Dentistry 2024-2025 Organelles PDF

MEDICAL BIOLOGY AND GENETICS Organelles Week 9 – 20.11.2024 Dr. Ceyhan Ceran Serdar – 2024 Reference Books  Online References Cell Organelles - Part 1 | Animation Video | Iken Edu: https://youtu.be/ZyWYID2cTK0 Cell Orga...

MEDICAL BIOLOGY AND GENETICS Organelles Week 9 – 20.11.2024 Dr. Ceyhan Ceran Serdar – 2024 Reference Books  Online References Cell Organelles - Part 1 | Animation Video | Iken Edu: https://youtu.be/ZyWYID2cTK0 Cell Organelles And Their Function Animation (BOTH 3D AND MICROSCOPIC VIEWS ) : https://www.youtube.com/watch?v=fKEaTt9heNM Biology: Cell Structure I Nucleus Medical Media: https://www.youtube.com/watch?v=URUJD5NEXC8&feature=emb_rel_pause Mitochondria: https://www.youtube.com/watch?v=vkYEYjintqU Mitochondria:https://www.youtube.com/watch?v=39HTpUG1MwQ Chloroplasts: https://www.youtube.com/watch?v=YeD9idmcX0w Inner Life Of the Cell: https://www.youtube.com/watch?v=wJyUtbn0O5Y Intermediate Filaments: https://www.youtube.com/watch?v=ll5MSxxHSCQ Cytoskeletal Structure and Function: https://www.youtube.com/watch?v=YTv9ItGd050 Muscle Contraction: https://www.youtube.com/watch?v=sZuy356qkPM Microfilaments: https://www.youtube.com/watch?v=VVgXDW_8O4U Cell-ECM Interactions – through integrin: https://www.youtube.com/watch?v=LajvidhBK2Y Cell Junctions: https://www.youtube.com/watch?v=gJ9WTD0XEnc Cell Junctions: https://www.youtube.com/watch?v=gJ9WTD0XEnc Cell Junctions: https://www.youtube.com/watch?v=ARaj3Kz1cCQ  Learning Outcomes 1. Describe what a cell is and list the basic characteristics of cells. 2. Explain why eukaryotic cells use organelles. 3. Describe the terms cytoplasm and cytosol. 4. Compare animal cell and a plant cell and list the structures unique to each. 5. Describe the structure of ribosomes, list and briefly explain the functions of ribosomes. 6. Describe the structure of mitochondria, list and briefly explain the functions of mitochondria. 7. Describe the structure of chloroplasts, list and briefly explain the functions of chloroplasts. 8. List the components of endomembrane system. 9. Explain how endomembrane system regulates protein traffic and performs metabolic functions. 10. Describe the structures of rough ER and smooth ER, list and briefly explain their functions. 11. Describe what is pharmacogenetics. 12. Describe the role of Smooth ER in drug metabolism, explaining the contrasting outcomes in terms of toxicity and drug tolerance. 13. Describe the role of Smooth ER in carbohydrate metabolism, and in regulation glucose levels. 14. Describe the role of Smooth ER in calcium storage. 15. Explain the steps of membrane biosynthesis taking place in the ER. 16. Define the Golgi-structure, list and briefly explain the functions of Golgi. 17. Describe the structure of lysosomes, list and briefly explain the functions of lysosomes. 18. Describe the structure of peroxisomes, list and briefly explain the functions of peroxisomes. 19. List and briefly explain the functions of vacuoles in animal cells. 20. List different types of cytoskeletal elements found in cells; describe their structure and explain their functions. 21. List different components of Extracellular Matrix (ECM) found in animal and plant cells; describe their structure and explain their functions. 22. List different types of cell-cell attachments found in animal and plant cells, explaining their main function and the associated structures present in each junction type.  You Are Here Compartmentalization in a Eukaryotic Cell Nucleus Ribosomes Endomembrane System  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane Peroxisomes Mitochondria Chloroplasts Cytoskeletal Elements Extracellular Matrix Cell-Cell Attachments  Working Cell Neil A. Campbell, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky Biology: A Global Approach, Global Edition (12th Edition) Chapter:7 2020 Boston: Benjamin Cummings / Pearson.  Working Cell Neil A Campbell; Michael L Cain; Peter V Minorsky; Jane B Reece; Lisa A Urry Biology (Global Approach) (11th Edition) 2018 Boston: Benjamin Cummings / Pearson. Sizes of Cells and Their Compartments Karp's Cell and Molecular Biology: Concepts and Experiments, 8th Edition Chapter 1, 2015 Wiley  You Are Here Compartmentalization in a Eukaryotic Cell Nucleus Ribosomes Endomembrane System  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane Peroxisomes Mitochondria Chloroplasts Cytoskeletal Elements Extracellular Matrix Cell-Cell Attachments  The Need for Adequate Concentrations of Reactants and Catalysts For a reaction to occur, the appropriate reactants must collide with and bind to a particular enzyme The frequency of such collisions is greatly increased by higher concentrations of enzymes and reactants As cell size increases, the number of molecules increase proportionately with volume Eukaryotic Cells Use Organelles to Compartmentalize Cellular Function A solution to the concentration problem is the compartmentalization of activities within specific regions of the cell Most eukaryotic cells have a variety of organelles, membrane-bounded compartments that are specialized for specific functions e.g. cells in a plant leaf have most of the materials needed for photosynthesis compartmentalized into structures called chloroplasts Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 7 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Geometric relationships between surface area and volume Metabolic requirements set upper limits on the size of cells The surface area to volume ratio of a cell is critical As the surface area increases by a factor of n2, the volume increases by a factor of n3 Small cells have a greater surface area relative to volume Figure 7.7 Geometric relationships between surface area and volume. In this diagram, cells are represented as boxes. Using arbitrary units of length, we can calculate the cell’s surface area (in square units, or units2), volume (in cubic units, or units3), and ratio of surface area to volume. A high surface-to-volume ratio facilitates the exchange of materials between a cell and its environment. Neil A Campbell; Michael L Cain; Peter V Minorsky; Jane B Reece; Lisa A Urry Biology (Global Approach) (11th Edition) Chapter:7 2018 Boston: Benjamin Cummings / Pearson. The Cytoplasm of Eukaryotic Cells Contains the Cytosol and Cytoskeleton The cytoplasm of a eukaryotic cell is the interior of the cell not occupied by the nucleus The cytosol is the semifluid substance in which the organelles are suspended These take place in the cytosol  synthesis of fats  synthesis of proteins  the initial steps in releasing energy from sugars The cytosol is permeated by the cytoskeleton Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Protoplasm, Cytoplasm, Cytosol https://www.youtube.com/watch?v=TptsLsxc2lQ  Tour of an Animal Cell Neil A. Campbell, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky Biology: A Global Approach, Global Edition (12th Edition) Chapter:7 2020 Boston: Benjamin Cummings / Pearson. Tour of an Plant Cell Neil A. Campbell, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky Biology: A Global Approach, Global Edition (12th Edition) Chapter:7 2020 Boston: Benjamin Cummings / Pearson. Silli, bazı hayvan hücrelerinde bulunan, Endoplazmik retikulum, zarla çevrili kese ve tüplerden Çekirdekçik, ribozom üretiminde yer alan, zarla çevrili olmayan bir yapıdır ve çekirdek, bir veya daha fazla çekirdekçik içerir. plazma zarı uzantısı oluşan, membran sentezi ve diğer sentetik ve Kromatin, DNA ve proteinlerden oluşan bir maddedir ve bölünen hücrede, bireysel olarak yoğunlaşmış kromozomlar şeklinde içinde mikrotübüllerden oluşan bir kümeye sahip metabolik süreçlerde aktif olan bir ağdır. Hem pürüzlü görülebilir. olan, hareket yeteneği ribozomlarla kaplı hem de düz bölgeleri vardır. sağlayan bir yapıdır. A Panoramic View of an Animal Cell - A eukaryotic cell has internal membranes that partition the cell into organelles Plant and animal cells have most of the same organelles Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson. A Panoramic View of a Plant Cell Vakuol, hücre içinde bulunan ve genellikle sıvı ile dolu olan, zarla çevrili büyük bir kesedir. Bitki hücrelerinde, su, besin maddeleri, atıklar ve pigmentler gibi maddeleri depolamak, hücreyi turgor basıncı ile desteklemek ve atık maddeleri zararlı hale gelmeden depolamak gibi işlevlere sahiptir. Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson.  Animal Cells vs Plant Cells 3. Sitozkeleton lifleri, hücresel zarı destekleyen, organelleri organize eden ve hücre hareketine katılan ağlar ve demetler oluşturur. Rough endoplazmik retikulum, 4. salgılanan proteinlerin, lizozomal Mikrovilluslar, çevredeki proteinlerin ve bazı membran ortamdan besin maddelerinin proteinlerinin sentezi, işlenmesi emilimi için yüzey alanını artırır. ve sıralanmasında görev alır. 5. Hücre duvarı, Golgi kompleksi, pürüzlü büyük ölçüde selülozdan oluşur, endoplazmik retikulumda hücrenin şeklini korumaya sentezlenen salgılanan yardımcı olur ve mekanik strese proteinleri, lizozomal proteinleri karşı koruma sağlar. ve membran proteinlerini işler ve 6. Vakuol, su, sıralar. iyonlar ve besin maddelerini depolar, makromolekülleri parçalar ve büyüme sırasında hücre tonusunda işlev görür. 7. Kloroplastlar, fotosentez yapan organellerdir, çift katmanlı zarla çevrilidir ve iç membranlardan oluşan bir ağ olan tilakoitleri içerir. 8. Plazmodesmata, hücre duvarını aşan ve bitki hücrelerinin komşu sitoplazmalarını birbirine bağlayan hücre bağlantılarıdır. Exploring Eukaryotic Cells Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson.  Eukarya Protistler, çoğunlukla tek hücreli ökaryotlardır ve bazıları nispeten basit çok hücreli akrabalara sahiptir. Burada, gölet suyunda yaşayan protistlerin bir karışımı yer almaktadır. Bilim insanları, protistleri evrimsel ilişkilerini doğru şekilde yansıtan bir şekilde nasıl sınıflandıracaklarını tartışmaktadır This domain includes three kingdoms of multicellular eukaryotes: kingdom Plantae: Multicellular, produce their own sugars and other food molecules by photosynthesis. kingdom Fungi: can be single celled or very complex multicellular, absorb dissolved nutrients from their surroundings; many decompose dead organisms and organic wastes (such as leaf litter and animal feces) and absorb nutrients from these sources. kingdom Animalia: obtain food by ingestion, which is the eating and digesting of other organisms. kingdom Protists: Single-celled eukaryotes, numerous and diverse and are more closely related to multicellular eukaryotes such as animals and fungi than they are to each other (some do photosynthesis). Neil A Campbell; Michael L Cain; Peter V Minorsky; Jane B Reece; Lisa A Urry Biology (Global Approach) (11th Edition) Chapter:1 2018 Boston: Benjamin Cummings / Pearson. Protista Krallığı: Tek hücreli ökaryotlar, sayıca çok ve çeşitlidir ve birbirlerine göre hayvanlar ve mantarlar gibi çok hücreli ökaryotlarla daha yakından ilişkilidir (bazı protistler fotosentez yapar).  You Are Here Compartmentalization in a Eukaryotic Cell Nucleus Ribosomes Endomembrane System  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane Peroxisomes Mitochondria Chloroplasts Cytoskeletal Elements Extracellular Matrix Cell-Cell Attachments  Presence of a Membrane-Bounded Nucleus A eukaryotic cell has a true, membrane bounded nucleus The nuclear envelope consists of two membranes The nucleus also includes the nucleolus, the site of  ribosomal RNA synthesis and  ribosome assembly The genetic information of a bacterial or archaeal cell is folded into a compact structure called the nucleoid and is attached to the cell membrane Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 7 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The Nucleus: Information Central The nucleus contains most of the DNA in a eukaryotic cell Ribosomes use the information from the DNA to make proteins The nucleus contains most of the cell’s genes and is usually the most conspicuous organelle The nuclear envelope encloses the nucleus, separating it from the cytoplasm The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  The Nucleus: Information Central Pores regulate the entry and exit of molecules from the nucleus The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein In the nucleus, DNA is organized into discrete units called chromosomes Each chromosome is composed of  a single DNA molecule  associated with proteins The DNA and proteins of chromosomes are together called chromatin Chromatin condenses to form discrete chromosomes as a cell prepares to divide The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson.  Organization of DNA Bacterial DNA is present in the cell as a circular molecule associated with few proteins Eukaryotic DNA is organized into linear molecules complexed with large amounts of proteins called histones Archaeal DNA is circular and complexes with proteins similar to eukaryotic histone proteins Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 7 Pearson Education, Inc., publishing as Pearson Benjamin Cummings “Kompleksleşmek,” bir veya daha fazla molekülün bir araya gelerek daha karmaşık bir yapı oluşturması anlamına gelir. Bu, özellikle biyolojik bağlamda, proteinlerin veya diğer moleküllerin birbirleriyle etkileşime girerek bir kompleks (birleşik yapı) oluşturmasını ifade eder. Örneğin, DNA’nın histonlarla kompleksleşmesi, DNA’nın histon proteinleriyle birleşerek daha düzenli ve sıkı bir yapı oluşturmasıdır.  DNA packaging The circular DNA of bacteria or archaea is much longer than the cell itself and so must be folded and packed tightly, equivalent to packing about 60 feet of thread into a thimble Most eukaryotic cells have more than 1000 times more DNA than prokaryotes and encode only 5-10 times more proteins The excess noncoding DNA has been referred to as junk DNA but may have important functions in gene regulation and evolution DNA packaging The problem of DNA packaging is solved among eukaryotes by organizing the DNA into chromosomes Chromosomes contain equal amounts of histones and DNA Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 7 Pearson Education, Inc., publishing as Pearson Benjamin Cummings https://en.wikipedia.org/wiki/Human_genome  Chr 1: ~200.000.000 bp ~2.000 gene ~1.500 pseudogene Each gene: ~10.000 – 20.000 bp Chr 1: ~ 40.000.000 bp gene-coding region ~ 30.000.000 bp gene-coding region Pseudogen, işlevsel olmayan ve genellikle bozulmuş bir gen kopyasını ifade eder. Bu kopyalar, orijinal genin benzerini taşır ancak mutasyonlar veya diğer genetik değişiklikler nedeniyle fonksiyonel protein üretme yeteneğini kaybetmişlerdir. Pseudogenler, evrimsel süreçler sonucu ortaya çıkabilir ve bazıları geçmişte işlevsel olan genlerin artık işlevsiz hale gelmiş kopyalarıdır. https://en.wikipedia.org/wiki/Human_genome.  Fig. 2 Number of LCNS (long conserved noncoding sequences) on each chromosome. The size of LCNS extractable genomic sequences (noncoding and nonrepetitive sequences) and number of LCNS extracted from human. The total bp of coding and repetitive sequences (upper white bars) and noncoding and nonrepetitive sequences (lower gray bars) are shown for each chromosome. The total bp (left axis) represents the length of each chromosome. The numbers of LCNS on each chromosome are indicated by the black dots and numbers on the right axis. https://en.wikipedia.org/wiki/Human_genome. Şekil 2: Her kromozomda bulunan uzun korunan kodlamayan dizilerin (LCNS) sayısı. İnsan genomundan çıkarılabilen LCNS dizilerinin boyutu Mamm Genome (2008) 19:703–712 (kodlamayan ve tekrarsız diziler) ve çıkarılan LCNS sayısı. Her kromozom için kodlayan ve tekrarlayan dizilerin toplam baz çiftleri (üst beyaz çubuklar) ve kodlamayan ve tekrarsız dizilerin toplam baz çiftleri (alt gri çubuklar) gösterilmiştir. Toplam baz çiftleri (sol eksen), her kromozomun uzunluğunu temsil eder. Her kromozomdaki LCNS sayıları, sağ eksendeki siyah noktalar ve sayılarla belirtilmiştir.  Nuclear Proteins Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  You Are Here Compartmentalization in a Eukaryotic Cell Nucleus Ribosomes Endomembrane System  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane Peroxisomes Mitochondria Chloroplasts Cytoskeletal Elements Extracellular Matrix Cell-Cell Attachments  Ribosomes: Protein Factories Ribosomes are particles made of ribosomal RNA and protein Ribosomes carry out protein synthesis in three locations – In the cytosol (free ribosomes) – On the outside of the endoplasmic reticulum or – On the nuclear envelope (bound ribosomes) Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  Ribosomes: Protein Factories Ribosomes are not really organelles because they are not enclosed by a membrane They are found in all cells but differ slightly in bacteria, archaea and eukarya in their size and composition Each cell type has a unique type of ribosomal RNA Ribosomes are very small Ribosomes can only be seen under the electron microscope They have sedimentation coefficients in keeping with their small size Sedimentation coefficient: a measure of how rapidly a particle sediments in an ultracentrifuge, expressed in Svedberg units (S) Ribosomes have values of  80S (eukaryotes) or  70S (bacteria and archaea) Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 21 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Ribosome subunits Ribosomes have two subunits, the large and small subunits, with sedimentation coefficients of 60S and 40S respectively (for eukaryotes) Bacteria and archaea have large and small subunits of 50S and 30S, respectively The S values of large and small subunits does not add up to the value for the complete ribosome, because S values depend on both size and shape Ribosome are numerous and ubiquitous Ribosomes are much more numerous than most other cellular structures (prokaryote cells contain thousands, eukaryote cells may contain millions) Ribosomes in mitochondria and chloroplasts are similar size and composition to those of bacteria This is particularly true of the nucleotide sequences of their rRNAs Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 21 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  You Are Here Compartmentalization in a Eukaryotic Cell Nucleus Ribosomes Endomembrane System  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane Peroxisomes Mitochondria Chloroplasts Cytoskeletal Elements Extracellular Matrix Cell-Cell Attachments  Endomembrane System An appreciation of eukaryotic cells depends on understanding the role of intercellular membranes and the compartmentalization of function within organelles Movement of lipids and proteins between organelles (called trafficking) must be tightly regulated The endomembrane system regulates protein traffic and performs metabolic functions in the cell Components of the endomembrane system – Nuclear envelope – Endoplasmic reticulum – Golgi apparatus – Lysosomes – Vacuoles – Plasma membrane These components are either continuous or connected via transfer by vesicles Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter:12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Plasma Membrane Plasma membrane  provides protection for a cell  provides a fixed environment inside the cell.  transport nutrients into the cell and also transports toxic substances out of the cell.  has proteins on it which interact with other cells.  the proteins which stick outside of the plasma membrane will allow for one cell to interact with another cell.  provides some structural support for a cell https://www.genome.gov/genetics-glossary/Plasma-Membrane#:~:text=The%20plasma%20membrane%2C%20or%20the,substances%20out%20of%20the%20cell.  Nuclear Membrane The nucleus contains most of the genetic material for a eukaryotic cell, but this genetic material needs to be protected. Nucleus is protected by the nuclear membrane, which is a double membrane that encloses all the nuclear genetic material and all the other components of the nucleus. There are some small holes or pores that are in the nuclear membrane that allow the messenger RNA and the proteins to move between the nucleus and the cytoplasm. But the nuclear membrane is regulating what material should be in the nucleus in contrast to what material should be in the cytoplasm. https://www.genome.gov/genetics-glossary/Nuclear-Membrane  Endomembrane System The endoplasmic reticulum and the Golgi complex are sites for  protein synthesis, processing, and sorting  also lipid synthesis Endosomes  carry and  sort material brought into the cell Lysosomes  digest ingested material and unneeded cellular components Vacuoles  temporary storage  transport  turgor pressure  and some hydrolytic functions Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The Endoplasmic Reticulum The endoplasmic reticulum (ER) is a continuous network of flattened sacs, tubules, and vesicles through the cytoplasm of a eukaryotic cell  The membrane-bound sacs are called ER cisternae,  The space inside them is the ER lumen The enzymes associated with the ER are involved in synthesis of proteins for  Incorporation into the plasma membrane  Organelles of the endomembrane system  Export from the cell The ER is also involved in lipid synthesis Biyoloji alanında entegrasyon, genellikle farklı biyolojik sistemlerin veya bileşenlerin bir araya gelerek bir bütün olarak işlev görmesi anlamında kullanılır. Bu, hücresel, organizmalık veya ekolojik düzeyde olabilir. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings https://studiousguy.com/smooth-endoplasmic-reticulum-structure-functions-and-diagram/  The Two Basic Kinds of Endoplasmic Reticulum Differ in Structure and Function Rough endoplasmic reticulum (rough ER) is characterized by ribosomes on the cytosolic side of the membrane A subdomain of rough ER, the transitional elements (TEs) plays a role in the formation of transition vesicles that  shuttle lipids and proteins from the ER to the Golgi complex Smooth ER lacks ribosomes and has other roles in the cell Rough ER membranes form large flattened sheets Smooth ER membranes form tubular structures Transitional elements of the rough ER are an exception; they resemble the smooth ER The lumenal spaces of rough and smooth ER are continuous Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Variation in Amounts of Rough and Smooth ER Both types of ER are present in most eukaryotic cells, but there is variation in the relative amounts Cells involved in synthesis of secretory proteins have prominent rough ER networks Cells producing steroid hormones tend to have extensive networks of smooth ER The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells The ER membrane is continuous with the nuclear envelope There are two distinct regions of ER – Smooth ER, which lacks ribosomes – Rough ER, surface is studded with ribosomes Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Rough ER vs Smooth ER Smooth endoplasmic reticulum found within muscle is known as the sarcoplasmic reticulum and serves a specialised function. Functions of Rough ER Functions of Smooth ER The rough ER The smooth ER – Has bound ribosomes, – Synthesizes lipids – Secrete glycoproteins (proteins covalently – Metabolizes carbohydrates bonded to carbohydrates) – Detoxifies drugs and poisons – Distributes transport vesicles, proteins – Stores calcium ions surrounded by membranes – Is a membrane factory for the cell Reece, J. B., & Campbell, N. A. (9th Edition). Campbell biology. Chapter: 6 Boston: Benjamin Cummings / Pearson.  The Endoplasmic Reticulum: Biosynthetic Factory Rough ER Is Involved in the Biosynthesis and Processing of Proteins Ribosomes on the cytosolic side of the rough ER membrane synthesize both membrane-bound and soluble proteins for the endomembrane system Newly synthesized proteins are inserted into the endomembrane system through a pore complex as they are synthesized (cotranslationally) Rough ER is the site for  The initial steps of addition of carbohydrates to glycoproteins  The folding of polypeptides  Recognition and removal of misfolded proteins  Assembly of multimeric proteins Rough ER Has a Role in Quality Control  In ER-associated degradation (ERAD), proteins that are incorrectly folded, modified, or assembled are exported for degradation  Degradation occurs in cytosolic proteasomes Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Properties of Rough ER The rough endoplasmic reticulum is a part of the endomembrane system that is present in the cytoplasm of the cell. The organelle is involved in the  synthesis,  folding,  modification, and  transport of proteins to different organelles within the cell or outside of the cell. The name ‘rough’ ER is given due to the appearance of ribosomes on the surface as appears under the microscope. Found both in plant and animal cells, the RER membrane is continuous with the nuclear membrane. It is usually located near the Golgi apparatus, and the protein synthesized in the ribosomes on RER are packaged into vesicles and transported to the Golgi body. https://microbenotes.com/rough-vs-smooth-endoplasmic-reticulum/  Properties of Rough ER Modifiye etmek, bir şeyin değiştirilmesi Rough ER is closely associated with the formation of lysosomes. veya düzeltilmesi anlamına gelir. Biyolojik ve kimyasal Rough ER also plays a significant role in quality control during the folding of the bağlamda, bir proteins where the ratio of sheets to tubules is changed when the quantity of molekülün yapısal unfolded proteins increases in the cell. veya kimyasal özelliklerinin değiştirilmesiyle ilgili Sometimes, apoptosis is initiated in the cell as a result of the increase in the bir terimdir. Bu content of unfolded proteins. değişiklikler, genellikle bir Similarly, rough ER also contains multiple enzymes that are involved in RNA molekülün metabolism that function to bind and modify RNA. fonksiyonunu, aktivitesini veya etkileşimlerini However, different diseases might result from the misfolding of proteins in RER. düzenlemek amacıyla yapılır.  Disease like spondyloepimetaphyseal dysplasia is attributed due to the accumulation of misfolded collagen proteins in the RER. https://microbenotes.com/rough-vs-smooth-endoplasmic-reticulum/  Smooth ER Smooth ER Is Involved in  lipid biosynthesis  oils  phospholipids  steroids  drug detoxification,  carbohydrate metabolism,  calcium storage Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Smooth ER - Drug Detoxification Drug detoxification often involves hydroxylation Adding hydroxyl groups to hydrophobic drugs  increases their solubility,  making them easier to excrete from the body Hydroxylation is catalyzed by a member of the cytochrome P-450 family of proteins, also called monooxygenases Hydroxylation Occurs via Electron Transport  Electrons from NADPH or NADH are transferred to a heme group in cytochrome P-450 INFORMATION  An electron is donated to O2, where one oxygen atom forms H2O BOX and the other is added to the substrate as a hydroxyl group Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Drug Tolerance - Drug Synergy Drug Tolerance Injection of phenobarbital into rats causes rapid increases in  the barbiturate-detoxifying enzymes and  a proliferation of smooth ER This means that higher doses of the drug are needed to achieve the same effect, a phenomenon known as tolerance The enzymes involved can decrease the effectiveness of other drugs as well Drug Synergy Synergy is an effect in which the combined effect of two substances is stronger than expected from just the sum of their individual effects Synergistic effects could lead to potential toxicity or lethality Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Smooth ER - Drug Metabolism Drug Detoxification in the Smooth ER Another cytochrome P-450 is part of a complex called INF aryl hydrocarbon hydroxylase, which metabolizes BOX polycyclic hydrocarbons The products can be more toxic than the original compounds; some are associated with spontaneous cancers in mice Cigarette smoke is a potent inducer of aryl hydrocarbon carboxylase Burada “indükleyici”, sigara dumanının aril hidrokarbon karboksilaz enziminin üretimini veya aktivitesini artıran bir faktör olduğunu ifade ediyor. Bu enzim, genellikle vücuda giren yabancı maddelerin (örneğin, kimyasalların veya toksinlerin) metabolize edilmesinde rol oynar. Ancak, bu aktivitenin artışı, metabolik süreçlerin yan ürünleri olarak daha toksik bileşiklerin oluşmasına neden olabilir. Dolayısıyla, sigara dumanı bu enzimi tetikleyerek hem kimyasal süreçleri hızlandırıyor hem de bu süreçlerin sonucu olarak zararlı etkiler doğurabiliyor. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Smooth ER - Drug Metabolism Pharmacogenetics Differences in activities and side effects of certain medications can result from differences in presence or activity of particular cytochrome P-450 genes in different patients A new field of study, called pharmacogenetics, investigates how inherited differences in genes and lead to differential responses to drugs and medications Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Smooth ER - Carbohydrate Metabolism Smooth ER in liver cells is involved in breakdown of stored glycogen;  it contains glucose-6-phosphatase, an enzyme unique to smooth ER Glucose-6-phosphatase hydrolyzes the phosphate from glucose-6-phosphate to form free glucose Regulation of Glucose  The liver stores glucose as glycogen in granules associated with smooth ER  When glucose is needed by the body, glycogen is broken down by phosphorolysis, producing glucose-6-phosphate  This must be converted to free glucose in order to leave the cell and enter the bloodstream Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings INFORMATION Smooth ER - Carbohydrate Metabolism BOX Buradaki “stepwise”, işlemin adım adım, kademeli bir şekilde gerçekleştiğini ifade ediyor. Yani, karaciğer glikojeninin parçalanması bir anda değil, bir dizi ardışık kimyasal reaksiyonla aşamalı olarak gerçekleştiriliyor. FIGURE 12-3 The Role of the Smooth ER in the Catabolism of Liver Glycogen. (a) This electron micrograph of a monkey liver cell shows numerous granules of glycogen closely associated with smooth ER (TEM). (b) The breakdown of liver glycogen involves the stepwise removal of glucose units as glucose-1-phosphate, followed by the conversion of glucose-1-phosphate to glucose-6-phosphate by enzymes in the cytosol. Removal of the phosphate group depends on glucose-6-phosphatase, an enzyme associated with the smooth ER membrane. Free glucose is then transported out of the liver cell into the blood by a glucose transporter in the plasma membrane. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Smooth ER - Calcium Storage The sarcoplasmic reticulum of muscle cells is an example of smooth ER that specializes in calcium storage The ER lumen contains high concentrations of calcium-binding proteins Calcium ions are pumped into the ER by ATP- dependent calcium ATPases and are released when needed for muscle contraction Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Calcium in cell injury and death, Zheng Dong, Pothana Saikumar, Joel M.Weinberg,and Manjeri A. Venkatachalam Annual Review of Pathology Mechanisms of Disease · February 2006 INFORMATION Smooth ER - Calcium Storage BOX Figure 1 Calcium homeostasis in normal cells. Ionized calcium (Ca2+) in the cytosol is normally maintained at 10–100 nM against steep gradients by transport of the ion to the extracellular space and cisternae of the endoplasmic reticulum (ER), and by protein binding. Physiological increases of cytosolic Ca2+ take place by entry through plasma membrane Ca2+ channels (leak channels, ligand-gated channels, and voltage-gated channels), release of Ca2+ from the ER or sarcoplasmic reticulum (SR) lumina upon binding of inositol trisphosphate (IP3) to the inositol trisphosphate receptor (IP3R), or release of Ca2+ from the SR (in muscle cells) upon Ca2+ binding to the ryanodine receptor (RyR) by a process called calcium-induced calcium release (CICR). Transport of Ca2+ across the plasma membrane to the extracellular space takes place via the plasma membrane calcium ATPase (PMCA) and the Na+/Ca2+ exchanger. The sarco-endoplasmic reticulum calcium ATPase (SERCA) transports Ca2+ into the ER in nonexcitable cells, or the SR in muscle cells. Mitochondrial membranes can also buffer Ca2+ by transport of the ion into the mitochondrial matrix via Ca2+ uniporters. Abnormal increase of mitochondrial matrix Ca2+ concentration is prevented by transport in the reverse direction via mitochondrial Na+/Ca2+ exchangers. Calcium in cell injury and death, Zheng Dong, Pothana Saikumar, Joel M.Weinberg,and Manjeri A. Venkatachalam Annual Review of Pathology Mechanisms of Disease · February 2006 Sitoplazmadaki Kalsiyum (Ca²⁺) Düzeylerinin Düzenlenmesi Normal Düzeyler: Sitoplazmada iyonize kalsiyum (Ca²⁺) konsantrasyonu genellikle 10–100 nanomolar (nM) seviyelerinde tutulur. Bu denge, kalsiyumun hücre dışına, endoplazmik retikulumun (ER) depolarına taşınması ve proteinlere bağlanmasıyla sağlanır. Fizyolojik Artışlar: Plazma Zarındaki Kanallar: Kalsiyum iyonları, plazma zarındaki sızıntı kanalları, ligandla açılan kanallar veya voltaja duyarlı kanallar yoluyla hücreye girer. ER veya SR’den Salınım: İnositol trisfosfat (IP3) molekülü, ER ya da kas hücrelerindeki sarkoplazmik retikulum (SR) depolarından kalsiyum salınımını tetiklemek için IP3 reseptörlerine (IP3R) bağlanır. Kas hücrelerinde, kalsiyumun ryanodin reseptörüne (RyR) bağlanmasıyla gerçekleşen kalsiyum kaynaklı kalsiyum salınımı (CICR) adı verilen süreç, SR’den kalsiyum salınımına neden olur. Kalsiyumun Hücre Dışına Taşınması: Hücre zarından kalsiyumun dışarı taşınması, plazma zarı kalsiyum ATPazı (PMCA) ve sodyum/kalsiyum değiştiricisi (Na⁺/Ca²⁺ değiştirici) aracılığıyla gerçekleşir. SERCA: Non-uyarılabilir hücrelerde ER’ye, kas hücrelerinde ise SR’ye kalsiyum taşınmasını sağlar. Mitokondride Kalsiyum Düzenlenmesi: Mitokondri zarları, kalsiyum iyonlarını tek yönlü taşıma sistemleri (Ca²⁺ taşıyıcıları) aracılığıyla mitokondri matrisine alarak tampon görevi görür. Mitokondri matrisinde aşırı kalsiyum birikimini önlemek için kalsiyum, mitokondriyal sodyum/kalsiyum değiştiriciler aracılığıyla ters yönde taşınır. Bu mekanizmalar, hücre içinde kalsiyumun dengeli bir şekilde düzenlenmesini sağlar ve hem normal fizyolojik işlevler hem de anormal durumların önlenmesi için hayati önem taşır.  Smooth ER - Steroid Biosynthesis Smooth ER in some cells is the site of  cholesterol and steroid hormone synthesis Large amounts of smooth ER are found in cells that synthesize these Smooth ER has also been found associated with plastids in some plants and may be involved in phytohormone synthesis Cholesterol Cholesterol, cortisol, and steroid hormones share a four- ring structure but differ in the number and arrangement of carbon side chains and hydroxyl groups Hydroxymethylglutaryl-CoA reductase (HMG-CoA reductase) is the committed step in cholesterol INFORMATION biosynthesis BOX It is found in smooth ER of liver cells and is targeted by cholesterol-lowering drugs called statins Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  The ER Plays a Central Role in the Biosynthesis of Membranes Fosfatidiletanolamin, hücre zarlarının yapısında bulunan bir fosfolipid türüdür. Ethanolamine grubu, fosfatidik asit ile bağlanarak bu molekülü oluşturur. In eukaryotic cells, the ER is the primary source of membrane lipids, Fosfatidiletanolamin, özellikle hücre with a few exceptions: zarlarının yapısal bütünlüğünü ve zar Mitochondria synthesize phosphatidylethanolamine geçirgenliğini sağlamak için önemli bir rol oynar. Ayrıca sinir Peroxisomes synthesize cholesterol hücrelerinde ve bazı biyolojik süreçlerde de yer alabilir. Chloroplasts contain enzymes for chloroplast-specific lipids Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  ER - Membrane Biosynthesis Fatty acids for membrane phospholipids are synthesized in the cytoplasm and incorporated into the ER membrane on the cytosolic side They are transferred to the lumenal side of the bilayer by enzymes called phospholipid translocators (flippases) The type of phospholipid molecules transferred across the membrane depends on the particular translocator present, leading to membrane asymmetry The distinct composition of cytosolic and lumenal monolayers established in the ER is transferred to other cellular membranes Movement of phospholipids from ER to mitochondria, chloroplasts, or peroxisomes is problematic Phospholipid exchange proteins (phospholipid transfer proteins) convey specific phospholipids to these organelles Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings INFORMATION Composition of ER and Plasma Membranes BOX Although the ER is the source of most membrane lipids, the compositions of other cellular membranes vary significantly from the composition of the ER membrane Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Cisternae (çoğul hali), hücre içinde bulunan cisterna yapılarının birden fazla olanını ifade eder. Cisterna, genellikle düzleşmiş ve zarla çevrili bir boşluktur ve hücre içindeki bazı organellerde bulunur. En yaygın olarak, endoplazmik retikulum (ER) ve Golgi aygıtı gibi organellerde cisternae bulunur. Bu yapılar, hücre içindeki madde taşıma, işleme ve depolama gibi önemli işlevlere sahiptir. Örneğin, Golgi aygıtında bir dizi cisterna, hücreye ait farklı bileşenlerin işlenmesi ve taşınması için görev yapar. The Golgi Apparatus: Shipping and Receiving Center Golgi apparatus – Modifies products of the ER – Manufactures certain macromolecules The Golgi apparatus consists of stacks of – Sorts and packages materials into associated, flattened sacs, or cisternae. Unlike transport vesicles the ER cisternae, these sacs are not physically connected. A Golgi stack receives and dispatches transport vesicles and the products they contain. A Golgi stack has a structural and functional directionality, with a cis face that receives vesicles containing ER products and a trans face that dispatches vesicles. The cisternal maturation model proposes that the Golgi cisternae themselves “mature,” moving from the cis to the trans face while carrying some proteins along. In addition, some vesicles recycle enzymes that had been carried forward in moving cisternae, transporting them “backward” to a less mature region where their functions are needed. Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  The Golgi Apparatus: Shipping and Receiving Center The Golgi complex is functionally and physically linked to the ER Here, glycoproteins and membrane lipids from the ER undergo  further processing and  are sorted and  packaged for transport Thus the Golgi complex plays a central role in membrane and protein trafficking in eukaryotic cells The Golgi Complex Consists of a Series of Membrane-Bounded Cisternae The Golgi complex is a series of flattened membrane-bounded cisternae A series of cisternae, usually three to eight, is called a Golgi stack Some cells have one large stack, and others, especially secretory cells, have hundreds or thousands of stacks Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Transport Vesicles Both ER and the Golgi complex are surrounded by numerous vesicles that carry lipids and proteins from the ER to the Golgi complex and then to various destinations in the cell The Golgi complex lumen (intracisternal space) is part of the endomembrane system Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Membrane Trafficking Sorting of proteins begins in the ER and early compartments of the Golgi There are mechanisms to retrieve or retain compartment-specific proteins The final sorting of material that will leave the Golgi complex occurs in the TGN Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Roles of the ER and Golgi Complex in Protein Trafficking Proteins synthesized in the rough ER must be directed to a variety of locations Once a protein reaches its destination, it must be prevented from leaving Each protein contains a specific “tag” targeting it to a transport vesicle that will take it to the correct location Protein Tags  A tag may be an amino acid sequence, a hydrophobic domain, oligosaccharide side chain, or some other feature  Tags can also exclude material from certain vesicles Lipid Tags  Membrane lipids may also be tagged to help vesicles reach their destinations  Lipid tags can be one or more phosphate groups attached to positions 3, 4, and/or 5 of a membrane phosphatidyl inositol phosphatidyl inositol Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings INFORMATION ER-Specific Proteins Contain Retention and Retrieval Tags BOX Protein composition in the ER is maintained by preventing some proteins from escaping the ER and by retrieving others from the Golgi Some proteins localized to the ER contain the sequence RXR (Arg-X-Arg; X is any amino acid) This is a retention tag and is also found in some proteins that are destined for the plasma membrane The RXR Tag The N-methyl-D-aspartate (NMDA) receptor, important in mammalian neurotransmission, has the RXR tag INFORMATION It is thought that the tripeptide causes subunits of NMDA to be BOX retained in the ER until the complex is completely assembled The RXR tag must be masked to allow the assembled complex to leave the ER Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings INFORMATION Retrieval Tags BOX Some proteins returned from the Golgi to the ER contain retrieval tags The tags are short C-terminal sequences such as  KDEL (Lys-Asp-Glu-Leu) or INFORMATION  KKXX in mammals and BOX  HDEL (His-Asp-Glu-Leu) in yeast When a protein with this tag binds a receptor, the receptor-ligand complex is packaged into a transport vesicle for return to the ER Evidence about the importance of retrieval tags comes from experiments involving chimeric proteins (fusion proteins) These are made by joining the DNA sequences for two polypeptide segments to allow production of a hybrid protein Proteins normally secreted from the cell that are altered to contain the retrieval tag end up in the ER Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Golgi-Specific Proteins Golgi complex proteins may be sorted according to the lengths of their membrane-spanning domains Some proteins resident to the Golgi complex also contain retention or retrieval tags Large complexes that are excluded from transport vesicles may play a role in maintaining the protein composition of the Golgi complex A third mechanism involves hydrophobic regions of Golgi proteins All Golgi-specific proteins are integral membrane proteins with one or more membrane- spanning domains Burada anlatılmak istenen, Golgi’ye özgü proteinlerin yapısal özellikleri ve zardaki konumlarıdır. Şöyle açıklayabiliriz: 1. Zarı Geçen Bölgeler: Golgi’ye özgü proteinlerin hepsi, zarın bir ucundan diğerine geçen (zarı delen) bir veya daha fazla bölgeye sahiptir. Bu bölgeler, proteinin zarın içine sabitlenmesini ve burada görev yapmasını sağlar. 2. Yerleşik Zar Proteinleri: Bu ifade, bu proteinlerin zara sıkı sıkıya bağlı olduklarını ve zardan kolayca ayrılmadıklarını vurgular. Yani, bu proteinler zarın bir parçası gibi davranır ve çoğunlukla zardaki işlevlerini sürdürürler (örneğin, molekül taşınması, sinyal iletimi veya Golgi işlevlerinin düzenlenmesi). 3. Anlamı: Bu özellik, Golgi’ye özgü proteinlerin yapısının ve işlevinin, zarla olan bu doğrudan ilişkisine dayandığını ifade eder. Bu sayede Golgi proteinleri, Golgi kompleksinde kalır ve taşınmaz ya da başka bir yere gitmez. Özetle, burada Golgi’ye özgü proteinlerin zara bağlı özel yapılar oldukları ve işlevlerini bu yapı üzerinden gerçekleştirdikleri anlatılıyor. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Golgi-Specific Proteins The length of the hydrophobic domains may determine into which cisternae each protein is incorporated The thickness of cellular membranes increases progressively from the  ER (5 nm) to the  plasma membrane (8 nm) The thickness of membranes in the Golgi increases from the CGN to the TGN Proteins move from compartment to compartment until the membrane thickness exceeds the length of the transmembrane domains This blocks further migration Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Roles of the ER and Golgi in Protein Glycosylation Much of the protein processing carried out in the ER and Golgi involves glycosylation, the addition of carbohydrate side chains to proteins Enzyme-catalyzed reactions involving the resulting glycoproteins then modify the oligosaccharide side chain Two General Kinds of Glycosylation  N-linked glycosylation (N-glycosylation) involves the addition of an oligosaccharide to the nitrogen atom of certain asparagine residues  O-linked glycosylation involves addition of the oligosaccharide to the oxygen atom on the hydroxyl group of certain serine or threonine residues INFORMATION BOX Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Roles of the ER and Golgi in Protein Glycosylation Initial Glycosylation Occurs in the ER The initial steps of N-glycosylation take place on the cytosolic surface of the ER membrane Later steps take place in the ER lumen All carbohydrate side chains initially have a common core oligosaccharide consisting of  two units of N-acetylglucosamine (GlcNAc),  nine mannose units,  and three glucose units INFORMATION BOX Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Cotranslational Glycosylation Usually the oligosaccharide is added to the recipient protein as the polypeptide is being synthesized This is called cotranslational glycosylation It helps to promote proper protein folding Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Further Glycosylation Occurs in the Golgi Complex Further processing of N-glycosylated proteins occurs in the Golgi complex as the glycoproteins move from the cis face through to the trans face These terminal glycosylations are variable and create great diversity Terminal glycosylation involves the removal of a few units of the core oligosaccharide and sometimes nothing more In some cases, more complex oligosaccharides are generated by adding GlcNAc or other monosaccharides Sometimes galactose units are added by galactosyl transferases The ER and Golgi contain hundreds of different glycosyl transferases Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Lysosome Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 7 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Lysosome Lysosomes  are single membrane organelles of the endomembrane system  contains digestive enzymes (hydrolases) capable of degrading all the major classes of biological macromolecules—lipids, carbohydrates, nucleic acids, and proteins.  degrade extracellular materials brought into the cell by endocytosis and digest intracellular structures and macromolecules that are damaged or no longer needed. These enzymes are sequestered to prevent them from digesting the contents of the cell A special carbohydrate coating on the inner lysosome membrane protects it from digestion Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 7 Pearson Education, Inc., publishing as Pearson Benjamin Cummings INFORMATION Targeting of Soluble Lysosomal Proteins to Endosomes and Lysosomes Is a BOX Model for Protein Sorting in the TGN Soluble lysosomal enzymes in the ER and early Golgi compartments undergo  N-glycosylation followed by  removal of glucose and mannose units The mannose residues on the side chains are phosphorylated within the Golgi complex, forming an oligosaccharide containing mannose-6-phosphate This tag ensures delivery of lysosomal proteins to the lysosomes The Mannose-6-Phosphate Tag  Phosphorylation of mannnose is catalyzed by two Golgi-specific enzymes  The first is a phosphotransferase that adds GlcNAc-1-phosphate to carbon 6 of mannose in an early Golgi compartment  The second, in a mid-Golgi compartment, removes GlcNAc, leaving behind the mannose-6-phosphate residue Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Ligand, biyoloji ve kimya alanlarında, bir molekülün başka bir molekülle bağlanan ve onunla bir kompleks oluşturan bir maddeyi ifade eder. Özellikle hücresel düzeyde, bir ligand genellikle bir reseptöre bağlanarak bir biyolojik yanıtın tetiklenmesine neden olur. Örneğin, hücre zarındaki bir reseptör, hormon veya nörotransmitter gibi bir ligand ile bağlanabilir, bu da hücredeki çeşitli işlevlerin başlamasına yol açar. Türkçeye doğrudan çevrilebilecek bir kelime olmamakla birlikte, genellikle “bağlayıcı” veya “bağlantı maddesi” gibi ifadelerle çevrilebilir. Ancak, biyolojik bağlamda ligand terimi özel bir anlam taşır. INFORMATION Destination of Lysosomal Proteins BOX Tagged lysosomal proteins bind to mannose-6-phosphate receptors (MPRs) The receptor-ligand complexes are packaged into transport vesicles and conveyed to an endosome In animal cells, lysosomal enzymes are transported from the TGN to organelles known as late endosomes Multivesicular Endosomes  Degradation and recycling of unneeded or damaged components are carried out by specialized late endosomes called multivesicular endosomes (MVEs)  They are sometimes called multivesicular bodies (MVBs)  These serve as an intermediate between early endosomes and lysosomes and sequester materials destined for degradation or recycling Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Destination of Lysosomal Proteins Targeting of Soluble Lysosomal Enzymes to Endosomes and Lysosomes by a Mannose-6-Phosphate Tag. (1) In the ER, soluble lysosomal enzymes undergo N- glycosylation followed by removal of glucose and mannose units. (2) Within the Golgi complex, mannose residues on the lysosomal enzymes are phosphorylated by two enzymes. The first one adds N-acetylglucosamine-1-phosphate to carbon atom 6 of mannose. The second one removes N-acetylglucosamine, leaving behind the phosphorylated mannose residue. (3) The tagged lysosomal enzymes bind to mannose-6-phosphate receptors in the TGN and are packaged into coated transport vesicles that convey the enzymes to a late endosome. (4) The acidity of the late endosomal lumen causes the enzymes to dissociate from their receptors. (5) The receptors are recycled in vesicles that return to the TGN. The late endosome either matures to form a lysosome or transfers its contents to an active lysosome. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Destination of Lysosomal Proteins Dissociation of the lysosomal enzymes prevents the retrograde movement of the enzymes back to the Golgi with the receptors The late endosome matures to form a new lysosome or delivers its contents to an active lysosome In the human genetic disorder I-cell disease, lysosomal enzymes are misdirected Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Secretory Pathways Transport Molecules to the Exterior of the Cell Secretory pathways move proteins from the ER through the Golgi complex to secretory vesicles and secretory granules The secretory granules then discharge their contents to the exterior of the cell Experiments using electron microscopy and autoradiography show the movement of proteins through secretory pathways Proteins were radioactively labeled briefly After three minutes, the proteins could be seen primarily in the rough ER A few minutes later, the proteins began to appear in the Golgi complex After 37 minutes, the protein was detected in vesicles budding from the Golgi (named condensing vacuoles by the researchers) After 117 minutes, the protein began to accumulate in dense zymogen granules, vesicles that discharge their contents out of the cell Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Zimojen granülleri, zimojenlerin depolandığı ve salgılanmaya hazır hale getirildiği hücresel yapılar olan granüllerdir. Zimojen, aktif hale gelmeden önce inaktif bir formda bulunan bir enzimi tanımlar. Bu tür enzimler genellikle sindirim enzimleri gibi biyolojik süreçlerde rol oynar. Zimojenler, genellikle salgı granüllerinde depolanır ve uygun bir uyarı ile aktive olduktan sonra, enzimatik faaliyetlerini gerçekleştirmek üzere salgılanır. Örneğin, pankreas hücrelerinde zimogen granülleri, sindirim enzimlerinin inaktif formlarını depolar ve bunlar, sindirim kanalına salındığında aktif hale gelir.  Constitutive Secretion After budding from the TGN, some vesicles  move directly to the cell surface and  immediately fuse with the plasma membrane This unregulated process is continuous and independent of external signals It is called constitutive secretion; one example is mucus secretion by the intestinal lining Constitutive secretion was once thought to be a default pathway for proteins synthesized by rough ER It was thought that proteins destined to stay in the endomembrane system must have a tag to avoid constitutive secretion Current evidence suggests that some tags may be required for constitutive secretion Güncel kanıtlar, bazı etiketlerin kalıtsal salgı için gerekli olabileceğini göstermektedir. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Regulated Secretion Secretory vesicles involved in regulated secretion accumulate in the cell and fuse with the plasma membrane only in response to specific signals An important example is neurotransmitter release Regulated secretory vesicles form by budding from the TGN as immature secretory vesicles Excluding Nonsecretory Proteins from Vesicles  Evidence suggests that high concentrations of secretory proteins lead to formation of protein aggregates  These aggregates, formed in the TGN, act to exclude nonsecretory proteins from the forming secretory vesicles  Proteins that do not form aggregates or enter secretory vesicles would be transported elsewhere Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Exocytosis Polarized Secretion In many cases, exocytosis of specific proteins is limited to a specific surface of the cell For example, intestinal cells secrete digestive enzymes only on the side of the cell that faces into the intestine This is called polarized secretion Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Exocytosis Releases Intracellular Molecules Outside the Cell In exocytosis, proteins in a vesicle are released to the exterior of the cell as the vesicle fuses with the plasma membrane Animal cells secrete hormones, mucus, milk proteins, and digestive enzymes this way Plant and fungal cells secrete enzyme and structural proteins for the cell wall Vesicles containing products for secretion move to the cell surface (1) The membrane of the vesicle fuses with the plasma membrane (2) Fusion with the plasma membrane discharges the contents of the vesicle (3) The membrane of the vesicle becomes part of the cell membrane (4) Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Exocytosis Orientation of Membrane When the vesicle fuses with the plasma membrane  The lumenal (inner) membrane of the vesicle becomes part of the outer surface of the plasma membrane  So, glycolipids and glycoproteins that were formed in the ER and Golgi lumens will face the extracellular space Mechanism of Exocytosis  The mechanism of the movement of exocytotic vesicles to the cell surface is not clear  Evidence points to the involvement of microtubules in vesicle movement  Vesicle movement stops when cells are treated with colchicine, a microtubule assembly inhibitor Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Endocytosis Imports Extracellular Molecules by Forming Vesicles from the Plasma Membrane Most eukaryotic cells carry out one or more forms of endocytosis for uptake of extracellular material  A small segment of the plasma membrane folds inward (1)  Then it pinches off to form an endocytic vesicle containing ingested substances or particles (2–4) Endocytic Vesicles  Endocytic vesicles develop into early endosomes, which fuse with vesicles from the TGN  They acquire digestive enzymes and form new lysosomes  In phagocytosis, solid particles are ingested  In pinocytosis, liquids are taken up Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Receptor Mediated Endocytosis During receptor-mediated endocytosis, (1) the molecules that will be internalized bind to specific receptors on the surface of the plasma membrane. (2) Receptor-ligand complexes accumulate in coated pits, where (3) invagination is facilitated by adaptor protein, clathrin, and dynamin on the cytosolic surface of the membrane. The result is (4) an internalized coated vesicle that quickly (5) loses its clathrin coat. The uncoated vesicle is now free to (6) fuse with other intracellular membranes, usually a membrane surrounding an early endosome, where internalized material is sorted. The fate of the receptors and the ingested molecules depends on the nature of the material. Transport vesicles often (7a) carry material to a late endosome for digestion. Alternative pathways include (7b) recycling to the plasma membrane or (7c) transport to another region of the plasma membrane and exocytosis (called transcytosis). Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Phagocytosis Particles or microorganisms bind to receptors on the cell surface, triggering the onset of phagocytosis. Folds of membrane called pseudopods gradually surround the particle. Eventually, the pseudopods meet and engulf the particle, forming a phagocytic vacuole. The vacuole then fuses with an early endosome or forms transient connections (indicated by dashed lines) with early and late endosomes and matures into a lysosome, in which digestion of the internalized material occurs. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Lysosomes  Lysosomes isolate digestive enzymes from the rest of the cell  Lysosomes develop from endosomes  Lysosomal enzymes are important for several different digestive processes Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Membrane Flow Endocytosis and exocytosis have opposite effects in terms of membrane flow Exocytosis adds lipids and proteins to the plasma membrane, whereas endocytosis removes them The steady-state composition of the plasma membrane results from a balance between the two processes Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  Lysosomes: Digestive Compartments A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids Lysosomal enzymes work best in the acidic environment inside the lysosome Some types of cells can engulf another cell by phagocytosis; this forms a food vacuole A lysosome fuses with the food vacuole and digests the molecules Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  Lysosomes: Digestive Compartments (a) Phagocytosis. In phagocytosis, lysosomes digest (hydrolyze) materials taken (b) Autophagy. In autophagy, lysosomes recycle intracellular materials. Top: In into the cell. Top: In this macrophage (a type of white blood cell) from a rat, the the cytoplasm of this rat liver cell is a vesicle containing two disabled organelles lysosomes are very dark because of a stain that reacts with one of the products (TEM). The vesicle will fuse with a lysosome in the process of autophagy, which of digestion inside the lysosome (TEM). Macrophages ingest bacteria and viruses recycles intracellular materials. Bottom: This diagram shows fusion of such a and destroy them using lysosomes. Bottom: This diagram shows a lysosome vesicle with a lysosome. This type of vesicle has a double membrane of unknown fusing with a food vacuole during the process of phagocytosis by a unicellular origin. The outer membrane fuses with the lysosome, and the inner membrane eukaryote. is degraded along with the damaged organelles. Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson. Lysosomes Synthesis and Intracellular Transport of Lysosomal Enzymes Lysosomal enzymes are synthesized in the ER and transported to the Golgi apparatus. Undergo a variety of post-translational modifications, including attachment of terminal mannose-6-phosphate groups. These phosphorylated mannose residues are "address labels“ recognized by specific receptors on the inner surface of the Golgi membrane. Thus lysosomal enzymes bind to these receptors and are thereby segregated from the numerous other secretory proteins within the Golgi. Small transport vesicles containing the receptor-bound enzymes are pinched off from the Golgi and proceed to fuse with the lysosomes. Vinay Kumar, Abul K. Abbas, Jon C. Aster Robbins & Cotran Pathologic Basis of Disease 2014 Elsevier Health Sciences INFORMATION Pathology - Lysosomal Storage Disease BOX Figure 5-10 Pathogenesis of lysosomal storage diseases. In the example shown, a complex substrate is normally degraded by a series of lysosomal enzymes (A, B, and C) into soluble end products. If there is a deficiency or malfunction of one of the enzymes (e.g., B), catabolism is incomplete and insoluble intermediates accumulate in the lysosomes. In addition to this primary storage, secondary storage and toxic effects result from defective autophagy. Vinay Kumar, Abul K. Abbas, Jon C. Aster Robbins & Cotran Pathologic Basis of Disease 2014 Elsevier Health Sciences  Abnormalities of Membranes INFORMATION BOX Harper's Illustrated Biochemistry 30th Edition, Victor W. Rodwell, David A. Bender, Kathleen M. Botham, Peter J. Kennelly, P. Anthony Weil,  Vacuoles Some cells contain a membrane-bounded vacuole In animal and yeast cells they are used to temporary storage or transport Phagocytosis leads to the formation of a membrane bound particle, called a phagosome When this type of vacuole fuses with a lysosome, the contents are hydrolyzed to provide nutrients to a cell Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Vacuoles: Diverse Maintenance Compartments A plant cell or fungal cell may have one or several vacuoles, derived from endoplasmic reticulum and Golgi apparatus Food vacuoles are formed by phagocytosis Contractile vacuoles, found in many freshwater protists, pump excess water out of cells Central vacuoles, found in many mature plant cells, hold organic compounds and water The central vacuole is usually the largest compartment in a plant cell; the rest of the cytoplasm is often confined to a narrow zone between the vacuolar membrane and the plasma membrane (TEM). Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  The Plant Vacuole: A Multifunctional Organelle Most mature plant cells contain a single large vacuole called a central vacuole The main function of the central vacuole is to maintain the turgor pressure that keeps the plant from wilting Tissues wilt when the central vacuole no longer presses against the cell contents (fails to provide adequate pressure) Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Endomembrane System: flow of membrane lipids and proteins through the various organelles. Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.  You Are Here Compartmentalization in a Eukaryotic Cell Nucleus Ribosomes Endomembrane System  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane Peroxisomes Mitochondria Chloroplasts Cytoskeletal Elements Extracellular Matrix Cell-Cell Attachments  Peroxisomes Peroxisome Structure  Peroxisomes resemble lysosomes in size and appearance  (like the Golgi complex, endosomes, and lysosomes,) are surrounded by a single membrane and perform several functions depending on cell type  Peroxisomes are not derived from the endoplasmic reticulum and are therefore not part of the endomembrane system  Peroxisomes are found in most cell types, but especially prominent in the liver and kidney cells of animals  How peroxisomes are related to other organelles is still unknown  Animal peroxisomes contain a crystalline core, consisting of Kristalin: “Kristalin” terimi, bir maddede crystalline urate oxidase kristal yapıların bulunması durumunu tanımlar. Yani, bir madde “kristalin” olarak adlandırıldığında, moleküler yapısının düzenli ve  Plant peroxisomes contain crystalline catalase. In higher plants, belirli bir yapıya sahip olduğunu ifade eder. Ayrıca peroxisomes contain also a complex battery of antioxidative “kristalin” terimi, genellikle bir yapının ya da maddelerin özelliklerini tanımlar (örneğin, enzymes such as superoxide dismutase. kristalin yapıda bir madde). Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Peroxisomes Function of Peroxisomes  perform several distinctive functions that differ with cell type (plant/animal), but they have the common property of both generating and degrading hydrogen peroxide (H2O2).  Reduce reactive oxygen species.  defining characteristic is the presence of catalase, an enzyme essential for the degradation of hydrogen peroxide  detoxify other harmful compounds, and catabolize unusual substances  In animals, they play roles in oxidative breakdown of fatty acids, especially longer chain fatty acids (up to 22 carbon atoms)  Some serious human diseases result from defects in one or more peroxisomal enzymes, normally involved in degrading long-chain fatty acids Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Biogenesis of Peroxisomes and Protein Import Peroxisome Biogenesis Occurs by Division of Preexisting Peroxisomes New peroxisomes typically arise by the division of existing peroxisomes rather than by fusion of vesicles from the Golgi complex. (1) Lipids and membrane proteins can be added to existing peroxisomes via cytosolic sources. (2) Polypeptides for peroxisomal matrix enzymes are synthesized on cytosolic ribosomes and are threaded through the membrane via a transmembrane peroxin transport protein. The enzyme shown here is catalase, a tetrameric protein that requires a heme cofactor. (3) Heme enters the peroxisomal lumen via a separate pathway, and the catalase polypeptides are folded and assembled with heme to form the active tetrameric protein. (4) After lipids and protein are added, new peroxisomes are formed by the division of the existing peroxisomes. (5) Some researchers believe that peroxisomes can obtain proteins or form de novo from protoperoxisomal vesicles that are derived from the ER. Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith, Becker's World Of The Cell 8th Ed. Chapter: 12 Pearson Education, Inc., publishing as Pearson Benjamin Cummings INFORMATION Peroxisomes in Plants BOX In plants and algae, peroxisomes are involved in several specific aspects of cellular energy metabolism Leaf Peroxisomes are prominent in photosynthetic tissue because of their role in photorespiration, the light-dependent uptake of oxygen and release of carbon dioxide characteristic large, prominent leaf peroxisomes often appear in close contact with chloroplasts and mitochondria The spatial proximity of the three organelles probably reflects their mutual involvement in the glycolate pathway also called the photorespiratory pathway because it involves the light-dependent uptake of O2 and release of CO2. Several enzymes of this pathway, including a peroxide-generating oxidase and two aminotransferases, are confined to leaf peroxisomes. Reece, J. B., & Campbell, N. A. (11th – Global Edition). Campbell biology. Chapter: 7 Boston: Benjamin Cummings / Pearson.