A3 Systematic 1+2+3+4 Dr.Rafeik 2025 PDF

Systematic Eukaryotic & Prokaryotic cellular organizations ▪ The broadest unit of classification is Kingdom...

Systematic Eukaryotic & Prokaryotic cellular organizations ▪ The broadest unit of classification is Kingdom ▪ Each division (phylum) is include / subdivided into Classes ‫وهكذا‬ Systematic Prokaryotes Eukaryotes ▪ All classes are grouped ‫ تتجمع‬into phylum Systematic = ▪ Science of description, identification, Name ▪ Pro = before ▪ Eu = true Three domain System Taxonomy naming, classification of objects or ▪ Karyon = nucleus ▪ Karyon = nucleus organisms. 3 domain system Example ▪ bacteria ▪ animals & plants Absent Present ▪ By carl woese Membrane bound ▪ ▪ Historical Evolution organelles ▪ Based on small-subunit ribosomal RNA, living world is divided into 3 domains Scientist System Notes 1) Eubacteria Ancient Greeks 2 kingdom ▪ Vegetalia + animalia Note that 2) Archaebacteria (Archaea). 3) Eukarya Classification ▪ Placing plants in categories based on Theophrastus Plants ▪ Classify plants into 4 types particular system according to Size : ▪ Note that : 2 domains are prokaryotes (Bacteria & archaea) 1) Trees ▪ Basic process of classification is grouping + 2) Shrubs ‫شجيرات‬ ranking Domain Features ‫خصائص‬ 3) Half shrubs 4) Herbs ‫العشب‬ Grouping ▪ Sorting of organisms with 1. Eubacteria ▪ Prokaryotic cell (No nucleus + Organelles) common features into groups ▪ Only one chromosome (single) Carolus 2 Kingdom ▪ Published “System Nature” Ranking ▪ Organization of large group ▪ Binomial Nomenclature 2. archaea ▪ Prokaryotic cell (No nucleus + Organelles) Linnaeus into smaller groups ✓ (Structurally resemble eubacteria) Ernest Haeckel 3 kingdom ▪ Protista ✓ Primitive ‫بدائي‬ ▪ Their genes + biochemical features indicate Species ▪ Group of morphologically similar organisms, ✓ Microorganisms ✓ they are more close to eukarya than that can interbreed together and produce eubacteria ‫الكائنات الدقيقة‬ fertile offspring ‫نسل قادر علي الانجاب‬ Whittaker 5 kingdom ▪ Prokaryotes = Monera ▪ Live in extreme environments system ▪ Fungi ‫الفطريات‬ ▪ Protista 3. Eukarya ▪ Higher organisms with nucleus + organelles ▪ Plantae Taxon (taxa ‫)جمعها‬ ▪ Animalia ▪ DNA is carried on several chromosomes ▪ General term to describe any unit of classification ▪ Divided into 4 kingdoms ✓ Protista + Fungi + Plants + Animals Binomial Nomenclature Rules Five kingdom System ▪ By whittaker ▪ Living organisms divided into 5 kingdoms : Latin language 2 parts (Genus + Species) Italic or underlined 1. Monera (prokaryote) 2. Fungi 3. Protista 4. Plantae 5. Animalia  Life forms Steps ▪ viral DNA is incorporated ‫ يدخل‬to host chromosome, Shapes of viruses then known as (prophage) ‫مهم‬ Sub – cellular Cellular 1. helical ‫( حلزوني‬ex : TMV) ▪ when bacteria divide, viral genome replicates Virus Prokaryotes + Eukaryotes 2. Icosahedral (polyhedral with 20 face) ‫متعدد الأضلاع أو الأوجه‬ (prophage = Viral DNA + bacterial DNA) ✓ (ex: Adenovirus) 3. complex ‫معقد بمعني بيجمع بين الشكلين اللي فوق‬ ✓ 3 parts : head + tail + tail fibers Note ▪ phage genome remain silent in bacteria ✓ Ex) Bacteriophage ✓ but in case of environmental conditions as radiation it become active Life cycle of virus ▪ Ex) Bacteriophage ‫الفيرس اللي بيصيب البكتيريا‬ ▪ 2 life cycle ✓ lytic cycle ✓ lysogenic cycle 1) lytic Cycle Lytic ▪ Reproductive cycle of virus ‫ دورة تكاثرية للفيرس‬that ends Sub cellular forms (Virus) cycle with death of host cell Virus Virulent ▪ Virus that depend on lytic cycle to reproduce virus ▪ Small infectious particles ▪ replicate only inside host (living cell). ‫يتضاعف داخل العائل‬ Steps Kingdom : Prokaryote ✓ host may be (bacteria, plant, animal) 1) Attachment ▪ Capsid combine with receptors ✓ Virus outside host called (virion) ‫مهمة جدااا‬ ‫المستقبلات اللي ع البكتيريا‬ Division 1 : Bacteriophyta ▪ viruses are too small to be seen with optical microscope. ▪ bacterium derived from Greek word (bacterion) : small stick. 2) Penetration ▪ Viral DNA enter host (bacteria) ✓ (1%) size of bacterium Features of ▪ Very small prokaryotic cell. 3) Biosynthesis ▪ Viral components synthesized ▪ widely distributed in nature. ‫منتشرة في الطبيعة‬ bacteria ‫خصائص‬ Structure & shape of virus 4) Maturation ▪ Assembly of viral components ▪ have very high surface to volume ratio (900 :1) ✓ high metabolic activity Structure of virus “Nucleocapsid” = genome + capsid 5) Release ▪ New viruses leave host ▪ most of bacteria are harmless Genome ▪ RNA or DNA.. double or single strand ✓ But some cause diseases + spoilage of ▪ Function : carry genetic information food + corrosion of Pipes 1. Lysogenic cycle Capsid ▪ protein coat, built from Protein subunit called (capsomeres) Lysogenic ▪ Reproduce viral genome ‫يضاعف المادة الوراثية للفيرس‬ ▪ Function : surround + protect genetic material cycle without destroying host Envelope ▪ in some viruses (virus can be enveloped or naked( Temperate ▪ Viruses capable of 2 different life cycle in bacteria ▪ Naked virus : has NO envelope.. virus (lytic + lysogenic) ▪ made of lipid ▪ surround protein coat (capsid) Morphology of bacteria Note ▪ Specific transport system 3. Cytoplasm ✓ active transport ‫نقل بيحتاج طاقة‬ Shape Arrangement Structure ▪ granular in appearance + rich in RNA. ✓ passive transport ‫نقل لا يحتاج طاقة‬ 1) Spherical ▪ Single (ex: Micrococcus) Function ▪ contain enzymes + salt + sugars + amino acid. (Cocci) ▪ Pairs (Diplococcus) ▪ chains (streptococcus) 2. Cell wall ▪ cube “8” (Sarcina) 4. Mesosome Structure ▪ 10 - 40% of total dry weight. ▪ contain murein (peptidoglycan or mucopeptide) Structure ▪ Folded invagination in plasma membrane ▪ irregular cluster (Staphylococcus) Function 1) Play role in cell division Peptidoglycan ▪ found only in prokaryotes 2) phosphorylation (ATP production) 3) secretion of enzymes Function 1) give rigidity + shape of bacteria 2) Rod (bacilli) ▪ Single 2) protect cell against osmotic stress shock ▪ chain (Streptobacilli) 5. Ribosome ▪ ex: Bacillus Note ▪ According to cell wall structure, bacteria differentiated into 2 groups : Structure ▪ Large granules in cytoplasm. ▪ Composed of rRNA + protein. 3) Spiral (helical) ▪ ex: spirochete ✓ Gram +ve bacteria ✓ Gram -ve bacteria ▪ Size of ribosome measured in Svedberg (s) unites depend on mass & shape of ribosome. ▪ ex: Vibrio “curved” ▪ Ribosomes of prokaryotes are (70s) smaller than ribosome Of eukaryotes (80 s). Function ▪ sites of protein synthesis Bacterial Cell Structure (2 Types ) Invariant structure ▪ found in all bacteria 6. bacterial chromosome Variant structure ▪ found in some bacterial cell Structure ▪ Single chromosome (large + circular + ds DNA) 7. reserve materials a) Invariant Structures Cell wall Gram +ve Gram -ve Structure ▪ lipid like molecules, glycogen, Sulfur granules, volutin (polyphosphate) 1. Cytoplasmic membrane ( Plasma membrane ) Structure ▪ Thick, monolayer ▪ Thin, triple layer ▪ not bounded by membranes Structure ▪ Thin structure under cell wall, surrounds cytoplasm Composition ▪ 90% ▪ 5-20% ▪ Composed of phospholipid layer ‫ طبقتين‬+ protein. peptidoglycan peptidoglycan ▪ Low lipid (1-4%) ▪ higher lipid (11- a) Variant Structures Function 1) Control movement of molecules by specific 22%) transport system. Resistance to ▪ More resistant ▪ Less resistant 1. Photosynthetic membranes 2) Sustain cell permeability ‫بيحافظ علي نفاذية الخلية‬ physical disruption ✓ Selective permeability In green ▪ Cylindrical vesicles ‫حويصلات‬ Susceptibility to ▪ more susceptible ▪ less susceptible = photosynthetic ▪ attached to cytoplasmic membrane 3) Enzyme of respiration are part of membrane penicillin or = less resistant more resistant bacteria ✓ so Play role in cell respiration lysozyme In cyanobacteria ▪ occur within cytoplasm Peritrichous ▪ Cluster of flagella arranged over 7. Bacterial Endospore the whole bacterial Cell ▪ not bounded by membrane ▪ ‫علي كل جسم البكتيريا‬ Structure ▪ bodies produced within bacterial cells as defense ▪ Known as (thylakoids) mechanism for unfavorable conditions ‫بتحم‬ ‫ي‬ ‫وسيلة‬ ‫نفسها من الظروف الصعبة‬ 2. Plasmid Position of ▪ central ‫يف النص‬ Structure ▪ Small circular macromolecules of DNA. ▪ terminal ‫طرفي‬ spore in ▪ exist in some bacteria ▪ sub terminal ‫طرف‬ ‫شبه‬ cell ‫ي‬ ▪ replicate independently. ‫يتضاعف ذاتيا‬ 4. Pili (fimbria) ▪ able to integrate ‫ يدخل‬into chromosome & replicate under control of chromosome replication (episomes). Structure ▪ short hair projections on surface of many bacteria ▪ thinner, shorter, numerous than flagella(‫) مهم جدا‬. Episome ▪ plasmid integrated into chromosome Function 1) attachment 2) F pilus (sex pilus) : help in bacterial mating & Function ▪ Contain limited amount of specific genes found in donor cell Bacterial Reproduction 5. Capsule Bacterial reproduction 3. Flagella Structure ▪ Some bacteria form capsule external to cell wall. Method of ▪ by asexual process of binary fission. Structure ▪ long, thread-appendages of uniform diameter. ▪ (vary between species) ▪ made of (flagellin) protein Reproduction ▪ polysaccharides & proteins. ▪ not seen by light microscope Steps of binary fission 1) chromosomal DNA duplication Capsulated ▪ Smooth + glistering colonies ‫مستعمرات لامعة‬ 2) membrane + cell wall grow inward to Function 1) motility (rods bacteria + few cocci) bacteria ▪ Called S-colonies meet one another 2) Allow bacteria to escape from environment 3) cell division into 2 daughter cells. Non capsulated ▪ Rough colonies bacteria ▪ Called (R-colonies) 3) Chemotaxis ‫الحركة تجاه أو بعيدا عن مادة كيميائية‬ ✓ Permit bacteria to move toward nutrient or away from stress Function 1) Protection against phagocytes ‫تحمي البكتيريا من الالتهام‬ Flagella 2) Act as protective cover ‫طبقة حماية‬ of 3) Determine pathogenicity of bacteria arrangement capsule Monotrichous ▪ single polar flagellum 4) Reservoir of stored food ‫مخزن للغذاء‬ 6. Slime layer (glycocalyx) Lophotrichous ▪ Cluster of flagella at one end. Structure ▪ similar to capsules in composition ✓ but loosely attached ‫غير متماسكة‬ ✓ form diffuse layer around cells Function 1) Protection against dehydration + Nutrient loss Amphitrichous ▪ one or Cluster of flagella at both 2) bind cells together. ends 3) Attachment to solid surface ( dental plague).  Importance of bacteria Gene transfer in bacteria 1. Decomposition of dead organisms, so recycling nutrients in soil. ▪ Bacteria able to exchange genes 2. Fix atmospheric nitrogen into compounds utilizable by plants. ▪ may occur between different families of bacteria 3. bacteria that live in intestine synthesize vitamins ▪ 3 mechanisms of gene exchange : 1) Conjugation Reproduction ▪ No sexual reproduction 2) Transduction 3) Transformation bacteria used in industrial + environmental applications as: Asexual reproduction 1) Manufacture of butter + cheese Unicellular ▪ by binary fission 3 Mechanisms of gene exchange 2) production of antibiotics + organic acids (lactic, Propionic acid). Colonial + ▪ Fragmentation, 1. Conjugation ▪ requires cell-to-cell contact 3) production of biogas (methane). ▪ Formation of non-motile spores ▪ F+ bacteria : has fertile plasmid filamentous 4) Recovery of petroleum + heavy metals ▪ F- bacteria : has NO plasmid 5) Wastes & waste water treatments ▪ genes move from : fertile strain (F+) into Ecology ▪ Freshwater, marine or wet soil cyanobacteria infertile strain (F-) Division II: Cyanophyta Importance ▪ Cultivation of rice : increase soil fertility by Steps of 1. donor cell approach + attaches to recipient ✓ Production of organic matter conjugation through sex tube (pilus). Kingdom I : Prokaryotae (photosynthesis) 2. Donor DNA replicate + copy passes Division II : Cyanophyta ✓ conversion of atm. N2 into usable form (Cyanobacteria or Blue-Green Algae) through tube to recipient bacteria as nitrate (nitrogen fixation by heterocysts) 1. Transformation ▪ Bacteria take free DNA from environment Cyanobacteria ▪ prokaryotic photoautotrophs + integrate it into recipient genome ▪ contain chlorophyll a masked by blue pigment Examples ▪ Nostoc + Oscillatoria phycocyanin 2. Transduction ▪ DNA is transferred using bacteriophage as vector. Color ▪ Often blue-green Nutrition ▪ Photosynthetic Pigments ▪ Chlorophyll a ▪ Phycocyanin + phycoerythrin (type of phycobilins which is protein-bound pigment). Stored food ▪ Cyanophycean starch (glycogen + protein) Morhpology ▪ Unicellular, colonial or filamentous ▪ Absence of motile (NO flagellated stage) Heterocyst ▪ Large cell interrupt chain of cells In filamentous species ▪ lack photosynthetic pigments ▪ function : nitrogen fixation hormogonium ▪ Sections between heterocysts ▪ Function : photosynthesis