CHAPTER 6: A TOUR OF THE CELL AP BIOLOGY 2011

CHAPTER 6: A TOUR OF THE CELL AP BIOLOGY 2011 1 IMPORTANCE OF CELLS ALL ORGANISMS ARE MADE OF CELLS CELLS ARE THE SMALLEST LIVING UNIT STRUCTURE IS CORRELATED TO FUNCTION ALL CELLS ARE RELATED BY THEIR DESCENT FROM EARLIER CELLS 2 10 m MICROSCOPY LIGHT MICROSCOPE 1 m 0.1 m 1 cm Human height Length of some nerve and muscle cells Chicken egg Unaided eye PASS VISIBLE LIGHT THROUGH A SPECIMEN MAGNIFY CELL STRUCTURES WITH LENSES 1 mm 100 µm 10 µm 100 nm 10 nm Frog egg Human egg Most plant and animal cells Most bacteria Smallest bacteria Viruses Ribosomes Proteins Light microscopy Superresolution microscopy Electron microscopy FIG. 6.2 1 nm Lipids 0.1 nm Atoms Small molecules 3

ELECTRON MICROSCOPE FOCUS A BEAM OF ELECTRONS THOUGH A SPECIMEN (TEM) OR ONTO ITS SURFACE (SEM) TECHNIQUE (a) Scanning electron microscopy (SEM). Micrographs taken with a scanning electron microscope 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. RESULTS Cilia 4 ELECTRON MICROSCOPE (b) Transmission electron microscopy (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. Longitudinal section of cilium Cross section of cilium 5 TECHNIQUE CELL FRACTIONATION TAKES CELLS APART AND SEPARATES THE MAJOR ORGANELLES FROM ONE ANOTHER CENTRIFUGES USED TO FRACTIONATE CELLS INTO THEIR COMPONENTS PARTS ENABLES SCIENTISTS TO DETERMINE THE FUNCTIONS OF ORGANELLES (BIOCHEMISTRY AND CYTOLOGY HELP CORRELATE CELL FUNCTION WITH STRUCTURE) FIG. 6.4 Homogenization Tissue cells Homogenate Centrifuged at 1,000 g (1,000 times the Centrifugation force of gravity) for 10 min Supernatant poured into next tube Differential centrifugation 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 chloroplasts if cells are from a plant) Pellet rich in microsomes (pieces of plasma s and cells internal s) Pellet rich in ribosomes 6

CELL TYPES PROKARYOTIC (DOMAINS BACTERIA AND ARCHAEA) EUKARYOTIC (DOMAIN EUKARYA) BOTH ARE: BOUNDED BY A PLASMA MEMBRANE CONTAIN CYTOSOL CONTAIN CHROMOSOMES HAVE RIBOSOMES 7 PROKARYOTIC CELLS Fimbriae DO NOT CONTAIN A NUCLEUS HAVE DNA LOCATED IN A REGION CALLED A NUCLEOID NO MEMBRANE- BOUND ORGANELLES Bacterial chromosome (a) A typical rod-shaped bacterium Nucleoid Ribosomes Plasma Cell wall Capsule Flagella 0.5 µm (b) A thin section through the bacterium Bacillus coagulans (TEM) FIG. 6.5 8 EUKARYOTIC CELLS CONTAIN A TRUE NUCLEUS BOUNDED BY A MEMBRANOUS NUCLEAR ENVELOPE MEMBRANE-BOUND ORGANELLES Total surface area [sum of the surface areas (height width) of all box sides number of boxes] 1 Surface area increases while total volume remains constant 5 6 150 750 1 GENERALLY BIGGER THAN PROKARYOTIC CELLS Total volume [height width length number of boxes] 1 125 125 CELL METABOLISM LIMITS CELL SIZE Surface-to-volume (S-to-V) ratio [surface area volume] 6 1.2 6 FIG. 6.7 9

PLASMA MEMBRANE (a) TEM of a plasma Outside of cell FUNCTIONS AS A SELECTIVE BARRIER THAT ALLOWS SUFFICIENT PASSAGE OF OXYGEN, NUTRIENTS, AND WASTE Inside of cell 0. Carbohydrate side chains Hydrophilic region Hydrophobic region STRUCTURED AS A DOUBLE LAYER OF PHOSPHOLIPIDS Hydrophilic region Phospholipid Proteins (b) Structure of the plasma FIG. 6.6 10 10 µm Animal Cells ANIMAL CELL ENDOPLASMIC RETICULUM (ER) Flagellum Nucleolus Nuclear envelope Rough Smooth ER ER Cell Human cells from lining Nucleolus Chromatin NUCLEUS of uterus (colorized TEM) Fungal Cells Centrosome Parent cell Plasma Buds 5 µm CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Ribosomes Yeast cells budding (colorized SEM) Microvilli Golgi apparatus Cell wall Vacuole Peroxisome Lysosome FIG. 6.8 A single yeast cell (colorized TEM) 11 PLANT CELL Plant Cells NUCLEUS Nucleolus Chromatin Rough endoplasmic reticulum Cell 5 µm Nuclear envelope Cell wall Smooth endoplasmic reticulum Nucleolus Cells from duckweed (colorized TEM) Ribosomes Central vacuole Golgi apparatus Microfilaments Intermediate filaments CYTOSKELETON Protistan Cells Flagella Microtubules Peroxisome Nucleolus Plasma Cell wall Wall of adjacent cell Vacuole Plasmodesmata FIG. 6.8 Cell wall Chlamydomonas (colorized TEM) 12

NUCLEUS Nucleolus Chromatin CELL S GENETIC INSTRUCTIONS ARE HOUSED IN THE NUCLEUS NUCLEAR ENVELOPE - ENCLOSES THE NUCLEUS, SEPARATES ITS CONTENTS FROM THE CYTOPLASM 0.25 µm Surface of nuclear envelope Pore complexes (TEM) Nuclear envelope: Inner Outer Nuclear pore Pore complex Ribosome Close-up of nuclear envelope Chromatin Nuclear lamina (TEM) Rough ER FIG. 6.9 13 RIBOSOMES MADE UP OF RIBOSOMAL RNA AND PROTEIN 0.25 µm CARRY OUT PROTEIN SYNTHESIS IN TWO LOCATIONS (CYTOSOL = FREE RIBOSOMES; ER = BOUND RIBOSOMES) PROKARYOTES = 70S RIBOSOMES TEM showing ER and ribosomes Free ribosomes in cytosol Endoplasmic reticulum (ER) Ribosomes bound to ER Large subunit Small subunit Diagram of a ribosome FIG. 6.10 EUKARYOTES = 80S RIBOSOMES 14 ENDOMEMBRANE SYSTEM REGULATES PROTEIN TRAFFIC AND PERFORMS METABOLIC FUNCTIONS IN THE CELL COMPONENTS: NUCLEAR ENVELOPE ENDOPLASMIC RETICULUM GOLGI APPARATUS LYSOSOMES VACUOLES PLASMA MEMBRANE 15

ENDOPLASMIC RETICULUM ENDOPLASMIC RETICULUM Rough ER Smooth ER Nuclear envelope ACCOUNTS FOR MORE THAN HALF OF THE TOTAL MEMBRANE IN EUKARYOTIC CELLS CONTINUOUS WITH THE NUCLEAR ENVELOPE SMOOTH ER - LACKS RIBOSOMES ER lumen Cisternae Ribosomes Transport vesicle Smooth ER Rough ER Transitional ER 200 nm ROUGH ER - CONTAINS RIBOSOMES FIG. 6.11 16 SMOOTH ER VS. ROUGH ER SMOOTH ER SYNTHESIZES LIPIDS METABOLIZES CARBOHYDRATES STORES CALCIUM DETOXIFIES POISON ROUGH ER HAS BOUND RIBOSOMES WHICH SECRETE GLYCOPROTEINS PRODUCES PROTEINS AND MEMBRANES WHICH ARE DISTRIBUTED BY TRANSPORT VESICLES 17 RECEIVES MANY OF THE TRANSPORT VESICLES PRODUCED IN THE ROUGH ER GOLGI APPARATUS CONSISTS OF FLATTENED MEMBRANOUS SACS CALLED CISTERNAE cis face ( receiving side of Golgi apparatus) Cisternae 0. MODIFIES THE PRODUCTS OF THE ROUGH ER MANUFACTURES CERTAIN MACROMOLECULES SORTS AND PACKAGES MATERIALS INTO TRANSPORT VESICLES trans face ( shipping side of Golgi apparatus) TEM of Golgi apparatus FIG. 6.12 18

LYSOSOME FIG. 6.13 Lysosome MEMBRANOUS SAC OF HYDROLYTIC ENZYMES Digestive enzymes Lysosome Plasma Digestion Food vacuole CAN DIGEST ALL KINDS OF MACROMOLECULES (a) Phagocytosis Vesicle containing two damaged organelles CARRY OUT INTRACELLULAR DIGESTION THROUGH PHAGOCYTOSIS fragment Peroxisome fragment Lysosome Peroxisome Vesicle (b) Autophagy Digestion 19 VACUOLES PLANT OR FUNGAL CELLS MAY HAVE ONE OR SEVERAL VACUOLES FOOD VACUOLES - FORMED BY PHAGOCYTOSIS Central vacuole Cytosol CONTRACTILE VACUOLES - PUMP EXCESS WATER OUT OF PROTIST CELLS CENTRAL VACUOLES - FOUND IN PLANT CELLS AND HOLD RESERVES OF IMPORTANT ORGANIC COMPOUNDS AND WATER Cell wall Central vacuole FIG. 6.14 5 µm 20 ENDOMEMBRANE SYSTEM REVIEW 1 Nuclear envelope is connected to rough ER, which is also continuous with smooth ER Rough ER 2 Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golgi Smooth ER Nuclear envelop cis Golgi 3 Golgi pinches off transport Vesicles and other vesicles that give rise to lysosomes and Vacuoles trans Golgi Plasma FIG. 6.15 4 Lysosome available 5 Transport vesicle carries 6 Plasma expands for fusion with another proteins to plasma by fusion of vesicles; proteins vesicle for digestion for secretion are secreted from cell 21

MITOCHONDRIA AND CHLOROPLASTS CHANGE ENERGY FROM ONE FORM TO ANOTHER MITOCHONDRIA - SITES OF CELLULAR RESPIRATION FOUND IN NEARLY ALL EUKARYOTIC CELLS CHLOROPLASTS - THE SITE OF PHOTOSYNTHESIS FOUND ONLY IN PLANT CELLS 22 EVOLUTION OF MITOCHONDRIA AND CHLOROPLASTS HAVE SIMILARITIES WITH BACTERIA HAVE A DOUBLE MEMBRANE CONTAIN FREE RIBOSOMES AND CIRCULAR DNA GROW AND REPRODUCE INDEPENDENTLY IN CELLS ENDOSYMBIONT THEORY EARLY ANCESTOR OF EUKARYOTIC CELLS ENGULFED PROKARYOTIC CELL HOST AND ENDOSYMBIONT MERGED INTO A SINGLE ORGANISM Endoplasmic reticulum Engulfing of oxygen- Nuclear using nonphotosynthetic envelope prokaryote, which becomes a mitochondrion Nonphotosynthetic eukaryote At least one cell Ancestor of eukaryotic cells (host cell) Engulfing of photosynthetic prokaryote Photosynthetic eukaryote FIG. 6.16 23 MITOCHONDRIA ENCLOSED BY TWO MEMBRANES SMOOTH OUTER MEMBRANE INNER MEMBRANE FOLDED INTO CRISTAE FIG. 6.17 10 µm Inter space Outer Mitochondria Free ribosomes in the mitochondrial matrix DNA Inner Cristae Matrix (a) Diagram and TEM of mitochondrion 0. Mitochondrial DNA Nuclear DNA (b) Network of mitochondria in a protist cell (LM) 24

CHLOROPLAST CAPTURE LIGHT AND ENERGY SPECIALIZED MEMBER OF A FAMILY OF CLOSELY RELATED PLANT ORGANELLES CALLED PLASTIDS CONTAINS CHLOROPHYLL FOUND IN LEAVES AND OTHER GREEN ORGANS OF PLANTS AND IN ALGAE STRUCTURE INCLUDES THYLAKOIDS (MEMBRANOUS SACS) AND STROMA (INTERNAL FLUID) 50 µm Ribosomes Stroma Inner and outer s Granum DNA Inter space Thylakoid (a) Diagram and TEM of chloroplast s (red) FIG. 6.18 (b) s in an algal cell 25 PEROXISOMES Peroxisome PRODUCE HYDROGEN PEROXIDE AND CONVERT IT TO WATER FIG. 6.19 26 NETWORK OF FIBERS THAT ORGANIZES STRUCTURES AND ACTIVITIES OF THE CELL EXTENDS THROUGHOUT THE CYTOPLASM GIVES MECHANICAL SUPPORT TO THE CELL 10 µm CYTOSKELETON ATP Vesicle Receptor for motor protein Motor protein Microtubule (ATP powered) of cytoskeleton (a) Microtubule INVOLVED IN CELL MOTILITY (USING MOTOR PROTEINS) Vesicles 0.25 µm FIG. 6.21 (b) 27

10 µm 10 µm 5 µm Column of tubulin dimers 25 nm Actin subunit Keratin proteins Fibrous subunit (keratins coiled together) α β Tubulin dimer 7 nm 8-12 nm 28 MICROTUBULES SHAPE THE CELL Centrosome Microtubule GUIDE MOVEMENT OF ORGANELLES Centrioles 0.25 µm HELP SEPARATE THE CHROMOSOME COPIES IN DIVIDING CELLS Longitudinal section of one centriole CAN GROW OUT OF CENTROSOMES Microtubules Cross section of the other centriole FIG. 6.22 29 CILIA AND FLAGELLA 0. Outer microtubule doublet Plasma Dynein proteins CONTAIN SPECIALIZED ARRANGEMENTS OF MICROTUBULES Microtubules Plasma Basal body (b) Cross section of motile cilium Central microtubule Radial spoke Cross-linking proteins between outer doublets LOCOMOTOR APPENDAGES OF SOME CELLS (a) 0.5 µm 0. Longitudinal section of motile cilium Triplet SHARE SOME COMMON STRUCTURES (c) Cross section of basal body FIG. 6.24 30

CILIA AND FLAGELLA (a) Motion of flagella. A flagellum usually undulates, its snakelike motion driving a cell in the same direction as the axis of the flagellum. Propulsion of a human sperm cell is an example of flagellatelocomotion (LM). Direction of swimming (b) Motion of cilia. Cilia have a backand-forth motion that moves the cell in a direction perpendicular to the axis of the cilium. A dense nap of cilia, beating at a rate of about 40 to 60 strokes a second, covers this Colpidium, a freshwater protozoan (SEM). Figure 6.23 B 31 MOVEMENT Microtubule doublets ATP DYNEIN - PROTEIN RESPONSIBLE FOR BENDING MOVEMENT OF CILIA AND FLAGELLA Dynein protein (a) Effect of unrestrained dynein movement Cross-linking proteins between outer doublets ATP Anchorage in cell (b) Effect of cross-linking proteins 1 3 2 FIG. 6.25 (c) Wavelike motion 32 MICROFILAMENTS BUILT FROM MOLECULES OF THE PROTEIN ACTIN FOUND IN MICROVILLI WHEN FUNCTIONING IN CELLULAR MOTILITY IT MUST ALSO CONTAIN THE PROTEIN MYOSIN Microvillus Plasma Microfilaments (actin filaments) Intermediate filaments 0.25 µm FIG. 6.36 33

MOVEMENT Muscle cell Actin filament Myosin filament Myosin head (a) Myosin motors in muscle cell contraction 0.5 µm Cortex (outer cytoplasm): gel with actin network Inner cytoplasm: sol with actin subunits 100 µm Extending pseudopodium (b) Amoeboid movement FIG. 6.27 (c) Cytoplasmic streaming in plant cells 30 µm 34 INTERMEDIATE FILAMENTS SUPPORT CELL SHAPE FIX ORGANELLES IN PLACE 35 CELL WALL EXTRACELLULAR STRUCTURE FOUND IN PLANTS MADE OF CELLULOSE FIBERS EMBEDDED IN OTHER POLYSACCHARIDES AND PROTEINS Central vacuole Cytosol Secondary cell wall Primary cell wall Middle lamella Plasma Plant cell walls HAVE MULTIPLE LAYERS Plasmodesmata FIG. 6.28 36

EXTRACELLULAR MATRIX ANIMAL CELLS LACK CELL WALLS SO ECM IS MADE UP OF GLYCOPROTEINS AND OTHER MACROMOLECULES FUNCTIONS OF THE ECM: SUPPORT, ADHESION, MOVEMENT, AND REGULATION FIG. 6.30 Collagen EXTRACELLULAR FLUID Polysaccharide molecule Proteoglycan complex Carbohydrates Fibronectin Core protein Integrins Plasma Proteoglycan molecule Proteoglycan complex Microfilaments CYTOPLASM 37 CELLULAR JUNCTIONS: PLASMODESMATA FOUND IN PLANTS CHANNELS THAT PERFORATE PLANT CELL WALLS Cell walls Interior of cell Interior of cell Figure 6.30 0.5 µm Plasmodesmata Plasma s 38 INTERCELLULAR JUNCTIONS IN ANIMAL CELLS Tight junctions prevent fluid from moving across a layer of cells Tight junction 0.5 µm TIGHT JUNCTIONS At tight junctions, the s of neighboring cells are very tightly pressed against each other, bound together by specific proteins (purple). Forming continuous seals around the cells, tight junctions prevent leakage of extracellular fluid across A layer of epithelial cells. DESMOSOMES Tight junctions Intermediate filaments Desmosome Desmosomes (also called anchoring junctions) function like rivets, fastening cells Together into strong sheets. Intermediate Filaments made of sturdy keratin proteins Anchor desmosomes in the cytoplasm. Gap junctions GAP JUNCTIONS Space between Plasma s cells of adjacent cells Figure 6.31 Extracellular matrix Gap junction 0. Gap junctions (also called communicating junctions) provide cytoplasmic channels from one cell to an adjacent cell. Gap junctions consist of special proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass. Gap junctions are necessary for communication between cells in many types of tissues, including heart muscle and animal embryos. 39