AP Biology, Chapter 7
A Tour of the Cell

Summary
Introduction

HOW WE STUDY CELLS
	Intro
	Microscopes provide windows to the world of the cell
		1. Distinguish magnification and resolving power.
			a. Magnification 
				i. = enlargement of image
				ii. Depends on quality of the original
			b. Resolving power
				i. = quality or clarity of image
				ii. Technically, the minimum observable distance between two points
				iii. Depends on wavelength and diameter of lens
		2. Describe the principles, advantages, and limitations of the light microscope, 
		transmission electron microscope, and scanning electron microscope.
			a. Compound light microscope invented by Galileo
				i. Total magnification = eyepiece x objective (x1000 max.)
				ii. Cheap and easy to use
				iii. Limited by wavelength of light, quality of lenses
			b. Transmission EM
				i. Shorter wavelength, focused by magnets (x ~ 106)
				ii. Limited to fixed, metal-stained material in thin slices
			c. SEM
				i. Uses electrons, high resolving power like TEM
				ii. Shows surfaces
	Cell biologists can isolate organelles to study their functions
		3. Describe the major steps of cell fractionation and explain why it is a useful technique.
			a. Homogenization
				i. Break up organ in a mortar or blender
				ii. Best done in a cold buffer to stabilize the products
			b. Differential centrifugation
				i. A series of successively faster spins each giving pellet and supernatant
				ii. Largest cell parts pellet first: nuclei and large debris
				iii. Then mitochondria/chloroplasts
				iv. Then other membranes including plasma membrane
				v. Very hard spins pellet ribosomes

A PANORAMIC VIEW OF THE CELL
	Intro
	Prokaryotic and eukaryotic cells differ in size and complexity
		4. Distinguish prokaryotic and eukaryotic cells.
			a. Features of all cells
				i. Plasma membrane
				ii. Aqueous cytoplasm
					.Storage
					.Glycolysis
					.Protein synthesis 
				iii. DNA storing traits
				iv. RNA and ribosomes for expressing traits
			b. Prokaryotes
				i. May also have complex stacked internal membranes
				ii. May also have double outer membrane and a cell wall
				iii. May also have rigid "flagella", pili, and mucoid capsule
				iv. Includes Domain Bacteria and Domain Archaea
			c. Eukaryotes
				i. Membrane-bound nucleus
				ii. Membrane-bound organelles 
		5. Explain why there are both upper and lower limits to cell size.
			a. Lower limit (Mycoplasma): must have DNA, ribosomes, enzymes
			b. Upper limit
				i. Volume increases as a cube, surface area as a square
					. All materials enter and leave through the surface
					. Large cells have low surface-to-volume ratios
				ii. One set of DNA not enough to run a large cell 
	Internal membranes compartmentalize the functions of a eukaryotic cell
		6. Explain why compartmentalization is important in eukaryotic cells.
			a. Differentiated chemistry; specialization for efficiency
			b. Separation of dangerous components like digestive enzymes
			c. Membranes and fluids have specialized functions as in mitochondria

THE NUCLEUS AND RIBOSOMES
	The nucleus contains a eukaryotic cell's genetic library
		7. Describe the structure and function of the nucleus and briefly explain how the nucleus 
		controls protein synthesis in the cytoplasm.
			a. Structure
				i. Large
				ii. Double membrane with large pores/pore complexes
				iii. Internally organized by internal lamina and matrix
				iv. DNA present mainly as dispersed chromatin (uncoiled chromosomes)
				v. Granular nucleolus
			b. Functions
				i. Protect DNA
				ii. Allow/control transcription and replication
				iii. Enable separation during mitosis
				iv. Assemble ribosomes
			c. Control of protein synthesis
				i. Genes selectively transcribed into mRNA
				ii. Edited by splicing out/adding pieces
				iii. Finished mRNA transported to cytoplasm
	Ribosomes build a cell's proteins
		8. Describe the structure and function of the eukaryotic ribosome.
			a. Structure
				i. 3rRNAs and >50 proteins; mainly RNA by mass
				ii. Two subunits clamp onto mRNA
				iii. Three tRNA binding slots
			b. Function
				i. Clamp onto mRNA
				ii. Allow complementary binding of mRNA codons and tRNA anticodons
				iii. Form peptide bonds
				iv. Move along mRNA one codon at a time
			c. Localization
				i. Free ribosomes make cytoplasmic proteins
				ii. ER-bound ribosomes make membrane and secreted proteins
THE ENDOMEMBRANE SYSTEM
	Intro
	The endoplasmic reticulum manufactures membranes and performs many other 
	biosynthetic functions
		9. List the components of the endomembrane system, describe their structures and 
		functions, and summarize the relationships among them.
			a. Components
				i. Endoplasmic reticulum
					.Tubes and sacs continuous with nuclear membrane
					.Smooth: lipid synthesis, carbohydrate metabolism, 
					detoxification, store Ca
					.Rough: synthesis and modification of membrane and secreted 
					Proteins
					.Transport vesicles bud off
				ii. Golgi apparatus
					.Stacks of membrane sacs with associated vesicles
					.Transport vesicles fuse at the cis side
					.Membranes and contents are modified and sorted as they pass 
					to trans side
					.Finished vesicles bud off the trans side
					.Also makes some secreted polysaccharides
	The Golgi apparatus finishes, sorts, and ships cell products
	Lysosomes are digestive compartments
		10. Summarize the importance of lysosomal function in organismal defense, cellular 
		recycling, and development.
			a. Lysosomes contain digestive enzymes with acid pH optima
			b. Roles
				i. Defense: after phagocytosis, lysosomes digest bacteria
				ii. Recycling (autophagy): old organelles are engulfed and digested
				iii. Development: cells that need to die (tadpole tails) are completely 
				recycled
			c. Lysosomal storage diseases
				i. Genetic lack of a lysosomal enzyme; substrates build up
				ii. Ex.: Tay-Sachs, Fabry, Gaucher
	Vacuoles have diverse functions in cell maintenance
		11. Describe the different structures and functions of vacuoles.
			a. Food vacuoles contain particles/bacteria being digested
			b. Contractile in freshwater organisms gather and expel excess water
			c. Central vacuole in plants 
				i. Maintains cell shape
				ii. Stores ions, wastes, pigments

OTHER MEMBRANEOUS ORGANELLES
	Mitochondria and chloroplasts are the main energy transformers of cells
		12. Describe the structure of a mitochondrion and explain the importance of 
		compartmentalization in mitochondrial function.
			a. Structure
				i. Outer smooth membrane
				ii. Intermembraneous space
				iii. Inner membrane folded into cristae
				iv. Matrix is innermost fluid with its own DNA and ribosomes
			b. Function
				i. Glycolysis in cytoplasm, Krebs cycle in matrix
				ii. Both feed high-E electrons into electron transport on the cristae
				iii. H+ pumped into intermembraneous space
				iv. Proton gradient used to make ATP
		13. Distinguish amyloplasts, chromoplasts, and chloroplasts.
			a. Amyloplasts store starch
			b. Chromoplasts store pigments like carotene
			c. Chloroplasts have thylakoids with chlorophyll
		14. Identify the three functional compartments of a chloroplast. Explain the importance 
		of compartmentalization in chloroplast function.
			a. Compartments
				i. Smooth outer membrane
				ii. Intermembraneous space
				iii. Stacks of thylakoids (grana) floating in liquid stroma
			b. Functions
				i. Thylakoids provide surface area for chlorophyll  electron transport
				ii. Carbohydrates made in the stroma using ATP and high-E electrons 
				from thylakoids
		15. Explain the roles of mitochondria and chloroplasts.
			a. Mitochondria complete aerobic respiration making a lot of ATP
			b. Chloroplasts capture radiant energy and store it in carbohydrates
			c. In summary:  6CO2 + 6H2O + energy  C6H12O6 + 6O2

	Peroxisomes consume oxygen in various metabolic functions
		16. Explain the role of peroxisomes in eukaryotic cells.
			a. Function: confine harmful oxidative reactions and break down H2O2
			b. Examples: dismantle fatty acids, detoxify ethanol, uric acid oxidation

THE CYTOSKELETON
	Intro
	Providing structural support to the cell, the cytoskeleton also functions in cell motility 
	and regulation
		17. Describe the functions of the cytoskeleton.
			a. Mechanical support and shape maintenance 
				i. Anchors organelles and cytoplasmic enzymes
				ii. Can be quickly dis- and reassembled for changing shape
			b. Motility
				i. ATP-requiring proteins pull on microtubules in cilia and flagella
				ii. Pull organelles along microtubules
				iii. Pull to change cell shape and location
				iv. Pull of cell membrane during phagocytosis
			c. Regulate by transmitting mechanical forces
		18. Describe the structure, monomers, and functions of microtubules, microfilaments, 
		and intermediate filaments.
			a. Microtubules
				i. Hollow tubulin helical polymers organized by centrioles
				ii. 9+2 in cilia and flagella
				iii. Resist compression, can be pulled against
			b. Microfilaments
				i. Twisted double actin filaments
				ii. Resist tension, form network/gel under plasma membrane
				iii. Pulled on by myosin in muscle cells, pseudopodia
			c. Intermediate filaments
				i. More permanent network
				ii. Maintains cell shape, organelle position
		19. Explain how the ultrastructure of cilia and flagella relate to their functions.
			a. Both have 9+2 microtubule pairs
			b. Outer 9 pairs connected by dynein
			c. Dynein uses ATP to walk along microtubule

CELL SURFACES AND JUNCTIONS
	Intro
	Plants cells are encased in cell walls
		20. Describe the development of plant cell walls.
			a. Thin primary lamella with cellulose
			b. Next gluey middle lamella with pectin
			c. Thicker secondary cell wall last
	The extracellular matrix (ECM) of animal cells functions in support, adhesion, 
	movement, and regulation
		21. Describe the structure and list four functions of the extracellular matrix in animal 
		cells.
			a. Structure
				i. Fibronectin attaches to integral plasma membrane proteins
				ii. Collagen fibers and proteoglycans attach to fibronectin
			b. Functions
				i. Anchor and protect cells
				ii. Direct cell migration during development and healing
				iii. Control some gene expression
				iv. Coordinate tissue function
	Intercellular junctions help integrate cells into higher levels of structure and function
		22. Describe the structures of intercellular junctions found in plant and animal cells and 
		relate those structures to their functions.
			a. Desmosomes: heavily reinforced plates between mechanically 				stressed cells
			b. Gap junctions/plamodesmata:tubular connections; allow solutes, 
			electrical impulses to pass for coordination
			c. Tight junctions: many tiny attachments between cells; act as a 
			barrier to strong solutes		
	The cell is a living unit greater than the sum of its parts