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Chapters 6

Chapters 6. The Cytoplasm & Organelles. The Typical Cell. typical cell: 1. nucleus 2. cell membrane 3. cytoplasm -cytosol -cytoskeleton 4. cytoplasmic organelles -membranous -non-membranous. Cytoplasm. semi-fluid-like jelly within the cell

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Chapters 6

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  1. Chapters 6 The Cytoplasm & Organelles

  2. The Typical Cell • typical cell: 1. nucleus • 2. cell membrane • 3. cytoplasm • -cytosol • -cytoskeleton • 4. cytoplasmic organelles • -membranous • -non-membranous

  3. Cytoplasm • semi-fluid-like jelly within the cell • division into three subdivisions: cytosol, cytoskeleton & organelles

  4. Cytosol ECF • lower K+ • higher Na+ • lower concentration • of dissolved and • suspended proteins • higher concentration • of carbohydrates • smaller reserves of amino • acids • higher K+ • lower Na+ • higher concentration • of dissolved and • suspended proteins • (enzymes, organelles) • lower concentration • of carbohydrates • (due to catabolism) • larger reserves of amino • acids (anabolism) The Cytosol – Eukaryotic Cells • eukaryotic cells – part of the cytoplasm • about 55% of the cell’s volume • about 70-90% water PLUS • ions • dissolved nutrients – e.g. glucose • soluble and insoluble proteins • waste products • macromolecules and their components - amino acids, fatty acids • ATP • unique composition with respect to extracellular fluids

  5. Cytoskeleton: • internal framework of the cell • gives the cytoplasm flexibility and strength • provides the cell with mechanical support • gives the cell its shape • can be rapidly disassembled in one area of the cell and reassembled in another • anchorage points for organelles and cytoplasmic enzymes • also plays a role in cell migration and movement by the cell

  6. The Cytoskeleton and Cell motility Vesicle ATP Receptor formotor protein • motility = changes in cell location and the limited movements in parts of the cell • the cytoskeleton is involved in many types of motility • requires the interaction of the cytoskeleton with motor proteins • some roles of motor proteins: • 1. motor proteins interact with microtubules (or microfilaments) and vesicles to “walk” the vesicle along the cytoskeleton • 2. motor protein, the cytoskeleton and the plasma membrane interact to move the entire cell along the ECM • 3. motor proteins result in the bending of cilia and flagella Microtubuleof cytoskeleton Motor protein(ATP powered) (a) Microtubule Vesicles 0.25 m (b)

  7. Cytoskeleton: • three major components • 1. microfilaments • 2. intermediate filaments • 3. microtubules

  8. 5 m 10 m 10 m Column of tubulin dimers Keratin proteins Actin subunit Fibrous subunit (keratinscoiled together) 25 nm 812 nm 7 nm Tubulin dimer  

  9. 1. microfilaments = thin filaments made up of a protein called actin -twisted double chain of actin subunits -forms a dense network immediately under the PM (called the cortex) -also found scattered throughout the cytoplasm

  10. microfilaments = -function: 1.anchor integral proteins and attaches them to the cytoplasm 2. interaction with myosin = interacts with larger microfilaments made up of myosin - results in active movements within a cell (e.g. muscle cell contraction) 3. provide much of the mechanical strengthof the cell – resists pulling forces within the cell 4. give the cell its shape 5. also provide support for cellular extensions called microvilli(small intestines)

  11. Examples of Actin/Myosin: Muscle cell 0.5 m Actin In muscle cells – motors within filaments made of myosin “slide” along filaments containing actin = Muscle Contraction filament Myosin filament Myosin head (a) Myosin motors in muscle cell contraction Cortex (outer cytoplasm):gel with actin network 100 m In amoeba – interaction of actin with myosin causes cellular contraction and pulls the cell’s trailing edge (left) forward -can also result in the production of Pseudopodia (for locomotion, feeding) Inner cytoplasm: solwith actin subunits Extendingpseudopodium (b) Amoeboid movement In plant cells – a layer of cytoplasm cycles around the cell -streaming over a “carpet” of actin filaments may be the result of myosin motors attached to organelles Chloroplast 30 m (c) Cytoplasmic streaming in plant cells

  12. 2. intermediate filaments = more permanent part of the cytoskeleton than other filaments • five types of IF filaments – type I to type V • made up of proteins such as vimentin, desmin, or keratin • each cell type has a unique complement of IFs in their cytoskeleton • all cells have lamin IFs – but these are found in the nucleus • some cells also have specific IFs • e.g neurons also posses IFs made of neurofilaments type I IFs = acidic keratins type II IFs = basic keratins type III IFs = desmin, vimentin type IV IFs = neurofilaments type V IFs = nuclear lamins kidney cell - vimentin

  13. 2. intermediate filaments = function: 1. impart mechanical strengthto the cytoskeleton – specialized for bearing tension (like microfilaments) 2. support cell shape e.g. forms the axons of neurons 3. anchor & stabilize organelles e.g. anchors the nucleus in place 4. transport materials e.g. movement of neurotrasmitters into the axon terminals

  14. 3. microtubules= hollow rods or “straws” - made of repeating units of proteins called tubulin - function: 1. cell shape & strength 2. organelles: anchorage & movement 3. mitosis - form the spindle (chromosome movement) 4. form many of the non-membranous organelles - cilia, flagella, centrioles • components of: • mitotic spindle • cilia and flagella • axons of neurons b-tubulin a-tubulin

  15. 3. microtubules-the basic microtubule is a hollow cylinder = 13 rows of tubulin called protofilaments • tubulin is a dimer – two slightly different protein subunits • called alpha and beta-tubulin -alternate down the protofilament row b-tubulin a-tubulin

  16. -animal cells – microtubule assembly occurs in the MTOC(microtubule organizing center or centrosome) -area of protein located near the nucleus -within the MTOC/centrosome : 1. a pair of modified MTs called centrioles 2. pericentriolar material – made up of factors that mediate microtubule assembly 3. “-” end of assembling microtubules (MTs grow out from the centrosome) -other eukaryotes – there is no MTOC -have other centers for MT assembly • can be found as a single tube a doublet and a triplet

  17. Microtubule Assembly within the MTOC: -MTs are easy to assemble and disassemble – by adding or removing tubulin dimers -one end accumulates or releases tubulin dimers much faster than the other end called the plus end -the tubulin subunits bind and hydrolyze GTP – determines how they polymerize into the MT -MT disassembly is a mechanism of certain chemotherapy drugs http://www.nature.com/nrc/journal/v4/n4/fig_tab/nrc1317_F4.html

  18. Non-membranous Organelles A. Centrioles:short cylinders of tubulin - 9 microtubule triplets -called a 9+0 array(9 peripheral triplets, 0 in the center) -grouped together as pairs – arranged perpendicular to one another -make up part of the centrosome or MTOC -role in MT assembly?? -also have a rolein mitosis - spindle and chromosome alignment

  19. B. Cilia & Flagella • cilia = projections off of the plasma membrane of eukaryotic cells – covered with PM BUT NOT MEMBRANOUS ORGANELLES • beat rhythmically to transport material – power & recovery strokes • found in linings of several major organs covered with mucus where they function in cleaning e.g. trachea, lungs Trachea

  20. 0.1 m Plasma membrane Outer microtubuledoublet B. Cilia & Flagella Dynein proteins Centralmicrotubule • cytoskeletal framework of a cilia or flagella = axoneme(built of microtubules) • contain 9 groups of microtubule doublets surrounding a central pair= called a 9+2 array • cilia is anchored to a basal body just beneath the cell surface Radialspoke Microtubules Cross-linkingproteins betweenouter doublets (b) Cross section ofmotile cilium Plasmamembrane Basal body 0.1 m 0.5 m (a) Longitudinal sectionof motile cilium Triplet (c) Cross section ofbasal body

  21. flagella = resemble cilia but much larger • 9+2 array • found singly per cell • functions to move a cell through the ECF -DO NOT HAVE THE SAME STRUCTURE AS BACTERIAL FLAGELLA

  22. Cilia, Flagella and Dynein “motors” • in flagella and motile cilia – flexible cross-linked proteins are found evenly spaced along the length • blue in the figure • these proteins connect the outer doublets to each other and to the two central MTs of a 9+2 array • each outer doublet also has pairs of proteins along its length • these stick out and reach toward its neighboring doublet • called dynein motors • responsible for the bending of the microtubules of cilia and flagella when they beat Microtubuledoublets Cross-linking proteinsbetween outer doublets Dynein protein

  23. Microtubuledoublets Cilia, Flagella and Dynein “motors” ATP • dynein “walking” moves flagella and cilia • dynein protein has two “feet” that walk along the MT • dyneins alternately grab, move, and release the outer microtubules • BUT: without any cross-linking between adjacent MTs - one doublet would slide along the other • elongate the cilia or flagella rather than bend it • so to bend the MT  must have proteins cross-linking between the MT doublets (blue lines in figure) • protein cross-links limit sliding • forces exerted by dynein walking causes doublets to curve = bending the cilium or flagellum Dynein protein (a) Effect of unrestrained dynein movement Cross-linking proteinsbetween outer doublets ATP Anchoragein cell (b) Effect of cross-linking proteins 1 3 2 (c) Wavelike motion

  24. Membranous Organelles • completely surrounded by a phospholipid bilayer similar to the PM surrounding the cell • allows for isolation of each individual organelle - so that the interior of each organelle does not mix with the cytosol -known as compartmentalization • BUT - cellular compartments must “talk” to each other • therefore the cell requires a well-coordinated transport system in order for the organelles to communicate and function together -”vesicular transport” -active process – requires ATP

  25. Membranous Organelles • major functions of the organelles • 1. protein synthesis – ER and Golgi • 2. energy production – mitochondria • 3. waste management – lysosomes and peroxisomes

  26. Membranous Organelles • the organelles of a eukaryotic cell are not constructed de novo • they require information in the organelle itself • when a cell divides – it must duplicate its organelles also • in general – the cell enlargens existing organelles by incorporating new phospholipids and proteins into them • the bigger organelle then divides when the daughter cell divides during cytokinesis

  27. The Endomembrane System: A Review • endomembrane system is a complex and dynamic player in the cell’s compartmental organization • divides the cell into compartments • includes the: • Nucleus • Endoplasmic Reticulum • Golgi apparatus • lysosomes, endosomes • vacuoles and vesicles

  28. The Endomembrane System: A Review • proteins travelling through the ER and Golgi are destined for • 1. Secretion outside the cell • 2. Plasma membrane • 3. Lysosome

  29. Endoplasmic reticulum (ER) = series of membrane-bound, flattened sacs in communication with the nucleus and the PM -each sac or layer = cisternae -inside or each sac =lumen (10% of total cell volume) -distinct regions of the ER are functionally specialized – Rough ER vs. Smooth ER

  30. -three functions: 1. synthesis – phospholipids, lipids and proteins • proteins • phospholipids & lipids • 2. storage – intracellular calcium • 3. transport – site of transport vesicle production

  31. Endoplasmic reticulum (ER) -two types: Rough ER - outside studded with ribosomes -continuous with the nuclear membrane -protein synthesis, phospholipid synthesis -also the initial site of processing and sorting of proteins

  32. Endoplasmic reticulum (ER) -the import of proteins into the RER is a co-translational process -import of proteins into an organelle = translocation -proteins are imported as they are being translated by ribosomes -in contrast to the import of proteins into other organelles (e.g. chloroplasts, mitochondria, peroxisomes) and the nucleus = post-translational process

  33. Co-translational Protein Synthesis two kinds of proteins enter the ER: • ER proteins – transmembrane proteins that stay stuck in the ER membrane PLUS ER lumen proteins that remain in the ER 2. proteins destined for the Golgi, PM or lysosome or secretion

  34. Co-translational Protein Synthesis • transport from the ribosome across the ER membrane requires the presence of an ERsignal sequence (red in the figure) • 16-30 amino acids at the beginning of the peptide sequence (N-terminal)

  35. Co-translational Protein Synthesis • a complex of proteins will bind this signal in the cytoplasm = signal recognition particle/SRP • the ER membrane has receptor for the SRP and ribosome – SRP receptor (yellow protein in figure) • the ribosome is “docked” next to a “hole” in the ER membrane (blue protein in figure) = translocon • translocon recognizes the signal sequence and binds it “guides” the rest of the translating polypeptide into the ER lumen • once the polypeptide is fed into the ER lumen – a peptidase (located in the SRP receptor complex) cleaves the signal sequence off

  36. Translocation • try this animation – it might be a bit complicated – but give it a try anyway • http://www.rockefeller.edu/pubinfo/proteintarget.html • here’s a figure from a molecular biology text that summarizes the process

  37. once the polypeptide is fed into the ER lumen – a peptidase cleaves the signal sequence off = PRODUCES A SOLUBLE PROTEIN • localizes to the ER lumen • the presence of another sequence of amino acids within the polypeptide – stop-transfer sequence – the translocator stops translocating and transfers the polypeptide into the ER membrane = PRODUCES A TRANSMEMBRANE PROTEIN

  38. Modifications in the RER • 1. folding of the peptide chain • actually a spontaneous process – due to the side chains on the amino acids • only properly folded proteins get transported to the Golgi for additional processing and transport • many proteins located in the ER which supervise this folding • 2. formation of disulfide bonds • help stabilize the tertiary and quaternary structure of proteins

  39. Modifications in the RER • 3. breaking of specific peptide bonds – proteolytic cleavage or proteolysis • 4. assembly into multimeric proteins (more than one chain) for an animation go to http://sumanasinc.com/webcontent/animations/content/proteinsecretion_mb.html

  40. Modifications in the RER • 5. addition and processing of carbohydrates = glycosylation • N-linked glycosylation = attachment of 14 sugar residues as a group to an asparagine amino acid within the protein • the sugar is actually built and then transferred as one unit to the nearby translating protein by a transferase protein • needs to be trimmed down in order to allow protein folding most proteins made in the ER undergo N-linked glycosylation

  41. Endoplasmic reticulum (ER) Smooth ER – extends from the RER • free of ribosomes main function is transport vesicle synthesis – area where this happens can be called transitional ER

  42. but other cell types have SER with enzymes embedded in it for additional functions: • lipid and steroid biosynthesis for membranes 2. detoxification of toxins and drugs 3. cleaves glucose so it can be released into the bloodstream 4. uptake and storage of calcium

  43. 2. Ribosomes = can be considered a nonmembranous organelle • made in the nucleolus • 2 protein subunits in combination with rRNA -large subunit = 28SrRNA, 5.8SrRNA, 5 rRNA + 50 proteins -small subunit = 18SrRNA + 33 proteins • proteins are translating in the cytoplasm and imported into the nucleus • rRNA is transcribed in the nucleolus • ribosomes found in association with the ER = where the peptide strand is fed into from the ribosome • also float freely within the cytoplasm as groups = polyribosomes

  44. 3. Golgi Apparatus = stacks of membranes called cisternae (cisterna, singular) -the first sac in the stack = cis-face (faces the ER) -the last sac in the stack = trans-face -the ones in the middle = medial cisterna or cisternae Named after Camillo Golgi in 1897

  45. 3. Golgi Apparatus -associated with the cis and trans faces are additional networks of interconnected cisternal structures -called the cis Golgi network (CGN) and trans Golgi network (TGN) -the TGN has a critical role in protein sorting

  46. 3. Golgi Apparatus • site of final protein modification and packaging of the finished protein • functions: • 1. protein modification • A. glycosylation - creation of glycoproteins and proteoglycans • B. site for phosphate addition to proteins = phosphorylation • C. protein trimming • 2. production of sugars • Golgi makes many kinds of polysaccharides • 3. formation of the lysosome • 4. packaging of proteins and transport to their final destination • TGN acts as a sorting station for transport vesicles

  47. Modifications in the Golgi • glycosylation = produces a glycoprotein or a proteoglycan • most plasma membrane and secreted proteins have one or more carbohydrate chains • sugars help target proteins to their correct location; are important in cell-cell and cell-matrix interactions • two kinds: N-linked and O linked • O-linked sugars are added one at a time in the Golgi to the amino acids serine, threonine or lysine (usually one to four saccharide subunits total) • N-linked sugars are added as a group (about 14 sugars!) in the ER Proteoglycan

  48. glycosylation: • glycosylation starts in the ER • N-linked glycosylation – addition of N-linked oligosaccharides • many of these N-linked sugar residues are trimmed off within the ER • important for folding of the protein • glycosylation continues in the cisternae of the Golgi • addition of O-linked oligosaccharides to proteins • PLUS modification of the N-linked oligosaccharides - either addition or removal of sugar residues

  49. Why Glycosylation? • the vast abundance of glycoproteins suggests that glycosylation has an important function • N-linked is found in all eukaryotes – including single-celled yeasts • a type of N-linked can even be found in archaea – in their cell walls • WHY GLYCOSYLATION? • N-linked in the ER is important for proper protein folding • N-linked also limits the flexibility of the protein • the sugar residues can prevent the binding of pathogens • sugar residues also function as signaling chemicals • sugar residues function in cell interactions

  50. Why Glycosylation? • O-linked glycosylation • O-linked are added one at a time in the Golgi to the amino acids serine, threonine or lysine (one to four saccharide subunits total) • added on by enzymes called glycosyltransferases • human A, B and O antigens are sugars added onto proteins and lipids in the plasma membrane of the RBC • everyone has the glycosyltransferase needed to produce the O antigen • those with blood type A have an additional Golgi glycosyltransferase enzyme which modifies the O antigen to make the A antigen • a different glycosyltransferase is required to make the B antigen • both glycosyltransferases are required for the creation of the AB antigen • coded for by specific gene alleles on chromosome 9 (ABO locus)

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