Chapter 6 A Tour of the Cell

Overview: The Fundamental Units of Life All organisms are made of cells The cell is the simplest collection of matter that can live Cell structure is correlated to cellular function All cells are related by their descent from earlier cells For the Discovery Video Cells, go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 6-1 Figure 6.1 How do cellular components cooperate to help the cell function?

Concept 6.1: To study cells, biologists use microscopes and the tools of biochemistry Though usually too small to be seen by the unaided eye, cells can be complex Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Microscopy In a light microscope (LM), visible light passes through a specimen and then through glass lenses, which magnify Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The quality of an image depends on Magnification, the ratio of an object’s image size to its real size Resolution, the measure of the clarity of the image, or the minimum distance of two distinguishable points Contrast, visible differences in parts of the sample Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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 Fig. 6-2 10 m Human height 1 m Length of some nerve and muscle cells 0.1 m Unaided eye Chicken egg 1 cm Frog egg 1 mm 100 µm Most plant and animal cells Light microscope 10 µm Nucleus Most bacteria 1 µm Mitochondrion Figure 6.2 The size range of cells Smallest bacteria Electron microscope 100 nm Viruses Ribosomes 10 nm Proteins Lipids 1 nm Small molecules 0.1 nm Atoms

LMs can magnify effectively to about 1,000 times Various techniques enhance contrast (staining or labeling) Most subcellular structures, including organelles (membrane-enclosed compartments), are too small to be resolved by an LM Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

(a) Brightfield (unstained specimen) Fig. 6-3ab TECHNIQUE RESULTS (a) Brightfield (unstained specimen) 50 µm (b) Brightfield (stained specimen) Figure 6.3 Light microscopy

(d) Differential-interference- contrast (Nomarski) Fig. 6-3cd TECHNIQUE RESULTS (c) Phase-contrast (d) Differential-interference- contrast (Nomarski) Figure 6.3 Light microscopy

50 µm (e) Fluorescence TECHNIQUE RESULTS Fig. 6-3e Figure 6.3 Light microscopy 50 µm

(f) Confocal 50 µm TECHNIQUE RESULTS Fig. 6-3f Figure 6.3 Light microscopy 50 µm

TEMs are used mainly to study the internal structure of cells 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

(b) Transmission electron microscopy (TEM) Longitudinal section of Fig. 6-4 TECHNIQUE RESULTS 1 µm (a) Scanning electron microscopy (SEM) Cilia (b) Transmission electron microscopy (TEM) Longitudinal section of cilium Cross section of cilium 1 µm Figure 6.4 Electron microscopy

Ultracentrifuges fractionate cells into their component parts Cell Fractionation Cell fractionation takes cells apart and separates the major organelles from one another Ultracentrifuges fractionate cells into their component parts Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Differential centrifugation Fig. 6-5a TECHNIQUE Homogenization Figure 6.5 Cell fractionation, part 1 Tissue cells Homogenate Differential centrifugation

(1,000 times the force of gravity) Fig. 6-5b TECHNIQUE (cont.) 1,000 g (1,000 times the force of gravity) 10 min 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) Figure 6.5 Cell fractionation, part 2 Pellet rich in “microsomes” (pieces of plasma membranes and cells’ internal membranes) Pellet rich in ribosomes

Prokaryotic cells: domains Bacteria and Archaea 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 cells: domains Bacteria and Archaea Eukaryotic cells: Protists, fungi, animals, and plants Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Comparing Prokaryotic and Eukaryotic Cells Basic features of all cells: Plasma membrane Semifluid substance called cytosol Chromosomes (carry genes) Ribosomes (make proteins) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

A typical rod-shaped bacterium (b) Fig. 6-6 Fimbriae Nucleoid Ribosomes Plasma membrane Bacterial chromosome Cell wall Capsule 0.5 µm Flagella (a) A typical rod-shaped bacterium (b) A thin section through the bacterium Bacillus coagulans (TEM) Figure 6.6 A prokaryotic cell

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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The plasma membrane is a selective barrier allows passage of oxygen, nutrients, and waste to service the volume of every cell a double layer of phospholipids Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Carbohydrate side chain Fig. 6-7 (a) TEM of a plasma membrane Outside of cell Inside of cell 0.1 µm Carbohydrate side chain Hydrophilic region Figure 6.7 The plasma membrane Hydrophobic region Hydrophilic region Phospholipid Proteins (b) Structure of the plasma membrane

Small cells have a greater surface area relative to volume Limits on the size of cells - The surface area to volume ratio of a cell is critical As the surface area increases by a factor of n2, the volume increases by a factor of n3 Small cells have a greater surface area relative to volume Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

A Panoramic View of the Eukaryotic Cell A eukaryotic cell has internal membranes that partition the cell into organelles Plant and animal cells have most of the same organelles BioFlix: Tour Of An Animal Cell BioFlix: Tour Of A Plant Cell Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

ENDOPLASMIC RETICULUM (ER) Nucleolus NUCLEUS Rough ER Smooth ER Fig. 6-9a Nuclear envelope ENDOPLASMIC RETICULUM (ER) Nucleolus NUCLEUS Rough ER Smooth ER Flagellum Chromatin Centrosome Plasma membrane CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Ribosomes Figure 6.9 Animal and plant cells—animal cell Microvilli Golgi apparatus Peroxisome Mitochondrion Lysosome

Rough endoplasmic reticulum Fig. 6-9b Nuclear envelope Rough endoplasmic reticulum NUCLEUS Nucleolus Chromatin Smooth endoplasmic reticulum Ribosomes Central vacuole Golgi apparatus Microfilaments Intermediate filaments CYTO- SKELETON Microtubules Figure 6.9 Animal and plant cells—plant cell Mitochondrion Peroxisome Chloroplast Plasma membrane Cell wall Plasmodesmata Wall of adjacent cell

The nucleus contains most of the DNA in a eukaryotic cell Concept 6.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes The nucleus contains most of the DNA in a eukaryotic cell Ribosomes use the information from the DNA to make proteins Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The Nucleus: Information Central The nucleus contains most of the cell’s genes and is usually the most conspicuous organelle The nuclear envelope encloses the nucleus The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Close-up of nuclear envelope Fig. 6-10 Nucleus 1 µm Nucleolus Chromatin Nuclear envelope: Inner membrane Outer membrane Nuclear pore Pore complex Rough ER Surface of nuclear envelope Ribosome 1 µm Figure 6.10 The nucleus and its envelope 0.25 µm Close-up of nuclear envelope Pore complexes (TEM) Nuclear lamina (TEM)

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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Chromatin condenses to form discrete chromosomes 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

Ribosomes: Protein Factories Ribosomes are particles made of ribosomal RNA and protein Ribosomes carry out protein synthesis in two locations: In the cytosol (free ribosomes) On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes) For the Cell Biology Video Staining of Endoplasmic Reticulum, go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Endoplasmic reticulum (ER) Fig. 6-11 Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes Large subunit Figure 6.11 Ribosomes Small subunit 0.5 µm TEM showing ER and ribosomes Diagram of a ribosome

Components of the endomembrane system: Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell Components of the endomembrane system: Nuclear envelope Endoplasmic reticulum Golgi apparatus Lysosomes Vacuoles Plasma membrane These components are either continuous or connected via transfer by vesicles Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The Endoplasmic Reticulum: Biosynthetic Factory The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells The ER membrane is continuous with the nuclear envelope There are two distinct regions of ER: Smooth ER, which lacks ribosomes Rough ER, with ribosomes studding its surface For the Cell Biology Video ER and Mitochondria in Leaf Cells, go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Functions of Smooth ER The smooth ER Synthesizes lipids Metabolizes carbohydrates Detoxifies poison Stores calcium Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Functions of Rough ER The rough ER Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates) Distributes transport vesicles, proteins surrounded by membranes Is a membrane factory for the cell Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The Golgi Apparatus: Shipping and Receiving Center The Golgi apparatus consists of flattened membranous sacs called cisternae Functions of the Golgi apparatus: Modifies products of the ER Manufactures certain macromolecules Sorts and packages materials into transport vesicles For the Cell Biology Video ER to Golgi Traffic, go to Animation and Video Files. For the Cell Biology Video Golgi Complex in 3D, go to Animation and Video Files. For the Cell Biology Video Secretion From the Golgi, go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

(“receiving” side of Golgi apparatus) 0.1 µm Fig. 6-13 cis face (“receiving” side of Golgi apparatus) 0.1 µm Cisternae Figure 6.13 The Golgi apparatus trans face (“shipping” side of Golgi apparatus) TEM of Golgi apparatus

Lysosomes: Digestive Compartments A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids Animation: Lysosome Formation Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Nucleus 1 µm Lysosome Digestive enzymes Lysosome Plasma membrane Fig. 6-14a Nucleus 1 µm Lysosome Digestive enzymes Lysosome Figure 6.14a Lysosome—phagocytosis Plasma membrane Digestion Food vacuole (a) Phagocytosis

two damaged organelles 1 µm Fig. 6-14b Vesicle containing two damaged organelles 1 µm Mitochondrion fragment Peroxisome fragment Lysosome Figure 6.14b Lysosomes—autophagy Peroxisome Mitochondrion Digestion Vesicle (b) Autophagy

Vacuoles: Diverse Maintenance Compartments A plant cell or fungal cell may have one or several vacuoles Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Video: Paramecium Vacuole Food vacuoles are formed by phagocytosis Contractile vacuoles, found in many freshwater protists, pump excess water out of cells Central vacuoles, found in many mature plant cells, hold organic compounds and water Video: Paramecium Vacuole Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Central vacuole Cytosol Nucleus Central vacuole Cell wall Chloroplast Fig. 6-15 Central vacuole Cytosol Nucleus Central vacuole Figure 6.15 The plant cell vacuole Cell wall Chloroplast 5 µm

The Endomembrane System: A Review The endomembrane system is a complex and dynamic player in the cell’s compartmental organization Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Nucleus Rough ER Smooth ER Plasma membrane Fig. 6-16-1 Figure 6.16 Review: relationships among organelles of the endomembrane system Plasma membrane

Nucleus Rough ER Smooth ER cis Golgi Plasma membrane trans Golgi Fig. 6-16-2 Nucleus Rough ER Smooth ER cis Golgi Figure 6.16 Review: relationships among organelles of the endomembrane system Plasma membrane trans Golgi

Nucleus Rough ER Smooth ER cis Golgi Plasma membrane trans Golgi Fig. 6-16-3 Nucleus Rough ER Smooth ER cis Golgi Figure 6.16 Review: relationships among organelles of the endomembrane system Plasma membrane trans Golgi

Peroxisomes are oxidative organelles Concept 6.5: Mitochondria and chloroplasts change energy from one form to another Mitochondria are the sites of cellular respiration, a metabolic process that generates ATP Chloroplasts, found in plants and algae, are the sites of photosynthesis Peroxisomes are oxidative organelles For the Cell Biology Video ER and Mitochondria in Leaf Cells, go to Animation and Video Files. For the Cell Biology Video Mitochondria in 3D, go to Animation and Video Files. For the Cell Biology Video Chloroplast Movement, go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Mitochondria and chloroplasts Are not part of the endomembrane system Have a double membrane Have proteins made by free ribosomes Contain their own DNA Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Chloroplasts: Capture of Light Energy The chloroplast is a member of a family of organelles called plastids Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis Chloroplasts are found in leaves and other green organs of plants and in algae Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Chloroplast structure includes: Thylakoids, membranous sacs, stacked to form a granum Stroma, the internal fluid Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Inner and outer membranes Fig. 6-18 Ribosomes Stroma Inner and outer membranes Granum 1 µm Thylakoid Figure 6.18 The chloroplast, site of photosynthesis

Peroxisomes: Oxidation Peroxisomes are specialized metabolic compartments bounded by a single membrane Peroxisomes 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

Chloroplast Peroxisome Mitochondrion 1 µm Fig. 6-19 Figure 6.19 A peroxisome 1 µm

Centrosomes and Centrioles In many cells, microtubules grow out from a centrosome near the nucleus The centrosome is a “microtubule-organizing center” In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Longitudinal section of one centriole Microtubules Cross section Fig. 6-22 Centrosome Microtubule Centrioles 0.25 µm Figure 6.22 Centrosome containing a pair of centrioles Longitudinal section of one centriole Microtubules Cross section of the other centriole

Video: Paramecium Cilia Cilia and Flagella Microtubules control the beating of cilia and flagella, locomotor appendages of some cells Cilia and flagella differ in their beating patterns Video: Chlamydomonas Video: Paramecium Cilia Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Direction of organism’s movement Fig. 6-23 Direction of swimming (a) Motion of flagella 5 µm Direction of organism’s movement Figure 6.23a A comparison of the beating of flagella and cilia—motion of flagella Power stroke Recovery stroke (b) Motion of cilia 15 µm

Animation: Cilia and Flagella Cilia and flagella share a common ultrastructure: A core of microtubules sheathed by the plasma membrane A basal body that anchors the cilium or flagellum A motor protein called dynein, which drives the bending movements of a cilium or flagellum Animation: Cilia and Flagella Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Cross section of cilium Fig. 6-24 Outer microtubule doublet Plasma membrane 0.1 µm Dynein proteins Central microtubule Radial spoke Protein cross-linking outer doublets Microtubules (b) Cross section of cilium Plasma membrane Basal body 0.5 µm (a) Longitudinal section of cilium 0.1 µm Figure 6.24 Ultrastructure of a eukaryotic flagellum or motile cilium Triplet (c) Cross section of basal body

How dynein “walking” moves flagella and cilia: Dynein arms alternately grab, move, and release the outer microtubules Protein cross-links limit sliding Forces exerted by dynein arms cause doublets to curve, bending the cilium or flagellum For the Cell Biology Video Motion of Isolated Flagellum, go to Animation and Video Files. For the Cell Biology Video Flagellum Movement in Swimming Sperm, go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

(a) Effect of unrestrained dynein movement Fig. 6-25a Microtubule doublets ATP Figure 6.25a How dynein “walking” moves flagella and cilia Dynein protein (a) Effect of unrestrained dynein movement

Cross-linking proteins inside outer doublets Fig. 6-25b ATP Cross-linking proteins inside outer doublets Anchorage in cell (b) Effect of cross-linking proteins 1 3 Figure 6.25b, c How dynein “walking” moves flagella and cilia 2 (c) Wavelike motion

Microfilaments (actin filaments) Fig. 6-26 Microvillus Plasma membrane Microfilaments (actin filaments) Figure 6.26 A structural role of microfilaments Intermediate filaments 0.25 µm

Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells At 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 Animation: Tight Junctions Animation: Desmosomes Animation: Gap Junctions Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Tight junctions prevent fluid from moving across a layer of cells Fig. 6-32a Tight junctions prevent fluid from moving across a layer of cells Tight junction Intermediate filaments Desmosome Gap junctions Figure 6.32 Intercellular junctions in animal tissues—tight junctions Extracellular matrix Space between cells Plasma membranes of adjacent cells

Tight junction 0.5 µm Fig. 6-32b Figure 6.32 Intercellular junctions in animal tissues—tight junctions 0.5 µm

Fig. 6-32c Figure 6.32 Intercellular junctions in animal tissues—desmosomes junctions Desmosome 1 µm

Fig. 6-32d Gap junction Figure 6.32 Intercellular junctions in animal tissues—gap junctions 0.1 µm

Fig. 6-33 5 µm Figure 6.33 The emergence of cellular functions

Fig. 6-UN1a Cell Component Structure Function Concept 6.3 Nucleus Surrounded by nuclear envelope (double membrane) perforated by nuclear pores. The nuclear envelope is continuous with the endoplasmic reticulum (ER). Houses chromosomes, made of chromatin (DNA, the genetic material, and proteins); contains nucleoli, where ribosomal subunits are made. Pores regulate entry and exit os materials. The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes (ER) Ribosome Two subunits made of ribo- somal RNA and proteins; can be free in cytosol or bound to ER Protein synthesis

Fig. 6-UN1b Cell Component Structure Function Concept 6.4 Endoplasmic reticulum Extensive network of membrane-bound tubules and sacs; membrane separates lumen from cytosol; continuous with the nuclear envelope. Smooth ER: synthesis of lipids, metabolism of carbohy- drates, Ca2+ storage, detoxifica- tion of drugs and poisons The endomembrane system regulates protein traffic and performs metabolic functions in the cell (Nuclear envelope) Rough ER: Aids in sythesis of secretory and other proteins from bound ribosomes; adds carbohydrates to glycoproteins; produces new membrane Golgi apparatus Stacks of flattened membranous sacs; has polarity (cis and trans faces) 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 sub- stances cell macromolecules, and damaged organelles for recycling Lysosome Membranous sac of hydrolytic enzymes (in animal cells) Vacuole Large membrane-bounded vesicle in plants Digestion, storage, waste disposal, water balance, cell growth, and protection

Fig. 6-UN1c Cell Component Structure Function Concept 6.5 Mitochondrion Bounded by double membrane; inner membrane has infoldings (cristae) Cellular respiration Mitochondria and chloro- plasts change energy from one form to another Chloroplast Typically two membranes around fluid stroma, which contains membranous thylakoids stacked into grana (in plants) Photosynthesis Peroxisome Specialized metabolic compartment bounded by a single membrane Contains enzymes that transfer hydrogen to water, producing hydrogen peroxide (H2O2) as a by-product, which is converted to water by other enzymes in the peroxisome