1. Cell Structure and Biology Advanced Placement Biology Chapter 6

2. Robert Hooke, 1665

3. Hooke’s First Microscope

4. History of the Cell 1665- Robert Hooke described cork as composed of cellulae (cell). A few years later-Anton van Leeuwenhoek described live cells. 1838 and 1839- Schleiden and Schwann developed the cell theory.

5. Schleiden and Schwann- Cell Theory All organisms are composed of cells or at least one. Cells are the smallest unit of life (a collection of metabolic processes + heredity). All cells come from other cells. None spontaneously arise.

6. Different types of microscopes –Can be used to visualize different sized cellular structures Unaided eye 1 m 0.1 nm 10 m 0.1 m 1 cm 1 mm 100 µm 10 µ m 1 µ m 100 nm 10 nm 1 nm Length of some nerve and muscle cells Chicken egg Frog egg Most plant and Animal cells Smallest bacteria Viruses Ribosomes Proteins Lipids Small molecules Atoms Nucleus Most bacteria Mitochondrion Light microscope Electron microscope Figure 6.2 Human height 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

7. Use different methods for enhancing visualization of cellular structures TECHNIQUE RESULT 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 6.3

8. 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)

9. The scanning electron microscope (SEM) –Provides for detailed study of the surface of a specimen TECHNIQUE RESULTS 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. (a) Cilia 1 µm Figure 6.4 (a)

10. The transmission electron microscope (TEM) –Provides for detailed study of the internal ultrastructure of cells 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. (b) Longitudinal section of cilium Cross section of cilium 1 µm Figure 6.4 (b)

11. 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. The process of cell fractionation APPLICATION TECHNIQUE Figure 6.5

12. Tissue cells Homogenization Homogenate 1000 g (1000 times the force of gravity) 10 min Differential centrifugation Supernatant poured into next tube 20,000 g 20 min Pellet rich in nuclei and cellular debris 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 150,000 g 3 hr 80,000 g 60 min Figure 6.5

13. What’s the world’s largest living cell? Surface to Volume Ratio

14. A smaller cell –Has a higher surface to volume ratio, which facilitates the exchange of materials into and out of the cell Surface area increases while total volume remains constant 5 1 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 1 6 150 125 12 750 125 6 Figure 6.7

15. (b) A thin section through the bacterium Bacillus coagulans (TEM) 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 0.5 µm Bacterial chromosome Figure 6.6 A, B

16. Prokaryote vs. Eukaryote Archaebacteria and Eubacteria. Lack membrane-bound organelles. DNA in a nucleoid region. Have plasma membrane. Cell wall of peptidoglycan. Use 70S ribosome. Unique flagella-flagellin protein. Animalia, Plantae, Protista, Fungi. Have true membrane- bound organelles. DNA in a nucleus. Have plasma membrane. Plants and some protists have a cell wall of cellulose. Use different ribosomes.

17. Cell structure is correlated to cellular function 10 µm Figure 6.1

18. A Composite Eukaryotic Cell

19. A animal cell: Rough ERSmooth ER Centrosome CYTOSKELETON Microfilaments Microtubules Microvilli Peroxisome Lysosome Golgi apparatus Ribosomes In animal cells but not plant cells: Lysosomes Centrioles Flagella (in some plant sperm) Nucleolus Chromatin NUCLEUS Flagelium Intermediate filaments ENDOPLASMIC RETICULUM (ER) Mitochondrion Nuclear envelope Plasma membrane Figure 6.9

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

25. Corn Plant Cell

26. Plasma Membrane

27. Cytosol and Membranes

28. What is the function of organelles? To compartmentalize chemical reactions that may proceed simultaneously. To provide membranes on which to catalyze reactions.

29. Nuclear Envelope –Encloses the nucleus, separating its contents from the cytoplasm Figure 6.10 Nucleus Nucleolus Chromatin Nuclear envelope: Inner membrane Outer membrane Nuclear pore Rough ER Pore complex Surface of nuclear envelope. Pore complexes (TEM). Nuclear lamina (TEM). Close-up of nuclear envelope Ribosome 1 µm 0.25 µm

30. EM of Nucleus

31. 1. The Nucleus Largest organelle, centralized in animal cells. Stores and protects the cell’s genetic information. Surrounded by two phospholipid bilayer membranes-nuclear envelope. Where both layers are fused - nuclear pores + transport protein.

32. The Nucleolus Site within the nucleus of ribosomal subunits are manufactured- rRNA + ribosomal proteins. Ribosomes leave the nucleus as subunits through the nuclear pore and are later reassembled. May be free (in the cytoplasm) or attached to the ER (rough ER ).

33. The Ribosome (40S and 60S)

35. Rough ER EM

36. Endoplasmic Reticulum (ER) Means “little net within the cytoplasm” Internal membrane system with a lipid bilayer + proteins. Weaved in sheets- forming channels. Outer membrane of the nuclear envelope is continuous with the ER membrane. Some regions have embedded ribosomes.

37. The ER Membrane –Is continuous with the nuclear envelope Smooth ER Rough ER ER lumen Cisternae Ribosomes Transport vesicle Smooth ER Transitional ER Rough ER 200 µm Nuclear envelope Figure 6.12

38. Two Types of (ER) 1. Rough ER: heavily studded with ribosomes- protein synthesis. Proteins have signal sequences which direct to a docking site on the surface of the ER. 2. Smooth ER: lack ribosomes; have enzymes embedded in membrane for carbohydrate and lipid synthesis. 3. Both secrete finished products in transport vesicles.

39. Functions of Smooth ER The smooth ER: –Synthesizes lipids –Metabolizes carbohydrates –Stores calcium –Detoxifies poison

40. The Golgi Complex Flattened stacks of membranes in the cytoplasm-cisternae. Collection, packaging and distribution of proteins and lipids. Transport vesicles from RER and SER fuse with the Golgi membrane.

42. Golgi apparatus TEM of 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 Golgi cisternae Cisternae trans face (“shipping” side of Golgi apparatus) 0.1 0 µm 1 6 5 2 3 4 Functions of the Golgi Apparatus Figure 6.13

43. Transport of Proteins

44. Proteins Leaving the Golgi

45. The Golgi Complex Proteins (from RER) may have short sugar chains added--> glycoproteins. Lipids (from SER) may have short sugar chains added-->glycolipids. Both collect at flattened ends-cisternae. Cisternae membranes pinch off the glycoproteins and glycolipids into secretory vesicles (liposomes). Liposomes may fuse with plasma membane or organelle membranes.

46. Lysosomes Membrane-bound organelle with digestive enzymes. Breakdown protein, nucleic acid, carbos, lipids. Digest old organelles and invading bacterial cells. Digestive enzymes only active at low pH.

47. Lysosomes

48. Inactive lysosomes-Primary Lysosomes, high pH, enzymes are inactive. Once fused with food vacuole- pump H+ into compartment- active, Secondary Lysosomes. Involved in normal cell death and programmed cell death (apoptosis). Ex. Tadpole tail tissue; webbing between human fingers.

49. Peroxisomes: Oxidation Peroxisomes: –Produce hydrogen peroxide and convert it to water. Chloroplast Peroxisome Mitochondrion 1 µm Figure 6.19

50. EM of Peroxisome

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

52. Mitochondrion EM

53. Mitochondria

54. Mitochondrion (ia) Rod-shaped organelle, 1-3 micrometers long. Bounded by two membranes- outer is smooth; inner is folded into continuous layers-cristae. Two compartments- matrix-inside the inner membrane and intermembrane space between the two membranes. Enzymes for oxidative metabolism are embedded in the inner membrane.

55. Mitochondria are enclosed by two membranes –A smooth outer membrane –An inner membrane folded into cristae Mitochondrion Intermembrane space Outer membrane Free ribosomes in the mitochondrial matrix Mitochondrial DNA Inner membrane Cristae Matrix 100 µm Figure 6.17

56. Mitochondria Contain a circular piece of DNA for many of the proteins in oxidative metabolism. Also has its own rRNA and ribosomal proteins--> own protein synthesis. Involved in its own replication. Circular DNA? Two membranes? Own Genes? Own replication? What does that sound like?

57. The Plastids Chloroplasts Leucoplasts Amyloplasts Chromoplasts

58. EM of Chloroplast

59. Chloroplasts –Are found in leaves and other green organs of plants and in algae. Chloroplast DNA Ribosomes Stroma Inner and outer membranes Thylakoid 1 µm Granum Figure 6.18

60. Chloroplasts Algae and plants have organelles for photosynthesis. Two membranes- outer and inner membranes. A closed, stacked network of membranes- granum (a). Fluid-filled space around grana-stroma. Disc-shaped structures-thylakoids. Light-capturing enzymes are embedded on thylakoids.

61. Chloroplasts Have DNA which encode many enzymes necessary for photosynthesis. Do all plant cells have chloroplasts? May lose internal structure-leucoplasts. A leucoplast that stores starch- amyloplast. Found in root cells. A leucoplast that stores other pigments- chromoplasts.

62. Centriole Barrel-shaped organelles in animals and protists, NOT plants. Usually found in pairs around the nuclear membrane. Hollow cylinders made of microtubules (protein). Have their own DNA. Help move chromosome during cell division.

63. Centriole

64. Other Organelles Central Vacuole or Tonoplast: in plants, for protein, water, and waste storage. Vesicles: in animals, usually smaller sacs used for storage and transport of materials.

65. Central Vacuoles –Are found in plant cells –Hold reserves of important organic compounds and water Central vacuole Cytosol Tonoplast Central vacuole Nucleus Cell wall Chloroplast 5 µm Figure 6.15

66. The Cytoskeleton!

67. Cytoskeleton –Is a network of fibers extending throughout the cytoplasm Microtubule 0.25 µm Microfilaments Figure 6.20

68. There are three main types of fibers that make up the cytoskeleton: Table 6.1

70. Actin Filaments Made of globular protein monomers- actin Actin monomers polymerize to form actin filaments Filaments are connected to proteins within the plasma membrane.

71. How do you put actin together?

72. Actin Filaments Actin filaments are thinner, cause cellular movements like ameboid movements, cell pinching during division. Provide shape for the cell.

73. Actin that function in cellular motility –Contain the protein myosin in addition to actin Actin filament Myosin filament Myosin motors in muscle cell contraction. (a) Muscle cell Myosin arm Figure 6.27 A

74. Microtubules 2 globular monomers-  tubulin and  tubulin polymerize to form 13 protofilaments Filaments form wide, hollow tubes- microtubules. Form from nucleation centers (near nucleus) and radiate out.

75. A Microtubule

76. Treadmilling of a Microtubule

77. Microtubules Constantly polymerize and depolymerize- GTP-binding at ends. Ends are + (away from center) or - (toward center). Cellular movements and intracellular movement of materials and organelles.

78. Microtubules Use specialized motor proteins to move organelles along the microtubule. Kinesins- move organelles toward the + end (toward cell periphery) Dyneins- move them toward the - end (toward the center of cell)

80. Microtubule and Motor Proteins

81. How do kinesins work?

82. How do dyneins work?

83. Could a simple defect in a kinesin affect a whole organism?

84. Wild-type Drosophila larva

85. Wild-type (Normal) Drosophila Movement

86. Mutant Kinesins in Drosophila (khc6 mutant)

87. Intermediate Filaments Most durable protein filament- tough fibrous filaments of overlapping tetramers of protein (rope-like). Between actin and microtubules in size. Stable Ex. of Fibers- vimentin and keratin

89. EM of Intermediate Filaments

90. Intermediate Filaments Anchored to proteins embedded into plasma membrane. Provide mechanical support to cell.

91. Plants: Plasmodesmata Plasmodesmata –Are channels that perforate plant cell walls Interior of cell Interior of cell 0.5 µm Plasmodesmata Plasma membranes Cell walls Figure 6.30

92. The Extracellular Matrix (ECM) of Animal Cells Animal cells –Lack cell walls –Are covered by an elaborate matrix, the ECM

93. Types of Intercellular Junctions in animals 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 6.31

94. Cilia