A Tour of the Cell: Importance, Structure, and Function

1. Chapter 6 A Tour of the Cell

2. Overview The Importance of Cells • All organisms are made of cells • The cell is the simplest collection of matter that can live • The cell demonstrates all properties of living things • Unicellular vs. Multicellular • Although, cells can differ from each other, they share certain common characteristics

3. 10 µm • Cell structure is correlated to cellular function Figure 6.1

4. Concept 6.1: Microscopy • 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

5. Light microscopes (LMs) • Pass visible light through a specimen • Magnify cellular structures with lenses • First invented by Robert Hooke in 1665. • Visible light is focused on a specimen with a condenser lense. • Light passing through the specimen is refracted with an objective lense and an ocular lense.

6. Magnification: How much larger the object is made to appear compared to its real size • Resolving Power(resolution): Minimum distance between two points that can still be distinguished as two separate units • Resolution of light microscope is limited by the wave length of visible light • Maximum resolution is 200 nm(0.2μm) • Highest magnification is 1000 times

7. 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 Small molecules Figure 6.2 Atoms 0.1 nm • Different types of microscopes • Can be used to visualize different sized cellular structures Unaided eye 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

8. Electron microscopes (EMs) • Focus a beam of electrons through a specimen (TEM) or onto its surface (SEM) • Resolving power is about 0.002 nm

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 • it has a great depth of field and produces three-dimensional image Figure 6.4 (a)

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) • electrons transmitted through the specimen • used to study internal cellular structures Figure 6.4 (b)

11. APPLICATION TECHNIQUE Isolating Organelles by Cell Fractionation • The process of 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 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. Figure 6.5

12. APPLICATION RESULTS TECHNIQUE 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. In the original experiments, the researchers used microscopy to identify the organelles in each pellet, establishing a baseline for further experiments. In the next series of experiments, researchers used biochemical methods to determine the metabolic functions associated with each type of organelle. Researchers currently use cell fractionation to isolate particular organelles in order to study further details of their function. Figure 6.5

13. 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

14. Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions • Two types of cells make up every organism • Prokaryotic • Eukaryotic

15. 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 • The entire region between the nucleus and the cell membraneis calledCytoplasm • They contain chromosomes • They all have ribosomes

16. Prokaryotic cells • Do not contain a nucleus • Have their DNA located in a region called the nucleoid

17. 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

18. Eukaryotic cells • Contain a true nucleus, bounded by a membranous nuclear envelope • Are generally quite a bit bigger than prokaryotic cells

19. 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 • The logistics of carrying out cellular metabolism sets limits on the size of cells • 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

20. Outside of cell Hydrophilic region (a) 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. 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

21. 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

22. 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 Flagella (in some plant sperm) Lysosome Mitochondrion • A animal cell Figure 6.9

23. 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

24. Concept 6.3: The Nucleus: Genetic Library of the Cell The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes • The nucleus • A membrane bound cellular organelle which contains most of the genes that control the entire cell • average diameter about 5 um • Enclosed by a nuclear envelope • Contains most of the genes in the eukaryotic cell

25. 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). • The nuclear envelope • Encloses the nucleus, separating its contents from the cytoplasm • Two lipid bilayer membrane separated by a space • Attached to proteins of the envelope’s nuclear side is a network of protein filaments, the nuclear lamina, which stabilizes nuclear shape. • Is perforated by pores Figure 6.10

26. Chromatin • is a complex of proteins and DNA inside the nucleus. • Appears as mass of material in nondividing cells • Makes up chromosomes in eukaryotic cells Chromosomes • long thread like associations of genes • Each species has a characteristic chromosome number • Human somatic cells have 46 chromosomes

27. Nucleolus: • roughly spherical region in the nucleus of nondividing cells • May be two or more in a cell • Packages ribosomal subunits from: • rRNA transcribed in the nucleolus • RNA produced elsewhere • Ribosomal proteins produced and imported from the cytoplasm • ribosomal subunits pass through nuclear pores to the cytoplasm.

28. Ribosomes: Protein Factories in the Cell • Ribosomes • a cytoplasmic organelle which is the site for protein synthesis. • Are complexes of RNA and protein. • Constructed in the nucleus in eukaryotic cells. • Cells with high rate of protein synthesis have prominent nucleoli and many Ribosomes, e.g. human liver cells have few millions

29. Free ribosomes: • ribosomes are suspended in the cytosol • most proteins made by free ribosomes will function in the cytosol. Bound ribosomes: • ribosomes attached to the outside of the endoplasmic reticulum. • generally make proteins that are destined for membrane inclusion or export. • cells specialized in protein secretion have many bound ribosomes, e.g. pancreatic cells.

30. Ribosomes Cytosol Free ribosomes Bound ribosomes Large subunit Small subunit 0.5 µm TEM showing ER and ribosomes Diagram of a ribosome Ribosomes: Protein Factories in the Cell ER Endoplasmic reticulum (ER) Figure 6.11

31. Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell • Many membranes of the eukaryotic cell are part of an endomembrane system. • Membranes may be interrelated directlythrough physical contact. • Membranes may be related indirectly through vesicles. • Vesicles:Membrane enclosed sacs that are portions of membranes moving from the site of one membrane to another.

32. The endomembrane system includes: 1. Nuclear envelope 2. Endoplasmic reticulum 3. Golgi apparatus 4. Lysosomes 5. Vacuoles

33. The Endoplasmic Reticulum: Biosynthetic Factory • The endoplasmic reticulum (ER) • Extensive membranous network of tubules and sacs (cisternae) • Accounts for more than half the total membrane in many eukaryotic cells • Most extensive portion of endomembrane system • Continuous with other membrane of the nuclear envelope

34. 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

35. There are two distinct regions of ER • Smooth ER, which lacks ribosomes • Rough ER, which contains ribosomes

36. Functions of Smooth ER • The smooth ER • Synthesizes lipids, phospholipids and steroids • Metabolizes carbohydrates • Stores calcium • Detoxifies poison

37. Functions of Rough ER • The rough ER • Appears rough because its cytoplasmic side is studded with ribosomes. • Produces proteins and membranes, which are distributed by transport vesicles • It is continuous with the outer membrane of the nuclear envelope. • Manufactures secretary proteins and membranes.

38. Ribosomes attached to rough ER synthesize secretory proteins↓Growing polypeptide enters through ER membrane into the cisternal space↓Protein folds into its conformation↓Protein departs in a transport vesicle to its destination

39. The Golgi Apparatus: Shipping and Receiving Center • Organelle made of stacked, flattened sacs (cisternae) that modifies,stores and routes products of the ER. • Receives many of the transport vesicles produced in the rough ER

40. Functions of the Golgi apparatus include • Modification of the products of the rough ER (oligosaccharide portion of glycoproteins) • Manufacture of certain macromolecules • Alters some membrane phospholipids • Target products for various parts of the cell • Sorts products for secretion

41. There are two sides in Golgi apparatus:1. cis face: (forming face):closely associated with the ER, receiving products by accepting transport vesicles.2. trans face: (maturing face): pinches off vesicles from Golgi and transport molecules to other sites.Each cisternae between cis and trans faces contain unique enzymes

42. 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 Figure 6.13 TEM of Golgi apparatus

43. Lysosomes: Digestive Compartments • A lysosome An organelle which is a membrane–enclosed bag (sac) of hydrolytic enzymes that digest all major classes of macromolecules ·Enzymes include lipase, carbohydrase, proteases and nucleases. ·  Optimal pH for these enzymes is pH 5· Lysosomes probably pinched off from the trans face of the Golgi·  Lysosomal membrane do two important functions: 1.Isolates strong hydrolytic enzymes from the cytosol 2. Keeps the optimal acidic environment for enzymatic activity by pumping hydrogen ions inward from the cytosol

44. 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: Cellular process of ingestion where plasma membrane engulfs food substances and pinches off to form particle-containing vacuole. Lysosomes fuse with these vacuoles and their hydrolytic enzymes digest the food. Figure 6.14 A

45. Autophagy (recycles cell own organic material) • lysosomes may engulf other cellular organelles or part of the cytosoland digest them with the hydrolytic enzymes • resulting monomers are released into the cytosol where they can berecycled into new macromolecules

46. 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 Figure 6.14 B

47. Lysosomes and human diseases Lack of specific lysosomal enzymes interfere with lysosomal metabolism and cellular functions.Examples:i. Pompe’s disease: the enzyme which breaks down glycogen is missing. The result is glycogen accumulation and damage of the liverii. Tay-Sachs disease: lysosomal lipase is missing. The result is accumulation of lipids in the brain

48. Vacuoles: Diverse Maintenance Compartments • Vacuole: Organelle which is a membrane enclosed sac that is larger than a vesicle • A plant or fungal cell may have one or several vacuoles • Food vacuoles • Are formed by phagocytosis • Contractile vacuoles • found in some freshwater protozoathat Pumps excess water from the cell.

49. Central vacuole Cytosol Tonoplast Nucleus Central vacuole Cell wall Chloroplast 5 µm Central vacuoles • Found in most mature plant cells. • is enclosed by a membrane called tonoplast • has many functions: • Store organic compounds (e.g. protein storage in seeds). • store inorganic ions. • isolate dangerous by-products from the cytoplasm. • contains soluble pigments in some cells. • may contain poisons to protect the plant from predators. • play a role in plant growth by absorbing water and elongate the cell. • hold reserves of important organic compounds and water Figure 6.15

50. The Endomembrane System: A Review • The endomembrane system • Is a complex and dynamic player in the cell’s compartmental organization