1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 6: A Tour of the Cell

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A cell and its skeleton viewed by fluorescence microscopy 10 µm

3. Concept 6.1: Biologists use microscopes and the tools of biochemistry to study cells Though usually too small to be seen by the unaided eye, cells can be complex Scientists use microscopes to visualize cells too small to see with the naked eye In a light microscope (LM), visible light is passed through a specimen and then through glass lenses Lenses refract (bend) the light, so that the image is magnified © 2011 Pearson Education, Inc.

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The size range of cells Nucleus Most bacteria 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 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 Human height Length of some nerve and muscle cells Chicken egg Frog egg Most plant and animal cells Mitochondrion Smallest bacteria Viruses Ribosomes Proteins Lipids Small molecules Atoms Unaided eye Light microscope Electron microscope nucleus Most bacteria

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Research Method Light Microscopy TECHNIQUERESULTS 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

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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)

7. 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 © 2011 Pearson Education, Inc.

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Research Method Electron Microscopy TECHNIQUERESULTS 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) 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) Cilia 1 µm Longitudinal section of cilium Cross section of cilium 1 µm

9. 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 Organisms of the domains Bacteria and Archaea consist of prokaryotic cells Protists, fungi, animals, and plants all consist of eukaryotic cells © 2011 Pearson Education, Inc.

10. Comparing Prokaryotic and Eukaryotic Cells Basic features of all cells –Plasma membrane –Semifluid substance called cytosol –Chromosomes (carry genes) –Ribosomes (make proteins) © 2011 Pearson Education, Inc.

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

12. 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 © 2011 Pearson Education, Inc.

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exploring Animal and Plant Cells Animal Cell (Eukaryotic Cells) Intermediate filaments ENDOPLASMIC RETICULUM (ER) Rough ERSmooth 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

14. 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 © 2011 Pearson Education, Inc.

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Geometric relationships between surface area and volume 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 1.2 750 125 6

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The plasma membrane Carbohydrate side chain Outside of cell Inside of cell Hydrophilic region Hydrophobic region Hydrophilic region (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

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Animal and Plant Cells: Plant Cell Ribosomes ( small brown dots ) Central vacuole Microfilaments Intermediate filaments Microtubules Rough endoplasmic reticulum Smooth endoplasmic reticulum 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 Cell wall Plasmodesmata Tonoplast CYTOSKELETON

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The nucleus and its envelope Pore complexes (TEM). Each pore is ringed by protein particles. Nuclear lamina (TEM). The netlike lamina lines the inner surface of the nuclear envelope. Nucleus 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

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ribosomes ER Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes Large subunit Small subunit TEM showing ER and ribosomes Diagram of a ribosome 0.5 µm

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Endoplasmic reticulum (ER) Smooth ER Rough ER ER lumen Cisternae Ribosomes Transport vesicle Smooth ER Transitional ER Rough ER 200 µm Nuclear envelope

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Golgi apparatus 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) TEM of Golgi apparatus 0.1 0 µm 1 6 5 2 3 4

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Lysosomes Lysosome Nucleus 1 µm 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 fragment Lysosome fuses with vesicle containing damaged organelle Hydrolytic enzymes digest organelle components Vesicle containing damaged mitochondrion Digestion Food vacuole Plasma membrane Lysosome Digestive enzymes (a) Phagocytosis: lysosome digesting food (b) Autophagy: lysosome breaking down damaged organelle Lysosome Digestion Lysosome

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The plant cell vacuole Central vacuole Cytosol Tonoplast Central vacuole Nucleus Cell wall Chloroplast 5 µm

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Review: relationships among organelles of the endomembrane system 3 Nuclear envelope Nuclear envelope is connected to rough ER, which is also continuous with smooth ER Nucleus Rough ER Smooth ER 1

25. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 3 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

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 3 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

27. Mitochondria and chloroplasts have similarities with bacteria –Enveloped by a double membrane –Contain free ribosomes and circular DNA molecules –Grow and reproduce somewhat independently in cells © 2011 Pearson Education, Inc. The Evolutionary Origins of Mitochondria and Chloroplasts

28. The Endosymbiont theory –An early ancestor of eukaryotic cells engulfed a nonphotosynthetic prokaryotic cell, which formed an endosymbiont relationship with its host –The host cell and endosymbiont merged into a single organism, a eukaryotic cell with a mitochondrion –At least one of these cells may have taken up a photosynthetic prokaryote, becoming the ancestor of cells that contain chloroplasts © 2011 Pearson Education, Inc.

29. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The mitochondrion, site of cellular respiration Mitochondrion Intermembrane space Outer membrane Free ribosomes in the mitochondrial matrix Mitochondrial DNA Inner membrane Cristae Matrix 100 µm

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The chloroplast, site of photosynthesis Granum Chloroplast DNA Ribosomes Stroma Inner and outer membranes Thylakoid 1 µm

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Peroxisomes Chloroplast Peroxisome Mitochondrion 1 µm

32. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The cytoskeleton Microtubule 0.25 µm Microfilaments

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Centrosome containing a pair of centrioles Centrosome Microtubule Centrioles 0.25 µm Longitudinal section of one centriole Microtubules Cross section of the other centriole

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Plasmodesmata between plant cells Cell walls Interior of cell Interior of cell 0.5 µm Plasmodesmata Plasma membranes

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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