Lecture 5. Cytoplasm and Nucleus 2 PDF

Cell Organelles: Part I Cytoplasm and Cell Nucleus Contents 1. Cytoplasm Basics 2. Theories on Physical Nature of Cytoplasm 3. Structural Features and Composition of Cytoplasm 4. Parts and Function of Cytoplasm: Cytosol 5. Parts and Function of Cytoplasm: Cell...

Cell Organelles: Part I Cytoplasm and Cell Nucleus Contents 1. Cytoplasm Basics 2. Theories on Physical Nature of Cytoplasm 3. Structural Features and Composition of Cytoplasm 4. Parts and Function of Cytoplasm: Cytosol 5. Parts and Function of Cytoplasm: Cell Organelles 6. Parts and Function of Cytoplasm: Cytoplasmic Inclusions 7. Overall Functions of Cytoplasm 8. Cytoplasmic Inclusions 9. Cell Organelles: Definition and Function 10. Nucleus 11. Parts and Function of Nucleus 11.1. Nuclear Envelope and Nuclear Pores 11.2. Nuclear Lamina and Nucleoplasm 11.3. Nucleolus 11.4. Chromatin and Chromosome  Cytoplasm Basics  The cytoplasm is a rich, semifluid material present in cells of organisms that are closed off by the cell membrane. It contains various cytoplasmic components, such as the 1). cytosol, 2). cytoplasmic organelles and 3). Inclusion bodies.  The cytoplasm is found within the cell. In an eukaryotic cell — such as an animal cell and a plant cell, the cytoplasm is between the cell membrane and the nuclear envelope. As for a prokaryotic cell such as a bacterial cell, lacking a well-defined nucleus, the cytoplasm contains everything that is inside the cell, surrounded by a cell membrane.  The cytoplasm is defined as the cellular component inside the cell between the cell membrane and the nuclear envelope of the nucleus.  All cells have cytoplasm. However, the size of the cytoplasm may vary from one cell to another.  The watery component (fluid segment) of the cytoplasm is called cytosol. The cytosol is made up of mostly water with a few other dissolved salts and ions. 14-09-2024 Cell Morphology 2  Theories on Physical Nature of Cytoplasm  Sol-Gel Form: Cytoplasm is known to behave similarly to that of a sol-gel. A sol-gel is a mixture of molecules that sometimes act like a liquid (sol) and other times acts like a solid (gel) integrated network.  As a Glass: Cytoplasm sometimes have glass-like behavior as well. This is when the cytoplasm acts as though it is approaching the glass transition as a glass-forming liquid. This comes off the theory that sometimes that cytoplasm may contain many solid components and hence the cytosol needs to act as glass and hold the solid components together so that they do not move excessively. This behavior still allows however for the movement of organelles and other inclusions across the cytoplasm and membrane if needed. This ability of the cytoplasm to somewhat “freeze” everything in place actually becomes very handy as a self-defense mechanism. This frozen stature would prevent harmful physical effects to the cell while still allowing cellular activities to take place whenever the goes back to a more fluid state.  Non-Brownian Motion of Cytoplasmic Components: Constituents of cytoplasm move as a separate entity. These are theorized to be channeled by motor proteins which assist with this non-Brownian motion within the cells versus actually having random forces causing the movements. 14-09-2024 Cell Morphology 3  Structural Features and Composition of Cytoplasm 14-09-2024 Cell Morphology 4  Parts and Function of Cell Cytoplasm: Cytosol  The cytosol is the part of the cytoplasm that is the liquid-like portion. It is mostly made up of water, dissolved minerals, and cytoskeleton filaments.  It, however, does not contain any organelles but holds them within the cell as part of the entire cytoplasm.  It consists of water, organic molecules, and dissolved ions. The highest percentage of cytosol component is water, i.e. about 70%.  The typical ions in the mammalian cytosol are potassium, magnesium, calcium, sodium, chloride, bicarbonate, amino acids in proteins.  The cytosol serves as the site where many chemical reactions take place. In prokaryotes, it is where most metabolic reactions take place (others occur in the cell membrane). In eukaryotes, it is where the organelles and other cytoplasmic structures are suspended. Since the cytosol contains dissolved ions, it plays a role in osmoregulation and cell signaling. It is also involved in generating action potentials in cells, such as nerve, and muscle cells. 14-09-2024 Cell Morphology 5  Parts and Function of Cell Cytoplasm: Cell Organelles  Organelles are specialized structures within cells that carry out specific tasks for the cell. The term “organelles” is based on the organs, as the organs in animals and humans work similarly in carrying out a specific task for the body.  In eukaryotic cells, the nucleus, for instance, is the organelle that contains the genetic material, and therefore it controls cellular activities such as metabolism, growth, and reproduction by regulating gene expression.  Chloroplasts are plastids containing green pigments essential for photosynthesis.  Mitochondria are the organelles that synthesize energy for multifarious metabolic processes.  The endoplasmic reticulum occurs as an interconnected network of flattened sacs or tubules involved in lipid synthesis, carbohydrate metabolism, drug detoxification, and attachment of receptors on cell membrane proteins. It is also involved in intracellular transport, such as the transport of the products (of the rough endoplasmic reticulum) to other cell parts like the Golgi apparatus.  Golgi apparatus is made up of membrane-bound stacks. It is involved in glycosylation, packaging of molecules for secretion, transporting of lipids within the cell, and giving rise to lysosomes. Other cytoplasmic structures found in the cytoplasm are vacuoles and ribosomes.  Ribosomes, the site of protein synthesis, are comprised of protein and RNA. Some ribosomes are unbound whereas the others are attached to the endoplasmic reticulum. 14-09-2024 Cell Morphology 6  Parts and Function of Cell Cytoplasm: Cytoplasmic Inclusions  Cytoplasmic inclusions are part of the cytosol but are not membrane-bound so they are not considered organelles. Instead, they are suspended in the cytosol as small, insoluble particles.  Cytoplasmic inclusions depend on the type of cell they are in. Cytoplasmic inclusions called lipid droplets are used by both plant and animals cells to store lipids like fatty acids. Lipid droplets are made of both lipids and proteins so that they don’t dissolve into the cytosol. Cytoplasmic inclusions in plant cells stores excess glucose during photosynthesis in plants. 14-09-2024 Cell Morphology 7  Overall Functions of Cytoplasm The cytoplasm (of both eukaryotes and prokaryotes) is where the functions for cell expansion, growth, and metabolism are carried out. Numerous chemical reactions including cellular metabolism take part in the cytoplasm as it acts as a bridge between the cell membrane and most organelles. The cytoplasm also has many other functions including: 1. Support and Structure  To aid with cell structure and turbidity. It helps the cells to maintain their shape which is important for the arrangement of cells.  To keep organelles in place. The cytoplasm keeps the membrane-bound organelles in place within the cell and prevents them from making unnecessary movements.  The cytosol – part of the cytoplasm – fills up the empty spaces in the cell that are not covered by the organelles. 14-09-2024 Cell Morphology 8  Overall Functions of Cytoplasm 2. Protection  To protect the cell and its components from damage. The cytoplasm in helping keep cell shape but also being able to keep organelles in place which act as a major part in the cell’s defense strategies.  Often the cytoplasm acts as a shock-absorber when the cell is attacked and cushions that blow to the cell. 3. Storage  It contains materials such as storage units and enzymes that are essential for many metabolic activities.  In plant cells, they include important storage units that are used to store excess glucose made during photosynthesis. 4. Transport  Through the process of cytoplasmic streaming, the cytoplasm assists with the transport of organelles and cytoplasmic inclusions all over the cell.  The cytoplasm also transports waste material out of the cells. If there was no cytoplasm in the cell, the cell would not be able to function. It would be flat and have no shape. In addition, the organelles would not be able to be suspended in the cell either. 14-09-2024 Cell Morphology 9  Cytoplasmic Streaming Cytoplasmic streaming occurs when the cytoplasm itself moves within the cell membrane in a plant or animal cell. The movement is made mainly as a transportation system in the cell to get the necessary components to the places they need to be. For instance, to move organelles around for metabolic activities or to get proteins and nutrients to the nucleus and other organelles. Cytoplasmic streaming is not completely understood in the way it works. However, it is believed that with a mixture of motor proteins and adenosine triphosphate (ATP) the process occurs and is able to transport molecules all over the cell 14-09-2024 Cell Morphology 10  Cell Organelles: Definition and Functions  The cellular components in a cell are enclosed in structures/compartments called cell organelles.  These cell organelles include both membrane and non-membrane bound organelles, present within the cells and are distinct in their structures and functions.  They coordinate and function efficiently for the normal functioning of the cell. A few of them function by providing shape and support, whereas some are involved in the locomotion and reproduction of a cell.  There are various organelles present within the cell and are classified into three categories based on the presence or absence of membrane.  Organelles without membrane: Ribosomes, and Cytoskeleton are non-membrane-bound cell organelles. They are present both in the prokaryotic cell and the eukaryotic cell.  Single membrane-bound organelles: Vacuole, Lysosome, Golgi Apparatus, Endoplasmic Reticulum are single membrane-bound organelles present only in a eukaryotic cell.  Double membrane-bound organelles: Nucleus, Mitochondria and Chloroplast are double membrane-bound organelles present only in a eukaryotic cell. 14-09-2024 Cell Morphology 11 14-09-2024 Cell Morphology 12 Nucleus  The nucleus is a double membrane-bound organelle located centrally only in a eukaryotic cell, enclosing the DNA, the genetic material. It is the most important and defining feature of all higher organisms, including plant and animal cells, whose main function is to control and coordinate the functioning of the entire cell.  The word ‘nucleus’ (plural: nuclei) is derived from the Latin word ‘nucleus‘, meaning ‘kernel’ or ‘seed’. Structure and Characteristics  The largest and most prominent organelle in the cell, the nucleus, accounts for almost 10% of the volume of the entire cell.  In mammalian cells, the average diameter of the nucleus is approximately 6 µm in size.  Mostly the shape of the nucleus is found to be either spherical or oblong.  Eukaryotes usually contain a single nucleus, however erythrocytes and platelets are without a nucleus and osteoclasts of bones have many of them. 14-09-2024 Cell Morphology 13 Nuclear Envelope and Nuclear Pores Parts and Function of Nucleus  Surrounding the nucleus, the nuclear envelope is made of a phospholipid bilayer, similar to cell membranes, and contains tiny openings called nuclear pores over them.  The two membranes are often referred to as the inner and outer nuclear membranes with a fluid-filled region called perinuclear space in between.  The perinuclear space has a thickness of 20 to 40 nm. The outer membrane is attached to ribosomes and is continuous with the cell’s endoplasmic reticulum, a system that helps to package, transport, and export substances outside the cell.  Nuclear pores enable the selective transport of water soluble molecules through the nuclear membrane are themselves composed of a large number of proteins (several hundred in mammals). Although many larger biomolecules, including proteins and RNA, are unable to passively diffuse through these pores they may be actively transported in conjunction with importin/karyopherin proteins and the RanGTP family of small GTPases.  Functions  Nuclear envelope separates the nuclear content from the cytoplasm an is selectively permeable in nature.  Nuclear pores regulate the flow of molecules into and out of the nucleus. 14-09-2024 Cell Morphology 14  Parts and Function of Nucleus Nuclear Lamina  They are meshwork of protein filaments organized in a net-like fashion that line below the inner nuclear membrane.  The proteins that make up the nuclear lamina are known as lamins, which are intermediate filament proteins.  Functions Nucleoplasm  Also  Supports theas known nuclear envelope,itmaintaining karyoplasm, the overall is found inside shape and the nucleus, structure and of the nucleus. is a gelatinous substance similar to the cytoplasm, being composed mainly of water with dissolved salts, enzymes, and suspended organic molecules.  Functions  Protects the nuclear content by providing a cushion around the nucleolus and the chromosome.  Supports the nucleus to hold its shape.  Provides a medium through which enzymes and fragments of genetic materials (DNA or RNA), can be transported throughout the nucleus. 14-09-2024 Cell Morphology 15  Parts and Function of Nucleus Nucleolus  Nucleolus was first described by F. Fontana is a non-membrane bound dynamic body which disappears in the late prophase and reappears in the telophase stage of cell division.  Each nucleolus is produced by a Nucleolar-Organizing Region (NOR) of a chromosome which is termed as nuclear organizing chromosome.  All the eukaryotic cell contain at least one such chromosome. Its number may be one or more (several hundred per nucleus), but 1 to 4 being the most common.  The number of nucleoli per nucleus also differs.  The yeast cell contains one relatively large nucleolus with respect to its nuclear volume.  At the other extreme , Xenopus oocytes contain over 1000 nucleoli per nucleus.  It is a site of transcription of ribosomal RNA and assembly of ribosome.  It is responsible for synthesizing a large nascent precursor ribosomal RNA (pre-rRNA). The concomitant assembly of these RNAs with incoming ribosomal proteins generates small and large ribosomal subunits that then pass into the cytoplasm. 14-09-2024 Cell Morphology 16  Parts and Function of Nucleus Nucleolus Structure : It consists of three major regions.  Fibrillar centres : Containing rRNA genes in the form of partly condensed chromatin.  Dense Fibrillar component: Surrounds the fibrillar center, which contains RNA molecules in the process of transcription.  Granular regions: Contains mature ribosomal precursor particles (pre-ribosome assembly). Nucleolar-Organizing Regions (NORs)  The nucleolus organizing region or nucleolar organizer is a region of chromosome around which the nucleolus forms.  In the human, the five chromosomes contains the NORs, which can be identified as secondary constriction on the metaphase chromosomes.  The area of chromosome distal to a nucleolar organizer is called satellite. A chromosome with a secondary constriction usually associated with a nucleolus is called SAT-chromosome. 14-09-2024 Cell Morphology 17  Parts and Function of Nucleus Chromatin and Chromosome  A chromatin is an organized structure of DNA and protein that is found in the nucleus of eukaryotic cells. It contains a single dsDNA in coiled and condensed form.  Chromatin and chromosomes are basically the same thing. The difference is that chromatin is less condensed and extended DNA while chromosomes are highly condensed and extended DNA.  The word chromosome comes from the Greek word “chroma” which means colour and “soma” which means body due their property of being very strongly stained by particular dyes.  The extent of chromatin condensation varies during the life cycle of the cell.  In non-dividing as well as interphase stages of the cell, most of the chromatin remain relatively decondensed. The light- staining, less condensed portions of the chromatin is termed euchromatin. The region is transcriptionally active and contains most of the transcribing genes.  The darkly stained and highly condensed region of the chromatin is termed as heterochromatin. Because of its condensed state, this heterochromatin is generally believed to be transcriptionally silent. 14-09-2024 Cell Morphology 18 Centromere Parts and Function of Nucleus  The constricted region of linear chromosomes is known as the centromere.  It is usually located exactly in the center of the chromosome and in some cases is located almost at the chromosome's end.  The regions on the either side of the centromere are referred to as the chromosome's arms.  The centromeres serve both as the sites of association of sister chromatids and as the attachment sites for microtubules of the mitotic spindle. Telomere  Telomeres are specialized structures, which cap the ends of eukaryotic chromosomes.  It consists of a long array of short, tandemly repeated sequences.  Sequencing of telomeres from different organisms has shown that most are repetitive sequences with a high G content in the strand with its 3' end. Origin of Replication  The origin of replication (also called the replication origin) is a particular sequence in a chromosome at which replication is initiated. One chromosome contains multiples origin replication. 14-09-2024 Cell Morphology 19 Chromosome Number Parts and Function of Nucleus  All eukaryotic cells have multiple linear chromosomes.  Every cell maintains a characteristic number of chromosomes.  The number of chromosomes in a species has no specific significance nor does it indicate any relationship between two species which may have the same chromosome number.  The majority of eukaryotic cells are diploid that is they contain two copies of each chromosome. Function of Nucleus 1. Contains genetic information 2. Governs genetic expression and other vital functions of cell 3. Facilitates DNA replication for mitosis 4. Produces ribosomes responsible for protein synthesis 14-09-2024 Cell Morphology 20