Cell Biology 1 z 211 Lecture Notes PDF

Cell Biology1 z 211 Prof/ Dr: Amel Ibrahim Othman 1 Mitochondria, Ribosomes & Endomembrane System Lecs.7,8,9 2 The Mitochondria 3  The Mitochondria * Discovered by Altmann in 1890, named “Bioblasts”, stained with (Altmann’s aci...

Cell Biology1 z 211 Prof/ Dr: Amel Ibrahim Othman 1 Mitochondria, Ribosomes & Endomembrane System Lecs.7,8,9 2 The Mitochondria 3  The Mitochondria * Discovered by Altmann in 1890, named “Bioblasts”, stained with (Altmann’s acid fuchsin). * Benda in 1937, introduced mito=thread+ chondrion= granules. * Hans Krebs described the Krebs cycle (TCA cycle). * Its number and distribution = energy demands = needs to the energy. * Shape: variable “rods, filaments” , about 0.5-1 µm in diameter with variable length. * Origin: by binary fission from pre-existing ones. * Contain its requirements for replication. * In mammals: mitochondrial genes are maternally** inherited. 4 Ultrastructure and Biochemical Composition * First extensive EM study by Palade in 1953. *Smooth outer Membrane covers the entire organelle. *Folded inner membrane into Cristae to increase the surface area. *Inter-membrane space between outer and inner membrane called outer chamber filled with fluid. *Space inside cristae called the Matrix. *Mitochondrial protein: matrix=67% - inner-membrane=21% - outer membrane=6% - inter-membrane 5 space=6% * 3 major ways for ATP production 1) By Glycolysis: - Occurs in the Cytoplasm - Anaerobic (Doesn't need Oxygen) - one sugar molecule 2 ATPs - Glucose 2 Pyruvate molecules 2) By Chloroplasts in plant cells using sun light. 3) By Mitochondria ( TCA cycle & ETC) Produces 36 ATPs 6  ATP Adenosine TriPhosphate Organic molecule containing high-energy Phosphate ponds 7 * Adenine Base 3 Phosphates Ribose Sugar 8  * ATP ATP-ase Synthetase Enzyme adding of phosphate group removable of phosphate group Synthesis Break down 9  make energy 1 { energy needed ATP even at rest eat activity food temperature control 2 synthesis (building) { growth reproduction repair 3 storage { glycogen (animal starch) fat 10  * Occurs across Cristae Occurs in Cytoplasm Occurs in Matrix 11  major reproduction of ATP FADH2 12 13 * Matrix: contains hundred of enzymes required for oxidation of pyruvate and fatty acids, mitochondrial DNA genome, ribosomes, tRNAs, enzymes for gene expression. * Inner-membrane: contain 3 major types of proteins: (1) proteins carry the redox-reactions of respiratory chain. (2) an enzyme complex, ATP-ase. (3) specific transport proteins regulate the passage of metabolites in & out of the matrix. * Inter membrane space: contains several enzymes using ATP for nucleotide phosphorylation. * Outer membrane: contains large channel proteins, permeable for all 14 proteins 10,000 daltons or less, enzymes act on lipid substrates.  Outer Mitochondrial Membrane * Thinner, with lesser proteins and more lipids than Inner-membrane. * PROTEINS= enzymes converting lipids metabolized form in matrix. = Porin: a protein responsible for easy permeability of 10,000 daltons/less molecules. =Enzymes for… oxidation of epinephrine, degradation of tryptophan, elongation of fatty acids. = Specific receptors for passing of some enzymes; cytochrome C from cytosol. 15  Outer Mitochondrial Membrane * LIPIDS= large amount of cholesterol for mechanical stabilization and preventing hydrocarbon of fatty acid tails from coming together and crystallization. = Phospholipids: 3-4 times more than inner-membrane. The Inter-membrane Space * = Several Enzymes : using ATP for nucleotide phosphorylation = Cytochrome C: shuttling electrons from complex III complex IV. and it has the ability to be converted into from ferric to ferrous and vise verca 16  Inner Mitochondrial Membrane * Thicker, with more proteins and less lipids ratio than outer-membrane. * The protein : lipid ratio ~~~ 4:1. * PROTEINS= Complexes: I, II, III, IV, Cytochromes and Ubiquinone that carrying out the oxidation reactions. = Enzymes: α-glycerophosphate dehydrogenase, Succinate dehydrogenase, and ATP-synthetase: (active site). = Specific Transport Proteins, regulating the movements of metabolites in & out of the matrix. * LIPIDS= Phospholipid called Cardiolipin: responsible limited permeability of the inner membrane to the ions. * There is NO cholesterol. 17  The Matrix * Enzymes= for oxidation of pyruvate and fatty acids acetyl CoA =for oxidation of acetyl CoA CO2 + NADH + FADH2 (main source of e- ETC), in the TCA cycle. =for TCA cycle ,except succinate dehydrogenase. =for the synthesis of mitochondrial DNA, RNA and proteins. *Proteases for removal of leader sequence attached to proteins (from cytosol to matrix) *Catalase and Dismutase …(safety device) getting rid of free radicals *Mitochondrial DNA, RNA and ribosomes. *Calcium stored in the form of Ca3(PO4)2 Granules. 18  The Mitochondrial Functions 1) Production of energy (ADP ATP). 2) Oxidation of fatty acids and other lipids. 3) Formation of some unites of Cytochromes. 4) Production of heme in animals. iron 5) Regulation of the conc. of Ca++ (bring to matrix). 19  The Mitochondrial Functions  The Glyoxylate cycle: A modified form of TCA-cycle, associated with the conversion of acetate Oxaloacetate  Fatty Acid Chain Elongation: (Synthesis in ?)/ Contain certain enzymes catalyzing the elongation of saturated fatty acids; palmitic acid; by successive addition of acetyl CoA to COOH-end- (in SER, elongation by the addition of malonyl CoA)  SOD and Catalase: Protective enzymes 2O-2 + 2H+ SOD H2O2 + O2 H2O2 Catalase H2O + 1/2O2 20  The Mitochondrial Functions  Amphibolic and Anaplerotic Reactions: The intermediates of TCA- cycle can act in both catabolic and anabolic Replacing reactions that pathways compensate the depletion of Oxaloacetate concentrations functioning in TCA-cycle 21 FADH2 22 23  Ribosomes (R) The Genetic Code Reader Ribosomes, because of RNA content. Two subunits, its sedimentation coefficient 80S (40S and 60S). Called protein factories. Cells have high rates of protein synthesis contain large number of ribosomes.. Formed in the nucleolus, in nuclear organizer region (NOR), then pass through the nuclear pores to reach the cytoplasm. 24  Chemical Structure Made of ribosomal RNA, rRNA (60%) and protein (40%). CHO and lipids are absent. Mg++ play an important role in maintaining its structure. Large subunit contains 40 type of proteins. Small subunit contains (28S, 5.8S, and 5S RNAs). 5.8S and 28S are transcribed in the 30 type of proteins. NOR. 18S RNA (transcribed in the The gene of the 5S RNA is outside the NOR) NOR. 25  Assembly of Ribosomes 1. 45S RNA molecule: a high molecular weight precursor of 18S, 5.8S and 28S RNAs + spacer sequences. 2. 45S + protein a giant ribonucleicprotein complex, RNP complex. 3. During processing, certain protein are released Ribosomal proteins, Nuclear proteins, become part of the reutilized completed subunits 26  Assembly of Ribosomes 4. RNP complex+ enzymes 3 fragments About ½ of the complex = spacer and 18S RNA+ 41S fragment nuclear proteins r-protein (28S+5.8S+r-proteins) Hydrolyzed Small, 40S and reutilized subunit Combined with 5S,an extranuclear rRNA, Large, 60S subunit 5. The final steps of ribosome maturation occur in the cytoplasm??? 27  Assembly of Ribosomes Ribosomal proteins are synthesized in the cytoplasm, then re-enter the nucleus. Complete assembly of r-subunits takes about An hour for the ½ an hour for larger subunit smaller subunit 28 Morphology of Ribosomes 29  Types of Ribosomes 1) Free ribosomes: Concerned with the synthesis of structural proteins (growth proteins), that will be in the cytosol. 2) Bound ribosomes: Bounded to nuclear envelop or rER membranes. Concerned with the synthesis of membrane-bound or secretory proteins. Ex: plasma proteins in the liver cells Thyroglobulin in thyroid gland cells. Lysosomal and peroxisomal enzymes.  Interestingly enough, free and bound ribosomes are interchangeable and the cell can change their numbers according to metabolic needs.  As one ribosome released at the end of mRNA, a new one is attached at the beginning of the message? 30  Mitochondrial Ribosomes Mitochondria contain its own ribosomes. Either free in the matrix or attached to the membrane of the cristae. Are smaller than the cytoplasmic ribosomes. Have sedimentation coefficient = 50-60S. Contain only two species of rRNA, and lesser proteins. 31 32 33  The endomembrane system A series of membranous organelles that work together and communicate by means of transport vesicles. Consists of Several types of Nuclear vesicles envelop Endoplasmic Reticulum Golgi 34 apparatus 35 36  Microbodies Heterogeneous group of small vesicle-like organelles. Mostly, concerned with oxidation. Usually, spherical or oval, bounded by a single membrane. 37 Peroxisomes 38  Peroxisomes  Generate H2O2 (both use and destruction).  About 0.5–1.5 µm in size.  Numerous (1∕4 mitochondria).  Increase in number by splitting.  Like the mitochondria, they are the major sites of oxygen utilization.  Abundant specially in kidney and liver cells. 39  Peroxisomes  STRUCTURE: A single smooth membrane-bounded organelles, specialized for metabolic oxidation.  Rich in enzymes that catalyze oxidation reactions such as peroxidase , acid oxidase and …..  The main source of 3 enzymes, D-a.a oxidase, , urate oxidase & catalase.  ORIGEN: by budding from SER.  Their enzymes and particular membrane are synthesized in RER.  Some enzymes (urate oxidase) are synthesized by free ribosomes & transported by specific recognition processes of peroxisomal membrane. 40  Peroxisomes  NUMBER: vary according to the cell type and circumstances of the body.  Abundant specially in kidney and liver cells.  Few in yeast cells grow in sugar solution.  Numerous in yeast cells grow in fatty acid solution (fatty as actyle CoA), and methanol.  20 min. after phenobarbital inj. SER & peroxisomes are numerous, ….. After detoxification the excess are removed by lysosomes. 41  Peroxisomes FUNCTION:  Fatty acid oxidation actyle CoA, that enter to mitochondria for sharing in Krebs cycle.  Detoxification: by oxidation using molecular oxygen H2O2 oxidation reactions are catalyzed by urate oxidases & a.ac. oxidase (RH2 + O2 R + H2O2 //// H2O2+ R-H2 R-+H2O).  Breakdown excess of purines (AMP,GMP) to uric acid.  Participate in the synthesis of cholesterol, bile acids and lipids used in myelin. 42  Resemblance between Peroxisomes and mitochondria  Oxygen utilization: (Consume 20% of oxygen in liver cells).  Fatty acid oxidation into acetyle CoA (1∕4 - 1∕5)  Presence of catalase: (prevent H2O2 accumulation).  Production of glyoxylates glycine mitochondria Incorporated into heme Another a.ac. 43  Lysosomes Membranous sacs, bounded by single smooth membrane Contain ≈ 60 hydrolytic enzymes that act in acid medium(pH 5-6) (intracellular digestion). Excessive leakage of lysosomes can destroy the cell by Auto-digestion. Originate by budding from Golgi complex.  Functions:  Aid in cell renewal.  Break down old cell parts.  Digests invaders. 44  Lysosomes  Intracellular digestion: 1) Heterophagy: Engulf and destroy foreign antigen by phagocytosis “recognition mechanism” – important in feeding in protozoa, and in body defense in metazoa. 2) Autophagy: 1ry lysosome+ old or damaged organelle autophagosome.  half life of liver mitochondria is about 10 days. 45  Lysosomes Autolysis: As the cell died, the lysosomal membranes are ruptured and Sooner, the lysosomal enzymes are discharged to digest the cell contents. e.g. the cells of the tail in tadpole larva.. Extracellular Digestion:  The lysosomal enzymes are discharged outside the cell by exocytosis to digest particles outside the cell. e.g bone remodeling. 46  Lysosomes  Intracellular digestion: Lysosomes can digest substances either: From outside the cell taken by endocytosis (heterophagy). From inside the cell as damaged organelles (autophagy). 47  Lysosomes Lysosomal membrane: 1) Resist the digestion: The lysosomal membrane on the inner side is lined with heavily glycosylated LMPs (lysosome associated membrane proteins), which protect the membrane from self-degradation by lysosomal hydrolases 2) Impermeable to both the enzymes and substrates. 3) Permeable to the final products digestion to excreted or reutilized by the cell. 4) Contain ATP-dependent proton (H+) pump that responsible for the internal acidic environment of lysosomes, in order to maintain the pH of the lumen at 5. 48  Lysosomes Types of Lysosomes: 1) Primary lysosomes: pure, original and newly formed, containing pure hydrolytic enzymes but no substrate. (a) Phagocytosis 2) Secondary lysosomes: formed when primary lysosomes fuse with phagosomes/endosome. 49 (b) Autophagy  Acrosome development in sperm (involvements in the formation of a cellular organelles ) Acrosome= membrane bound structure at the anterior end of the sperm cells. Contains= hydrolytic enzymes (hyaluronidase is the most important for egg penetration). Has been suggested as a Giant Lysosome. As the acrosome grows, the Golgi body becomes reduced in size, and may disappears entirely in many mature sperms. 50 Fate of Secondary Lysosomes:  Secondary lysosomes can be recycled  Contain : useful substances + useless wastes  Accumulated 2ry lysosomes with wastes = Residual Bodies.  Residual Bodies in a cell indicates cell senility.  Residual bodies in the cells of Lower invertebrates =exocytosed Higher organisms= accumulated & interfered with the normal activities of the cell, resulting in cell death. 51  Distribution of Lysosomes: According to the cell type Few: muscle cell, acinar cells Very numerous: in WBCs of pancreas Numerous: in kidney, intestine, lung, uterus & reticulo-endothelial system 52  Lysosomal Enzymes: enzymes Substrate  Proteases  proteins  Nucleases  Nucleic acids  Glycosidases  Polysaccharides  Lipases  Lipids  phosphatases  Organic- linked phosphates 53 Lysosomes and diseases: A) Lung diseases: 1. Silicosis: inhalation of silica particles ”taken up by phagocytes” silica+phagocytic membrane rupture stimulation of fibroblasts fibrosis. (used in the glass, construction, ceramics, paints, plastics, rubber and the chemical industry,, also, silica sand is used in water filtration and agriculture.) 2.Asbestosis: inhalation of asbestos fibers. (most commonly used materials in industries such as construction, shipbuilding.) 3. Black Lung disease: breathing in coal dust. 54 B. Lysosomal Storage Diseases Lacking of certain hydrolytic enzymes needed for the breakdown of macromolecules (proteins, polysaccharides, lipids or nucleic acids). Usually due to a defect in gene encoding. The accumulation of these macromolecules can interfere with other activities of the cell. Neurons of the central nervous system are particularly susceptible to damage.. 55 B. Lysosomal storage diseases Pomp’s disease: absence of glycosidase. Tay-Sachs disease: absence of lipase. Hurler’s disease: massive accumulation of glycosaminoglycans,.…. absence of α-L-iduronidase 56 C. Inclusion (I) Cell Diseasse:  Deficiency in N-acetyl glucosaminyl phosphotranferase activity: no tagging with mannose-6-phosphate not recognized by Golgi-sorting machinery their secretion.  Absence of mannose-6-phosphate receptors from Golgi or plasma membrane escape from Golgi sorting process. 57  Inflammation, arthritis or auto immune diseases Lysosomal enzymes are released from phagocytes damage cell death. Cortisone and aspirin stabilize the lysosomal membrane reduce the tendency to abnormal enzyme release. Lysosomal rupture abnormal stimulation to mitosis development of tumors. 58 59 60  *The Nucleus *The control center of the cell. *Discovered by James Watson, Francis Crick, & Rosalind Franklin (1953). *Contain a complete set of all the instructions required for the construction of an individual organism and for proper functioning. *Enclosed by nuclear envelope= two membranes, the outer one is continuous with the rER. *Have pores, for material exchange. 61  *The Nucleus The nuclear matrix. One/or more nucleoli chromosomes , extended as nucleoprotein fibers, the chromatin. Nucleoplasm 62  The Chromatine: The structural representation of the chromosomes during interphase. Chromocenters a deeply stained nuclear area, as its chromosomes remain in the condensed state through the cell cycle. Euchromatin: lightly stained, dispersed = active, contain the structural genes. Heterochromatin: darkly stained, condensed = inactive, regulates gene expression. Constitutive heterochromatin permanently condensed, inactive Facultative heterochromatin dispersed active 63 64  Chemical Structure of Chromatin Consists of DNA + protein + few RNA, may also present. Most proteins are histonses. Nonhistones , serving as a catchall for other proteins. Histones contain high proportion of lysine and arginine (+vely charged a.ac)?? Histonses= five types,H1, H2A, H2B, H3 and H4. H2A, H2B, H3 and H4 are nucleosomal histones. H1: responsible for packing the together. Histones : responsible for packing the long DNA molecule. Nucleosomes give the chromatin its “bead-on-a-string”. 65  Chemical Structure of Chromatin Nucleosome beads can be removed by nuclease enzyme. Each nucleosome (structural unite of chromosome) contains a set of 8 histones (2 copies), of H2A, H2B, H3 and H4 + 146 base pair of DNA. Linear DNA : a separating portion of DNA between the nucleosomes = 60 base pair of DNA. 66  Chromatin Fibers Nucleosomes are packed together forming a regular higher-order structure to generate regular arrays of highly condensed DNA of 30 nm chromatin fibers. H1molecules are responsible for packing nucleosomes into the 30 nm chromatin fibers. 67  The Chromatosome The linker DNA + histone H1 68  The Solenoid Chromatin fibers arranged in diameter of 10 nm /and 30 nm. 10 nm= linear array of nucleosomes 30 nm= helical coiling of 10 nm fibers as 6 nucleosomes / turn by the aid of histone H1. Successive turns form a structure called a solenoid 69  Supercoiling 1. The first level= the coiling of 2 polypeptide chains of DNA to form the conventional double-helix structure. 2. The second level= the double-helix wound around the histone core making nucleosomes. 3. The nucleosomes are arranged into solenoid. 4. The solenoid are arranged in loops each of 36,000 base pair = 315 nucleosomes. 5. Human cell containing about 1 m length of 70 DNA, arranged in 50,000 loops / nucleus. 71  The Nucleolus A ribosome-producing machine. Contains loops of DNA having rRNA genes in the NOR. 3 2 Has no membrane 1 Distinguished into 3 regions: 1- A pale-staining component: contains DNA of the NOR. 2- A granular component: contains 15 nm particles of mature ribosomal precursor particles. 3- A dense fibillar component: many fin fibers of 5 nm ribonucleoprotein fibers (RNA transcripts) 72  The Nucleolus Its size reflects its activity. As the cell approaches mitosis, it decrease in size as the chromosomes condensed and no need for RNA synthesis. In human, ribosomal genes are near the tips of 5 different chromosomes (n),10 chromosomes of diploid (2n) cells:13, 14, 15, 21, & 22. 73  The Nuclear Envelope Two membranes separated by 20-40 nm of perinuclear space. The outer membrane is continuous with the ER and have ribosomes. The connection of the membranes of the nucleus and ER facilitates the growth, expand, breakdown and reformation of the nuclear membrane. The two membranes are continuous at the regions of the nuclear pores. The double membrane system maintain double interaction between the contents of the nucleoplasm and cytoplasm. 74  The Nuclear Lamina An electron-dense layer on the nucleoplasmic side of the inner nuclear membrane. Play a critical role in maintaining and organizing both, the nuclear envelope and the underlying chromatin. STRUCTURE: composed of a fibrous meshwork containing specialized proteins that form pores in the nuclear membrane. Are of 3 major proteins bind to a specific integral protein of the membrane. 75  The Nuclear Lamina FUNCTION: 1- Outer surface: play an important role in holding the nuclear pores in place and shaping the nuclear envelope. 2- Inner surface: holding and organizing the interphase chromosomes inside the nucleus. 76  Nuclear Transport and Nuclear Pores The nuclear pore complex: a large supramolecular structure surround the nuclear pores, organized and held in place by the nuclear lamina. The complex is defined by 8 large protein granules arranged in octagonal pattern. Act as channel for water soluble molecules 9 nm diameter/ 15 nm long. Small particles pass rapidly, the larger takes variable time. A typical mammalian cell contains 3000-4000 pore complexes- 11 pore/ square µm of membrane area. 77  Nuclear Transport and Nuclear Pores A cell synthesizing DNA needs 103 histone molecules from cytoplasm/3 mins = 100 histone mole/min/pore. In rapidly growing cell need 3 assembled ribosomes/ pore to the cytoplasm. Large ribosomal subunit (15 nm), and large molecules such as DNA and RNA polymerasees (100,000/200,000 Daltons)may transported by active transport / or special receptor proteins on the pore margin. Annulated lamellae 78  The Nucleoplasm A fluid substance in which the solutes of the nucleus are dissolved. Proteinic in nature, containing some RNA and a number of hydrolytic enzymes. The Nuclear Matrix It is a protein-containing fibrillar net work. Involved in regulation of transcription and replication processes and contains binding sites for some hormones affecting these processes. Concerned with the processing of newly synthesized RNA molecules. 79 80