Contents of Cytoplasm

CYTOPLASM AND ITS CONTENTS

1. CYTOPLASM - DEVIKA K V I MDS

2. SYNOPSIS INTRODUCTION CYTOPLASMIC MATRIX CELL MEMBERANE CELL JUNCTION MITOCHONDRIA ROUGH AND SMOOTH ENDOPLASMIC RETICULUM. RIBOSOMES GOLGI APPARATUS LYSOSOMES PEROXISOMES MICROTUBULES CILIA FILAMENTS CONCLUSION REFERENCES

3. INTRODUCTION The cell was first discovered by  Robert Hooke  in 1665, which can be found to be described in his book, Micrographia The cytoplasm is the part of the cell designed to perform principal metabolic activities. To carry out a broad range of different functions, the cytoplasm is equipped with several different kinds of cytoplasmic organelles, cytoplasmic matrix and cytoskeleton.

4. COMPONENTS OF THE CELL CYTOPLASM MEMBERANEOUS ORGANELLES CELL MEMBERANE MITOCHONDRIA ROUGH SURFACED ENDOPLASMIC RETICULUM SMOOTH ENDOPLASMIC RETICULUM GOLGI APPARATUS SECRETORY VESICLES LYSOSOMES ENDOSOMES PEROXISOMES NON MEMBERANEOUS ORGANELLES RIBOSOMES MICROTUBULES CILIA AND FLAGELLA CENTRIOLES FILAMENTS CYTOPLASMIC INCLUSION STORED FOOD Glycogen Fat PIGMENTS EXOGENOUS Carotene, Carbon particles ENDOGENOUS Haemoglobin Hemosiderin Bilirubin Melanin Lipofuscin

5. C YTOPLASMIC MATRIX/ CYTOSOL N on organelle component of the cytoplasm. L iquid component? M icrotrabecular lattice (6nm thick) represent part of the gel structure of the matrix. This network hold the organelle in position. cytoplasm EM H & E

6. Cell memberane / plasma memberane / PLASMALEMMA Outer memberane of the cell Cannot be seen in the LM because the memberane is only 8-10nm thick In EM – trilaminar structure The cell memberane posess a unique outer region made up of ( glycocalyx or cell coat)

7. FUNCTIONS Cell memberane is the part of the cell that determines which constituent are able to enter or leave the cytoplasm Cell memberane plays a role in receiving chemical messages from other cells (A receptor is defined as a protein molecule with in a cell or on the cell surface to which a substance like hormone, a drug, or an antigen can bind to it , and cause a change in the cell activity)

8. MOLECULAR STRUCTURE OF THE CELL MEMBERANE

9. CELL MEMBERANE PROTEINS Memberane proteins furnish transmemberane channels for the passage of ions and molecules present in aqueous solution. Intrinsic or integral memberane proteins and peripheral or extrinsic memberane proteins FLUID MOSAIC MODEL by Singer and Nicholson(1972) Lipids are organised in a double layer or bilayer. Membrane lipids are amphipathic. Memberane proteins can be associated either to the lipid bilayer polar head groups (peripheral proteins) or to the hydrophobic matrix (integral proteins) Both the lipids and the proteins are in the constant motion. Three main modes of motion are rotational, translational and transbilayer .

10. ASYMMETRY OF THE CELL MEMBERANE Glycocalyx present only on the outer side Two constituent layer of the lipid bilayer have substatially different lipid compositions Different proteins can be present in inner and outer parts

11. CELL JUNCTIONS Tight/occluding junction Anchoring/ adhering junction Gap junction

12. MITOCHONDRIA

13. “ Mitos , thread; chondrion , granule” Ovoid elongated thread like structures present in the cytoplasm 0.5-1 um in diameter and 5-10um in length It contain both DNA( mt DNA) and RNA Site of the cell involved in the oxidation process- “power House of the cell” Contains the enzymes responsible for respiratory metabolism-( ATP)

14. In Electron microscopy i)outer memberane (permeable) ii) inner memberane (7 nm thick, selectively permeable) ii) Intermemberaneos space iv) Cristae v)Mitochondrial matrix vi)Matrix granules STRUCTURE OF MITOCHONDRIA

15. FUNCTIONS Mitochondrial structure is related to various enzymatic and electrochemical reactions that bring about oxidative phosphorylation Mitochondial enzymes catalyse a number of different reactions involved in the breakdown of various end products of glycolysis, fatty acid metabolism, aminoacid metabolism

16. ENZYMATIC REACTIONS IN MITOCHONDRIA In the cytosol, mammalian cells utilize an oxygen independent pathway to degrade glucose in the cytosol The aerobic pathway comes into effect once pyruvate has been produced through glycolysis Pyruvate is taken in through both the memberanes to the mitochondrial matrix, which is where the enzymes of the citric acid cycle are situated The enzymes catalyse a number of different reactions involved in the break down of various end products of 1) glycolysis, 2) fatty acid metabolism 3)amino acid metabolism

17. Within the mitochondrial matrix, glycolytic end products are gradually oxidised to carbon dioxide by the enzymes of the citric acid cycle During these process there is release of hydrogen atoms, some of which become transferred to NAD, and others to FAD The electrons of the hydrogen are then passed along the series of respiratory enzymes called flavoproteins and cytochromes The energy obtained from the transfer of electron carriers is used to generate ATP from ADP and inorganic phosphate The various enzymes involved in the electron transport chain and oxidative phosphorylation form integrated complexes on the inner mitochondrial memberane and its cristae

18. mi MITOCHONDRIA APPEAR TO BE DESCENDED FROM AEROBIC BACTERIA It contains both DNA and RNA They also contain ribosomes Thus mitochondria posess the basic requirement of an independent existence Mitochondrial DNA, RNA and ribosomes are similar to their counterparts in the bacteria Mitochondrial DNA directs the synthesis of proteins The mitochondrial genes have become integrated in the cell’s own genome

19. MITOCHONDRIAL DISORDERS

20. Rounded ribonucleoprotein particles 20-30nm in diameter Present as unbound particles and also as bound state attached to the endoplasmic reticulum They are composed of rRNA and ribosomal proteins and the don’t posess a memberane (non memberaneous organelle) LM In H & E staining the cytoplasm are either tinged with blue or is definitely blue in cells that are actively producing proteins Cytoplasmic basophiia - strong affinity of rRNA for hematoxylin . DIFFUSE LOCALIZED

21. ELECTRON MICROSCOPIC VIEW

22. FUNCTIONS I t provides the intracellular sites where aminoacid molecules are linked together to form polypeptides Translation

23. RIBOSOMIOPATHIES Treacher Collins syndrome (TCS ) Diamond- blackfan anemia (DBA ) Robert syndrome (RBS ) Shwachman -diamond syndrome (SDS ) Bowen- conradi syndrome (BWCNS ) North American Indian childhood cirrhosis (NAIC)

24. ROUGH ENDOPLASMIC RETICULUM

25. Endo:within the cytoplasm; Reticulum:network by PORTER Largest organelle in the cell and is the major site of protein synthesis and transport, protein folding, lipid biogenesis, calcium storage Endoplasmic reticulum with ribosomes attached Regions of cytoplasm that exhibits intense loca l basophilia Memberaneous organelle Seen in cells that elaborate secretory proteins or glycoprotein

26. ELECTRON MICROSCOPIC VIEW

27. SEGREGATION OF LYSOSOMAL ENZYMES AND SECRETORY PROTEINS rER is required by all the cells eventhough they are not secretory, for the synthesis and segregation of lysosomal enzymes. SIGNAL HYPOTHESIS BY BLOBEL AND SABATANI

28. + SITE OF INCORPORATION OF INTEGRAL MEMBERANE PROTEINS AND MEMBERANE LIPIDS. Integral protein and glycoprotein molecules extend partially through the rER SITE OF MODIFICATION OF SEGREGATED PROTEINS Once protein are synthesised , protein destined for secretion must undergo proper folding and modifications, with the aid of chaperons Following the removal of the signal sequence, the molecule fold up because of the formation of S-S bonds, a configurational change that helps to keep segregation unidirectional From the rER memberane segregated proteins are delivered by means of small vesicles to the golgi apparatus

29. PROCESS OF PROTEIN SYNTHESIS RNA is transcribed from DNA RNA transcript mRNA is spliced and modified to mRNA which is moved from nucleus to the cytoplasm The mRNA attaches to the ribosome Each aminoacids attaches to the proper tRNA with the help of enzymes & ATP A succession of tRNAs add their aminoacids to the polypeptide chains as the MRNA is moved through the ribosome one codon at a time

30. LIPID BIOGENESIS ER is a site of bulk memberane lipid biogenesis Proteins and phospholipids are transferred and biochemically modified in the region of the ER and Golgi apparatus This region is known as ERGIC CALCIUM METABOLISM Ca 2+ concentration in the lumen of the ER is 100-800uM. ER contains several calcium channels, ryanodine receptors and inositol 1,4,5 tri phosphate receptors that are responsible for releasing calcium from the ER into the cytoplasm when the intracellular levels are low

31. 1. Lack of protein due to ER retention Cystic fibrosis and associated diseases Congenital goiter and hypothyroidism due to thyroglobulin deficiency Osteogenesis imperfecta Procollagen type I, II, IV deficiency Albinism/ tyrosinase deficiency 2.Toxic protein or protein aggregates Diabetes insipidus Liver disease in a1-antitrypsin deficiency 3 . Defective transport machinery Abetalipoproteinemia ENDOPLASMIC RETICULUM DISORDERS

32. SMOOTH ENDOPLASMIC RETICULUM Devoid of ribosomes, hence it cannot synthesise proteins. It consists of tubules that branch and anastomose in an irregular manner FUNCTIONS sER is the site of intracellular synthesis of lipids and cholestrol . Steroid hormone secretion It is believed to detoxify many drugs including alcohol It is involved in hepatic glycogen metabolism (glycogen synthase phosphatase & phosphorylase phosphatase) Regulation of intracellular distribution of calcium ions.

33. EM

34. N amed after Camillo Golgi, Italian neurologist A pale staining area seen near the nucleus The main structural unit of the golgi apparatus is flattened memberaneous vesicle described as a G olgi saccule Golgi saccules are arranged in golgi stacks that contains 3-10 saccules The saccules are fenestrated known as a network of anastomosing tubules Saccules in each stacks are interconnected with those of other stacks by complex of anastomosing tubules. This network is termed as golgi complex

35. Structure of

36. ELECTRON MICROSCOPIC VIEW

37. FUNCTIONS Modify the secretory products ROUTE TAKEN BY THE SEGREGATORY PROTEINS G olgi stack contain 3 compartment cis medial trans ( mannose) (N- glucosamine) ( galactose & sialic acid) Glycosylation by glucosyl transferase Sulfation by sulfotransferase Golgi memberane

38. Golgi sorts and packages its segregated proteins into two distinct intracellular compartments golgi apparatus sort out the secretory products and package them as secretory granules It manages to segregate the acid hydrolases and sequester these in lysosomes The golgi apparatus is the main center for memberane traffic within the cell It serves as a major distribution centre for newly synthesised memberane constituents and it redirects much of the recycled memberane that returns to it in the form of coated vesicles The golgi apparatus plays a role in both lipoprotein secretion and prohormone processin g

39. MAKING PROTEINS; A REVIEW

40. AFFECTED GENE DISEASE PRIMARY CLINICAL MANIFESTATION CELLULAR EFFECT RAB1, RAB2, RAB8, STX5 Parkinson’s disease Neurological disease Altered expression of the proteins leads to Golgi fragmentation ABCB6 Dyschromatosis universalis hereditaria Skin disorder Mutation leads to retention of the protein ATP6V0A2 Cutis laxa Connective tissue disorder Mutations lead to abnormal glycosylation of serum proteins and impairment of Golgi trafficking ATP7B Wilson disease Hepatic and neurological disorders Protein is localized to the TGN and is essential for copper metabolism. UBE3A Angelman syndrome Neurodevelopmental Disorder Loss of protein expression leads to an altered Golgi morphology and pH

41. Golgi Endoplasmic Reticulum Lysosomal complex (GERL) by Novikoff . GERL may provide a more direct route for certain enzymes synthesised in the rER to reach the sites from which lysosomes and the secretory vesicles arise. When a GERL is present it receives the luminal contents of Golgi saccules before they are delivered to the secretory vesicles or lysosomes.

42. SECRETORY VESICLES They are vesicles bounded by a unit memberane Large secretory granules are called zymogen granules. It contain enzymes in the precursor forms It is stained vivid red in H&E staining due to their high protein concentration The mechanism by which the secretory products are releases to the cell surface is termed as exocytosis

43. LYSOSOMES Described in 1950 by Christian de Duve Spherical memberaneous organelle 0.2-0.4um diameter They are centre for degradation and recycling of macromolecules delivered by endocytosis, phagocytosis and autophagy STRUCTURE OF LYSOSOMES 7-10 nm phospholypid bilayer high carbohydrate content (glycosylated lysosomal memberane protein Lysosomal memberane proteins include LAMP-1,2, lysosomal integral memberane Proteins(LIMP) &CD63 Intralysosomal memberane is rich in phospholipids Lysosome contain upto 600uM calcium

44. ELECTON MICROSCOPIC VIEW

45. FUNCTIONS Degradation of macromolecules 60 resident hydrolases including proteases, peptidases, phosphatases, nucleases, glycosidases , sulfatases and lipases have different target substrates and their collective action permits the degradation of macromolecules The best known lysosomal hydrolases are cathepsin family of proteases The characteristic acidic pH of lysosomes are the result of action of the vacuolar H+-ATPase

46. Endocytosis Process by which cells internalize the plasma memberane along with the cell surface receptors and soluble molecules Cells have multiple mechanism for endocytosis, including clatherin dependent and independent routes phagocytosis pinocytosis

47. Autophagy Chaperon mediated autophagy, microautophagy and macroautophagy Chaperon mediated autophagy is a process by which cytosolic proteins harboring specific recognition motifs are delivered to the lysomes via the action of a chaperon and the lysosomal receptor LAMP-2A Micro autophagy involves the direct engulfment of the cytoplasmic cargo at the limiting lysosomal memberane During macroautophagy , sequestration of small portion of the cytoplasm including soluble materials and organelles, within a newly generated double memberane called the isolation memberane ( phagophore ) result in the formation of autophagosomes Autophagosomes fuse with the lysosomes for the degradation and recycling of their contents

48. Exocytosis Damage to the plasma memberane resulting in calcium influx Lysosomes are translocated to the periphery, and fuse with the plasma memberane Calcium binds to the synaptotagmin VII and facilitates interaction with the SNAREs Lysosomal exocytosis plays an important role in immune responses, bone resorption , cell signalling and plasma memberane repair

49. CHOLESTROL HOMEOSTASIS The majority of cholestrol (80%) is found in the plasma memberane , where it constitutes 40% of all lipids In addition to the cholestrol synthesis in the ER, the uptake of low density lipoprotein via receptor mediated endocytosis is an important route for cholestrol entry into the cell LDL derived cholestrol esters are transported to the lysosomes Action of acid lipase liberates free esterified cholestrol

50. L ysosomal participation in cell death signalling Lysosomes were referred to as ‘suicide bags’ Partial permiabilization of the memberane induces apoptosis, and massive lysosomal rupture induces necrosis The executors of lysosomal mediated apoptosis are not the lysosomes themselves but their hydrolases, more specifically the cathepsins release of cathepsin to the cytosol by Lysosomal memberane permeablization (LMP) Cathepsin B induces typical apoptosis associated changes includes chromatin condensation, DNA fragmentation, phosphatidyl serine exposure, and plasma memberane blebbing

51. lys LYSOSOMES IN DISEASE Lysosomes have a central role in lysosomal storage disorders but an increasing evidence indicates that lysosomes are involved in alzhiemer’s disease and amyotropic lateral sclerosis Lysosomal storage disorders frequently involve the central nervous system Cathepsins contribute to the development and progression of cardiovascular diseases, including atherosclerosis and aneurysm formation

52. DISEASE ENZYME DEFICIENCY AGE AT ONSET CLINICAL SIGNS PATHOLOGY TAY - SACH’S DISEASE Hexosaminidase A, Gangliosides 3-8 months Psychomotor arrest, startle reflex, seizures, cherry red spots Storage in central and peripheral neurons NIEMANN PICK’S DISEASE TYPE A Sphyngoyelinase , shyngomyelin 1-6 months Psychomotor arrest, spleen enlargement, retinal cherry red spot sometimes Storage in neurons and spleen METACHROMATIC LEUKODYSTROPHY Cerebroside sulfatase Early childhood Progressive mental a nd motor deterioration Myelin deficits in CNS and often PNS, storage in glia KRABBE’S DISEASE Galactocerebroside8- galactosidase , galactocerebrosidase 3-6 months Irritability, crying, mental and motor deterioration, seizures Myelin deficits, gobloid cells (large mulinucleated macrophages

53. PEROXISOMES Memberane bound organelles Less than 1um, hence called as microbodies They contains peroxide forming enzymes and catalase and are involved in the formation and degradation of intracellular hydrogen peroxides FUNCTIONS Peroxisomes play a direct role in lipid metabolism (glucose from lipids) Hepatocyte peroxisomes can breakdown fatty acids by beta oxidation The oxidase enzymes in peroxisomes ( urate oxidase, D-amino oxidase and alpha hydroxy acid oxidase) produce hydrogen peroxide wherase catalase converts products into water and oxygen

54. ELECTRON MICROSCOPIC VIEW

55. MICROTUBULES Tubular or cylindrical structures Outer diameter is 25nm It contains a protein tubulin, that are arranged in rings stacked end to end FUNCTIONS I t provide internal support for the cell and present its main skeletal element Facilitate the intracellular transport of organelles, particles and macromolecules along the specific routes through the cytoplasm Microtubules are essential for the process of segregation of daughter chromosomes at mitosis

56. ELECTON MICROSCOPIC VIEW OF MICROTUBULES

57. CILIA

58. CILIA Motile hair like processes almost10 um length with a diameter of 0.2um They extend from the luminal border of most of the surface epithelial lining of certain internal passages and cavities Every cilium has a tiny associated structure known as basal body at the base The basal bodies of cilia and flagella are derived from the centrioles cilia

59. IN H&E STAINING IN ELECTRON MICROSCOPE

60. FILAMENTS Non memberaneous organelle Elongated thread like structures seen in decreasing diameters If they are seen under LM, they are called as fibres Those resolved under high power of LM is called as fibrils Those resolved by EM having smaller diameter are called as filaments Three different categories of filaments are Thin filaments/microfilaments Thick filaments Intermediate filaments

61. MICROFILAMENTS Slender rods with a diameter of 6-7nm. They are composed of actin associated with tropomyosin . In the thin filaments of skeletal and cardiac muscle contain troponin as well as actin and tropomyosin . THICK FILAMENTS 12-16 nm in diameter. It is composed of myosin. INTERMEDIATE FILAMENTS 7-11nm,also called as10nm filaments. They supplement microtubles in providing support and maintaining the shape of the various part of the cell. Ex: tonofilaments , desmin , neurofilament , glial filament, vimentin

62. MAIN CLASS OF INTERMEDIATE FILAMENTS CLASSES OF FILAMENTS CELL TYPES cytokeratin Epithelial cells desmin Muscle cells neurofilament neurons Glial filament Astrocytes, ependymal cells, schwann cells, pituicytes vimentin Mesenchymal derivative including endothelial cells, muscle cells, neuro ectodermal derivative including early differentiating neurons and most kind of glial cells, immature cells

63. THIN AND THICK FILAMENTS INTERMEDIATE FILAMENTS

64. REFERENCES 1.Ham’s Histology 2.”The Endoplasmic Reticulum: structure, function and response to cell signaling”; Dianne S. Schwarz, Michael D.Blower;Cell.Mol.Life Sci (2016) 73:79-74 3.’’The Golgi apparatus: an organelle with multiple complex functions’’; Cathal WILSON, Rosella VENDITT, Laura R. REGA, Antonino COLANZI, Giovanni D’ANGELO and M.Antonietta DE MATTEIS; Biochem . J, (2011) 433, 1-9 4.’’Lysosome: The story Beyond the Storage’’; Ursula Matte, Gabriela Pasqualim ; Journal of Inborn Errors of Metabolism and screening, 2016, volume 4: 1-7

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