Chapter 6 A Tour of the Cell

Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density, making the image appear almost 3D. 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. 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 (d) (e) (f)

Figure 6.3 Research Method Light Microscopy TECHNIQUE RESULTS 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.] (a) Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved). (b) Phase-contrast. Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells. (c) 50 µm

Figure 6.1 A cell and its skeleton viewed by fluorescence microscopy

Figure 6.2 The size range of cells 10 m Human height 1 m Length of some nerve and muscle cells 0.1 m Unaided eye Chicken egg 1 cm Frog egg 1 mm 100 µm Most plant and animal cells Light microscope 10 µm nucleus Nucleus Most bacteria Most bacteria Mitochondrion 1 µm Electron microscope Smallest bacteria 100 nm Viruses Ribosomes 10 nm Proteins Lipids Measurements 1 centimeter (cm) = 102 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 µm = 10 9 m 1 nm Small molecules 0.1 nm Atoms

Figure 6.6 A prokaryotic cell 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 Plasma membrane: membrane enclosing the cytoplasm Cell wall: rigid structure outside the plasma membrane Capsule: jelly-like outer coating of many prokaryotes Flagella: locomotion organelles of some bacteria (a) A typical rod-shaped bacterium (b) A thin section through the bacterium Bacillus coagulans (TEM) 0.5 µm

Figure 6.7 Geometric relationships between surface area and volume Surface area increases while total volume remains constant 5 1 Total surface area (height  width  number of sides  number of boxes) Total volume (height  width  length  number of boxes) Surface-to-volume ratio (surface area  volume) 6 150 125 12 750

Figure 6.8 The plasma membrane Carbohydrate side chain Outside of cell Inside of cell Hydrophilic region Hydrophobic (b) Structure of the plasma membrane Phospholipid Proteins 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. (a) 0.1 µm

Figure 6.9 Exploring Animal and Plant Cells Animal Cell ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Centrosome CYTOSKELETON Microfilaments Microtubules Microvilli Peroxisome Mitochondrion Lysosome Golgi apparatus Ribosomes Plasma membrane In animal cells but not plant cells: Lysosomes Centrioles Flagella (in some plant sperm) Nuclear envelope Nucleolus Chromatin NUCLEUS Flagelium Intermediate filaments

Animal and Plant Cells: Plant Cell Ribosomes ( small brown dots ) Central vacuole Microfilaments Intermediate filaments Microtubules Rough endoplasmic reticulum Smooth Chromatin NUCLEUS Centrosome Nuclear envelope Nucleolus Chloroplast Plasmodesmata Wall of adjacent cell Cell wall Plasma membrane Mitochondrion Golgi apparatus Peroxisome In plant cells but not animal cells: Chloroplasts Central vacuole and tonoplast Tonoplast CYTOSKELETON

Figure 6.10 The nucleus and its envelope Nucleolus Chromatin Nuclear envelope: Inner membrane Outer membrane Nuclear pore Rough ER Pore complex Surface of nuclear envelope. TEM of a specimen prepared by a special technique known as freeze-fracture. Close-up of nuclear envelope Ribosome 1 µm 0.25 µm Pore complexes (TEM). Each pore is ringed by protein particles. Nuclear lamina (TEM). The netlike lamina lines the inner surface of the nuclear envelope.

TEM showing ER and ribosomes Figure 6.11 Ribosomes Ribosomes ER Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes Large subunit Small TEM showing ER and ribosomes Diagram of a ribosome 0.5 µm

Figure 6.12 Endoplasmic reticulum (ER) Smooth ER Rough ER ER lumen Cisternae Ribosomes Transport vesicle Transitional ER 200 µm Nuclear envelope

Figure 6.13 The Golgi apparatus cis face (“receiving” side of Golgi apparatus) Vesicles move from ER to Golgi Vesicles also transport certain proteins back to ER Vesicles coalesce to form new cis Golgi cisternae Cisternal maturation: Golgi cisternae move in a cis- to-trans direction Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma mem- brane for secretion Vesicles transport specific proteins backward to newer Cisternae trans face (“shipping” side of TEM of Golgi apparatus 0.1 0 µm 1 6 5 2 3 4

Figure 6.14 Lysosomes 1 µm Nucleus Lysosome containing Lysosome contains active hydrolytic enzymes Food vacuole fuses with lysosome Hydrolytic enzymes digest food particles Lysosome containing two damaged organelles 1 µ m Mitochondrion fragment Peroxisome Lysosome fuses with vesicle containing damaged organelle Hydrolytic enzymes digest organelle components Vesicle containing damaged mitochondrion Digestion Food vacuole Plasma membrane Digestive (a) Phagocytosis: lysosome digesting food (b) Autophagy: lysosome breaking down damaged organelle

Figure 6.15 The plant cell vacuole Central vacuole Cytosol Tonoplast Central vacuole Nucleus Cell wall Chloroplast 5 µm

Figure 6.16 Review: relationships among organelles of the endomembrane system Nuclear envelope is connected to rough ER, which is also continuous with smooth ER 1 Nucleus Rough ER Smooth ER Nuclear envelope 3

Figure 6.16 Review: relationships among organelles of the endomembrane system Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes and vacuoles Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golgi 3 4 5 Nuclear envelope Nuclear envelope is connected to rough ER, which is also continuous with smooth ER 2 Nucleus Rough ER Smooth ER cis Golgi trans Golgi Lysosome available for fusion with another vesicle for digestion Transport vesicle carries proteins to plasma membrane for secretion Transport vesicle 1

Figure 6.16 Review: relationships among organelles of the endomembrane system Plasma membrane expands by fusion of vesicles; proteins are secreted from cell Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes and vacuoles Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golgi 3 4 5 6 Nuclear envelope Nuclear envelope is connected to rough ER, which is also continuous with smooth ER 2 Nucleus Rough ER Smooth ER cis Golgi trans Golgi Plasma membrane Lysosome available for fusion with another vesicle for digestion Transport vesicle carries proteins to plasma membrane for secretion Transport vesicle 1

Figure 6.17 The mitochondrion, site of cellular respiration Intermembrane space Outer membrane Free ribosomes in the mitochondrial matrix Mitochondrial DNA Inner Cristae Matrix 100 µm

Figure 6.18 The chloroplast, site of photosynthesis Granum Chloroplast DNA Ribosomes Stroma Inner and outer membranes Thylakoid 1 µm

Figure 6.19 Peroxisomes Chloroplast Peroxisome Mitochondrion 1 µm

Figure 6.20 The cytoskeleton Microtubule 0.25 µm Microfilaments

Figure 6.21 Motor proteins and the cytoskeleton Vesicle ATP Receptor for motor protein Motor protein (ATP powered) Microtubule of cytoskeleton (a) Motor proteins that attach to receptors on organelles can “walk” the organelles along microtubules or, in some cases, microfilaments. Vesicles 0.25 µm (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.)

Table 6.1 The Structure and Function of the Cytoskeleton

Figure 6.22 Centrosome containing a pair of centrioles Microtubule Centrioles 0.25 µm Longitudinal section of one centriole Microtubules Cross section of the other centriole

Figure 6.23 A comparison of the beating of flagella and cilia (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 flagellate locomotion (LM). (b) Motion of cilia. Cilia have a back- and-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). Direction of swimming Direction of organism’s movement Direction of active stroke recovery stroke 15 µm 1 µm

Figure 6.24 Ultrastructure of a eukaryotic flagellum or cilium Outer microtubule doublet (a) A longitudinal section of a cilium shows micro- tubules running the length of the structure (TEM). (c) Basal body: The nine outer doublets of a cilium or flagellum extend into the basal body, where each doublet joins another microtubule to form a ring of nine triplets. Each triplet is connected to the next by non-tubulin proteins (blue). The two central microtubules terminate above the basal body (TEM). (b) A cross section through the cilium shows the ”9 + 2“ arrangement of microtubules (TEM). The outer micro- tubule doublets and the two central microtubules are held together by cross-linking proteins (purple in art), including the radial spokes. The doublets also have attached motor proteins, the dynein arms (red in art). Dynein arms Central microtubule Outer doublet cross-linking proteins Radial spoke Microtubules Plasma membrane Basal body 0.5 µm 0.1 µm Cross section of basal body Triplet Plasma membrane

Figure 6.25 How dynein “walking” moves flagella and cilia Microtubule doublets ATP Dynein arm 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. (a)

Outer doublets cross-linking proteins Anchorage in cell ATP (b) In a cilium or flagellum, two adjacent doublets cannot slide far because they are physically restrained, so they bend. (Only two of the nine outer doublets in Figure 6.24b are shown here.)

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. (c) 1 3 2

Figure 6.26 A structural role of microfilaments Microvillus Plasma membrane Microfilaments (actin filaments) Intermediate filaments

Figure 6.27 Microfilaments and motility Muscle cell Actin filament Myosin filament Myosin motors in muscle cell contraction. Cortex (outer cytoplasm): gel with actin network Inner cytoplasm: sol with actin subunits Extending pseudopodium (a) (b) Amoeboid movement . Nonmoving cytoplasm (gel) Chloroplast Streaming cytoplasm (sol) Parallel actin filaments Cell wall (b) Cytoplasmic streaming in plant cells. Myosin arm

Figure 6.28 Plant cell walls Central vacuole of cell Plasma membrane Primary cell wall Middle lamella 1 µm Central vacuole of cell Central vacuole Cytosol Plant cell walls Plasmodesmata Secondary cell wall Plasma membrane

Figure 6.29 Extracellular matrix (ECM) of an animal cell A proteoglycan complex consists of hundreds of proteoglycan molecules attached noncovalently to a single long polysac- charide molecule. Collagen fibers are embedded in a web of complexes. Fibronectin attaches the ECM to integrins embedded in the plasma membrane. Plasma membrane EXTRACELLULAR FLUID Micro- filaments CYTOPLASM Integrins are membrane proteins that are bound to the ECM on one side and to associated proteins attached to microfilaments on the other. This linkage can transmit stimuli between the cell’s external environment and its interior and can result in changes in cell behavior. Polysaccharide molecule Carbo- hydrates Proteoglycan Core protein Integrin

Figure 6.30 Plasmodesmata between plant cells Cell walls Interior of cell 0.5 µm Plasmodesmata Plasma membranes

Figure 6.31 Exploring Intercellular Junctions in Animal Tissues Tight junctions prevent fluid from moving across a layer of cells Tight junction 0.5 µm 1 µm Space between cells Plasma membranes of adjacent cells Extracellular matrix Gap junction Tight junctions 0.1 µm Intermediate filaments Desmosome Gap junctions At tight junctions, the membranes of neighboring cells are very tightly pressed against each other, bound together by specific proteins (purple). Forming continu- ous seals around the cells, tight junctions prevent leakage of extracellular fluid across a layer of epithelial cells. 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. 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 commu- nication between cells in many types of tissues, including heart muscle and animal embryos. TIGHT JUNCTIONS DESMOSOMES GAP JUNCTIONS

Figure 6.32 The emergence of cellular functions from the cooperation of many organelles