Chapter 6 A Tour of the Cell The Importance of Cells All organisms are made of cells The cell is the simplest collection of living matter; the smallest unit of life. Figure 6.1 Microscopy To study cells, biologists use microscopes and the tools of biochemistry Scientists use microscopes to see cells too small to see with the naked eye Types of microscopes ◦ Light microscopes ◦ Electron microscopes Microscopy Magnification – The ratio of an object’s image size to its actual size Resolution – The measure of clarity of the object’s image; the minimum distance two distinct points can be separated by and still be distinguished as two points. Microscopy Light microscopes (LMs) ◦ Pass visible light through a specimen ◦ Magnify structures w/ lenses ◦ Limited magnification; cannot resolve detail finer than 2 μm, or 200 nm. ◦ Up to 1000x magnification 10 m 1m Human height Length of some nerve and muscle cells 0.1 m ◦ Can be used to visualize different sized cellular structures ◦ Have other disadvantages and advantages associated with them Figure 6.2 1 cm Frog egg 1 mm 100 µm Most plant and Animal cells 10 µ m Nucleus Most bacteria Mitochondrion 1µm 100 nm Smallest bacteria Viruses 10 nm Ribosomes Proteins 1 nm Lipids Small molecules 0.1 nm Atoms Measurements 1 centimeter (cm) = 102 meter (m) = 0.4 inch 1 millimeter (mm) = 10–3 m 1 micrometer (µm) = 10–3 mm = 10–6 m 1 nanometer (nm) = 10–3 mm = 10–9 m Electron microscope Different types of microscopes Electron microscope Chicken egg Light microscope Microscopy Microscopy RESULT TECHNIQUE (a) Brightfield (unstained specimen). Passes light directly through specimen. Unless cell is naturally pigmented or artificially stained, image has little contrast. [Parts (a)–(d) show a human cheek epithelial cell.] (b) Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved). (c) Phase-contrast. Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells. Figure 6.3 50 µm (d) Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density, making the image appear almost 3D. (e) Fluorescence. Shows the locations of specific molecules in the cell by tagging the molecules with fluorescent dyes or antibodies. These fluorescent substances absorb ultraviolet radiation and emit visible light, as shown here in a cell from an artery. 50 µm (f) Confocal. Uses lasers and special optics for “optical sectioning” of fluorescently-stained specimens. Only a single plane of focus is illuminated; out-of-focus fluorescence above and below the plane is subtracted by a computer. A sharp image results, as seen in stained nervous tissue (top), where nerve cells are green, support cells are red, and regions of overlap are yellow. A standard fluorescence micrograph (bottom) of this relatively thick tissue is blurry. 50 µm Microsopcy Electron microscopes (EMs) focus a beam of electrons either through or over the surface of a cell. ◦ Scanning Electron Microscope – Electrons pass over surface of cell; resulting image is a three dimensional view of the surface of a cell. ◦ Transmission Electron Microscope – Electrons pass through a cell (slice); resulting image shows internal structures of cell. Microscopy Scanning electron microscope (SEM) ◦ detail surface of a specimen (3D) TECHNIQUE RESULTS 1 µm Cilia (a) Scanning electron microscopy (SEM). Micrographs taken with a scanning electron microscope show a 3D image of the surface of a specimen. This SEM shows the surface of a cell from a rabbit trachea (windpipe) covered with motile organelles called cilia. Beating of the cilia helps move inhaled debris upward toward the throat. Figure 6.4 (a) Microscopy Transmission electron microscope (TEM) ◦ details internal ultrastructure of cells Longitudinal section of cilium (b) Transmission electron microscopy (TEM). A transmission electron microscope profiles a thin section of a specimen. Here we see a section through a tracheal cell, revealing its ultrastructure. In preparing the TEM, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections. Figure 6.4 (b) Cross section of cilium 1 µm Microscopy Biological samples stained with heavy metals Electrons on cell surface become excited and can be detected electronically. Uses electromagnets as lenses rather than glass. Microscopy Cytology – The study of cell structure Brainstorm: Compare and contrast the different types of microscopes. What are some advantages to each type? What are some disadvantages? Microscopy What type of microscope would be used to study: ◦ Changes in shape of a living white blood cell ◦ Details of the surface structure of a hair ◦ The detailed structure of an organelle? Isolating Organelles by Cell Fractionation Cell fractionation ◦ Takes cells apart & separates organelles from 1 another ◦ Centrifuge fractionates cells into their component parts Homogenization Tissue cells 1000 g Homogenate (1000 times the force of gravity) Differential centrifugation 10 min Supernatant poured into next tube 20,000 g 20 min Pellet rich in nuclei and cellular debris Figure 6.5 80,000 g 60 min 150,000 g 3 hr Pellet rich in mitochondria (and chloroplasts if cells are from a Pellet rich in plant) “microsomes” (pieces of plasma membranes and Pellet rich in cells’ internal ribosomes membranes) RESULTS In the original experiments, the researchers used microscopy to identify the organelles in each pellet, establishing a baseline for further experiments. In the next series of experiments, researchers used biochemical methods to determine the metabolic functions associated with each type of organelle. Researchers currently use cell fractionation to isolate particular organelles in order to study further details of their function. Figure 6.5 Prokaryotic and Eukaryotic Cells Review: What are the main differences between eukaryotic cells and prokaryotic cells? Create a venn diagram to compare and contrast the structures that are found in eukaryotic and prokaryotic cells. Define all of the terms (including a description of the function of organelles). Using those definitions, write a brief explanation of the different capabilities of each type of cell. Comparing Prokaryotic & Eukaryotic Cells Plasma membrane Cytoplasm Cytosol Chromosomes Ribosomes Brainstorm: What is the function of ribosomes? Hint: Look at the word. What other term does it remind you of? Prokaryotic Cells “Pro” + “karyon” (kernel) No nucleus DNA is found in the nucleoid Nucleoid is not bound by a membrane Pili: attachment structures on the surface of some prokaryotes Nucleoid: region where the cell’s DNA is located (not enclosed by a membrane) Ribosomes: organelles that synthesize proteins Bacterial chromosome (a) A typical rod-shaped bacterium Figure 6.6 A, B Plasma membrane: membrane enclosing the cytoplasm Cell wall: rigid structure outside the plasma membrane Capsule: jelly-like outer coating of many prokaryotes 0.5 µm Flagella: locomotion organelles of some bacteria (b) A thin section through the bacterium Bacillus coagulans (TEM) Eukaryotic Cells “Eu” + “karyon” Membrane bound nucleus ◦ Nuclear envelope Prokaryotes vs Eukaryotes Brainstorm: Why does the size of the cell matter? Prokaryotes vs Eukaryotes A smaller cell ◦ Has higher surface area to volume ratio ◦ Makes it easier to transport enough through membrane Surface area increases while total volume remains constant 5 1 1 Figure 6.7 Total surface area (height width number of sides number of boxes) 6 150 750 Total volume (height width length number of boxes) 1 125 125 Surface-to-volume ratio (surface area volume) 6 12 6 Eukaryotic Cells Plasma membrane acts as a selective barrier (semipermeable) ◦ Allows passage of nutrients Outside of cell & waste Carbohydrate side chain Hydrophilic region Inside of cell 0.1 µm Hydrophobic region Figure 6.8 A, B (a) TEM of a plasma membrane. The plasma membrane, here in a red blood cell, appears as a pair of dark bands separated by a light band. Hydrophilic region Phospholipid Proteins (b) Structure of the plasma membrane Eukaryotic Cells Membrane bound organelles ◦ Compartmentalize the cell ◦ Membranes participate in metabolic activity Brainstorm: Why is it important for eukaryotic cells to be compartmentalized? Eukaryotic Cells Plant cells vs animal cells ◦ Have most of the same organelles ◦ More similar to each other than either are to prokaryotic cells Practice: Just like you did for prokaryotes vs eukaryotes, create a venn diagram comparing and contrasting plant and animal cells. Focus on organelles, and include a key that defines each of the terms. A animal cell ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Nuclear envelope Nucleolus NUCLEUS Chromatin Flagelium Plasma membrane Centrosome CYTOSKELETON Microfilaments Intermediate filaments Ribosomes Microtubules Microvilli Golgi apparatus Peroxisome Figure 6.9 Mitochondrion Lysosome In animal cells but not plant cells: Lysosomes Centrioles Flagella (in some plant sperm) A plant cell Nuclear envelope Nucleolus Chromatin NUCLEUS Centrosome Rough endoplasmic reticulum Smooth endoplasmic reticulum Ribosomes (small brwon dots) Central vacuole Tonoplast Golgi apparatus Microfilaments Intermediate filaments CYTOSKELETON Microtubules Mitochondrion Peroxisome Plasma membrane Chloroplast Cell wall Plasmodesmata Wall of adjacent cell Figure 6.9 In plant cells but not animal cells: Chloroplasts Central vacuole and tonoplast Cell wall Plasmodesmata Eukaryotic Cells Genetic instructions are housed in the nucleus and carried out by the ribosomes Nucleus ◦ ◦ ◦ ◦ Genetic library of the cell Bound by nuclear envelope (double membrane) Usually the largest, most obvious organelle Protein studded surface Pore complex Nuclear Lamina – maintains shape Chromosomes – made of chromatin Nucleolus – cite of rRNA synthesis Eukaryotic Cells nuclear envelope ◦ Encloses the nucleus, separates contents from cytoplasm Nucleus 1 µm Nucleolus Chromatin Nucleus Nuclear envelope: Inner membrane Outer membrane Nuclear pore Pore complex Rough ER Surface of nuclear envelope. 1 µm Ribosome 0.25 µm Close-up of nuclear envelope Figure 6.10 Pore complexes (TEM). Nuclear lamina (TEM). Eukaryotic Cells Ribosomes ◦ Made of ribosomal RNA (rRNA) and protein ◦ Carry out protein synthesis (translation) ◦ Free ribosomes – suspended in cytosol ◦ Bound ribosomes – attached to rough ER or nuclear envelope ◦ Ribosomes can alternate roles Ribosomes ER Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes Large subunit 0.5 µm TEM showing ER and ribosomes Figure 6.11 Small subunit Diagram of a ribosome Eukaryotic Cells Endomembrane system Regulates protein traffic and performs metabolic functions in the cell ◦ Protein synthesis and transport ◦ Metabolism of lipids ◦ Detoxification Structural differences mediate function ◦ Endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, plasma membrane. The Endoplasmic Reticulum: Biosynthetic Factory Endoplasmic reticulum accounts for more than half of the total membrane in eukaryotic cells Net-like structure made up of membranous tubules and cisternae (sacs of liquid) Rough ER – Covered in ribosomes Smooth ER – Lacks ribosomes ER membrane ◦ continuous with/attached to the nuclear envelope Smooth ER Rough ER Nuclear envelope ER lumen Cisternae Ribosomes Transitional ER Transport vesicle Smooth ER Rough ER 200 µm Figure 6.12 Functions of Smooth ER ◦ Synthesizes lipids ◦ Metabolizes carbohydrates ◦ Stores Ca+ Releases into cytosol in response to nerve impulse, causing muscle contraction ◦ Detoxifies poison (adds hydroxyl groups to drugs) Functions of Rough ER ◦ Studded with ribosomes ◦ Makes proteins and membranes, distributed by transport vesicles (sacs of membrane) Secreted proteins Membrane-bound proteins ◦ Glycoproteins – secretory proteins, covalently bonded to carbohydrates ◦ Synthesizes membranes Phospholipids Embeds proteins directly into membrane The Golgi Apparatus: Shipping and Receiving Center Golgi apparatus ◦ ◦ ◦ ◦ gets transport vesicles from rough ER flattened membranous sacs called cisternae Modifies products of rough ER Makes certain macromolecules http://www.hhmi.org/bulletin/winter2014/express-shipping https://www.youtube.com/watch?v=jazs6sR Q2og http://www.ted.com/talks/david_bolinsky _animates_a_cell Golgi apparatus Golgi apparatus cis face (“receiving” side of Golgi apparatus) 1 Vesicles move 2 Vesicles coalesce to 6 Vesicles also form new cis Golgi cisternae from ER to Golgi transport certain Cisternae proteins back to ER 3 Cisternal maturation: Golgi cisternae move in a cisto-trans direction Figure 6.13 5 Vesicles transport specific proteins backward to newer Golgi cisternae 0.1 0 µm 4 Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma membrane for secretion trans face (“shipping” side of Golgi apparatus) TEM of Golgi apparatus Lysosomes: Digestive Compartments Membranous sacs Full of digestive enzymes Internally acidic Synthesized by the rough ER, processed by the Golgi Phagocytosis – intracellular digestion ◦ Cells engulf smaller objects (sometimes organisms), forming a food vacuole ◦ Food vacuole fuses with lysosome Lysosomes 1 µm Nucleus Lysosome Lysosome contains active hydrolytic enzymes Food vacuole fuses with lysosome Hydrolytic enzymes digest food particles Digestive enzymes Lysosome Plasma membrane Digestion Food vacuole Figure 6.14 A (a) Phagocytosis: lysosome digesting food Lysosomes Autophagy- self eating (vesicle surrounds damaged organelle) Lysosome containing two damaged organelles 1µm Mitochondrion fragment Peroxisome fragment Lysosome fuses with vesicle containing damaged organelle Hydrolytic enzymes digest organelle components Lysosome Vesicle containing damaged mitochondrion Digestion (b) Autophagy: lysosome breaking down damaged organelle Figure 6.14 B Vacuoles: Diverse Maintenance Compartments Plant or fungal cells have at least one vacuole Food vacuoles – surround ingested materials so that they can be broken down Contractile vacuoles – pump excess water out of a cell Central vacuole – enclosed by tonoplast, also works to maintain homeostasis. Cell sap – solution inside of the central vacuole Central Vacuole Central vacuole Cytosol Tonoplast Nucleus Central vacuole Cell wall Chloroplast Figure 6.15 5 µm The Endomembrane System: A Review Compartmental organization of a cell System of interconnected membranes Function, composition, and contents modified with progression from ER to vacuoles Brainstorm: How do transport vesicles serve to integrate the endomembrane system? Relationships within the endomembrane system Nuclear envelope is 1 connected to rough ER, which is also continuous with smooth ER Nucleus Rough ER 2 Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golgi Smooth ER cis Golgi Nuclear envelop Golgi 3 pinches off transport Vesicles and other vesicles that give rise to lysosomes and Vacuoles Plasma membrane trans Golgi 4 Lysosome available for fusion with another vesicle for digestion Figure 6.16 5 Transport vesicle carries 6 proteins to plasma membrane for secretion Plasma membrane expands by fusion of vesicles; proteins are secreted from cell Mitochondria and Chloroplasts Change energy from one form to another Mitochondria ◦ Sites of cellular respiration Chloroplasts ◦ Only in plants & plantlike protists; photosynthesis Mitochondria Chemical energy conversion – site of cellular respiration Generates ATP from fuel sources (sugars, fats, etc…) Double membrane ◦ Outer = smooth ◦ Inner = convoluted; infoldings called cristae Intermembrane space and mitochondrial matrix Number of mitochondria related to metabolic activity of a cell Mitochondria; enclosed by 2 membranes ◦ smooth outer membrane ◦ inner membrane folded into cristae Mitochondrion Intermembrane space Outer membrane Free ribosomes in the mitochondrial matrix Inner membrane Cristae Matrix Mitochondrial DNA 100 µm Brainstorm: Why is the inner membrane folded? Figure 6.17 Chloroplasts: Capture of Light Energy Plastids – family of plant organelles ◦ Amyloplast – colorless; stores starch ◦ Chromoplast – pigmented; gives color to flowers ◦ Chloroplast Chloroplast ◦ has chlorophyll – green pigment ◦ Enzymes and molecules that function in photosynthetic production Chloroplasts Leaves and green algae Chloroplast structure: ◦ Thylakoids- membranous sacs; flattened ◦ Stroma- internal fluid; contains chloroplast DNA Chloroplast Ribosomes Stroma Chloroplast DNA Inner and outer membranes Granum Figure 6.18 1 µm Thylakoid Peroxisomes: Oxidation ◦ Make H2O2 (hydrogen peroxide) and convert it to H2O ◦ Single membrane; transfers hydrogen ◦ Break down fatty acids to transfer to mitochondria Chloroplast Peroxisome Mitochondrion Brainstorm: What role would a peroxisome in a liver cell have? 1 µm Figure 6.19 The Cytoskeleton A network of fibers that organizes structures and activities in the cell Microtubule Figure 6.20 0.25 µm Microfilaments Roles of the Cytoskeleton: Support, Motility, and Regulation Cytoskeleton ◦ Gives mechanical support to the cell ◦ involved in cell motility, using motor proteins ATP Vesicle Receptor for motor protein Motor protein Microtubule (ATP powered) of cytoskeleton (a) Motor proteins that attach to receptors on organelles can “walk” the organelles along microtubules or, in some cases, microfilaments. Vesicles Microtubule 0.25 µm Figure 6.21 A, B (b) Vesicles containing neurotransmitters migrate to the tips of nerve cell axons via the mechanism in (a). In this SEM of a squid giant axon, two vesicles can be seen moving along a microtubule. (A separate part of the experiment provided the evidence that they were in fact moving.) 3 types of fibers make up the cytoskeleton Table 6.1 The wacky history of cell theory - Lauren Royal-Woods | TED-Ed Microtubules 1.) Microtubules ◦ Shape the cell ◦ Guide movement of organelles ◦ Help separate chromo copies (mitosis) Centrosomes and Centrioles Centrosome- “microtubule-organizing center” Cilia and Flagella Cilia & flagella ◦ have specialized arrangements of microtubules ◦ locomotor appendages of some cells Brainstorm: How are cilia and flagella similar? How are they different? Flagella beating pattern (a) Motion of flagella. A flagellum usually undulates, its snakelike motion driving a cell in the same direction as the axis of the flagellum. Propulsion of a human sperm cell is an example of flagellatelocomotion (LM). Direction of swimming Figure 6.23 A 1 µm Ciliary motion (b) Motion of cilia. Cilia have a backand-forth motion that moves the cell in a direction perpendicular to the axis of the cilium. A dense nap of cilia, beating at a rate of about 40 to 60 strokes a second, covers this Colpidium, a freshwater protozoan (SEM). Figure 6.23 B 15 µm Cilia and flagella share a common ultrastructure Outer microtubule doublet Dynein arms 0.1 µm Central microtubule Outer doublets cross-linking proteins inside Microtubules Radial spoke Plasma membrane Basal body (b) 0.5 µm (a) 0.1 µm Triplet (c) Figure 6.24 A-C Cross section of basal body Plasma membrane The protein dynein ◦ Is responsible for the bending movement of cilia and flagella Microtubule doublets ATP Dynein arm (a) Powered by ATP, the dynein arms of one microtubule doublet grip the adjacent doublet, push it up, release, and then grip again. If the two microtubule doublets were not attached, they would slide relative to each other. Figure 6.25 A ATP Outer doublets cross-linking proteins Anchorage in cell (b) In a cilium or flagellum, two adjacent doublets cannot slide far because they are physically restrained by proteins, so they bend. (Only two of the nine outer doublets in Figure 6.24b are shown here.) Figure 6.25 B 1 3 2 (c) Localized, synchronized activation of many dynein arms probably causes a bend to begin at the base of the Cilium or flagellum and move outward toward the tip. Many successive bends, such as the ones shown here to the left and right, result in a wavelike motion. In this diagram, the two central microtubules and the cross-linking proteins are not shown. Figure 6.25 C Microfilaments (Actin Filaments) Microfilaments are twisted double chains of actin ◦ ◦ ◦ ◦ ◦ Actin = globular protein Branching network connected by proteins Tension bearing (pulling forces) Connected with myosin (motor protein) Ameoboid movement (pseudopodia) and cytoplasmic streaming Microfilaments Microvillus Plasma membrane Microfilaments (actin filaments) Intermediate filaments Figure 6.26 0.25 µm Microfilaments Microfilaments that function in cellular motility ◦ Contain the protein myosin in addition to actin Muscle cell Actin filament Myosin filament Myosin arm Figure 6.27 A (a) Myosin motors in muscle cell contraction. Amoeboid movement ◦ Involves the contraction of actin & myosin filaments Cortex (outer cytoplasm): gel with actin network Inner cytoplasm: sol with actin subunits Extending pseudopodium Figure 6.27 B (b) Amoeboid movement Cytoplasmic streaming ◦ Is another form of locomotion created by microfilaments Nonmoving cytoplasm (gel) Chloroplast Streaming cytoplasm (sol) Parallel actin filaments Figure 6.27 C (b) Cytoplasmic streaming in plant cells Cell wall Intermediate Filaments Support cell shape Fixes organelles in space No set structure or function (diverse class of cytoskeletal elements) ◦ Constructed from proteins from specific family (e.g. keratin) More permanent than microtubules and microfilaments Cell Walls of Plants An extracellular structure of plant cells that distinguishes them from animal cells Cellulose fibers embedded in other polysaccharides and protein Middle lamina (sticky) Multiple layers ◦ Primary cell wall ◦ Secondary cell wall The Extracellular Matrix (ECM) of Animal Cells Animal cells do not have a cell wall Instead are connected by extracellular matrix Composed mostly of glycoproteins ◦ Collagen ◦ Proteoglycans ◦ Fibronectin Connected to proteins embedded in plasma membrane called integrins EXTRACELLULAR FLUID Collagen A proteoglycan complex Polysaccharide molecule Carbohydrates Core protein Fibronectin Plasma membrane Integrin Figure 6.29 Integrins Microfilaments CYTOPLASM Proteoglycan molecule Extracellular Matrix Functions ◦ ◦ ◦ ◦ Support Adhesion Movement Regulation Intercellular Junctions Plants: Plasmodesmata Plasmodesmata ◦ channels in plant cell walls Cell walls Interior of cell Interior of cell Figure 6.30 0.5 µm Plasmodesmata Plasma membranes Animals: Tight Junctions, Desmosomes, and Gap Junctions Animals have 3 types of intercellular junctions ◦ Tight junctions ◦ Desmosomes ◦ Gap junctions Types of intercellular junctions in animals TIGHT JUNCTIONS Tight junction Tight junctions prevent fluid from moving across a layer of cells 0.5 µm At tight junctions, the membranes of neighboring cells are very tightly pressed against each other, bound together by specific proteins (purple). Forming continuous seals around the cells, tight junctions prevent leakage of extracellular fluid across A layer of epithelial cells. DESMOSOMES Desmosomes (also called anchoring junctions) function like rivets, fastening cells Together into strong sheets. Intermediate Filaments made of sturdy keratin proteins Anchor desmosomes in the cytoplasm. Tight junctions Intermediate filaments Desmosome Gap junctions Space between Plasma membranes cells of adjacent cells Figure 6.31 1 µm Extracellular matrix Gap junction 0.1 µm GAP JUNCTIONS Gap junctions (also called communicating junctions) provide cytoplasmic channels from one cell to an adjacent cell. Gap junctions consist of special membrane proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass. Gap junctions are necessary for communication between cells in many types of tissues, including heart muscle and animal embryos. The Cell: A Living Unit Greater Than the Sum of Its Parts Cells rely on the integration of structures and organelles in order to function 5 µm Figure 6.32