Cell and Organelles PDF

Lecture 1 Cell Structure and Function Dr.Michael Jin The Fundamental Units of Life--Cells All organisms are made of cells The cell is the simplest collection of matter that can be alive (virus?) Cell structure is correlated to cellular function ...

Lecture 1 Cell Structure and Function Dr.Michael Jin The Fundamental Units of Life--Cells All organisms are made of cells The cell is the simplest collection of matter that can be alive (virus?) Cell structure is correlated to cellular function  Microscopy In a light microscope (LM), visible light is passed through a specimen and then through glass lenses Lenses refract (bend) the light, so that the image is magnified Three important parameters of microscopy – Magnification, the ratio of an object’s image size to its real size (LM max 1000X vs. EM 100,000X ) – Resolution, the measure of the clarity of the image, or the minimum distance of two distinguishable points (LM 200nm vs. EM 2nm ) – Contrast, visible differences in parts of the sample *Resolution is limited by the shortest wavelength of the radiation used for imaging  10 m Human height 1m Length of some nerve and The size range of cells Unaided eye muscle cells 0.1 m Chicken egg 1 cm Frog egg 1 mm Light microscopy Human egg 100 m Most plant and animal cells 10 m Nucleus most cells: 1-100 µm Most bacteria Electron microscopy Mitochondrion 1 m Smallest bacteria Super- 100 nm Viruses resolution microscopy Ribosomes 10 nm Proteins Lipids 1 nm Small molecules 0.1 nm Atoms Label the molecules with fluorescent dyes, which absorb ultraviolet radiation and emit visible light  GFP (Green Fluorescent Protein) Exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range Makes for an excellent tool in biology due to its ability to form internal chromophore without requiring any cofactors or enzymes/substrates Can be used in living cells or organisms  Electron Microscopes (EMs) Two basic types of EMs are used to study subcellular structures Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of a specimen, providing images that look 3-D Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen, and are used mainly to study the internal structure of cells  Three Domains of Life & Two types of cells Two types of cells: prokaryotic or eukaryotic Organisms of the domains Bacteria and Archaea consist of prokaryotic cells Protists, fungi, animals, and plants all consist of eukaryotic cells Comparing Prokaryotic and Eukaryotic Cells Basic features of all cells – Plasma membrane – Semifluid substance called cytosol – Chromosomes (carry genes in form of DNA) – Ribosomes (make proteins)  Prokaryotic cells are characterized by having – No nucleus – DNA in an unbound region called the nucleoid – No membrane-bound organelles – Most have cell wall  Eukaryotic cells are characterized by having – DNA in a nucleus that is bounded by a membranous nuclear envelope – Membrane-bound organelles cytosol  Plasma Membrane The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste The general structure of a biological membrane is a double layer of phospholipids Fluid Mosaic Model Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions A membrane is a fluid structure with a “mosaic” of various proteins embedded in it  Surface area to volume ratio (SA/V) Metabolic requirements set upper limits on the size of cells The surface area to volume ratio of a cell is critical (sufficient material exchange) As a cell increases in size, its volume increases much faster than its surface area Small cells have a greater surface area relative to volume  A Panoramic View of the Eukaryotic Cell A eukaryotic cell has internal membranes that partition the cell into organelles Plant and animal cells have most of the same organelles (what are the differences?) Animal Cell ENDOPLASMIC RETICULUM (ER) Nuclear Rough Smooth envelope Flagellum ER ER NUCLEUS Nucleolus Chromatin Centrosome Plasma membrane CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Ribosomes Microvilli Golgi apparatus Peroxisome Mitochondrion Lysosome  Nuclear Rough Plant Cell envelope endoplasmic NUCLEUS reticulum Smooth Nucleolus endoplasmic reticulum Chromatin Ribosomes Central vacuole Golgi apparatus Microfilaments Intermediate CYTOSKELETON filaments Microtubules Mitochondrion Peroxisome Plasma membrane Chloroplast Cell wall Plasmodesmata Wall of adjacent cell The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes The nucleus contains most of the DNA in a eukaryotic cell (where is the rest?) Ribosomes use the information from the DNA to make proteins The nuclear envelop encloses the nucleus, separating it from the cytoplasm The nuclear envelop is a double membrane; each membrane consists of a lipid bilayer Pores regulate the entry and exit of molecules from the nucleus The shape of the nucleus is maintained by the nuclear lamina, a network of protein filaments that maintains the shape of the nucleus  1 m Nucleus and its envelope Nucleus Nucleolus Chromatin Nuclear envelope: Inner membrane Outer membrane Nuclear pore Rough ER Pore complex Surface of nuclear envelope Ribosome Close-up 0.25 m of nuclear Chromatin envelope 1 m Pore complexes (TEM) Nuclear lamina (TEM)  In the nucleus, DNA is organized into discrete units called chromosomes Each chromosome is composed of a single DNA molecule associated with proteins (histones) 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 a densely stained region located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis and ribosome assembly  Ribosomes: Protein Factories Ribosomes are particles made of ribosomal RNA (rRNA) and protein Ribosomes carry out protein synthesis in two locations – In the cytosol (free ribosomes) – On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)  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  Endoplasmic Reticulum: Biosynthetic Factory 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 Functions of Smooth ER – Synthesizes lipids – Detoxifies drugs and poisons – Stores calcium ions Functions of Rough ER – Has bound ribosomes, the new polypeptide chains enter the ER lumen and are modified, like covalently attached to carbohydrates. These proteins are usually secretory or membrane proteins – Package proteins in transport vesicles, which go to Golgi Apparatus  Golgi Apparatus: Shipping and Receiving Center The Golgi apparatus consists of flattened membranous sacs called cisternae Functions of the Golgi apparatus – Modifies products of the ER – Sorts and packages materials into transport vesicles, and send them to their final destinations  Various Golgi enzymes modify the carbohydrate portions of glycoproteins. -- Carbohydrates are first added to proteins in rough ER. -- The carbohydrate on the resulting glycoprotein is modified as it passes through the rest of the ER and the Golgi. -- The Golgi removes some sugar monomers and substitutes others, producing a large variety of carbohydrates. （just one example） ABO blood type system  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 cell 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 Lysosomes A “road-map” of the secretory and endocytic pathways ER signal sequences direct ribosomes to the ER membrane  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  Mitochondria and chloroplasts change energy from one form to another Mitochondria are the sites of cellular respiration, a metabolic process that uses oxygen to generate ATP Chloroplasts are the sites of photosynthesis The Evolutionary Origins of Mitochondria and Chloroplasts Mitochondria and chloroplasts have similarities with bacteria – Enveloped by a double membrane, like engulfed bacteria – Contain free ribosomes and circular DNA molecules – Grow and reproduce somewhat independently in cells  Endosymbiont Theory – An early ancestor of eukaryotic cells engulfed a nonphotosynthetic prokaryotic cell, which formed an endosymbiont relationship with its host – The host cell and endosymbiont merged into a single organism, a eukaryotic cell with a mitochondrion – At least one of these cells may have taken up a photosynthetic prokaryote, becoming the ancestor of cells that contain chloroplasts  Mitochondria: Chemical Energy Conversion Mitochondria have a smooth outer membrane and an inner membrane folded into cristae The inner membrane creates two compartments: intermembrane space and mitochondrial matrix (the fluid-filled inner space) Some metabolic steps of cellular respiration are catalyzed in the matrix Cristae present a large surface area for enzymes that synthesize ATP  Chloroplasts: Capture of Light Energy Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis Chloroplasts are found in leaves and other green organs of plants and in algae Chloroplast structure includes – Thylakoids, membranous sacs, stacked to form a granum – Stroma, the internal fluid-filled space  Peroxisomes: Oxidation Peroxisomes are specialized metabolic compartments bounded by a single membrane Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen Peroxisomes produce hydrogen peroxide (toxic) and convert it to water Peroxisomes perform reactions with many different functions How peroxisomes are related to other organelles is still unknown  The cytoskeleton is a network of fibers that organizes structures and activities in the cell The cytoskeleton is a network of fibers extending throughout the cytoplasm It organizes the cell’s structures and activities, anchoring many organelles Three main types of fibers make up the cytoskeleton – Microtubules are the thickest of the three components – Microfilaments, also called actin filaments, are the thinnest components – Intermediate filaments are fibers Red: microfilaments (actins) Green: microtubules with diameters in a middle range  10 m Column of tubulin dimers 25 nm   Tubulin dimer  10 m Actin subunit 7 nm  5 m Keratin proteins Fibrous subunit (keratins coiled together) 812 nm  Microtubules Microtubules are hollow rods about 25 nm in diameter and about 200 nm to 25 microns long Functions of microtubules – Shaping the cell – Guiding movement of organelles – Separating chromosomes during cell division – Locomotion of the cell (cilia and flagella)  Vesicle Microtubule ATP Receptor for interacts with motor motor protein proteins to produce motility Motor protein Microtubule (ATP powered) of cytoskeleton (a) Microtubule Vesicles 0.25 m (b)  Centrosomes and Centrioles In many cells, microtubules grow out from a centrosome near the nucleus The centrosome is a “microtubule- organizing center” In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring Microtubules separate chromosomes during cell division Cilia and Flagella Microtubules control the beating of cilia and flagella, locomotor appendages of some cells Cilia and flagella share a common structure – A core of microtubules sheathed by the plasma membrane – A basal body that anchors the 9+2 cilium or flagellum – A motor protein called dynein, which drives the bending movements of a cilium or flagellum 9+0 Microfilaments (Actin Filaments) Microfilaments are solid rods about 7nm in diameter, built as a twisted double chain of actin subunits The structural role of microfilaments is to bear tension, resisting pulling forces within the cell They form a 3-D network called the cortex just inside the plasma membrane to help support the cell’s shape Bundles of microfilaments make up the core of microvilli of intestinal cells  Actin functions in muscle contraction together with the protein myosin In muscle cells, thousands of actin filaments are arranged parallel to one another Thicker filaments composed of myosin interdigitate with the thinner actin fibers  Localized contraction brought about by actin and myosin also drives amoeboid movement Pseudopodia (cellular extensions) extend and contract through the reversible assembly and contraction of actin subunits into microfilaments Extracellular components and connections between cells help coordinate cellular activities Most cells synthesize and secrete materials that are external to the plasma membrane These extracellular structures include – Cell walls of plants – The extracellular matrix (ECM) of animal cells – Intercellular junctions  Cell Walls of Plants The cell wall is an extracellular structure that distinguishes plant cells from animal cells Prokaryotes, fungi, and some protists also have cell walls The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein  Plant cell walls may have multiple layers – Primary cell wall: relatively thin and flexible – Secondary cell wall (in some cells): added between the plasma membrane and the primary cell wall Plasmodesmata are channels between adjacent plant cells  Extracellular Matrix (ECM) of Animal Cells Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM) The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin ECM proteins bind to receptor proteins in the plasma membrane called integrins  Cell Junctions Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact Intercellular junctions facilitate this contact There are several types of intercellular junctions – Plasmodesmata – Tight junctions – Desmosomes – Gap junctions  Plasmodesmata in Plant Cells Plasmodesmata are channels that perforate plant cell walls Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells At tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid Desmosomes (anchoring junctions) fasten cells together into strong sheets Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells