Chapter 6

1. Chapter 6 A Tour of the Cell

2. (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

3. TECHNIQUE RESULTS (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.] 50 µm Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved). (b) (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 Research Method Light Microscopy

4. 10 µm Figure 6.1 A cell and its skeleton viewed by fluorescence microscopy

5. 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 Light microscope Most plant and animal cells 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 Atoms 0.1 nm

6. Pili: attachment structures on the surface of some prokaryotes Nucleoid: region wherethe 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 0.5 µm Flagella: locomotion organelles of some bacteria (a) A typical rod-shaped bacterium (b) A thin section through the bacterium Bacillus coagulans (TEM) Figure 6.6 A prokaryotic cell

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

8. Outside of cell Carbohydrate side chain Hydrophilic region Inside of cell 0.1 µm Hydrophobic region (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 Figure 6.8 The plasma membrane

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

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

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

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

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

14. Golgi apparatus cis face (“receiving” side of Golgi apparatus) 4 2 5 6 3 1 Vesicles coalesce to form new cis Golgi cisternae Vesicles move from ER to Golgi 0.1 0 µm Vesicles also transport certain proteins back to ER 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 trans face (“shipping” side of Golgi apparatus) Vesicles transport specific proteins backward to newer Golgi cisternae TEM of Golgi apparatus Figure 6.13 The Golgi apparatus

15. 1 µm Nucleus Lysosome containing two damaged organelles 1 µ m Mitochondrion fragment Peroxisome fragment Lysosome Lysosome contains active hydrolytic enzymes Lysosome fuses with vesicle containing damaged organelle Hydrolytic enzymes digest organelle components Hydrolytic enzymes digest food particles Food vacuole fuses with lysosome Digestive enzymes Lysosome Lysosome Lysosome Plasma membrane Digestion Digestion Vesicle containing damaged mitochondrion Food vacuole (a) Phagocytosis: lysosome digesting food (b) Autophagy: lysosome breaking down damaged organelle Figure 6.14 Lysosomes

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

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

18. 1 Nuclear envelope is 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 envelope Transport vesicle 3 3 Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes and vacuoles trans Golgi Lysosome available for fusion with another vesicle for digestion 4 Transport vesicle carries proteins to plasma membrane for secretion 5 Figure 6.16 Review: relationships among organelles of the endomembrane system

19. 1 Nuclear envelope is 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 envelope Transport vesicle 3 3 Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes and vacuoles Plasma membrane trans Golgi Lysosome available for fusion with another vesicle for digestion 4 Transport vesicle carries proteins to plasma membrane for secretion 5 Plasma membrane expands by fusion of vesicles; proteins are secreted from cell 6 Figure 6.16 Review: relationships among organelles of the endomembrane system

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

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

22. Chloroplast Peroxisome Mitochondrion 1 µm Figure 6.19 Peroxisomes

23. Microtubule Microfilaments 0.25 µm Figure 6.20 The cytoskeleton

24. 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 Microtubule 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.) Figure 6.21 Motor proteins and the cytoskeleton Vesicle

25. Table 6.1 The Structure and Function of the Cytoskeleton

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

27. (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). Direction of swimming 1 µm (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 organism’s movement Direction of active stroke Direction of recovery stroke 15 µm Figure 6.23 A comparison of the beating of flagella and cilia

28. Outer microtubule doublet 0.1 µm Dynein arms Central microtubule Outer doublet cross-linking proteins Microtubules Radial spoke Plasma membrane (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). Basal body 0.5 µm 0.1 µm (a) A longitudinal section of a cilium shows micro- tubules running the length of the structure (TEM). Triplet (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). Cross section of basal body Figure 6.24 Ultrastructure of a eukaryotic flagellum or cilium Plasma membrane

29. 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 How dynein “walking” moves flagella and cilia

30. 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, so they bend. (Only two of the nine outer doublets in Figure 6.24b are shown here.)

31. 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.

32. Microvillus Plasma membrane Microfilaments (actin filaments) Intermediate filaments 0.25 µm Figure 6.26 A structural role of microfilaments

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

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

35. Collagen fibers are embedded in a web of proteoglycan complexes. A proteoglycan complex consists of hundreds of proteoglycan molecules attached noncovalently to a single long polysac- charide molecule. Polysaccharide molecule EXTRACELLULAR FLUID Carbo- hydrates Fibronectin attaches the ECM to integrins embedded in the plasma membrane. Core protein 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. Proteoglycan molecule Plasma membrane CYTOPLASM Micro- filaments Integrin Figure 6.29 Extracellular matrix (ECM) of an animal cell

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

37. TIGHT 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. Tight junction Tight junctions prevent fluid from moving across a layer of cells 0.5 µm 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 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 commu- nication between cells in many types of tissues, including heart muscle and animal embryos. Extracellular matrix Space between cells Gap junction Plasma membranes of adjacent cells 0.1 µm Figure 6.31 Exploring Intercellular Junctions in Animal Tissues

38. 5 µm Figure 6.32 The emergence of cellular functions from the cooperation of many organelles