Cell Biology Course Notes PDF

Cell Biology (24BT1101)  COURSE OUTCOMES (COs): CO No Course Outcomes Mapped BTL PO/PSO CO 1 Understand and apply the knowledge of cell PO1,PSO1 3 and nuclear organization...

Cell Biology (24BT1101)  COURSE OUTCOMES (COs): CO No Course Outcomes Mapped BTL PO/PSO CO 1 Understand and apply the knowledge of cell PO1,PSO1 3 and nuclear organization CO 2 PO1,PSO1 3 Understand and apply the principles of cell division and cellc ycle CO 3 PO4,PSO1 3 Apply the knowledge of tissues and receptors CO 4 PO1,PO4,PS 3 Apply the knowledge of membrane structure O1 and transport  SYLLABUS: CO1: Introductory cell- Types of microorganisms. Differences between Eukaryotic and prokaryotic organisms. Structure and function of Prokaryotic and Eukaryotic cell – bacterial cell, plant cell,animal cell, Cyanobacterial cell. Cell organelles – plasma membrane, mitochondria, Golgi complex, E.R, Lysosomes, Ribosomes. Cytoskeleton – Microtubules, microfilaments. CO2: Nuclear Organization- Nuclear ingredients – Nuclear membrane, Nature of thegenetic material, Nucleoproteins. Packaging of genetic material, Nucleosome model, Organization ofChromatin, Chromosome. Cell division and cell cycle-Cell Division: Mitosis and Meiosis. Steps in cell cycle, Go-G1 transition, cell cycle check points, Chromosome movements, regulation of cell division. Cell differentiation: cortical Differentiation, nuclear differentiation and cell death. CO3: Tissues & Receptors- Meristems, Simple, complex and special tissues.Growth patterns, Cell growth and mechanisms. Embryonicdevelopment, Organogenesis, metamorphosis,Cell signaling– Membrane receptors, Cell – Cell interactions. CO4: Membrane Structure and Transport- Thestructural and functional organization of cell membrane, the extra cellular matrix of eukaryote’s cell wall.Transport across cell membrane - passive and active transport, Na-K pump, Ca2+ ATPase pumps,Lysosomal and Vacuolar membrane ATP dependent proton pumps, Co-transport into prokaryotic cells,endocytosis, exocytosis, pinocytosis and phagocytosis.  Text Books :1. P.S. Verma and V.K. Agarwal,”Cell biology, Genetic, Molecular Biology, Evolution andEcology” edition, S. Chand and Company Ltd. George H fried, “Biology scham series”, edition, McGraw Hill. Reference Books :1. EDP Roberties & EMF Roberties ,”Cell Biology & Molecular Biology” Sauder College. G P Talwar and L.M. Srivatsava ,”Textbook of Biochemistry and Human biology “,Eastern Economy Edition Essential Cell Biology by Bruce Alberts (5th edition) Molecular cell Biology by Harvey Lodish, 6th edition Session 1 1. Classification of Organisms 2. Prokaryotes 3. Eukaryotes 4. Differences between Prokaryotes and Eukaryotes  How is Life Classified? Two kingdom: Life was classified into two kingdoms: Plant Kingdom – Animal Kingdom Three Kingdom: It was given by Ernst Haeckel. He divided organisms in the environment into 3 different categories based on their characteristics, functions, etc. The 3 kingdoms were: Animalia(animals), Plantae(plants) and protista(eukaryotes). Five kingdom: (From 1969 – 1990) Life was classified into 5 Kingdoms: Monera, Protista, Plantae, Fungi, Animalia, by R.H. Whittaker. Classification based on anatomy, morphology, embryology, and cell structure. BUT – the traditional 5 Kingdom system says nothing about how organisms within Kingdoms or between kingdoms may be related to each other via evolutionary relationships among the kingdoms. (Viruses are not in ANY of these kingdoms...remember that scientists do not classify them as 'alive').  Taxonomy Organizing, classifying and naming living things Formal system originated by Carl von Linné (1701-1778) Identifying and classifying organisms according to specific criteria Each organism placed into a classification system  Taxonomy Domain Kingdom Phylum Class Order Family Genus species  Naming Micoorganisms Binomial (scientific) nomenclature Gives each microbe 2 names: – Genus - noun, always capitalized – species - adjective, lowercase Both italicized or underlined – Staphylococcus aureus (S. aureus) – Bacillus subtilis (B. subtilis) – Escherichia coli (E. coli) Monera: Monera was a kingdom that contained unicellular organisms with a prokaryotic cell organization (having no nuclear membrane), such as bacteria. Archaebacteria constitute a domain or kingdom of single-celled microorganisms generally found in extreme environmental conditions. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells. Eubacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Protista: 5-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues. Fungi: A fungus is any member of the group of eukaryotic organisms that includes unicellular microorganisms such as yeasts and molds, as well as multicellular fungi that produce familiar fruiting forms known as mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants and animals. Plantae: Plants are multicellular, eukaryotic organisms of the kingdom plants. Animalia: Animals are multicellular, eukaryotic organisms of the kingdom Animalia (also called Metazoa).  Evolution - living things change gradually over millions of years Changes favoring survival are retained and less beneficial changes are lost All new species originate from preexisting species Closely related organism have similar features because they evolved from common ancestral forms Evolution usually progresses toward greater complexity Prokaryotes Kingdom Monera Species number low (~17, 000), but most numerous on Earth Two Divisions Eubacteria (Bacteria& Cyanobacteria) Archaebacteria Kingdom Monera Prokaryotic Single-celled Diverse energy types: Chemoautotrophic- Purple sulfur bacteria Photoautotrophic- cyanobacteria Heterotrophic- E. coli Kingdom Monera Some with cell walls, but cell walls composed of peptidoglycan, not cellulose (as in higher plants). Asexual and sexual reproduction  Eubacteria pneumonia cyanobacteria anthrax Basic shapes of Eubacteria ROD-SHAPED SPHERICAL SPIRILLA Prokaryotic cells Components of prokaryotic cells Cytoplasm Ribosomes Nuclear Zone DNA Plasmid Cell Membrane Mesosome Cell Wall Capsule (or slime layer) Flagellum Prokaryotic Form and Function  Bacterial Taxonomy Based on bacteria Bergey’s Manual Bergey’s Manual of Determinative Bacteriology – five volume resource covering all known procaryotes – classification based on genetic information– phylogenetic – two domains: Archaea and Bacteria – five major subgroups with 25 different phyla  Major Taxonomic Sub Groups of Bacteria Vol 1A: Domain Archaea – primitive, adapted to extreme habitats and modes of nutrition Vol 1B: Domain Bacteria Vol 2-5: – Phylum Proteobacteria – Gram-negative cell walls – Phylum Firmicutes – mainly Gram-positive with low G + C content – Phylum Actinobacteria – Gram-positive with high G + C content Eukaryotes  Eukaryotes Protista Fungi Plantae Animalia  Protozoan Classification Grouping is based on method of motility, reproduction, and life cycle 1. Mastigophora – primarily flagellar motility, some flagellar and amoeboid; sexual reproduction; cyst and trophozoite 2. Sarcodina – primarily amoeba; asexual by fission; most are free-living 3. Ciliophora – cilia; trophozoites and cysts; most are free- living, harmless 4. Apicomplexa – motility is absent except male gametes; sexual and asexual reproduction; complex life cycle – all parasitic  Fungal Classification Sexual reproduction – Spores are formed following fusion of male and female strains and formation of sexual structure 1. Zygomycota – zygospores; sporangiospores and some conidia 2. Ascomycota – ascospores; conidia 3. Basidiomycota – basidiospores; conidia 4. Deuteromycota – majority are yeasts and molds; no sexual spores known; conidia Eukaryotic cells  Eukaryotic cell Components Cytoplasm Lysosomes Nucleus Cytoskeleton Mitochondria Centriole Chloroplast Ribosomes Cilium and Flagellum RER Microvilli SER Cell membrane Golgi body Cell Wall Vacuoles  Comparison of features of prokaryotic and eukaryotic cells Prokaryotes Eukaryotes Typical organisms bacteria, archaea protists, fungi, plants, animals Typical size ~ 1–5 µm ~ 10–100 µm Type of nucleus nucleoid region; no true nucleus true nucleus with double membrane linear molecules (chromosomes) DNA circular (usually) with histone proteins RNA/protein RNA synthesis in the nucleus synthesis coupled in the cytoplasm protein synthesis in the cytoplasm Ribosomes 50S and 30S 60S and 40S Cytoplasmic highly structured by endomembranes and structure very few structures a cytoskeleton flagella and cilia containing microtubules; lamellipodia and Cell movement flagella made of flagellin filopodia containing actin Mitochondria none one to several thousand Chloroplasts none in algae and plants single cells, colonies, higher multicellular organisms Organization usually single cells with specialized cells mitosis (fission or budding) Cell division binary fission (simple division) meiosis Chromosomes single chromosome more than one chromosome Membranes cell membrane Cell membrane and membrane-bound organelles  Viruses Structure of a “Virus Particle” – Noncellular Biological Entity – Contains either DNA or RNA (not both) – Nucleic Acid is surrounded or coated by a protein shell (capsid) – Some viruses possess a membrane-like envelope surrounding the particle  Viruses Viral Replication – No independent metabolism or replication – Replicate only inside an infected host cell – Do not replicate via a process of cell division – Replicate via a process of: Attachment and Penetration Disassembly (uncoating) Synthesis of Viral Protein and Nucleic Acid Reassembly of new viral particles Release of new viral particles Thank you Session 2 1. Structure and function of Prokaryotic and Eukaryotic cell 2. Plant and animal cells The size range of organisms Light microscopes visible light is passed through the specimen and glass lenses the resolution is limited by the wavelength of the visible light magnification to 1000x the size of the actual specimen Electron microscope – focused a beam (current) of electrons, have the wavelength much shorter than visible light, 1 nm (0.1nm) TEM transmission: the beam through a thin specimen - ultrastructure SEM scanning: the electron beam scans the surface of the sample use the electromagnets instead of glass lenses  SEM Light microscope Prokaryotic Cell Structure Cellular Appendages A) Flagella B) Periplasmic Flagella C) Fimbrae D) Pilus Internal Structures Cellular Envelope A) Cytoplasm B) Chromatin Body A) Glycocalyx C) Plasmid D) Ribsomes B) Cell Wall E) Endospores C) Cell Membrane A) Flagella a) Filament i) Whip-like, helical structure b) Hook i) Holds the filament ii) Attached to the rod portion of the basal body c) Basal body i) A complex structure consisting of a rod, 4 rings and a motor contained within the cell envelope ii) ii) Activation of the motor causes the hook (and therefore the filament) to swivel Four types of flagellar arrangements a) Monotrichous i) A single flagella at one end b) Lophotrichous i) Multiple flagella at one end c) Amphitrichous i) Flagella located at each end d) Peritrichous i) Flagella are found randomly over the cell’s surface B) Periplasmic Flagella 1) A type of modified flagella 2) Found in a special bacteria known as spirochetes 3) Consist of a filament and hook but the entire structure is located between the cell wall and membrane (the periplasmic space) 4) The filament is wrapped around the cell and is free to contract & relax causing a twisting, flexing movement of the entire cell C) Fimbrae 1) Small, hair-like fibers on the surface of the cell 2) Tend to stick to each other as well as other surfaces D) Pilus 1) Elongated, tubular structure 2) Only present on certain species of Gram- negative bacteria 3) Primarily involved in attachment, movement, and conjugation a) The transfer of DNA from one bacterium to another Cellular Envelope A) Glycocalyx Refers to the gel-like outer covering of some bacteria 2 types a) Slime layer i) diffuse & irregular structure b) Capsule i) distinct & gelatinous structure Functions a) Protection against phagocytosis i) Encapsulated bacteria tend to have a greater pathogenicity because of glycocalyx b) Helps bacteria adhere to its environment or other bacteria c) Helps prevent the loss of water and nutrients B) Cell Wall 1) Lies immediately below the glycocalyx 2) Provides the bacteria with structure and protection from lysis a) Certain drugs, including penicillin, destroy the cell wall allowing cell lysis to occur  3) Composed primarily of peptidoglycan a) basic structure i) composed of 2 repeating subunits (a) N-acetylmuramic acid (NAM) (b) N-acetylglucosamine (NAG) (i) covalently bonded together to form a glycan chain ii) adjacent glycan chains are held together by tetrapeptide chains attached to each NAM (a) tetrapeptide chains are directly-linked in Gram-negative bacteria (b) tetrapeptide chains are cross- linked in Gram- positive bacteria 4) Bacteria are lumped into 2 groups based on the staining of their cell walls a) Hans Christian Gram developed Gram staining in 1884 i) The result is a group of bacteria that stain violet (Gram-positive) and a group that stain red (Gram- negative) b) Gram-positive bacteria i) Cell wall composed of a thick layer of peptidoglycan ii) There is a narrow periplasmic space iii) Gram-positive bacteria are more permeable but less susceptible to lysis iv) Two molecules commonly found in bacteria (a) teichoic acid – binds together layers of peptidoglycan (b) lipoteichoic acid – link the peptidoglycan layers to the cell membrane c) Gram-negative bacteria i) Cell wall composed of a thin layer of peptidoglycan ii) There is a wider periplasmic space iii) Gram-negative bacteria are less permeable but more susceptible to lysis iv) Surrounded by an outer membrane (Lipo polysaccharides) – LPS layer is similar to cell membrane (lipid bilayer) with polysaccharides embedded in it C) Cell Membrane 1) Composed primarily of phospholipids 2) Membrane proteins provide the membrane with structure and functionality 3) cell membrane is bound to the cell wall (peptidoglycan) by lipoproteins Mesosomes are inward projections of the membrane a) Believed to increase surface area for membrane activities b) Functions primarily in controlling the movement of substances into and out of the cell 3. Internal Structures A) Cytoplasm 1) Fluid within the cell 2) Primarily water containing dissolved nutrients & wastes 3) Serves as a site for numerous metabolic reactions B) Chromatin body 1) A single, circular loop of essential DNA 2) Aggregated in a dense area of the cell known as the nucleoid C) Plasmids 1) Extra, nonessential pieces of DNA 2) Arranged in isolated loops or attached to the chromatin body 3) They are reproduced and passed on to the offspring 4) Often contain protective traits 5) Exchanged during conjugation D) Ribosomes (70S) 1) The site of protein production within the cell 2) Composed of rRNA and proteins 3) Comprised of 2 subunits a) Small subunit (30S) b) Large subunit (50S) F) Endospores (Spores) 1) Dormant bodies produced primarily by 3 groups of Gram-positive bacteria a) Bacillus sp., Clostridium sp. & Sporosarcina sp. 2) Function in the survival of the bacteria in hostile conditions 3) Spore producing bacteria have a two-phase life cycle a) Vegetative cell i) a metabolically active cell b) Endospore i) dormant body capable of becoming a vegetative cell 4) Sporulation – process of spore formation (takes about 6-8 hrs) a) Hostile conditions cause the vegetative cell to convert to a spore- forming cell known as a sporangium b) The DNA of the cell is duplicated c) A septum forms dividing the cell into unequal parts each with its own DNA d) The larger portion engulfs the smaller portion resulting in a forespore e) A thick peptidoglycan coat forms around the forespore making it impervious to other substances and heat resistant; it is now an endospore f) The endospore is released as the sporangium deteriorates g) The endospore remains dormant until conditions improve around it 5) Germination of endospores requires water and an environmental stimulus 6) Most endospore-forming bacteria are relatively harmless but with some bacteria the endospore play a vital role in their pathogenicity Anatomy of the Plant Cell Anatomy of the Animal Cell S.No Plant Cell Animal Cell 1 A plant cell is usually larger in size. An animal cell is comparatively smaller in size. 2 3 It cannot change its shape. An animal cell can often change its shape. 4 Plastids are present. Plant cells Plastids are usually absent. exposed to sunlight contain chloroplast. 5 A mature plant cell contains a large An animal cell often possesses many central vacuole. small vacuoles. 6 Nucleus lies on one side in the Nucleus usually lies in the centre. peripheral cytoplasm 7 Centrioles are usually absent except Centrioles are practically present in in motile cells of lower plants. animal cells 8 Lysosomes are rare. Lysosomes are always present in animal cells. 9 Glyoxysomes may be present. They are absent. 10 Tight junctions and desmosomes are Tight junctions and desmosomes are lacking. Plasmodesmata is present. present between cells. Plasmodesmata are usually absent. 11 Reserve food is generally in the Reserve food is usually glycogen. form of starch. 12 Plant cell synthesise all amino Animal cell cannot synthesise all the acids , coenzymes and vitamins amino acids, co enzymes and vitamins required by them. required by them. 13 Spindles formed during cell Spindle formed during cell division is divisions in anastral i.e. without amphiastral i.e. has an asters at each asters at opposite poles. pole. 14 Cytokinesis occurs by cell plate Cytokinesis occurs by construction or method. furrowing. 15 Plant cell does not burst if placed Animal cell lacking contractile in hypotonic solution due to the vacuoles usually burst, if placed in presence of the cell wall. hypertonic solution. Thank you Session 3 Cell organelles 1. Mitochondria 2. Golgi complex Mitochondria The sun is the ultimate source of energy for all organisms and cells  ATP- “the free-energy currency” – Every day, we build bones, move muscles, think, and perform many other activities with our bodies. All of these activities are based upon energy. – ATP: The Perfect Energy ? Currency for the Cell Mitochondria and Energy Conversion  Mitochondria- the power plants of ATP Mitochondria are double layer membrane-enclosed organelles distributed through the cytosol of most eukaryotic cells. Their main function is the conversion of the potential energy of food molecules into ATP. So mitochondria are also called “the powerhouse” of the cell. In addition to supplying cellular energy, mitochondria are involved in cell death, as well as the control of the cell cycle and cell growth. Mitochondrial Morphology and Structure I. Shape, size & number Mitochondria are often flexible, rod-shaped organelles that are about 0.5 to 1μm in width and as much as 7 μ m in length. Mitochondria vary considerably in size & shape. Their number correlate with the metabolic activities of the cell. II Ultra structure and Functional Localization 1. Outer membrane 2. Inner membrane 3. Inter membrane space 4. Translocation contact site 5.Matrix 6. Cristae II Ultra structure and Functional Localization 1. Outer membrane contains many complexes of integral membrane proteins that form channels through which a variety of molecules and ions move in and out of the mitochondrion. we called it porins. These porins form channels that allow molecules 5000 Daltons or less in molecular weight to freely diffuse from one side of the membrane to the other. 2. Inner membrane The inner membrane, which encloses the matrix space, is folded to form cristae. The area of the inner membrane is about five times as great as the outer membrane. This membrane is richly endowed with cardiolipin, a phospholipid that possesses four, rather than the usual two, fatty acyl chains. The presence of this phospholipid in high concentration makes the inner membrane nearly impermeable to ions, electrons, and protons. The inner membrane has a very high protein-to-phospholipid ratio (about 4:1 by weight). Impermeable to most charged molecules Inner membrane contains three major types of proteins: ①those that carry out the oxidation reactions of the respiratory chain NADH dehydrogenase Cytochrome b-c1 Cytochrome oxidase ② ATP synthase ③specific transport proteins 3. Inter membrane space contains several enzymes that use the ATP that passes out of the matrix to phosphorylate other nucleotides. 4. Translocation contact site TOM(Translocon of the outer membrane) TIM(Translocon of the inner membrane) Translocation into the Mitochondrial Matrix Depends on a Signal Sequence and Protein Translocators 5. Matrix contains hundreds of different enzymes including those required for ①the oxidation of pyruvate and fatty acids ②the citric acid cycle. It also contains small amounts of mitochordrial DNA genome, special mitochondrial ribosomes, tRNAs and various enzymes that required for the expression of the mitochondrial genes.  Chemical composition The outer membrane consists of 40% lipids and 60% proteins. The inner membrane is made up of 20% lipids and 80% proteins. The electron transport enzymes, proton secreting proteins are virtually buried in the core of the inner membranes. Mitochondrial matrix also consists of a wide variety of enzymes. There are more than 120 kinds of enzymes of mitochondria. Mitochondrial matrix also contains DNA, RNA molecules.  Because the growth and proliferation of mitochondria are controlled by both nuclear genome and it’s own genome. Mitochondria are usually called semiautonomous organelle. Mitochondrial proteins are first fully synthesized as precursor proteins in the cytosol and then translocated into mitochondria by a post translational mechanism.  Cellular respiration and Pathway of oxidation I: Glycolysis The series of reaction by which 1 molecule of glucose is converted to 2 molecule of pyruvic acid Yield: 2 ATP+ 2NADH2 Characteristics: Does not require oxygen Takes place in cytosol  II: Conversion of pyruvic acid to acetyl CoA 2 pyruvic acid 2 acetyl CoA (coenzyme A) Yield: 2 NADH2 takes place in matrix of mitochondria  III: Citric Acid Cycle( Krebs cycle, TCA cycle). Characteristics: Requires the presence of Oxygen (aerobic) takes place in the matrix and inner membrane of the mitochondria. 2FADH2+ 6NADH2+ 2 ATP The electrons of NADH and FADH 2 are transferred to the respiratory chain 1ATP IV: Electron transport system and oxidative phosphorylation The electron (hydrogen) transport chain is the final pathway for all electrons removed from substrate molecules during oxidation; consists mainly of enzymes of the cytochrome group.  Summary of glucose Oxidation Oxidative phosphorylation is the mechanism by which the free energy of electron is used to convert ADP to ATP : Each pair of electron in NADH2 generates 3 ATP Each pair of electron in FADH2 generates 2 ATP (1) Glycolysis: 2NADH2,each yielding 3ATP(total:6ATP) (2) Oxidation of pyruvic acid to acetyl CoA 2NADH2,each yielding 3ATP (total: 6ATP) (3)Oxidation of acetyl COA in Citric acid cycle. – 2FADH2,each yielding 4ATP – 6NADH2,each yielding 18ATP – (total: 22ATP)  The total yield of ATP is 34 ATP, about 90% of all the ATP generated by the oxidation of 1 glucose. Thus the complete oxidation of 1 glucose generates a grand total of 38 ATP (adding 2ATP produced directly during glycolysis and 2ATP during TCA cycle). Glucose + 6 O2 6 CO2 +6H2O +38ATP+heat  Diseases caused by mtDNA mutation Parkinson’s Disease Named after English doctor James Parkinson Affects 1-2% of individuals over 60 years old Motor syndrome Akinesia Rigidity Tremor imbalance  Golgi Apparatus The Golgi Apparatus is also known as the Golgi Complex or Golgi Body The Golgi Apparatus is found in most eukaryotic cells  Golgi Apparatus The Golgi structure is a smooth, curvy structure. It is a flattened stack of membranes. It has a front end and a back end. The front end is called the cis face and the back end is called the trans face. Golgi apparatus has cisternae are the flattened membrane folds and secretory vesicles which are what the cell discharges.  Golgi Apparatus The basic function of the Golgi apparatus is the transport of proteins within the cell. The Golgi receives materials for transportation through the cis face and sends the materials through to the trans face once they are packaged and modified into the vesicles. It functions in the collection, packaging, and distribution of material. The cisternae are the flattened membrane folds of the Golgi apparatus that push together pinching off secretory vesicles containing molecules which are then discharged into the cell.  The vesicles that pinch off from the Golgi apparatus move to the cell rer9 membrane and the material in the vesicle is released to the outside of the cell. Some of these pinched off vesicles also become lysosomes Along with protein modification, Golgi apparatus is involved in the transport of lipids around the cell  Golgi apparatus is found to play an important role in Alzheimer’s disease. Alzheimer’s disease is a brain disorder where brain cells are being destroyed. This is what gives a person memory loss and this disease can lead to death. As the death of neurons increases the affected brain region begins to shrink. The cause of this disease is because there is too little removal of a specific type of protein (Amyloid beta protein misfoalding). Therefore, the Golgi apparatus isn’t functioning as it is supposed to in collecting, transporting, and distributing the protein molecules.  Functions of Golgi Apparatus Golgi vesicles are often, referred to as the “traffic police” of the cell. They play a key role in sorting many of the cell's proteins and membrane constituents and in directing them to their proper destinations Golgi enzymes add signal or tag such as carbohydrates or phosphate residues to certain proteins to direct them to their proper destination. In plants, Golgi apparatus is mainly involved in the secretion of materials of cell walls (lipids, glycoprotein, cellulose, hemicellulose and lignin) Involved in the cell membrane formation of daughter cells. In animals Golgi apparatus is involved in the packaging and exocytosis of the i) Mucus (glycoprotein) ii) Lactoprotein secretion by mammary glands iii) secretion of collagen iv) formation of melanin and other pigments. It is also involved in the formation of cellular organelles like plasma membrane, lysosomes, acrosome of spermatozoa and granules of oocytes. Session 4 Endoplasmic Reticulum What is Endoplasmic Reticulum Made up of The endoplasmic reticulum is made out of a lipid membrane. The endoplasmic reticulum is still connected to the nuclear membrane that is wrap around the cell’s DNA. So there is a straight connection between the cells nucleus and the endoplasmic reticulum.  Where is it situated in the Cell The rough endoplasmic reticulum is located around the nucleus in the cells of both plants and animals. It function and transports proteins and lipids throughout the cell. The smooth endoplasmic reticulum is connected to the nuclear envelope of cells in plants and animals. It's primary function is to facilitate the metabolism of carbohydrates and steroids in the cell ❑ Endoplasmic Matrix  The space inside the tubules and vesicles is filled with a watery medium that is different from the fluid in the cytosol outside the ER.  Their walls are constructed of lipid bilayers membranes that contains large amount of proteins , similar to the cell membrane. Two Types : 1) Rough Endoplasmic reticulum 2) Smooth Endoplasmic reticulum ENDOPLASMIC RETICULUM ❑ ROUGH ENDOPLASMIC RETICULIM (RER)  The surface of the RER is studded with ribosome, giving it a rough appearance.  It mainly consists of cisternae.  The membrane of the RER forms large double membrane sheets  Which is located near and continuous with the outer layer of the nuclear envelope.  RER is very imp. in the synthesis and packaging of proteins e:g, Russell’s bodies of Eosinophils, nissel’s granules of nerve cell  Binding site of the ribosome on the RER is the translocon.  The ribosomes bound to the RER at any one time are not a stable part of this organelles structure  Because ribosomes are constantly being bound and released from the membranes.  Ribosomes only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol.  This special complex forms when a free ribosome begins translating the mRNA of a protein destined for the secretory pathway.  The first 5-30 amino acid polymerized encode a single peptide, a molecular message that is recognized and bound by a single recognition particle (SRP).  The ribosomes that become attached to the endoplasmic reticulum synthesize all trans membrane proteins.  Most secreted proteins that are stored in the Golgi apparatus, lysosomes, and endosomes. ❑ Protein Transport  As proteins are formed in the endoplasmic reticulum, they are transported through the tubules toward proteins of the SER that lie nearest to Golgi apparatus.  At this point, small transport vesicles composed of small envelopes of smooth ER continually break away and diffuse to the deepest layer of Golgi apparatus.  Inside this vesicles are the synthesized proteins and other product from the ER present. ❑ Transport vesicles  They are surrounded by coating protein called COP I, COP II.(Coat Protein complex)  COP II targets vesicles to the Golgi apparatus.  Transparent proteins from the RER to Golgi apparatus.  This process is termed as anterograde transport.  COP I transports proteins from the cis end of the Golgi complex back to the RER.  This process is termed as retrograde transport. ❑ FUNCTION OF RER-  Surface for Ribosomes- The RER provides space and ribophorins for the attachment of ribosomes to itself.  Surface for protein synthesis  Formation of Glycoprotein- Linking of sugars to for glycoprotein starts in the RER and is completed in Golgi complex.  Synthesis of precursors- The RER produce enzyme precursors for the formation of lysosomes by Golgi Complex.  Smooth ER formation- The RER gives rise to the smooth ER by loss of ribosomes. Smooth ER Smooth ER also has arrangement of tubules, vesicles The size and structure of the SER varies between the cells. The SER can change within a cells lifetime to allow the cell to adapt to changes in its function and requirements. There are no ribosome’s attached to the membrane surface. The SER is connected to the nuclear envelope  The network of the SER allows there to be enough surface area for the action or storage of key enzymes or the products of the enzymes.  The SER is less stable.  The SER is characteristic of cells in which synthesis of non-protein substances takes place. ❑ FUNCTION OF SER  The smooth endoplasmic reticulum lacks ribosomes and functions in lipid metabolism, carbohydrate metabolism, and detoxification and is especially abundant in mammalian liver and gonad cells.  It also synthesizes phospholipids. Cells which secrete these products, such as those in the testes, ovaries, and skin oil glands have a great deal of smooth endoplasmic reticulum.  Detoxification-The SER brings about detoxification in the liver , i.e., converts harmful materials(drugs, poisons) into harmless ones for excretion by the cell. (Cytochrome P450 :Monooxygenases)  Formation of organelles- The SER produces Golgi apparatus , lysosomes and vacuoles.  It also carries out the attachment of receptors on cell membrane proteins and steroid metabolism.  In muscle cells, it regulates calcium ion concentration  The smooth endoplasmic reticulum also contains the enzyme glucose-6-phosphatase, which converts glucose-6- phosphate to glucose, a step-in gluconeogenesis. Lysosomes 1  It is called "The Police Force of the Cell" or "suicide bags“ Lysosomes are produced in the Golgi Apparatus Lysosomes are spherical organelles that contain enzymes (acid hydrolases). They break up food so it is easier to digest. They are found in animal cells, while in yeast and plants the same roles are performed by lytic vacuoles. The size of lysosomes varies from 0.1–1.2 μm. Lysosomes are common in animal cells but rare in plant cells contain hydrolytic enzymes necessary for intracellular digestion. 2 Some important enzymes found within lysosomes include: Lipase, which digests lipids Amylase, which digest carbohydrates (e.g., sugars) Proteases, which digest proteins Nucleases, which digest nucleic acids phosphoric acid monoesters. All these hydrolytic enzymes are produced in the endoplasmic reticulum, and to some extent in cytoplasm are transported and processed through the Golgi apparatus. Through golgi apparatus they pinch off as single membrane vesicles. 3  A lysosome is a membrane bag containing digestive enzymes to digest food, the lysosome membrane fuses with the membrane of a food vacuole and squirts the enzymes inside. The digested food can then diffuse through the vacuole membrane and enter the cell to be used for energy or growth. 5 Functions of Lysosomes Lysosomes are the cells' garbage disposal system. They are used for the digestion of macromolecules from phagocytosis (ingestion of other dying cells or larger extracellular material, like foreign invading microbes). Endocytosis (where receptor proteins are recycled from the cell surface), and autophagy (wherein old or unneeded organelles or proteins, or microbes that have invaded the cytoplasm are delivered to the lysosome). Autophagy may also lead to autophagic cell death, a form of programmed self-destruction. Autophagy may also lead to autophagic cell death, a form of programmed self-destruction, or autolysis, of the cell, which means that the cell is digesting itself. 6  Lysosomal enzymes are synthesized in the cytosol and the endoplasmic reticulum, where they receive a mannose-6- phosphate tag that targets them for the lysosome. If the lysosomal enzymes do not reach the target, it causes inclusion-cell disease, resulting in accumulation of waste within these organelles. The only thing that keeps the cell itself from being digested is the membrane surrounding the lysosomes. 7  These enzymes work only at low pH (highly acidic) levels. However because they can only work at low pH levels and the rest of the cell has a neutral pH level, they can be neutralized if they accidentally escape from the lysosome In white blood cells that eat bacteria, lysosome contents are carefully released into the vacuole around the bacteria and serve to kill and digest those bacteria. Uncontrolled release of lysosome contents into the cytoplasm can also cause cell death (necrosis). 8 Ribosomes  Introduction  Ribosome are small organelles found in each type of cell i.e., Prokaryotic Eukaryotic  They are the only organelle found in prokaryotic cell  They are not membrane bounded  Discovery  Discovered in 1950 by a Romanian cell biologist George Palade  Appeared under microscope as dense granules  Can be seen through electron microscope  Structure  A ribosome has two main constituent elements Protein = 25-40% RNA = 37-62%  Two main subunits are present i.e., A larger subunit A smaller subunit  Structure PROKARYOTIC SUBUNITS: larger subunit = 50 S smaller subunit = 30 S Total ribosomal complex = 70 S Prokaryotic cell has almost 52 proteins  Structure EUKARYOTIC SUBUNITS: Larger subunit = 60S Smaller subunit = 40 S Total ribosomal complex = 80 S Eukaryotic cell has almost 82 proteins Ribosomal subunits:  SVEDBERG: It is the centrifugal unit depending on the density of the object (and in the cage of cell, organelles) determining that how quickly they sink to the depth when centrifuged Ribosome Whole Small Large Source Ribosome Subunit Subunit E. coli 70S 30S 50S 16S RNA 23S & 5S RNAs 21 proteins 31 proteins Rat 80S 40S 60S cytoplasm 18S RNA 28S, 5S & 5.8S 33 proteins RNAs 49 proteins Quantity:  Quantity of ribosomes vary depend upon the type of cell e.g.,  Bacteria = 20,000  Yeast = 200,000  Quantity depends upon the physiological ability of cell to produce proteins  Structure of prokaryotic Ribosomes LARGER SUBUNIT: Consists of two RNA strands A longer and a shorter strand wrap upon each other Strands are dotted with protein coats Proteins often glue RNA strands in their characteristic shape  Structure of prokaryotic Ribosomes SMALLER SUBUNIT: Consists of a single RNA strand It is also covered with a protein coat Smaller subunit though smaller than the larger subunit, is quite enormous than the normal proteins Location: Ribosomes can be found either:  Dispersed freely in the cytosol  Attatched to the surface of Endoplasmic Reticulum  On the basis of location ribosomes are divided into two types: Free ribosomes Bounded ribosomes Free Ribosomes  These ribosomes are found freely dispersed in the cytosol  They are involved in the synthesis of proteins that work inside the cytosol  They vary in number depending upon the functionality of the cell types and its need to synthesize proteins Bounded Ribosomes:  They are found attached to the surface of Endoplasmic reticulum making them “Rough Endoplasmic Reticulum”  The proteins assembled in these ribosomes are either transported to the outside of the cell or are included in the cell membrane Function:  Main function of ribosomes is the translation of genetic information encoded in nucleotide bases of DNA into amino acid sequence of proteins.  This is also known as “gene expression”  mRNA peptide polyribosome Translation Ribosome subunits 80S vs 70S Ribosomes 80 S ribosome 70S ribosome Present in Eukaryotes or all Present in Prokaryotes higher organisms (bacterium), Mitochondrion Organisms and chloroplast Consists of 2 subunits, 60S Consists of 2 subunits, 50S Subunits and 40S. and 30S. The 80S ribosomes are The 70S ribosomes are composed of 40% RNA andcomposed of 60% RNA and Composition 60% proteins. 40% proteins. The 60S subunit contains The 50S subunit contains two three rRNAs (28S, 5.8S andrRNAs (23S and 5S) 5S) complexed with ~49complexed with ~34 proteins. Larger Subunits proteins The 40S subunit contains The 30S subunit contains 16S 18S rRNAs complexed withrRNAs complexed with ~21 Smaller Subunit ~33 proteins. proteins.  Shine-Dalgarno (SD) sequence The Shine-Dalgarno sequence is a ribosomal binding site in prokaryotic messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon. The Shine-Dalgarno sequence exists both in bacteria and archaea. It is also present in some chloroplast and mitochondrial transcripts. The six-base consensus sequence is AGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while subsequence GAGG dominates in E. coli virus T4 early genes. The Shine-Dalgarno sequence was proposed by Australian scientists John Shine (b. 1946) and Lynn Dalgarno (b. 1935). Mutations in the Shine-Dalgarno sequence can reduce or increase translation in prokaryotes. This change is due to a reduced or increased mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the 3'- terminal 16S rRNA sequence can restore translation. Thank you Ultra structural of cell membrane  The Cell Membrane The cell membrane is a dynamic and intricate structure that regulates material transported across the membrane. The membrane is selectively permeable (or semi-permeable) meaning that certain molecules can cross the membrane and others cannot. 2  Understanding Membrane Structure Fluid Mosaic Model: Singer & Nicholson, 1972 Proteins embedded and floating in a sea of phospholipids Phospholipid bilayer Hydrophobic region of protein  Fluid Mosaic Model Proteins are "stuck" in the membrane like a mosaic. Proteins can be on just the surface (peripheral) or embedded in the membrane (intrinsic). Proteins that span the entire membrane are called “transmembrane” It is the different proteins that are responsible for the uniqueness of different membranes (plasma, eukaryotic, prokaryotic, organelle etc.) 5 The Plasma Membrane 6 Cytoskeleton Microtubules, Microfilaments and Intermediate filaments  Cytoskeleton The cytoskeleton is a network of fibers extending throughout the cytoplasm. The cytoskeleton organizes the structures and activities of the cell. Provides structural support to the cell Cytoskeleton functions in cell motility and regulation  Major functions of cytoskeleton Mechanical support – Maintains shape Provides anchorage for organelles Dynamic assembly – Dismantles in one spot and reassembles in another to change cell shape  Motility The cytoskeleton also plays a major role in cell motility. – This involves both changes in cell location and limited movements of parts of the cell. The cytoskeleton interacts with motor proteins. – In cilia and flagella motor proteins pull components of the cytoskeleton past each other. – This is also true in muscle cells.  Motor molecules also carry vesicles or organelles to various destinations along “monorails’ provided by the cytoskeleton. Interactions of motor proteins and the cytoskeleton circulates materials within a cell via streaming. There are three main types of fibers in the cytoskeleton: Microtubules Microfilaments and Intermediate filaments Microtubules : Microtubules, the thickest fibers, are hollow rods about 25 microns in diameter. – Microtubule fibers are constructed of the globular protein, tubulin, and they grow or shrink as more tubulin molecules are added or removed. They move chromosomes during cell division. Another function is as tracks that guide motor proteins carrying organelles to their destination.  In many cells, microtubules grow out from a centrosome near the nucleus. These microtubules resist compression to the cell. In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring.  Microtubules are the central structural supports in cilia and flagella. – Both can move unicellular and small multicellular organisms by propelling water past the organism. – If these structures are anchored in a large structure, they move fluid over a surface. For example, cilia sweep mucous carrying trapped debris from the lungs.  Cilia usually occur in large numbers on the cell surface. – They are about 0.25 microns in diameter and 2-20 microns long. There are usually just one or a few flagella per cell. – Flagella are the same width as cilia, but 10-200 microns long.  A flagellum has an undulatory movement. – Force is generated parallel to the flagellum’s axis.  Cilia move more like oars with alternating power and recovery strokes. – They generate force perpendicular to the cilia’s axis.  In spite of their differences, both cilia and flagella have the same ultrastructure. – Both have a core of microtubules sheathed by the plasma membrane. – Nine doublets of microtubules arranged around a pair at the center, the “9 + 2” pattern. – Flexible “wheels” of proteins connect outer doublets to each other and to the core. – The outer doublets are also connected by motor proteins. – The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a centriole.  The bending of cilia and flagella is driven by the arms of a motor protein, dynein. – Addition to dynein of a phosphate group from ATP and its removal causes conformation changes in the protein. – Dynein arms alternately grab, move, and release the outer microtubules. – Protein cross-links limit sliding and the force is expressed as bending. Microfilaments (Actin filaments) Microfilaments, the thinnest class of the cytoskeletal fibers, are solid rods of the globular protein actin. – An actin microfilament consists of a twisted double chain of actin subunits. Microfilaments are designed to resist tension. With other proteins, they form a three- dimensional network just inside the plasma membrane.  In muscle cells, thousands of actin filaments are arranged parallel to one another. Thicker filaments, composed of a motor protein, myosin, interdigitate with the thinner actin fibers. – Myosin molecules walk along the actin filament, pulling stacks of actin fibers together and shortening the cell.  In other cells, these actin-myosin aggregates are less organized but still cause localized contraction. – A contracting belt of microfilaments divides the cytoplasm of animals cells during cell division. – Localized contraction also drives amoeboid movement. Pseudopodia, cellular extensions, extend and contract through the reversible assembly and contraction of actin subunits into microfilaments.  In plant cells (and others), actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming. – This creates a circular flow of cytoplasm in the cell. – This speeds the distribution of materials within the cell. Intermediate filaments Intermediate filaments, intermediate in size at 8 - 12 nanometers, are specialized for bearing tension. – Intermediate filaments are built from a diverse class of subunits from a family of proteins called keratins. Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes. They reinforce cell shape and fix organelle location. Thank you Cell Nucleus Nucleoid DNA Structure 1. Cell growth 2. Growth patterns and mechanisms Cell Nucleus  Nucleus The nucleus is the genetic control center of a eukaryotic cell. In most cells, there is only one nucleus. It is spherical, and the most prominent part of the cell, making up 10% of the cell’s volume. It has a unique structure and function that is essential to cell. Structure of the Nucleus The Nucleus the nuclear envelope nucleoplasm chromatin the nucleolus Nuclear Envelope The nuclear envelope is a double-layered membrane perforated with pores, which control the flow of material going in and out of the nucleus. The outer layer is connected to the endoplasmic reticulum, communicating with the cytoplasm of the cell. The exchange of the large molecules (protein and RNA) between the nucleus and cytoplasm happens here. Nucleoplasm A jelly-like (made mostly of water) matrix within the nucleus All the other materials “float” inside Helps the nucleus keep its shape and serves as the median for the transportation of important molecules within the nucleus Nuclear Pore Complex Nuclear Pore Complex Nuclear Pore Complex (Functions) Chromatin & Chromosomes Chromosomes contain DNA in a condensed form attached to a histone protein. Chromatin is comprised of DNA. There are two types based on function. Heterochromatin: highly condensed, transcriptionally inactive mostly located adjacent to the nuclear membrane Eurochromatin: delicate, less condensed organization of chromatin, located in a transcribing cell * Transcribing means equivalent RNA copies are being made from the DNA to create proteins. DNA DNA, or deoxyribonucleic acid, contains the information needed for the creation of proteins (which include enzymes and hormones) and is stored in the nucleus, as already said, in the form of chromatin or chromosomes. The nucleus is the site of DNA duplication, which is needed for cell division (mitosis) and organism reproduction and growth. The Nucleolus The nucleolus is a non- membrane bound structure composed of proteins and nucleic acids found within the nucleus. The ribosomal RNA is transcribed in the nucleolus. Functions of Nucleus The nucleus is often compared to the “command center,” as it controls all functions of the cell. It is important in regulating the actions of the cells. It plays an important part in creating the cell’s proteins. It is involved in important processes dealing with DNA and other genetic molecules. Nucleoid The nucleoid is the region in the prokaryotic cell that contains the main DNA material. The nucleoid has an irregular shape compared to the nucleus of eukaryotic cells, which is circular. DNA in the nucleoid is circular and may have multiple copies at any given time. Additionally, DNA in the nucleoid may be supercoiled, meaning it has twists in the circular shape that makes it more compact. As the cells grow, the DNA in the nucleoid may extend into the cytosol, or cellular fluid.  What is the difference between Nucleus and Nucleoid? Nucleus is the structure where Eukaryotes store their genetic material while nucleoid is the place where Prokaryotes store their genetic material. Nucleus is large and well organized, whereas nucleoid is small and poorly organized. Nucleus is surrounded by a double layered membrane called “nuclear membrane” and separates from other cell organelles. Such membrane cannot be found in nucleoid. Nucleus contains many chromosomes while nucleoid generally has only one circular DNA molecule. Nucleolus and nucleoplasm are present inside the nucleus, whereas they are absent in nucleiod. DNA double helix DNA DNA : Basic chemical units Each nucleotide consists of 1. A 5 carbon sugar – Deoxyribose 2. Nitrogenous Bases Purines: Adenine and Guanine Pyrimidines : Thymine and Cytosine 3. Phosphate - link between sugars  Basic Structure of DNA BACKBONE OF DNA/RNA ATGCU Bases in DNA adenine Purines N9 guanine cytosine Pyrimidines N1 thymine  Four kinds of nucleotides are the building blocks for DNA. Purine (having double-ring structures) containing A G Pyrimidine (having single-ring structures) containing T C  Nucleoside and Nucleotide, the fundamental building block of DNA phosphoester bond glycosidic bond POLYNUCLEOTIDE…. Each strand is made up of a sugar covalently linked to a phosphate which is covalently linked to another sugar and so on. A DNA strand may contain thousands to millions of these sugar-phosphate units. Each sugar also has a Purine or Pyrimidine base attached to it through a covalent bond. Phosphodiester linkages: repeating, sugar-phosphate backbone of the polynucleotide chain  Watson and Crick model DNA was double strand (because of the 2 nm diameter) To maintain the uniform diameter, a double-ring base probably would pair with a single-ring base along the length of the molecule Adenine can hydrogen bond to thymine at 2 places. Guanine can hydrogen bond to cytosine at 3 places This explained Chargaff's findings that the amounts of adenine and thymine were the same, and the amounts of guanine and cytosine were the same for a species.  DNA Double Helix A DNA molecule consists of two strands which are coiled around each other in a double helix. The bases in the opposite strands are arranged such that where there is an adenine in one strand, the other strand has a Thymine and where there is a Guanine in one strand, the other strand has a cytosine.  Two strands of nucleotides, with their bases hydrogen-bonded to each other form a ladder if, and when, the sugar phosphate backbones ran in opposite directions to each other, or anti-parallel to each other, and twisted to form a double helix. This is where that 5' and 3' bonding gets important. The end of a DNA molecule will have a free sugar (3'end) on one side and a free phosphate (5' end) on the other side.  The constancy of the complementary base- pairing is critical to the structure of DNA. DNA of different species and of different genes shows variation in the sequence of base pairs in the DNA chain. The double helix has Minor and Major grooves  Summary of the Salient features of DNA double helix 1. Two polynucleotide chains are coiled around a central axis in the form of a right handed double helix. 2. Each polynucleotide chain is made up of 4 types of nucleotides. They are adenylate, guanidylate, thymidylate and cytidinilate. 3. Each polynucleotide chain has direction or polarity. Further each polynucleotide chain has 5’ phosphorylated and 3’ hydroxyl ends. 4. The backbone of each strand consists of alternating sugar and phosphate. The bases project inwards and they are perpendicular to the central axis. 5. The 2 strands run in opposite direction (ie.) they are antiparallel. 6.The strands are complementary to each other. Base composition of one strand is complementary to the opposite strand. If adenine appears in one strand, thymine is found in the opposite strand and vice versa. When guanine is found in one strand, cytosine is present in the opposite strand and vice versa. 7.Bases of opposite strands are involved in pairing. Pairing occurs through hydrogen bonding and it is specific. Adenine pairs with thymine through two hydrogen bonds. Guanine pairs with cytosine with three hydrogen bonds. 8. Major and minor grooves are present on the double helix. They arise because glycosidic linkages of base pairs are not opposite to each other. Protein interact with DNA through the minor and major grooves without disrupting the DNA strands. 9. According to Chargaff’s observation, the number of adenine base is equal to thymine base and the number of guanine base is equal to number of cytosine base. Also A + T = G + C and the ratio of A+T /G+C = nearly 1.0. The total number of purine bases = the total number of pyrimidine bases. The ability to form hydrogen bonds makes the base pairs more stable structurally.  Functions of DNA 1. DNA is the genetic material of living organisms. 2. DNA contain all the information required for the information of an individual organism. 3. The genetic information in DNA is converted to characteristic features of living organisms like color of the skin and eye, height, intelligence, ability to metabolize particular substance, ability to withstand stress, susceptibility to disease and ability to produce or synthesize certain substances. 4. DNA is the source of information for the synthesis of all cellular proteins. The segment of DNA that contain information for a protein is known as gene. 5. DNA is transmitted from parents to offsprings and hence transmit genetic information from one generation to another. 6. The amount of DNA in any given species or cell is constant and is not affected by nutritional and metabolic states.  DNA Organization in Eukaryotic Chromosomes  Eukaryotic chromosomal organization Many eukaryotes are diploid (2N) The amount of DNA that eukaryotes varies from organism to organism Eukaryotic chromosomes are integrated with proteins that help it fold (protein + DNA = chromatin) Chromosomes become visible during cell division DNA of a human cell is 2.3 m (7.5 ft) in length if placed end to end while the nucleus is a few micrometers; packaging/folding of DNA is necessary 2 main groups of proteins involved in folding/packaging eukaryotic chromosomes ◼ Histones = positively charged proteins filled with amino acids lysine and arginine that bond ◼ Nonhistones = less positive Nucleosome Model: Chromatin is linked together by histones for every 200 bps Chromatin arranged like “beads on a string” 8 histones in each nucleosome 147 bps per nucleosome core particle with 53 bps for linker DNA (H1) Left-handed superhelix Histone proteins ◼ Abundant ◼ Histone protein sequence is highly conserved among eukaryotes—conserved function ◼ Provide the first level of packaging for the chromosome; compact the chromosome by a factor of approximately 7 ◼ DNA is wound around histone proteins to produce nucleosomes; stretch of unwound DNA between each nucleosome  DNA wraps twice round the core DNA strand DNA held in place by another histone (H1) = the nucleosome H1 Nucleosomes are joined by linker DNA Linker DNA Histone proteins ◼ 5 main types H1—attached to the nucleosome and involved in further compaction of the DNA (conversion of 11 nm chromatin to 30 nm chromatin) H2A H2B Two copies in each nucleosome H3 ‘histone octomer’; DNA wraps H4 around this structure1.75 times ◼ This structure produces 11nm chromatin A possible nucleosome structure Nucleosomes connected together by linker DNA and H1 histone to produce the “beads-on-a-string” extended form of chromatin Histone octomer H1 Linker DNA 11 nm chromatin is produced in the first level of packaging. Solenoidal model ◼ DNA is further compacted when the DNA nucleosomes associate with one another to produce 30 nm chromatin ◼ Mechanism of compaction is not understood, but H1 plays a role (if H1 is absent, then chromatin cannot be converted from 11 to 30 nm) ◼ DNA is condensed to 1/6th its unfolded size Packaging of nucleosomes into the 30-nm chromatin fiber (Solenoidal model) Nonhistone proteins ◼ Other proteins that are associated with the chromosomes ◼ Amount of nonhistone protein varies from cell to cell ◼ May have role in compaction or be involved in other functions requiring interaction with the DNA ◼ Many are acidic and negatively charged; bind to the histones 300 nm Chromatin loops  Compaction continues by forming looped domains from the 30 nm chromatin, which seems to compact the DNA to 300 nm chromatin  Human chromosomes contain about 2000 looped domains  30 nm chromatin is looped and attached to a nonhistone protein scaffolding  DNA in looped domains are attached to the nuclear matrix via DNA sequences called MARs (matrix attachment regions) Model for the organization of 30-nm chromatin fiber into looped domains that are anchored to a nonhistone protein chromosome scaffold The many different orders of chromatin packing that give rise to the highly condensed metaphase chromosome DNA compaction Level of DNA compaction changes throughout the cell cycle; most compact during M and least compact during S 2 types of chromatin; related to the level of gene expression Euchromatin—defined originally as areas that stained lightly Heterochromatin—defined originally as areas that stained darkly  Euchromatin—chromosomes or regions therein that exhibit normal patterns of condensation and relaxation during the cell cycle ◼ Most areas of chromosomes in active cells ◼ Usually areas where gene expression is occurring  Heterochromatin—chromosomes or regions therein that are condensed throughout the cell cycle  Provided first clue that parts of eukaryotic chromosomes do not always encode proteins. Chromosomes Chromosomes  All eukaryotic cells store genetic information in chromosomes. ◼ Most eukaryotes have between 10 and 50 chromosomes in their body cells. ◼ Human cells have 46 chromosomes. ◼ 23 nearly-identical pairs  Structure of Chromosomes Chromosomes are composed of a complex of DNA and protein called chromatin that condenses during cell division. DNA exists as a single, long, condensed double-stranded fiber extending chromosome’s entire length. Each unduplicated chromosome contains one DNA molecule, which may be several inches long Structure of Chromosomes  The centromere is a constricted region of the chromosome containing a specific DNA sequence, to which is bound 2 discs of protein called kinetochores.  Kinetochores serve as points of attachment for microtubules that move the chromosomes during cell division Metaphase chromosome Centromere region of chromosome Kinetochore Kinetochore microtubules Sister Chromatids Chromosomes  A diploid cell has two sets of each of its chromosomes  A human has 46 chromosomes (2n = 46)  In a cell in which DNA synthesis has occurred all the chromosomes are duplicated and thus each consists of two identical sister chromatids Maternal set of chromosomes (n = 3) 2n = 6 Paternal set of chromosomes (n = 3) Two sister chromatids of one replicated chromosome Centromere Two nonsister Pair of homologous chromatids in chromosomes a homologous pair (one from each set) Homologues  Homologous chromosomes: Look the same Control the same traits May code for different forms of each trait Independent origin - each one was inherited from a different parent  Chromosome Duplication  Because of duplication, each condensed chromosome consists of 2 identical chromatids joined by a centromere.  Each duplicated chromosome contains 2 identical DNA molecules Non-sister chromatids Centromere Duplication Sister Sister Two unduplicated chromatids chromatids chromosomes Two duplicated chromosomes Copyright © The McGraw-Hi ll Companies, Inc. Permis sion requi red for reproducti on or di splay.  TYPES OF CHROMOSOMES SHORT ARM 1. SUB-METACENTRIC:- Here the centromere is not at the middle position CENTROMERE of the chromosomes. So the arms are unequal and it is ‘L-Shaped’ in appearance. LONG ARM TWO EQUAL ARMS 2. METECENTRIC:- The centromere is at the middle position. So the arms are equal CENTROMERE and it is ‘V-Shaped’ in appearance.  TYPES OF CHROMOSOMES 3. TELOCENTRIC:- The centromere CENTROMERE is present at the end of the chromosomes. LONG ARM SHORT ARM CENTROMERE 4)ACROCENTRIC:-The centromere is almost terminal. It LONG ARM has one large and another very small arm. FUNCTION OF CHROMOSOMES ❖ Regulate the proteins of cells. ❖ Determine the gender of an individual. ❖ Influence or determine the traits of the entire organism. ❖ Determine height, eye color. ❖ Contain the genetic instructions to control cell processes. ❖ Contain instructions to form new cells. ❖ The codes in chromosomes determine what proteins the cell will produce.