1. A Tour of the Cell

2. Eukaryotic cells have internal membranes that compartmentalize their functions Basic features of all cells: plasma membrane, cytosol, chromosomes, ribosomes Prokaryotic vs Eukaryotic cells – prokaryotic cells  Bacteria and Archaea No nucleus DNA in an unbound region called the nucleoid No membrane-bound organelles Cytoplasm bound by the plasma membrane – eukaryotic cells  Protists, fungi, animals and plants DNA in a nucleus bounded by nuclear envelope Membrane-bound organelles Cytoplasm in the region between the plasma membrane and nucleus Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

3. Fig. 6-6 Fimbriae Nucleoid Ribosomes Plasma membrane Cell wall Capsule Flagella Bacterial chromosome 0.5 µm Prokaryotic cell

4. Fig. 6-9a ENDOPLASMIC RETICULUM (ER) Smooth ERRough ER Flagellum*** (not in plants) Centrosome CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Microvilli Peroxisome Mitochondrion Lysosome*** (not in plants/prokaryotes) Golgi apparatus Ribosomes Plasma membrane Nuclear envelope Nucleolus Chromatin NUCLEUS Eukaryotic Animal Cell

5. Fig. 6-9b NUCLEUS Nuclear envelope Nucleolus Chromatin Rough endoplasmic reticulum Smooth endoplasmic reticulum Ribosomes Central vacuole*** Microfilaments Intermediate filaments Microtubules CYTO-SKELETON Chloroplast*** Plasmodesmata*** Wall of adjacent cell Cell wall*** Plasma membrane Peroxisome Mitochondrion Golgi apparatus Eukaryotic Plant Cell ***specific to plants

6. Organelles to know Nucleus – Genetic information Ribosomes – protein factories Endoplasmic Reticulum – protein trafficking and metabolic functions Golgi Apparatus – shipping and receiving center Lysosomes – digestive compartments Vacuoles – maintenance compatments Mitochondria – chemical energy conversion (site of cellular respiration) Chloroplasts – light energy conversion (site of photosynthesis) Peroxisomes - oxidation Cytoskeleton – support, motility and regulation Extracellular Matrix – support, adhesion, movement, regulation Intercellular Junctions – facilitate contact between cells

7. Nucleus: Information Central – nuclear envelope encloses the nucleus, separating it from the cytoplasm – nuclear membrane is a double membrane; each membrane consists of a lipid bilayer – Pores regulate the entry and exit of molecules from the nucleus – The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein – In the nucleus, DNA and proteins form genetic material called chromatin – Chromatin condenses to form discrete chromosomes – The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

8. Fig. 6-10 Nucleolus Nucleus Nuclear lamina Close-up of nuclear envelope 1 µm 0.25 µm Ribosome Pore complex Nuclear pore Nuclear envelope Chromatin Surface of nuclear envelope Pore complexes

9. Ribosomes: Protein factories – particles made of ribosomal RNA and protein – Protein synthesis occurs here Free ribosomes are localized to the cytosol Bound ribosomes are on the ER or the nuclear envelope Fig. 6-11 Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes Large subunit Small subunit Diagram of a ribosome

10. Endoplasmic Reticulum (ER): Protein Trafficking – The ER membrane is attached to the nuclear envelope – There are two distinct regions of ER: Smooth ER  lacks ribosomes – Synthesizes lipids – Metabolizes carbohydrates – Detoxifies poison – Stores calcium Rough ER  with ribosomes – Secretes glycoproteins (proteins covalently bonded to carbohydrates) – Distributes transport vesicles, proteins surrounded by membranes – membrane factory for the cell Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

11. Fig. 6-12 Smooth ER Rough ER Nuclear envelope Rough ER Smooth ER Transport vesicle Ribosomes

12. Golgi apparatus: Shipping and Receiving Center – shipping and receiving center – consists of flattened membranous sacs called cisternae – Functions: Modifies products of the ER Manufactures certain macromolecules Sorts and packages materials into transport vesicles Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Cisternae

13. Lysosome: Digestive Compartment – a membranous sac of hydrolytic enzymes that can digest macromolecules – Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids After phagocytosis (engulfing of another cell) lysosomes fuse with the food vacuole and digests the molecules Autophagy uses enzymes to recycle the cell’s own organelles and macromolecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Digestive enzymes Lysosome Plasma membrane Food vacuole Digestion Peroxisome Vesicle Lysosome Mitochondrion Digestion (a) Phagocytosis (b) Autophagy

14. – Diverse Maintenance Compartments – Food vacuoles are formed by phagocytosis – Contractile vacuoles pump excess water out of cells – Central vacuoles (in many mature plant cells) hold organic compounds and water Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 6-15 Central vacuole Cytosol Central vacuole Nucleus Cell wall Chloroplast Vacuoles: Maintenance Compartment

15. The Endomembrane System: A Review The endomembrane system is a complex and dynamic player in the cell’s compartmental organization – Nuclear envelope – ER – Golgi apparatus – Lysosomes – Vacuoles – Plasma membrane Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

16. Fig. 6-16-3 Smooth ER Nucleus Rough ER Plasma membrane Golgi Nuclear envelope is connected to rough ER Proteins produced by the ER flow in transport vessicles to the Golgi Golgi pinches off vessicles that give rise to lysosomes, vessicles and vacuoles Lysosomes can fuse with another vessicle for digestion Transport vessicle carries proteins to plasma membrane for secretion Plasma membrane expands by fusion of vessicles; proteins are secreted from the cell Transport vessicle Lysosome

17. Mitochondria: Chemical Energy Conversion – sites of cellular respiration, a metabolic process that generates ATP – Have a double membrane – Contain their own DNA – Mitochondria are in nearly all eukaryotic cells – They have a smooth outer membrane and an inner membrane folded into cristae Cristae present a large surface area for enzymes that synthesize ATP – The inner membrane creates two compartments: intermembrane space and mitochondrial matrix Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

18. Fig. 6-17 Free ribosomes in the mitochondrial matrix Intermembrane space Outer membrane Inner membrane Cristae Matrix 0.1 µm

19. Chloroplasts: Light Energy Conversion – Capture light energy, are the sites of photosynthesis – found in plants and algae – Have a double membrane (similar to mitochondria) – Contain their own DNA (similar to mitochondria) – contain chlorophyll and other molecules that function in photosynthesis – found in leaves and other green organs of plants and in algae Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Ribosomes Thylakoid Stroma Granum Inner and outer membranes 1 µm

20. – oxidative organelles – specialized metabolic compartments bounded by a single membrane – produce hydrogen peroxide and convert it to water – Oxygen is used to break down different types of molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 1 µm Chloroplast Peroxisome Mitochondrion Peroxisome: Oxidation

21. Cytoskeleton: Support, Motility and Regulation – a network of fibers extending throughout the cytoplasm – organizes the cell’s structures and activities, anchoring many organelles – composed of three types of molecular structures: Microtubules are the thickest of the three components Microfilaments, also called actin filaments, are the thinnest components Intermediate filaments are fibers with diameters in a middle range – helps to support the cell and maintain its shape – interacts with motor proteins to produce motility Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

22. Functions – Shaping the cell – Guiding movement of organelles – Separating chromosomes during cell division Centrosomes – The centrosome is a “microtubule-organizing center” – microtubules grow out from a centrosome near the nucleus and attach to chromosomes during mitosis Cilia and Flagella – Microtubules control the beating of cilia and flagella – A core of microtubules sheathed by the plasma membrane Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Microtubules

23. Fig. 6-22 Centrosome Microtubule centrosome microtubules Microtubules separate chromosomes during mitosis

24. Fig. 6-23 (a) EX: Motion of flagella in sperm(b) EX: Motion of cilia in aquatic life Microtubules assist in motility

25. Fig. 6-24 (c) Cross section of basal body (a)Longitudinal section of cilium Plasma membrane Basal body Microtubules (b)Cross section of cilium Plasma membrane Microtubule structure in cilia

26. Microfilaments (Actin Filaments) Microfilaments are solid rods built as a twisted double chain of actin subunits The structural role: bear tension and resist pulling forces within the cell Cellular function: cellular motility – Myosin and actin contribute to this Examples – Muscle contraction – Ameoboid movement occurs through Pseudopodia – Cytoplasmic streaming Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Microvillus Microfilaments (actin filaments) Intermediate filaments

27. Intermediate Filaments They support cell shape and fix organelles in place more permanent cytoskeleton fixtures than the other two classes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

28. Cell Walls of Plants Prokaryotes, fungi, and some protists also have cell walls Functions: protects the plant cell, maintains its shape, prevents excessive uptake of water made of cellulose fibers Plant cell walls may have multiple layers: – Primary cell wall: relatively thin and flexible – Middle lamella: thin layer between primary walls of adjacent cells – Secondary cell wall (in some cells): added between the plasma membrane and the primary cell wall Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

29. Fig. 6-28 Secondary cell wall Primary cell wall Middle lamella Central vacuole Cytosol Plasma membrane Plant cell walls Plasmodesmata 1 µm

30. The Extracellular Matrix (ECM) of Animal Cells Functions – Support – Adhesion – Movement – Regulation made up of glycoproteins (collagen, proteoglycans, and fibronectin) ECM proteins bind to receptor proteins in the plasma membrane called integrins Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings EXTRACELLULAR MATRIX Collagen Fibronectin Micro- filaments CYTOPLASM Integrins Proteoglycan complex

31. Intercellular Junctions Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact Intercellular junctions facilitate this contact There are several types of intercellular junctions – Plasmodesmata – channels that perforate cell walls – Tight junctions - membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid – Desmosomes (anchoring junctions) fasten cells together into strong sheets – Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

32. Fig. 6-32 Tight junction 0.5 µm Desmosome Gap junction Extracellular matrix 0.1 µm Plasma membranes of adjacent cells Space between cells Gap junctions Desmosome Intermediate filaments Tight junction Tight junctions prevent fluid from moving across a layer of cells Desmosomes fasten cells together in sheets Gap junctions all cells to communicate with one another via cytoplasmic channels

33. Fig. 6-UN1 Cell Component Structure Function Houses chromosomes, made of chromatin (DNA, the genetic material, and proteins); contains nucleoli, where ribosomal subunits are made. Pores regulate entry and exit of materials. Nucleus (ER) Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes Ribosome Concept 6.4 Endoplasmic reticulum The endomembrane system regulates protein traffic and performs metabolic functions in the cell (Nuclear envelope) Concept 6.5 Mitochondria and chloro- plasts change energy from one form to another Golgi apparatus Lysosome Vacuole Mitochondrion Chloroplast Peroxisome Two subunits made of ribo- somal RNA and proteins; can be free in cytosol or bound to ER Extensive network of membrane-bound tubules and sacs; membrane separates lumen from cytosol; continuous with the nuclear envelope. Membranous sac of hydrolytic enzymes (in animal cells) Large membrane-bounded vesicle in plants Bounded by double membrane; inner membrane has infoldings (cristae) Typically two membranes around fluid stroma, which contains membranous thylakoids stacked into grana (in plants) Specialized metabolic compartment bounded by a single membrane Protein synthesis Smooth ER: synthesis of lipids, metabolism of carbohy- drates, Ca 2+ storage, detoxifica- tion of drugs and poisons Rough ER: Aids in synthesis of secretory and other proteins from bound ribosomes; adds carbohydrates to glycoproteins; produces new membrane Modification of proteins, carbo- hydrates on proteins, and phos- pholipids; synthesis of many polysaccharides; sorting of Golgi products, which are then released in vesicles. Breakdown of ingested substances, cell macromolecules, and damaged organelles for recycling Digestion, storage, waste disposal, water balance, cell growth, and protection Cellular respiration Photosynthesis Contains enzymes that transfer hydrogen to water, producing hydrogen peroxide (H 2 O 2 ) as a by-product, which is converted to water by other enzymes in the peroxisome Stacks of flattened membranous sacs; has polarity (cis and trans faces) Surrounded by nuclear envelope (double membrane) perforated by nuclear pores. The nuclear envelope is continuous with the endoplasmic reticulum (ER).