor proteins can transport neurotransitter vesicles along actin microfilaments Cilia and flagella share a common ultrastructure: A core of microtubules sheathed by the plasma membrane -A basal body that anchors the cilliim or flagellum -A motor protein called dynein,which drives the bending movements of a cilliim or flagellum -Dynein arms alternatively grab, move, and release the outer microtubules -Protein cross-links limit sliding -Forces exerted by dynein arms cause doublets to curve, blinding the cilliim or flagella -Dynein arms can ‘walk’ along microtubules towards the basal body bending and rotating the cillia/ flagella Plasma Membrane & Transport Simple Diffusion: Unassisted Movement down the gradients -The most straightforward way for a solute to cross a membrane is through simple diffusion, the unassisted net movement of a solute from high to lower concentration -Typically this is only possible for gases, non polar molecules, or small polar molecules such as water, glycerol, or ethanol => Osmosis: -If two solution are separated by a selectively permeable membrane, permeable to the water but not the solutes, the water will move toward the region of higher concentration, osmosis. For most cells, water tends to move inward. => Water balance of cells: -Isotonicsolution: solute concentration is the same as that inside of the cell; no net water movement across the plasma membrane -Hypertonic solution: solute concentration is greater than that inside the cell; cell loses water -Hypotonicsolution: solute concentration is less than that inside the cell; cell gains water Facilitated Diffusion: protein-mediated movement down the gradient -Most substances in the cell are too large or too polar to cross membranes by simple diffusion -Tases can only move in and out of cells with the assistance of transport proteins -Facilitated diffusion; the solute diffuses as dictated by its concentration gradient =>Carrier proteins and Channel proteins:
-The membrane potential is maintained by active transport of potassium ions inward and sodium ions outward -Special press or channels allow water and ions to enter or leave the cell rapidly and needed EXTRACELLULAR FLUID Cytoplasmic Na+binds to the sodium -potassium pump. The affinity for Na+is high when the proteinhas this shape. Na+binding stimulates phosphorylation by ATP. Phosphorylation leads to a change inprotein shape, reducingits affinity for Na+, which is released outside.The new shape has ahigh affinity for K+, whichbinds on the extracellular side and triggers releaseof the phosphate group. => Bulk transport: -Small molecules and water enter or leave the cell through the lipids bilayer or via transport proteins -Large molecules, such as polysaccharides and proteins, cross the membrane in bulk via vesicles -Bulk transport requires energy -The two mechanisms are exocytosis and endocytosis Exocytosis: -In exocytosis, transport vesicles migrate to the membrane, fuse with it, and releasetheir contents outside the cell -A membrane bound spherical vesicles buds from the golgi apparatus and moves along a microtubule to the plasma membrane -The membrane of the vesicles fuses with the plasma membrane , allowing the contents to spill out into the extracellular space =>Calcium independent & dependent: -Ca2+ independent secretion happens continuously e.g newly synthesised membrane proteins -Ca2+ dependentsecretion requires the influx of calcium to occur e.g. insulin secretion -Types of endocytosis; phagocytosis (“cellular eating”), pinocytosis (“cellular drinking”), receptor-mediated enodcytosis
- Phagocytosis→ In phagocytosis, the cell forms a ‘pseudopodia’ around an extracellular particle, surrounding it in a large vacuole -This vacuole will then fuse with a lysosome, forming a‘phagolysome’to digest the engulfed contents -An example is the engulfment of pathogens by immune cells such as macrophages Pinocytosis -In pinocytosis, small droplets are taken up when extracellular fluid is “gulped” into tiny vesicles -Non-specific processes -Epithelial cells in capillaries use pinocytosis to engulf the liquid portion of blood (plasma) at the capillary surface. The resulting vesicles travel across the capillary cells and relate their contents to surrounding tissues
=> Receptor mediated endocytosis: 1.The ligand binds to the membrane bound receptor 2.This signals for membrane clatharin coating and invagination 3.The clatharin coated vesicles is formed with both ligand and receptor contained within 4.The vesicles becomes an early endgame, the receptor is rebased and recycled back to the cell surface is the uptake of LDL => Membrane transport and disease: -Membrane transporters and channels are involved in amigo range of cellular processes in all organs of the body -Defects in these due to genetic mutations, can have severe biological consequences Mitochondria -Mitochondria were self-contained separate cells -Harbour their own DNA -Protein folding machinery -Engulfed by another cell forming a relationship Endosymbiotic Theory Structure of mitochondria => What is the role of mitochondria? -Powerhouse of the cell -ATP generation via oxidative phosphorylation -Site of Kreb’s cycle -mtDNA (37 genes)& ribosme rich -Cell fate decisions (apoptosis) => Mitochondrial inheritance: -Mutations in the mitochondrial DNA (mtDNA) that affect mitochondria function -Unique characteristics due to: maternal inheritance, mitochondrial are critical to cell function -The subclass of these that have neurotransmitters disease symptoms are often called a mitochondrial myopathy => Mitochondrial Density -Relates to function of the cell it resides within -Energy utilisation dictates quantity of mitochondria -More energetics cell/tissue - more mitochondria => Mitochondrial structure -Two membranes: smooth outer membrane, highly folded inner membrane (Cristae) -Internal fluid-filled space: mitochondrial matrix, DNA, ribosomes & enzymes
cytochromes (each with an iron atom) to O -The electron transport chain generates no ATP -The chains function is to break the large free-energy drop from food to O2 into smaller steps that release energy in manageable amounts => TCA Cycle •The citric acid cycle has eight steps, each catalyzed by a specific enzyme •The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate •The next seven steps decompose the citrate back to oxaloacetate, making the process a cycle => Chemiosmosis -Electron transfer in the electron transport chain causes proteins to pump H+ from the mitochondrial matrix to the inter membrane space -H+ then moves back across the membrane, passing through channels in ATP synthase -ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP -This is an example of chemiosmosis, the use of energy in a H+ gradient to drive cellular work -The energy stored in a H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis -The H+ gradient is referred to as a proton-motive force, emphasising its capacity to do work ATP production - cellular respiration -During cellular respiration, most energy flows in this sequence; Glucose → NADH → electron transport chain → proton-motive force → ATP -About 40% of the energy in a glucose molecule is transferred to ATP during cellular respiration, making about 38 ATP Cytology and Cell Fractionation => Cytology -The study of the cell -Cytopathology is the science dealing with the structure of abnormal or diseased cells -A cell is the basic structural, functional and biological unit of a living organism -The tissues that form part of the body consists entirely of cells and extracellular matrix elaborated by cell -Most mammalian cells are microscopic => Types of microscopes -Light microscopy -Fluorescence microscopy -Confocal microscopy -Electron microscopy Cytology Specimens 1.Peritoneal, pericardial and pleural fluids 2.CSF 3.Nipple discharge
4.Bronchial brushings/washings 5.Sputum 6.Gastric washings 7.Urine sediment 8.Prostatic secretions 9.Cervicovaginal (paps) smear Cytology sampling techniques -Exfoliative cytology: cells shed from, or scrapped or brushed off epithelial surface -Fluid cytology:cells withdrawn with the fluid in which they suspended -Washings: cells flushed out of an organ using an irrigating fluid Cell is the structure and functional unit of life -Cell contain organelles which perform a variety of biological specific functions -Electron micrograph explains only the structure but not the function of cell organelles -To obtain precise information about the cells organelles, it is necessary to isolate then free from contamination organelles
