1. C HAPTER 6 A Tour of the Cell

2. H OW W E S TUDY C ELLS Biologists use microscopes and the tools of biochemistry to study cells Robert Hooke, Leeuwenhook used microscopes to study cells. Today’s microscopes are light microscopes where visible light is passed through a specimen and then through a glass lenses. Refraction of the light (bending it) allows magnification of the image.

3. M ICROSCOPES Microscopes function three ways: Magnification the ratio of an image size to the real size of an object light microscopes magnify 1000x very effectively Resolution is the clarity of the image – the minimum distance two points that can be separated and still be seen as two points. Contrast highlights differences in the parts of a sample we also use staining to highlight certain portions in specimens on a slide.

4. Size range of cells Note that light microscopes can not magnify as well as electron microscopes

5. Light Microscopy (LM) vs. Electron Microscopy (EM)

6. C OMPARISONS OF S COPES Visible light passes through specimen Refracts light so specimen is magnified Magnify up to 1000X Specimen can be alive/moving Color Focuses a beam of electrons through/onto specimen Magnify up to 1,000,000 times Specimen non-living and in vacuum Black and white Light Electron

7. E LECTRON M ICROSCOPY 2-D Creates a flat image with extreme detail Can enhance contrast by staining atoms with heavy metal dyes 3-D Used for detailed study of surface of specimen Gives great field of depth Transmission (TEM) Scanning (SEM)

8. Studying cell structure & function 1.Cell fractionation - take apart cells, separate major organelles 2.Ultracentrifuge - applies force 1 million times the force of gravity to separate further the cell organelles with the most dense at the bottom

9. 2 T YPES OF C ELLS : 1. Prokaryotes : Domain Bacteria & Archaea 2. Eukaryotes (Domain Eukarya): Protists, Fungi, Plants, Animals

10. A P ROKARYOTIC C ELL ( BACTERIA )

11. P ROKARYOTIC AND EUKARYOTIC CELLS SHARE : A selective barrier called the plasma membrane Cytosol, a jelly-like semifluid inside the cell where cell contents are found all cells have chromosomes which carry genes in the form of DNA All have ribosomes that make proteins according to instructions of genes.

12. P ROKARYOTE V S. E UKARYOTE “before” “nucleus” No nucleus DNA in a nucleoid Cytosol No organelles other than ribosomes Small size Primitive i.e. Bacteria & Archaea “true” “nucleus” Has nucleus and nuclear envelope Cytosol Membrane-bound organelles with specialized structure/function Much larger in size More complex i.e. plant/animal cell

13. C ELL S IZE AND S CALE http://learn.genetics.utah.edu/content/begin/cells/scale/ Scale of the Universe: http://www.onemorelevel.com/game/scale_of_the_unive rse_2012

14. Y OU MUST KNOW : 2A3 Eukaryotic cells have internal membranes that compartmentalize their functions Organisms must exchange matter with the environment in order to grow, reproduce and maintain organization. 1. As cells increase in volume, the relative surface area decreases and demand for material resources increases; more cellular structures are necessary to adequately exchange materials and energy with the environment. These limitations restrict cell size. Examples: root hairs, cells of villi, microvilli, cells of alveoli

15. Y OU MUST KNOW 2B3 eukaryotic cells maintain internal membranes that partition the cell into specialized regions a. Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface area where reactions can occur. b. Membranes and membrane-bound organelles in eukaryotic cells localize (compartmentalize) intracellular metabolic processes and specific enzymatic reactions. Examples Endoplasmic reticulum; Mitochondria; Chloroplasts; Golgi; Nuclear envelope Mitochondria specialize in energy capture and transformation, cristae increase the surface area

16. C ELL SIZE LIMITS Eukaryotic cells are much larger than prokaryotic cells. Size is a general feature of cell structure that relates to function. The logistics of carrying out cellular metabolism sets limits on cell size. Metabolic requirements also set upper limits on size that is practical for a single cell. The plasma membrane functions as a selective barrier allowing passage of oxygen nutrients and wastes.

17. surface area to volume ratio Cells must be small to maintain a large surface area to volume ratio Large S.A. allows  rates of chemical exchange between cell and environment

18. A NIMAL S URFACE A REA E XAMPLE (A NIMAL ): Small Intestine: highly folded surface to increase absorption of nutrients Villi Villi: finger-like projections on SI wall Microvilli Microvilli: projections on each cell

19. F OLDS  V ILLI  M ICROVILLI

20. P LANT S URFACE A REA E XAMPLE (P LANT ): Root hairs Root hairs : extensions of root epidermal cells; increase surface area for absorbing water and minerals

21. N UCLEUS Function: control center of cell Contains DNA Surrounded by double membrane ( nuclear envelope ) Continuous with the rough ER Nuclear pores : control what enters/leaves nucleus Chromatin : complex of DNA + proteins; makes up chromosomes Nucleolus : region where ribosomal subunits are formed

22. N UCLEUS Contains DNA Function: control center of cell Surrounded by double membrane ( nuclear envelope ) Continuous with the rough ER Nuclear pores : control what enters/leaves nucleus Chromatin : complex of DNA + proteins; makes up chromosomes Nucleolus : region where ribosomal subunits are formed

23. Parts of plant & animal cell p 108-109

25. Y OU MUST KNOW 4.A.2: The structure and function of subcellular components, and their interactions, provide essential cellular processes. a. Ribosomes are small, universal structures comprised of two interacting parts: ribosomal RNA and protein. In a sequential manner, these cellular components interact to become the site of protein synthesis where the translation of the genetic instructions yields specific polypeptides.

26. R IBOSOMES Function: protein synthesis Composed of rRNA + protein Large subunit + small subunit Types: 1. Free ribosomes : float in cytosol, produce proteins used within cell 2. Bound ribosomes : attached to ER, make proteins for export from cell

27. E NDOMEMBRANE S YSTEM : Regulates protein traffic & performs metabolic functions

28. E NDOMEMBRANE SYSTEM The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, various kinds of vesicles and vacuoles and the plasma membrane Functions: protein synthesis, and transport in/out of the cell, metabolism, lipid movement and detoxification. Membranes vary in: Thickness Molecular composition Types of chemical reactions

29. Y OU M UST K NOW b. Endoplasmic reticulum (ER) occurs in two forms: smooth and rough. 1. Rough endoplasmic reticulum functions to compartmentalize the cell, serves as mechanical support, provides site-specific protein synthesis with membrane-bound ribosomes and plays a role in intracellular transport.

30. E NDOPLASMIC R ETICULUM (ER) Network of membranes and sacs 1. Rough ER : ribosomes on surface Function: package proteins for secretion, send transport vesicles to Golgi, make replacement membrane 2. Smooth ER : no ribosomes on surface Function: synthesize lipids, metabolize carbs, detox drugs & poisons, store Ca 2+

31. S MOOTH ER Functions: metabolic processes like: Synthesis of lipids Carbohydrate metabolism Drug/poison detoxification Calcium ion storage Ca +2 Enzymes produced help make: oils, phospholipids and steroids Structure determines function: EX: Synthesis and secretion of hormones in the testes and ovaries are rich in smooth ER Drug detox: hydroxyl groups added, increases solubility, allows body to get rid of. Drugs in turn cause more smooth ER to be made which increases the rate of detox, increasing tolerance to that and other drugs.

32. E NDOPLASMIC R ETICULUM (ER)

33. Y OU MUST KNOW 2. In most cases, smooth ER synthesizes lipids. c. The Golgi complex is a membrane-bound structure that consists of a series of flattened membrane sacs (cisternae). 1. Functions of the Golgi include synthesis and packaging of materials (small molecules) for transport (in vesicles), and production of lysosomes.

34. G OLGI A PPARATUS Function: synthesis & packaging of materials (small molecules) for transport (in vesicles); produce lysosomes Series of flattened membrane sacs (cisternae) Cis face : receives vesicles Trans face : ships vesicles

36. G OLGI MODELS (a) According to the cisternae maturation model the cisternae progress forward from the cis to trans face, carrying and modifying their cargo as they move. (b) The vesicular transport model, where each cisterna remains in one place with unchanging enzymes, and the proteins move forward through the stack via vesicles that move from earlier to later cisternae (anterograde traffic).

37. Y OU MUST KNOW e. Lysosomes are membrane-enclosed sacs that contain hydrolytic enzymes, which are important in intracellular digestion, the recycling of a cell’s organic materials and programmed cell death (apoptosis). Lysosomes carry out intracellular digestion in a variety of ways.

38. L YSOSOMES Function: intracellular digestion; recycle cell’s materials; programmed cell death (apoptosis) Contains hydrolytic enzymes

39. L YSOSOME DIGESTION Phagocytosis ( phagein to eat, kytos vessel) Lysosomes digest (hydrolyze) materials taken into the cell and recycle intra cellular materials. TOP- a Macrophage (WBC) ingests bacteria and viruses and destroy them using lysosomes. The lysosomes are dark. Macrophages uses lysosomes to destroy ingested bacteria and viruses BOTTOM this diagram shows one lysosome fusing with a food vacuole during the process of phagocytosis of a protist

40. Y OU MUST KNOW A vacuole is a membrane-bound sac that plays roles in intracellular digestion and the release of cellular waste products. In plants, a large vacuole serves many functions, from storage of pigments or poisonous substances to a role in cell growth. In addition, a large central vacuole allows for a large surface area to volume ratio

41. V ACUOLES Function: storage of materials (food, water, minerals, pigments, poisons) Membrane-bound vesicles Eg. food vacuoles, contractile vacuoles Freshwater protists have contractile vacuoles to pump excess water out of the cell keeping the ionic concentration stable. Plants: large central vacuole -- stores water, ions in the cell sap Role in plant growth by absorption of water

42. (1)

43. (2) (3)

44. (4) (5) (6)

45. Mitochondria specialize in energy capture and transformation. 1. Mitochondria have a double membrane that allows compartmentalization within the mitochondria and is important to its function 2. The outer membrane is smooth, but the inner membrane is highly convoluted, forming folds called cristae. 3. Cristae contain enzymes important to ATP production; cristae also increase the surface area for ATP production. M ITOCHONDRIA

46. Function: site of cellular respiration Double membrane: outer and inner membrane Cristae : folds of inner membrane; contains enzymes for ATP production; increased surface area to  ATP made Matrix : fluid-filled inner compartment Video

47. Y OU MUST KNOW g. Chloroplasts are specialized organelles found in algae and higher plants that capture energy through photosynthesis. 1. The structure and function relationship in the chloroplast allows cells to capture the energy available in sunlight and convert it to chemical bond energy via photosynthesis. 2. Chloroplasts contain chlorophylls, which are responsible for the green color of a plant and are the key light-trapping molecules in photosynthesis. There are several types of chlorophyll, but the predominant form in plants is chlorophyll a. 3. Chloroplasts have a double outer membrane that creates a compartmentalized structure, which supports its function. Within the chloroplasts are membrane-bound structures called thylakoids. Energy- capturing reactions housed in the thylakoids are organized in stacks, called “grana,” to produce ATP and NADPH2, which fuel carbon-fixing reactions in the Calvin-Benson cycle. Carbon fixation occurs in the stroma, where molecules of CO2 are converted to carbohydrates.

48. C HLOROPLASTS Function: site of photosynthesis Double membrane Thylakoid disks in stacks (grana); stroma (fluid) Contains chlorophylls (pigments) for capturing sunlight energy

49. I LLUSTRATIVE E XAMPLES : 1.B.1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. b. Structural evidence supports the relatedness of all eukaryotes. b. Cytoskeleton (a network of structural proteins that facilitate cell movement, morphological integrity and organelle transport); c. Membrane-bound organelles (mitochondria and/or chloroplasts); Linear chromosomes; d. Endomembrane systems, including the nuclear envelope

50. E NDOSYMBIONT THEORY Mitochondria & chloroplasts share similar origin Prokaryotic cells engulfed by ancestors of eukaryotic cells Evidence: Double-membrane structure (other organelles have single) Have own ribosomes & DNA Reproduce independently within cell

51. P EROXISOMES Functions: break down fatty acids; detox alcohol Involves production of hydrogen peroxide (H 2 O 2 )

52. C YTOSKELETON : NETWORK OF PROTEIN FIBERS Function: support, motility, regulate biochemical activities

53. MicrotubulesMicrofilaments Intermediate Filaments Protein = tubulin Largest fibers Shape/support cell Track for organelle movement Forms spindle for mitosis/meiosis Component of cilia/flagella Protein = actin Smallest fibers Support cell on smaller scale Cell movement Eg. ameboid movement, cytoplasmic streaming, muscle cell contraction Intermediate size Permanent fixtures Maintain shape of cell Fix position of organelles 3 T YPES OF C YTOSKELETON F IBERS :

54. MicrotubulesMicrofilaments Intermediate Filaments 3 T YPES OF C YTOSKELETON F IBERS :

56. Centrosomes : region from which microtubules grow Also called microtubule organizing center Animal cells contain centrioles

57. C ILIA & F LAGELLA Flagella: long and few; propel through water Cilia: short and numerous; locomotion or move fluids Have “9+2 pattern” of microtubules

58. E XTRACELLULAR M ATRIX (ECM) Outside plasma membrane Composed of glycoproteins (ex. collagen) Function: Strengthens tissues and transmits external signals to cell

59. I NTERCELLULAR J UNCTIONS (A NIMAL CELLS ) Tight junctions : 2 neighboring cells are fused to form watertight seal preventing leakage Desmosomes : “rivets” that fasten cells into strong sheets. Attach muscle to muscle Gap junctions : channels through which ions, sugar, small molecules can pass from cell to cell Video

60. P LANT C ELLS Cell wall: protect plant, maintain shape, prevent excessive water uptake Composed of cellulose Plasmodesmata : channels between cells to allow passage of molecules

61. Plant Cells OnlyAnimals Cells Only Central vacuolesLysosomes ChloroplastsCentrioles Cell wall of celluloseFlagella, cilia Plasmodesmata Desmosomes, tight and gap junctions Extracellular matrix (ECM)

62. H ARVARD CELL VIDEO http://multimedia.mcb.harvard.edu/anim_innerlife.html