1. Chapter 6 A Tour of the Cell Cells rely on the integration of structures and organelles in order to function For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Cell: A Living Unit Greater Than the Sum of Its Parts

2. Fig. 6-33 5 µm

3. You should now be able to: 1.Distinguish between the following pairs of terms: magnification and resolution; prokaryotic and eukaryotic cell; free and bound ribosomes; smooth and rough ER 2.Describe the structure and function of the components of the endomembrane system 3.Briefly explain the role of mitochondria, chloroplasts, and peroxisomes 4.Describe the functions of the cytoskeleton Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

4. 5.Compare the structure and functions of microtubules, microfilaments, and intermediate filaments 6.Explain how the ultrastructure of cilia and flagella relate to their functions 7.Describe the structure of a plant cell wall 8.Describe the structure and roles of the extracellular matrix in animal cells 9.Describe the intercellular junctions Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

5. Overview: The Fundamental Units of Life All organisms are made of cells- cell theory The cell is the simplest collection of matter that can live Cell structure is correlated to cellular function All cells are related by their descent from earlier cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

6. Microscopy Scientists use microscopes to visualize cells too small to see with the naked eye In a light microscope (LM), visible light passes through a specimen and then through glass lenses, which magnify the image Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

7. Fig. 6-2 10 m 1 m 0.1 m 1 cm 1 mm 100 µm 10 µm 1 µm 100 nm 10 nm 1 nm 0.1 nm Atoms Small molecules Lipids Proteins Ribosomes Viruses Smallest bacteria Mitochondrion Nucleus Most bacteria Most plant and animal cells Frog egg Chicken egg Length of some nerve and muscle cells Human height Unaided eye Light microscope Electron microscope

8. Two basic types of electron microscopes (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 TEMs are used mainly to study the internal structure of cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

9. Fig. 6-4 (a) Scanning electron microscopy (SEM) TECHNIQUERESULTS (b) Transmission electron microscopy (TEM) Cilia Longitudinal section of cilium Cross section of cilium 1 µm

10. Fig. 6-5a Homogenization Homogenate Differential centrifugation Tissue cells TECHNIQUE

11. Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells Protists, fungi, animals, and plants all consist of eukaryotic cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

12. Comparing Prokaryotic and Eukaryotic Cells Basic features of all cells: – Plasma membrane – Semifluid substance called cytosol – Chromosomes (carry genes) – Ribosomes (make proteins) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

13. Prokaryotic cells are characterized by having – No nucleus – DNA in an unbound region called the nucleoid – No membrane-bound organelles – Cytoplasm bound by the plasma membrane Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

14. Fig. 6-6 Fimbriae Nucleoid Ribosomes Plasma membrane Cell wall Capsule Flagella Bacterial chromosome (a)A typical rod-shaped bacterium (b)A thin section through the bacterium Bacillus coagulans (TEM) 0.5 µm

15. Eukaryotic cells are characterized by having – DNA in a nucleus that is bounded by a membranous nuclear envelope – Membrane-bound organelles – Cytoplasm in the region between the plasma membrane and nucleus Eukaryotic cells are generally much larger than prokaryotic cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

16. The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell The general structure of a biological membrane is a double layer of phospholipids Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

17. Fig. 6-7 TEM of a plasma membrane (a) (b) Structure of the plasma membrane Outside of cell Inside of cell 0.1 µm Hydrophilic region Hydrophobic region Hydrophilic region PhospholipidProteins Carbohydrate side chain

18. 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 BioFlix: Tour Of An Animal Cell BioFlix: Tour Of An Animal Cell BioFlix: Tour Of A Plant Cell BioFlix: Tour Of A Plant Cell Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

19. Fig. 6-9a ENDOPLASMIC RETICULUM (ER) Smooth ERRough ER Flagellum Centrosome CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Microvilli Peroxisome Mitochondrion Lysosome Golgi apparatus Ribosomes Plasma membrane Nuclear envelope Nucleolus Chromatin NUCLEUS

20. Fig. 6-9b NUCLEUS Nuclear envelope Nucleolus Chromatin Rough endoplasmic reticulum Smooth endoplasmic reticulum Ribosomes Central vacuole Microfilaments Intermediate filaments Microtubules CYTO- SKELETON Chloroplast Plasmodesmata Wall of adjacent cell Cell wall Plasma membrane Peroxisome Mitochondrion Golgi apparatus

21. 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 DNA in a eukaryotic cell Ribosomes use the information from the DNA to make proteins Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

22. Fig. 6-10 Nucleolus Nucleus Rough ER Nuclear lamina (TEM) Close-up of nuclear envelope 1 µm 0.25 µm Ribosome Pore complex Nuclear pore Outer membrane Inner membrane Nuclear envelope: Chromatin Surface of nuclear envelope Pore complexes (TEM)

23. In the nucleus, DNA and proteins form genetic material called chromatin Chromatin condenses to form discrete chromosomes The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

24. Concept 6.4: 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

25. The 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, with ribosomes studding its surface Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

26. Fig. 6-12 Smooth ER Rough ER Nuclear envelope Transitional ER Rough ER Smooth ER Transport vesicle Ribosomes Cisternae ER lumen 200 nm

27. Ribosomes: Protein Factories Ribosomes are particles made of ribosomal RNA 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) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

28. Fig. 6-11 Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes Large subunit Small subunit Diagram of a ribosome TEM showing ER and ribosomes 0.5 µm

29. Functions of Smooth ER The smooth ER – Synthesizes lipids – Metabolizes carbohydrates – Detoxifies poison – Stores calcium Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

30. Functions of Rough ER The rough ER – Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates) – Distributes transport vesicles, proteins surrounded by membranes – Is a membrane factory for the cell Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

31. The Golgi apparatus consists of flattened membranous sacs called cisternae Functions of the Golgi apparatus: – Modifies products of the ER – Manufactures certain macromolecules – Sorts and packages materials into transport vesicles The Golgi Apparatus: Shipping and Receiving Center Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

32. Fig. 6-13 cis face (“receiving” side of Golgi apparatus) Cisternae trans face (“shipping” side of Golgi apparatus) TEM of Golgi apparatus 0.1 µm

33. 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 Animation: Lysosome Formation Animation: Lysosome Formation Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

34. 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

35. Fig. 6-14a Nucleus 1 µm Lysosome Digestive enzymes Plasma membrane Food vacuole Digestion (a) Phagocytosis

36. Fig. 6-14b Vesicle containing two damaged organelles Mitochondrion fragment Peroxisome fragment Peroxisome Lysosome Digestion Mitochondrion Vesicle (b) Autophagy 1 µm

37. Vacuoles: Diverse Maintenance Compartments A plant cell or fungal cell may have one or several vacuoles Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

38. 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 Video: Paramecium Vacuole Video: Paramecium Vacuole Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

39. Fig. 6-15 Central vacuole Cytosol Central vacuole Nucleus Cell wall Chloroplast 5 µm

40. The Endomembrane System: A Review The endomembrane system is a complex and dynamic player in the cell’s compartmental organization Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

41. Fig. 6-16-3 Smooth ER Nucleus Rough ER Plasma membrane cis Golgi trans Golgi

42. Concept 6.5: Mitochondria and chloroplasts change energy from one form to another Mitochondria are the sites of cellular respiration, a metabolic process that generates ATP Chloroplasts, found in plants and algae, are the sites of photosynthesis Peroxisomes are oxidative organelles Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

43. Mitochondria and chloroplasts – Are not part of the endomembrane system – Have a double membrane – Have proteins made by free ribosomes – Contain their own DNA Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

44. Mitochondria: Chemical Energy Conversion Mitochondria are in nearly all eukaryotic cells They have a smooth outer membrane and an inner membrane folded into cristae The inner membrane creates two compartments: intermembrane space and mitochondrial matrix Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix Cristae present a large surface area for enzymes that synthesize ATP Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

45. Fig. 6-17 Free ribosomes in the mitochondrial matrix Intermembrane space Outer membrane Inner membrane Cristae Matrix 0.1 µm

46. Chloroplasts: Capture of Light Energy The chloroplast is a member of a family of organelles called plastids 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

47. Chloroplast structure includes: – Thylakoids, membranous sacs, stacked to form a granum – Stroma, the internal fluid Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

48. Fig. 6-18 Ribosomes Thylakoid Stroma Granum Inner and outer membranes 1 µm

49. Fig. 6-19 1 µm Chloroplast Peroxisome Mitochondrion

50. 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 It organizes the cell’s structures and activities, anchoring many organelles It is composed of three types of molecular structures: – Microtubules – Microfilaments – Intermediate filaments Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

51. Fig. 6-20 Microtubule Microfilaments 0.25 µm

52. Roles of the Cytoskeleton: Support, Motility, and Regulation The cytoskeleton helps to support the cell and maintain its shape It interacts with motor proteins to produce motility Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton Recent evidence suggests that the cytoskeleton may help regulate biochemical activities Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

53. Fig. 6-21 Vesicle ATP Receptor for motor protein Microtubule of cytoskeleton Motor protein (ATP powered) (a) MicrotubuleVesicles (b) 0.25 µm

54. Components of the Cytoskeleton Three main types of fibers make up the cytoskeleton: – Microtubules are the thickest of the three components of the cytoskeleton – Microfilaments, also called actin filaments, are the thinnest components – Intermediate filaments are fibers with diameters in a middle range Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

55. Table 6-1a 10 µm Column of tubulin dimers Tubulin dimer   25 nm

56. Table 6-1b Actin subunit 10 µm 7 nm

57. Table 6-1c 5 µm Keratin proteins Fibrous subunit (keratins coiled together) 8–12 nm

58. 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Microtubules

59. Fig. 6-22 Centrosome Microtubule Centrioles 0.25 µm Longitudinal section of one centriole Microtubules Cross section of the other centriole

60. Cilia and Flagella Microtubules control the beating of cilia and flagella, locomotor appendages of some cells Cilia and flagella differ in their beating patterns Video: Chlamydomonas Video: Chlamydomonas Video: Paramecium Cilia Video: Paramecium Cilia Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

61. Fig. 6-23 5 µm Direction of swimming (a) Motion of flagella Direction of organism’s movement Power strokeRecovery stroke (b) Motion of cilia 15 µm

62. Fig. 6-24 0.1 µm Triplet (c) Cross section of basal body (a)Longitudinal section of cilium 0.5 µm Plasma membrane Basal body Microtubules (b)Cross section of cilium Plasma membrane Outer microtubule doublet Dynein proteins Central microtubule Radial spoke Protein cross- linking outer doublets 0.1 µm

63. How dynein “walking” moves flagella and cilia: − Dynein arms alternately grab, move, and release the outer microtubules – Protein cross-links limit sliding – Forces exerted by dynein arms cause doublets to curve, bending the cilium or flagellum Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

64. Fig. 6-25a Microtubule doublets Dynein protein (a) Effect of unrestrained dynein movement ATP

65. Fig. 6-25b Cross-linking proteins inside outer doublets Anchorage in cell ATP (b) Effect of cross-linking proteins (c) Wavelike motion 13 2

66. Fig. 6-26 Microvillus Plasma membrane Microfilaments (actin filaments) Intermediate filaments 0.25 µm

67. Concept 6.7: 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

68. 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

69. The 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

70. Fig. 6-30a Collagen Fibronectin Plasma membrane Proteoglycan complex Integrins CYTOPLASM Micro- filaments EXTRACELLULAR FLUID

71. Functions of the ECM: – Support – Adhesion – Movement – Regulation Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

72. Intercellular 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

73. Fig. 6-31 Interior of cell 0.5 µm PlasmodesmataPlasma membranes Cell walls

74. Fig. 6-32 Tight junction 0.5 µm 1 µm Desmosome Gap junction Extracellular matrix 0.1 µm Plasma membranes of adjacent cells Space between cells Gap junctions Desmosome Intermediate filaments Tight junction Tight junctions prevent fluid from moving across a layer of cells

75. Fig. 6-UN1a Cell Component Structure Function Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes Nucleus Surrounded by nuclear envelope (double membrane) perforated by nuclear pores. The nuclear envelope is continuous with the endoplasmic reticulum (ER). (ER) Houses chromosomes, made of chromatin (DNA, the genetic material, and proteins); contains nucleoli, where ribosomal subunits are made. Pores regulate entry and exit os materials. Ribosome Two subunits made of ribo- somal RNA and proteins; can be free in cytosol or bound to ER Protein synthesis

76. Fig. 6-UN1b Cell Component Structure Function Concept 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell Endoplasmic reticulum (Nuclear envelope) Golgi apparatus Lysosome Vacuole Large membrane-bounded vesicle in plants Membranous sac of hydrolytic enzymes (in animal cells) Stacks of flattened membranous sacs; has polarity (cis and trans faces) Extensive network of membrane-bound tubules and sacs; membrane separates lumen from cytosol; continuous with the nuclear envelope. Smooth ER: synthesis of lipids, metabolism of carbohy- drates, Ca 2+ storage, detoxifica- tion of drugs and poisons Rough ER: Aids in sythesis of secretory and other proteins from bound ribosomes; adds carbohydrates to glycoproteins; produces new membrane Modification of proteins, carbo- hydrates on proteins, and phos- pholipids; synthesis of many polysaccharides; sorting of Golgi products, which are then released in vesicles. Breakdown of ingested sub- stances cell macromolecules, and damaged organelles for recycling Digestion, storage, waste disposal, water balance, cell growth, and protection

77. Fig. 6-UN1c Cell Component Concept 6.5 Mitochondria and chloro- plasts change energy from one form to another Mitochondrion Chloroplast Peroxisome Structure Function Bounded by double membrane; inner membrane has infoldings (cristae) Typically two membranes around fluid stroma, which contains membranous thylakoids stacked into grana (in plants ) Specialized metabolic compartment bounded by a single membrane Cellular respiration Photosynthesis Contains enzymes that transfer hydrogen to water, producing hydrogen peroxide (H 2 O 2 ) as a by-product, which is converted to water by other enzymes in the peroxisome