Cell Architecture “Of the things of nature there are … two kinds: those which are brought into being and perish, and those which are free from these processes throughout all ages. The latter are of the highest worth and are divine… Aristotle 384-322 BC from Parts of Animals

Techniques to view cells & fractionate cellular components -Microscopy - Differential Centrifugation

When is magnification important? LE 6-2 10 m When is magnification important? Human height 1 m Length of some nerve and muscle cells When object becomes too small to see by eye ~1 mm 0.1 m Unaided eye Chicken egg When is resolving power or resolution important? 1 cm When details become blurry= the difference between two points is unclear Frog egg 1 mm 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 µm = 10–9 m 100 µm Light microscope Most plant and animal cells 10 µm Nucleus Most bacteria What is the relationship between resolution and Wavelength ) of light (electromagnetic spectrum)? Mitochondrion 1 µm Electron microscope Smallest bacteria 100 nm Viruses Higher resolution (more details) at shorter  Ribosomes 10 nm Proteins Lipids 1 nm Small molecules 0.1 nm Atoms

Forms of Light Microscopy LE 6a Forms of Light Microscopy Brightfield What is different about (a) vs (b)? 50 µm Brightfield Phase-contrast

Differential-interference-contrast (DIC) Conventional fluorescence LE 6-3b Differential-interference-contrast (DIC) (Nomarski) Fluorescence (Specific structures labeled with fluorescent tag) 50 µm Confocal (laser beam) Any difference? Conventional fluorescence

(cilia) Scanning electron microscopy (SEM) Surface of rabbit tracheal cells (cilia) Longitudinal section of cilium Transmission electron microscopy (TEM) Cross section of cilium 1 µm Section of tracheal tissue

Surface area increases while Total volume remains constant Total surface area (height x width x number of sides x number of boxes) 6 125 150 750 1 5 1.2 Total volume (height x width x length X number of boxes) Surface-to-volume ratio (surface area  volume) Surface area increases while Total volume remains constant LE 6-7 Why do cells tend to be small?

Isolating Organelles by Cell Fractionation

Differential centrifugation LE 6-5a Homogenization Tissue cells Homogenate Differential centrifugation

LE 6-5b 1000 g (1000 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) Pellet rich in “microsomes” (pieces of plasma membranes and cells’ internal membranes) Pellet rich in ribosomes

Cells Exhibit Evolutionary Relatedness by their Similarities & Differences

Prokaryote A typical rod-shaped bacterium A thin section through the bacterium Bacillus coagulans (TEM) 0.5 µm Pili Nucleoid Ribosomes Plasma membrane Cell wall Capsule Flagella Bacterial chromosome LE 6-6 Prokaryote

ENDOPLASMIC RETICULUM (ER Flagellum Centrosome CYTOSKELETON Microfilaments Intermediate filaments Microtubules Peroxisome Microvilli ENDOPLASMIC RETICULUM (ER Rough ER Smooth ER Mitochondrion Lysosome Golgi apparatus Ribosomes: Plasma membrane Nuclear envelope NUCLEUS In animal cells but not plant cells: Lysosomes Centrioles Flagella (in some plant sperm) Nucleolus Chromatin LE 6-9a Non-plant eukaryotic cell

Plant cell LE 6-9b Nuclear envelope Rough endoplasmic NUCLEUS reticulum In plant cells but not animal cells: Chloroplasts Central vacuole and tonoplast Cell wall Plasmodesmata Smooth Ribosomes (small brown dots) Central vacuole Microfilaments Intermediate filaments Microtubules CYTOSKELETON Chloroplast Wall of adjacent cell Nuclear envelope Nucleolus Chromatin NUCLEUS Centrosome Golgi apparatus Mitochondrion Peroxisome Plasma membrane LE 6-9b Plant cell

Basic features of ALL cells: Plasma membrane Semifluid substance called the cytosol Chromosomes (carry genes) Ribosomes (make proteins)

Plasma membrane LE 6-8 Outside of cell Carbohydrate side chain Hydrophilic region Hydrophobic Carbohydrate side chain Structure of the plasma membrane Phospholipid Proteins Outside of cell Inside of cell 0.1 µm TEM of a plasma membrane LE 6-8 Plasma membrane

Nucleus LE 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 0.25 µm Close-up of nuclear envelope Pore complexes (TEM) Nuclear lamina (TEM)

LE 6-12 Smooth ER Nuclear envelope Rough ER ER lumen Cisternae Ribosomes Transitional ER Transport vesicle 200 nm Smooth ER Rough ER

Functions of Smooth ER The smooth ER Synthesizes lipids Metabolizes carbohydrates Stores calcium Detoxifies poison

Functions of Rough ER The rough ER Has bound ribosomes that make proteins targeted for membranes or to be transported across membranes Is a membrane factory for the cell

Part of protein synthesis machinery LE 6-11 Ribosomes ER Cytosol Endoplasmic reticulum (ER) Free ribosomes Bound ribosomes TEM showing ER and ribosomes Large subunit 0.5 µm Small subunit Part of protein synthesis machinery Ribosome

Golgi Apparatus LE 6-13 Golgi apparatus cis face (“receiving” side of trans face (“shipping” side of Golgi apparatus) TEM of Golgi apparatus 0.1 µm Golgi apparatus cis face (“receiving” side of Vesicles coalesce to form new cis Golgi cisternae Vesicles also transport certain proteins back to ER Vesicles move from ER to Golgi Vesicles transport specific proteins backward to newer Golgi cisternae Cisternal maturation: 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 Cisternae LE 6-13 Golgi Apparatus

Lysosomes: Digestive Compartments Membranous sac of hydrolytic enzymes Hydrolyzes (breaks down) proteins, fats, polysaccharides, and nucleic acids Recycle organelles and macromolecules (autophagy) Hydrolyzes food taken up by the cell (phagocytosis)

Lysosomes: Digestive Compartments Formation of lysosomes with hydrolytic enzyme Animation: Lysosome Formation

Phagocytosis: lysosome digesting food 1 µm LE 6-14a Phagocytosis: lysosome digesting food 1 µm Plasma membrane Food vacuole Lysosome Nucleus Digestive enzymes Digestion Lysosome contains active hydrolytic fuses with lysosome Hydrolytic enzymes digest food particles

Autophagy: lysosome breaking down damaged organelle 1 µm LE 6-14b Autophagy: lysosome breaking down damaged organelle 1 µm Vesicle containing damaged mitochondrion Mitochondrion fragment Lysosome containing two damaged organelles Digestion Lysosome Lysosome fuses with vesicle containing Peroxisome Hydrolytic enzymes digest organelle components

Vacuoles: Diverse Maintenance Compartments Vesicles and vacuoles (larger versions of vesicles) are membrane-bound sacs with varied functions A plant cell or fungal cell may have one or several vacuoles

Video: Paramecium Vacuole Food vacuoles: form by phagocytosis Contractile vacuoles: pump excess water out of cells (in many freshwater protists) Central vacuoles (plant cells): hold organic compounds and water, maintain turgor pressure Video: Paramecium Vacuole

LE 6-15 5 µm Central vacuole Cytosol Tonoplast Central vacuole Nucleus Cell wall Chloroplast

Mitochondria and chloroplasts change energy from one form to another Mitochondria are the sites of cellular respiration Chloroplasts, found only in plants and algae, are the sites of photosynthesis Mitochondria and chloroplasts are not part of the endomembrane system Peroxisomes are oxidative organelles

Mitochondrion Intermembrane space Outer membrane Free ribosomes in the LE 6-17 Mitochondrion Intermembrane space Outer membrane Inner Cristae Matrix 100 nm Mitochondrial DNA Free ribosomes in the mitochondrial matrix

Chloroplasts move with plant cells: cytoplasmic streaming LE 6-18 Chloroplasts move with plant cells: cytoplasmic streaming video Chloroplast Ribosomes Stroma Chloroplast DNA Inner and outer membranes Granum 1 µm Thylakoid

Peroxisomes: Oxidation Specialized metabolic compartments bounded by a single membrane Peroxisomes produce hydrogen peroxide and convert it to water How does the the cell protect itself from the toxic effects of hydrogen peroxide?

Chloroplast Peroxisome Mitochondrion 1 µm LE 6-19

Summary -Microscopy and differential centrifugation are two powerful methods to examine cellular structure and function. -Optimal size for most cells is generally low to optimize surface area:volume ratio. -All cells have plasma membrane, cytosol, DNA and ribosomes. -Prokaryotic cells tend to be smaller than eukaryotic, and lack nuclei, cytoplasmic membranes systems and organelles. -Eukaryotic cells have evolved or acquired many membrane bound compartments for specialized functions.

Please, ask questions.

Eukaryotic Cell Structure: Part II

The Cytoskeleton Intermediate Filaments Microfilaments Microtubules

Dynamic: shorten and lengthen

Speculate on the how actin causes movement? LE 6-27b Cortex (outer cytoplasm): gel with actin network Amoeboid movement Inner cytoplasm: sol with actin subunits Extending pseudopodium Speculate on the how actin causes movement?

Intestinal cell Function of MF? Microvillus Plasma membrane LE 6-26 Microfilaments (actin filaments) Microvillus Plasma membrane Intermediate filaments 0.25 µm Intestinal cell Function of MF?

Muscle cell Actin filament Myosin filament Myosin arm LE 6-27a Muscle cell Actin filament Myosin filament Myosin arm Myosin motors in muscle cell contraction

Cytoplasmic streaming in plant cells Chloroplast LE 6-27c Nonmoving cytoplasm (gel) Cytoplasmic streaming in plant cells Chloroplast Streaming cytoplasm (sol) Cell wall Parallel actin filaments Vacuole

Dynamic: shorten and lengthen

LE 6-21b 0.25 µm Microtubule Vesicles

Vesicle Receptor for motor protein Microtubule of cytoskeleton LE 6-21a Vesicle Receptor for motor protein Microtubule of cytoskeleton Motor protein (ATP powered) ATP

Motile sperm flagellum Direction of swimming Undulating movement 5 µm LE 6-23a Motile sperm 5 µm Direction of swimming Motion of flagella flagellum Undulating movement

protozoan 15 µm Direction of organism’s movement Motion of cilia LE 6-23b 15 µm Direction of organism’s movement Motion of cilia Direction of active stroke recovery stroke protozoan

Microtubules: Power Flagella & Cilia Movement

Microtubule doublets Dynein arm Dynein “walking” ATP ATP LE 6-25a Dynein “walking” Microtubule doublets Dynein arm ATP ATP Molecular motor

Effect of cross-linking proteins LE 6-25b Wavelike motion Cross-linking proteins inside outer doublets ATP Anchorage in cell Effect of cross-linking proteins

MT organization in Flagella and Cilia LE 6-24 MT organization in Flagella and Cilia Outer microtubule doublet Plasma membrane 0.1 µm Dynein arms Central microtubule Cross-linking proteins inside outer doublets Microtubules Plasma membrane 9+2 Radial spoke Basal body 0.5 µm

Basal body Microtubule-containing structure at base of flagellum and cilium Organization: Nine triplets In contrast: MT organization in cilia and flagella is?_____________

Basal body anchors each flagellum and cilium LE 6-24 Basal body anchors each flagellum and cilium 9 doublets+2 Plasma membrane Basal body Basal Body 0.5 µm Triplet Nine triplets Cross section of basal body

Centrioles Occur in pairs oriented at right angle Similar nine triplet organization as basal body Present in animal cells Contained in centrosome:microtubule organizing center (MTOC) Note: plants cells have centrosomes but lack centrioles

LE 6-22 Microtubule Centrosome Centrioles Longitudinal section of one centriole Microtubules Cross section of the other centriole

Extracellular structures Secreted materials on the outside surface of plasma membrane: Cell walls (cellulose) of plants Extracellular matrix (ECM) of animal cells Intercellular junctions

Cell Walls of Plants Mixture of cellulose fibers plus other polysaccharides and protein Distinctive to plants. Not present on animal cells Protection against physical stress, predators and disease Maintainance of cell shape Prevention of excessive water uptake

LE 6-28 Central vacuole Plasma of cell membrane Secondary cell wall Primary cell wall Central vacuole of cell Middle lamella 1 µm Central vacuole Cytosol Plasma membrane Plant cell walls Plasmodesmata

Extracellular Matrix (ECM) of Animal Cells Proteoglycan complexes and other macromolecules Functions: Support Adhesion to other cells or surfaces Movement Regulation (influences binding of hormones or other factors to receptors on plasma membrane)

Proteoglycan complex EXTRACELLULAR FLUID Collagen fiber Fibronectin LE 6-29a Proteoglycan complex EXTRACELLULAR FLUID Collagen fiber Fibronectin Plasma membrane CYTOPLASM Integrin Micro- filaments

Proteoglycan complex Polysaccharide molecule Carbo- hydrates Core LE 6-29b Proteoglycan complex Polysaccharide molecule Carbo- hydrates Core protein Proteoglycan molecule

Intercellular Junctions Between adjacent cells Adhesion Communication

Plants: Plasmodesmata - Channels that perforate plant cell walls - Allow passage of water & small solutes between adjacent cells

Plasmodesmata LE 6-30 Cell walls Interior of cell Interior of cell Plasma membranes

Animals: Tight Junctions, Desmosomes, and Gap Junctions Tight junctions: on membranes of neighboring cells prevent leakage of extracellular fluid between cells 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

LE 6-31 Tight junctions prevent Tight junction fluid from moving across a layer of cells Tight junction 0.5 µm Tight junction Intermediate filaments Desmosome 1 µm Gap junctions Space between cells Plasma membranes of adjacent cells Gap junction Extracellular matrix 0.1 µm

The Cell: A Living Unit Greater Than the Sum of Its Parts Cells rely on the integration of structures and organelles in order to function Think of the structures and organelles involved in the function of the following cell

5 µm Macrophage: patrols for & destroys foreign objects bacteria LE 6-32 Macrophage: patrols for & destroys foreign objects 5 µm bacteria