A Tour of the Cell: From Chemical Evolution to Multicellularity

1. 10 µm 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 How old is the earth? How do we know? What was it like back then (young planet)? How did life 1st come about? The probable evolution of cells was posited by A. Oparin (1920’s): “chemical evolution” Inorganic compounds (CHONPS) organic molecules primitive cells

3. The chemical evolution of cells • Had to start with building blocks • The Miller-Urey experiment • The experiment used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). • The chemicals were all sealed inside a sterile array of glass tubes and flasks connected in a loop, with one flask half-full of liquid water and another flask containing a pair of electrodes. • The liquid water was heated to induce evaporation, sparks were fired between the electrodes to simulate lightning through the atmosphere and water vapor, and then the atmosphere was cooled again so that the water could condense and trickle back into the first flask in a continuous cycle.

4. The result: • At the end of one week of continuous operation, Miller and Urey observed that as much as 10–15% of the carbon within the system was now in the form of organic compounds. • Two percent of the carbon had formed amino acids that are used to make proteins in living cells, with glycine as the most abundant. • Sugars, lipids, and some of the building blocks for nucleic acids were also formed. (Wikipedia)

5. From organic molecules to cells… • It’s proposed that this “primordial soup” of organics in the young oceans may have puddled together, condensed/evaporated into self-sustaining “globs” = primitive cells? Some labs have since been able to replicate this process (make primitive “beginner-level” protocells) • Microspheres • Coacervates

6. Once upon a time, about 3.5 billion years ago… Self-replicating molecules First to appear were self-replicating molecules. Then these molecules became more complicated and evolved a membrane inside which they were protected from the changing external environment. These were the first cells that became primitive bacteria, termed Prokaryotes. • Archaebacteria • “Extremophiles”

7. Then what happened? • According to some more recent findings, many scientists have pushed back the origin of cells to around 3.8 billion years! • The first cells were likely heterotrophic and anaerobic • According to the heterotroph hypothesis, autotrophs developed after the evolution of heterotrophs partly because the primitive atmosphere of the earth lacked oxygen. • Oxygen built up as a result of photosynthesis. There is no evidence of plants or cyanobacteria in the fossil record before about 2 billion years ago. Also rocks containing oxides (elements combined with oxygen) don't appear until then either.

8. What about eukaryotic cells? Supporting evidence: • Both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (in being circular and in its size). • They are surrounded by two or more membranes, and the innermost of these shows differences in composition from the other membranes of the cell. The composition is like that of a prokaryotic cell membrane. • Evolved around 1.75 – 2 billion years ago • “The Endosymbiont Hypothesis” (Lynn Margulis) • narrated animation

9. Multicellularity • 1st multicellular eukaryotes seem to have evolved about a billion years ago • Algae, kelp, fungi • May have come about as colonial groups of individual cells that have division of labor

10. 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 Cell anatomy reflects function • Concept 6.1: 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 • Different types of microscopes • Can be used to visualize different sized cellular structures 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

11. Electron microscopes (EMs) • Focus a beam of electrons through a specimen (TEM) or onto its surface (SEM) • Light microscopes (LMs) • Pass visible light through a specimen • Magnify cellular structures with lenses

12. 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 Figure 6.4 (a)

13. 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) • Provides for detailed study of the internal ultrastructure of cells Figure 6.4 (b)

14. Isolating Organelles by Cell Fractionation • Cell fractionation • Takes cells apart and separates the major organelles from one another

15. The centrifuge • Is used to fractionate cells into their component parts

16. 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 • They contain chromosomes • They all have ribosomes

17. Two types of cells make up every organism Prokaryotic cells • Do not contain a nucleus • Have their DNA located in a region called the nucleoid • Eukaryotic cells • Have a membrane-bound nucleus • Have membrane-bound organelles that compartmentalize their functions

18. 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

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

20. 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 Limitations of Cell Size: Surface Area to Volume Ratio • A smaller cell has a higher surface to volume ratio, which facilitates the exchange of materials into and out of the cell • The logistics of carrying out cellular metabolism sets limits on the size of cells Figure 6.7

21. Outside of cell Hydrophilic region 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) Inside of cell 0.1 µm Hydrophobic region Hydrophilic region Phospholipid Proteins (b) Structure of the plasma membrane Cell Membrane • The plasma membrane • Functions as a selective barrier • Allows sufficient passage of nutrients and waste Carbohydrate side chain Figure 6.8 A, B

22. 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 • Tutorial on parts of a typical animal cell

23. 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

24. 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

25. The Nucleus: Genetic Library of the Cell • The nucleus • Contains most of the genes in the eukaryotic cell (where are the rest?) The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

26. 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). Nuclear membrane • The nuclear envelope • Encloses the nucleus, separating its contents from the cytoplasm Figure 6.10

27. 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 • Ribosomes • Are particles made of ribosomal RNA and protein • Carry out protein synthesis Endoplasmic reticulum (ER) Figure 6.11

28. Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell • The endomembrane system • Includes many different structures

29. Smooth ER Nuclear envelope Rough ER ER lumen Cisternae Ribosomes Transitional ER Transport vesicle 200 µm Smooth ER Rough ER The Endoplasmic Reticulum: Biosynthetic Factory • The endoplasmic reticulum (ER) • Accounts for more than half the total membrane in many eukaryotic cells • The ER membrane is continuous with the nuclear envelope Figure 6.12

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

31. Functions of Smooth ER • The smooth ER • Synthesizes lipids • Metabolizes carbohydrates • Stores calcium • Detoxifies poison Ex: liver cells

32. Functions of Rough ER • The rough ER • Has bound ribosomes • Produces proteins and membranes, which are distributed by transport vesicles

33. The Golgi Apparatus: Shipping and Receiving Center • The Golgi apparatus • Receives many of the transport vesicles produced in the rough ER • Consists of flattened membranous sacs called cisternae • Functions of the Golgi apparatus include • Modification of the products of the rough ER • Manufacture of certain macromolecules

34. cis face (“receiving” side of Golgi apparatus) 5 3 4 6 2 1 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 • Functions of the Golgi apparatus Golgi apparatus Figure 6.13 TEM of Golgi apparatus

35. 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: Digestive Compartments • A lysosome • Is a membranous sac of hydrolytic enzymes • Can digest all kinds of macromolecules • Lysosomes carry out intracellular digestion by phagocytosis

36. 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 Lysosomes • Autophagy Animation of how lysosomes work http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__lysosomes.html Figure 6.14 B

37. Vacuoles: Diverse Maintenance Compartments • A plant or fungal cell • May have one or several vacuoles • Water, food, or waste storage • In animal cells, these are called “vesicles”

38. Food vacuoles • Are formed by phagocytosis • animation • Contractile vacuoles • Pump excess water out of protist cells link

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

40. 1 Nuclear envelope is connected to rough ER, which is also continuous with smooth ER Nucleus Rough ER 2 Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golgi Smooth ER cis Golgi Nuclear envelop 3 Golgi pinches off transport Vesicles and other vesicles that give rise to lysosomes and Vacuoles Plasma membrane trans Golgi 4 5 6 Lysosome available for fusion with another vesicle for digestion Transport vesicle carries proteins to plasma membrane for secretion Plasma membrane expands by fusion of vesicles; proteins are secreted from cell • Relationships among organelles of the endomembrane system Figure 6.16

41. Concept 6.5: Mitochondria and chloroplasts change energy from one form to another • Mitochondria • Are the sites of cellular respiration • Chloroplasts • Found only in plants, are the sites of photosynthesis

42. Mitochondrion Intermembrane space Outer membrane Free ribosomes in the mitochondrial matrix Inner membrane Cristae Matrix Mitochondrial DNA 100 µm Mitochondria: Chemical Energy Conversion • Mitochondria are enclosed by two membranes • Are found in nearly all eukaryotic cells • A smooth outer membrane • An inner membrane folded into cristae Figure 6.17

43. Chloroplasts: Capture of Light Energy • The chloroplast • Is a specialized member of a family of closely related plant organelles called plastids • Choroplasts specifically contain chlorophyll

44. Chloroplast Ribosomes Stroma Chloroplast DNA Inner and outer membranes Granum 1 µm Thylakoid Chloroplasts Are found in leaves and other green organs of plants and in algae • Chloroplast structure includes • Thylakoids, membranous sacs • Stroma, the internal fluid Figure 6.18

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

46. Microtubule Microfilaments 0.25 µm Figure 6.20 Cytoskeleton Concept 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell

47. Roles of the Cytoskeleton: Support, Motility, and Regulation • Gives mechanical support to the cell • Is involved in cell motility, which utilizes motor proteins • The cytoskeleton • Is a network of fibers extending throughout the cytoplasm Animated, narrated tutorial http://www.wiley.com/college/pratt/0471393878/student/animations/actin_myosin/index.html

48. Table 6.1 Components of the Cytoskeleton • There are three main types of fibers that make up the cytoskeleton

49. Microtubules • Microtubules • Shape the cell • Guide movement of organelles • Help separate the chromosome copies in dividing cells

50. Centrosome Microtubule Centrioles 0.25 µm Longitudinal section of one centriole Cross section of the other centriole Microtubules Figure 6.22 Centrosomes and Centrioles • Contains a pair of centrioles • These form the spindle for chromosome division in mitosis/meiosis • The centrosome • Is considered to be a “microtubule-organizing center”