Chapter 6

1. Chapter 6 A Tour of the Cell

2. 10 µm Overview: The Importance of Cells • All organisms are made of cells • The cell is the simplest collection of matter that can live. • Cell structure is correlated to cellular function Figure 6.1 Lecturer/Iyad A. Elqouqa

3. Key Concepts • Concept 6.1 To study cells, biologists use microscopes and the tools of biochemistry. • Concept 6.2 Eukaryotic cells have internal membranes that compartmentalize their functions. • Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes. • Concept 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell • Concept 6.5 Mitochondria and chloroplasts change energy from one form to another • Concept 6.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell • Concept 6.7 Extracellular components and connections between cells help coordinate cellular activities Lecturer/Iyad A. Elqouqa

4. Microscopy • Concept 6.1. To study cells, biologists use microscopes and the tools of biochemistry • Scientists use microscopes to visualize cells too small to see with the naked eye. • Light microscopes (LMs) • Pass visible light through a specimen • Magnify cellular structures with lenses Lecturer/Iyad A. Elqouqa

5. 10 m Human height 1 m Length of some nerve and muscle cells 0.1 m Light microscope Chicken egg 1 cm Frog egg 1 mm 100 µm Most plant and Animal cells Electron microscope 10 µ m NucleusMost bacteriaMitochondrion 1 µ m Electron microscope Smallest bacteria 100 nm Viruses 10 nm Ribosomes Proteins Lipids 1 nm Figure 6.2 Small molecules Atoms 0.1 nm Unaided eye • Different types of microscopes • Can be used to visualize different sized cellular structures 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 mm = 10–9 m Lecturer/Iyad A. Elqouqa

6. 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.] 50 µm (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 • Use different methods for enhancing visualization of cellular structures Lecturer/Iyad A. Elqouqa

7. (d) (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 Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density, making the image appear almost 3D. Lecturer/Iyad A. Elqouqa

8. Electron microscopes (EMs) • Focus a beam of electrons through a specimen (TEM) or onto its surface (SEM) • The scanning electron microscope (SEM) • Provides for detailed study of the surface of a specimen. • The transmission electron microscope (TEM) • Provides for detailed study of the internal ultrastructure of cells Lecturer/Iyad A. Elqouqa

9. TECHNIQUE RESULTS 1 µm Cilia (a) Scanning electron micro- scopy (SEM). Micrographs taken with a scanning electron micro- scope 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. • The scanning electron microscope (SEM) • Provides for detailed study of the surface of a specimen Figure 6.4 (a) Lecturer/Iyad A. Elqouqa

10. Longitudinal section of cilium Cross section of cilium 1 µm (b) Transmission electron micro- scopy (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. • The transmission electron microscope (TEM) • Provides for detailed study of the internal ultrastructure of cells Figure 6.4 (b) Lecturer/Iyad A. Elqouqa

11. APPLICATION TECHNIQUE Isolating Organelles by Cell Fractionation • Cell fractionation • Takes cells apart and separates the major organelles from one another • The centrifuge • Is used to fractionate cells into their component parts • The process of cell fractionation Cell fractionation is used to isolate (fractionate) cell components, based on size and density. First, cells are homogenized in a blender to break them up. The resulting mixture (cell homogenate) is then centrifuged at various speeds and durations to fractionate the cell components, forming a series of pellets. Lecturer/Iyad A. Elqouqa

12. Homogenization Tissue cells 1000 g (1000 times the force of gravity) 10 min Homogenate Differential centrifugation Supernatant poured into next tube 20,000 g 20 min 80,000 g 60 min Pellet rich in nuclei and cellular debris 150,000 g 3 hr Pellet rich in mitochondria (and chloro- plasts if cells are from a plant) Pellet rich in “microsomes” (pieces of plasma mem- branes and cells’ internal membranes) Pellet rich in ribosomes Figure 6.5 Results Researchers currently use cell fractionation to isolate particular organelles in order to study further details of their function. Lecturer/Iyad A. Elqouqa

13. Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions • Two types of cells make up every organism • Prokaryotic • Eukaryotic Lecturer/Iyad A. Elqouqa

14. Comparing Prokaryotic and Eukaryotic Cells • All cells have several basic features in common • They are bounded by a plasma membrane. • They contain a semifluid substance called the cytosol • They contain chromosomes • They all have ribosomes • Prokaryotic cells • Do not contain a nucleus • Have their DNA located in a region called the nucleoid. Lecturer/Iyad A. Elqouqa

15. 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 Bacterialchromosome 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, B Lecturer/Iyad A. Elqouqa

16. Eukaryotic cells • Contain a true nucleus, bounded by a membranous nuclear envelope • Are generally quite a bit bigger than prokaryotic cells • The logistics of carrying out cellular metabolism sets limits on the size of cells Lecturer/Iyad A. Elqouqa

17. 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 • A smaller cell • Has a higher surface to volume ratio, which facilitates the exchange of materials into and out of the cell Figure 6.7 Lecturer/Iyad A. Elqouqa

18. Outside of cell Hydrophilic region 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) Inside of cell 0.1 µm Hydrophobic region Hydrophilic region Phospholipid Proteins (b) Structure of the plasma membrane • The plasma membrane • Functions as a selective barrier • Allows sufficient passage of nutrients and waste Carbohydrate side chain Figure 6.8 A, B Lecturer/Iyad A. Elqouqa

19. A Panoramic View of the Eukaryotic Cell • Eukaryotic cells • Have extensive and elaborately arranged internal membranes, which form organelles. • Plant and animal cells • Have most of the same organelles Lecturer/Iyad A. Elqouqa

20. Nuclear envelope ENDOPLASMIC RETICULUM (ER) NUCLEUS Nucleolus Rough ER Smooth ER Chromatin Flagelium Plasma membrane Centrosome CYTOSKELETON Microfilaments Intermediate filaments Ribosomes Microtubules Microvilli Golgi apparatus Peroxisome In animal cells but not plant cells: Lysosomes Centrioles Lysosome Mitochondrion • A animal cell Figure 6.9 Lecturer/Iyad A. Elqouqa

21. Nuclear envelope Rough endoplasmic reticulum Nucleolus NUCLEUS Chromatin Smooth endoplasmic reticulum Centrosome Ribosomes (small brwon dots) Central vacuole Tonoplast Golgi apparatus Microfilaments Intermediate filaments Microtubules Mitochondrion Peroxisome Plasma membrane Chloroplast Cell wall Plasmodesmata Wall of adjacent cell • A plant cell CYTOSKELETON In plant cells but not animal cells: Chloroplasts Central vacuole and tonoplast Cell wall Plasmodesmata Figure 6.9 Lecturer/Iyad A. Elqouqa

22. Concept 6.3. The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes. • The nucleus • Contains most of the genes in the eukaryotic cell. • The nuclear envelope • Encloses the nucleus, separating its contents from the cytoplasm Lecturer/Iyad A. Elqouqa

23. Nucleus Nucleus 1 µm Nucleolus Chromatin 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 Nuclear lamina (TEM). Pore complexes (TEM). • Nuclear envelope Figure 6.10 Lecturer/Iyad A. Elqouqa

24. Ribosomes: Protein Factories in the Cell • Ribosomes • Are particles made of ribosomal RNA and protein. • Carry out protein synthesis Lecturer/Iyad A. Elqouqa

25. Ribosomes Cytosol Free ribosomes Bound ribosomes Large subunit Small subunit 0.5 µm TEM showing ER and ribosomes Diagram of a ribosome ER Endoplasmic reticulum (ER) Figure 6.11 Lecturer/Iyad A. Elqouqa

26. The Endoplasmic Reticulum: Biosynthetic Factory • Concept 6.4. The endomembrane system regulates protein traffic and performs metabolic functions in the cell • The endomembrane system • Includes many different structures • The endoplasmic reticulum (ER)/ Accounts for more than half the total membrane in many eukaryotic cells. The ER membrane is continuous with the nuclear envelope. Lecturer/Iyad A. Elqouqa

27. Smooth ER Nuclear envelope Rough ER ER lumen Cisternae Ribosomes Transitional ER Transport vesicle 200 µm Smooth ER Rough ER • The ER membrane Figure 6.12 Lecturer/Iyad A. Elqouqa

28. There are two distinct regions of ER • Smooth ER, which lacks ribosomes • Rough ER, which contains ribosomes Lecturer/Iyad A. Elqouqa

29. Functions of Smooth ER • The smooth ER • Synthesizes lipids • Metabolizes carbohydrates • Stores calcium • Detoxifies poison Functions of Rough ER • The rough ER • Has bound ribosomes • Produces proteins and membranes, which are distributed by transport vesicles Lecturer/Iyad A. Elqouqa

30. The Golgi Apparatus: Shipping and Receiving Center • The Golgi apparatus • Receives many of the transport vesicles produced in the rough ER. • Consists of flattened membranous sacs called cisternae • Functions of the Golgi apparatus include • Modification of the products of the rough ER • Manufacture of certain macromolecules Lecturer/Iyad A. Elqouqa

31. cis face (“receiving” side of Golgi apparatus) 5 3 4 6 1 2 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 Golgi apparatus • Functions of the Golgi apparatus Figure 6.13 TEM of Golgi apparatus Lecturer/Iyad A. Elqouqa

32. Lysosomes: Digestive Compartments • A lysosome • Is a membranous sac of hydrolytic enzymes • Can digest all kinds of macromolecules Lecturer/Iyad A. Elqouqa

33. 1 µm Nucleus Lysosome Hydrolytic enzymes digest food particles Food vacuole fuses with lysosome Lysosome contains active hydrolytic enzymes Digestive enzymes Lysosome Plasma membrane Digestion Food vacuole (a) Phagocytosis: lysosome digesting food • Lysosomes carry out intracellular digestion by • Phagocytosis Figure 6.14 A Lecturer/Iyad A. Elqouqa

34. Lysosome containing two damaged organelles 1 µ m Mitochondrion fragment Peroxisome fragment Lysosome fuses with vesicle containing damaged organelle Hydrolytic enzymes digest organelle components Lysosome Digestion Vesicle containing damaged mitochondrion (b) Autophagy: lysosome breaking down damaged organelle • Autophagy Figure 6.14 B Lecturer/Iyad A. Elqouqa

35. Vacuoles: Diverse Maintenance Compartments • A plant or fungal cell • May have one or several vacuoles • Food vacuoles • Are formed by phagocytosis • Contractile vacuoles • Pump excess water out of protist cells Lecturer/Iyad A. Elqouqa

36. Central vacuole Cytosol Tonoplast Nucleus Central vacuole Cell wall Chloroplast 5 µm • Central vacuoles • Are found in plant cells • Hold reserves of important organic compounds and water Figure 6.15 Lecturer/Iyad A. Elqouqa

37. The Endomembrane System: A Review • The endomembrane system • Is a complex and dynamic player in the cell’s compartmental organization Lecturer/Iyad A. Elqouqa

38. 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 envelop 3 Golgi pinches off transport Vesicles and other vesicles that give rise to lysosomes and Vacuoles Plasma membrane trans Golgi 4 5 6 Lysosome available for fusion with another vesicle for digestion Transport vesicle carries proteins to plasma membrane for secretion Plasma membrane expands by fusion of vesicles; proteins are secreted from cell • Relationships among organelles of the endomembrane system Figure 6.16 Lecturer/Iyad A. Elqouqa

39. Concept 6.5 Mitochondria and chloroplasts change energy from one form to another • Mitochondria • Are the sites of cellular respiration • Chloroplasts • Found only in plants, are the sites of photosynthesis Lecturer/Iyad A. Elqouqa

40. Mitochondrion Intermembrane space Outer membrane Free ribosomes in the mitochondrial matrix Inner membrane Cristae Matrix Mitochondrial DNA 100 µm Mitochondria: Chemical Energy Conversion • Mitochondria • Are found in nearly all eukaryotic cells • Mitochondria are enclosed by two membranes • A smooth outer membrane • An inner membrane folded into cristae Figure 6.17 Lecturer/Iyad A. Elqouqa

41. Chloroplast Ribosomes Stroma Chloroplast DNA Inner and outer membranes Granum 1 µm Thylakoid Chloroplasts: Capture of Light Energy • The chloroplast • Is a specialized member of a family of closely related plant organelles called plastids • Contains chlorophyll • Chloroplasts • Are found in leaves and other green organs of plants and in algae • Chloroplast structure includes • Thylakoids, membranous sacs • Stroma, the internal fluid Figure 6.18 Lecturer/Iyad A. Elqouqa

42. Chloroplast Peroxisome Mitochondrion 1 µm Peroxisomes: Oxidation • Peroxisomes • Produce hydrogen peroxide and convert it to water Figure 6.19 Lecturer/Iyad A. Elqouqa

43. Microtubule Microfilaments 0.25 µm Figure 6.20 • Concept 6.6 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 Lecturer/Iyad A. Elqouqa

44. Roles of the Cytoskeleton: Support, Motility, and Regulation • The cytoskeleton • Gives mechanical support to the cell. • Is involved in cell motility, which utilizes motor proteins. • There are three main types of fibers that make up the cytoskeleton Lecturer/Iyad A. Elqouqa

45. Table 6.1 Lecturer/Iyad A. Elqouqa

46. Microtubules • Microtubules • Shape the cell • Guide movement of organelles • Help separate the chromosome copies in dividing cells Lecturer/Iyad A. Elqouqa

47. Centrosomes and Centrioles Centrosome Microtubule Centrioles 0.25 µm Longitudinal section of one centriole Cross section of the other centriole Microtubules Figure 6.22 Lecturer/Iyad A. Elqouqa • The centrosome • Is considered to be a “microtubule-organizing center”. • Contains a pair of centrioles

48. Cilia and Flagella • Cilia and flagella • Contain specialized arrangements of microtubules • Are locomotor appendages of some cells Lecturer/Iyad A. Elqouqa

49. (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 1 µm • Flagella beating pattern Figure 6.23 A Lecturer/Iyad A. Elqouqa

50. (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). Figure 6.23 B • Ciliary motion 15 µm Lecturer/Iyad A. Elqouqa