A.P. Biology Chapter 6 Notes

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A.P. Biology Chapter 6 Notes
2012-10-26 14:54:02
Biology Chapter Notes

A.P. Biology Chapter 5 Notes
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  1. Cell Theory
    • •All organisms are composed of cells or at least one.
    • •Cells are the smallest unit of life (a collection of metabolic processes + heredity).
    • •All cells come from other cells.  None spontaneously arise.
  2. SEM (Scanning Electron Microscope)
    Provides for detailed study of the surface of a specimen
  3. TEM (Transmission Electron Microscope
    Provides for detailed study of the internal ultrastructure of cells
  4. Cell Fractionation
    Cell fractionation is used to isolate(fractionate) cell components, based on size and density.
  5. Surface to Volume Ratio
    A smaller cell has a higher surface to volume ratio, which facilitates the exchange of materials into and out of the cell
  6. Pili
    Attachment structures onthe surface of some prokaryotes
  7. Nucleoid
    Region where the cell’s DNA is located (notenclosed by a membrane)
  8. Ribosomes
    Organelles that synthesize proteins
  9. Plasma Membrane
    • Membrane enclosing the cytoplasm
    • Functions as a selective barrier
    • Allows sufficient passage of nutrients and waste
  10. Cell Wall
    • Rigid structure outside the plasma membrane
    • Plant only
    • Are made of cellulose fibers embedded in other polysaccharides and protein
    • May have multiple layers
  11. Capsule
    Jelly-like outer coating of many prokaryotes
  12. Flagella
    Locomotion organelles of some bacteria
  13. Prokaryote
    • Archaebacteria and Eubacteria
    • Lack membrane-bound organelles
    • DNA in a nucleoid region
    • Have plasma membrane
    • Cell wall of peptidoglycan
    • Use 70S ribosome
    • Unique flagella-flagellin protein.
  14. Eukaryote
    • Animalia, Plantae, Protista, Fungi
    • Have true membrane-bound organelles
    • DNA in a nucleus
    • Have plasma membrane
    • Plants and some protists have a cell wall of cellulose
    • Use different ribosomes.
  15. Structure and Function
    Cell structure is correlated to cellular function
  16. Function of Organelles
    • To compartmentalize chemical reactions that may proceed simultaneously
    • To provide membranes on which to catalyze reactions
  17. Nuclear Envelope
    Encloses the nucleus, separating its contents from the cytoplasm
  18. Nucleus
    • Largest organelle, centralized in animal cells
    • Stores and protects the cell’s genetic information
    • Surrounded by two phospholipid bilayer membranes-nuclear envelope
    • Where both layers are fused - nuclear pores + transport protein.
    • The nuclear envelope encloses the nucleus, separating its contents from the cytoplasm; the nuclear envelope is a double membrane (each have a lipid bilayer with associated proteins); the nuclear envelope is perforated by pores; at the lip of each pore, the inner and outer membranes of the nuclear envelope are continuous; the nuclear matrix is a framework of fibers extending throughout the nuclear interior; each chromosome is made up of a material call chromatin, a complex of proteins and DNA; a prominent structure within the nondividing nucleus is the nucleolus
    • Contains most of the genes in the eukaryotic cell (some genes are located in mitochondria and chloroplasts); translates and transcribes (see next column for more details)
    • An intricate protein structure called a pore complex lines each pore and regulates the entry and exit of certain large macromolecules and particles; except at the pores, the nuclear side of the envelope is lined by the nuclear lamina, a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope; within the nucleus, DNA is organized into discrete units call chromosomes, structures that carry the genetic information; the nucleolus synthesizes a special type of RNA call ribosomal RNA (rRNA) from instructions in the DNA; proteins imported from the cytoplasm are assembled with rRNA into large and small ribosomal subunits in the nucleolus; these subunits then exit the nucleus through the nuclear pores to the cytoplasm, where a large and a small subunit can assemble into a ribosome; process of transcribing and translating: directs protein synthesis by synthesizing messenger RNA (mRNA) according to instructions provided by the DNA; the mRNA is then transported to the cytoplasm via the nuclear pores; once an mRNA molecule reaches the cytoplasm, ribosomes translate the mRNA’s genetic message into the primary structure of a specific polypeptide
    • Animal and Plant
  19. Nucleolus
    • Site within the nucleus of ribosomal subunits are manufactured- rRNA + ribosomal proteins
    • Ribosomes leave the nucleus as subunits through the nuclear pore and are later reassembled
    • May be free (in the cytoplasm) or attached to the ER (rough ER).
  20. Endoplasmic Reticulum (ER)
    • Means “little net within the cytoplasm
    • ”Internal membrane system with a lipid bilayer + proteins
    • Weaved in sheets- forming channels
    • Outer membrane of the nuclear envelope is continuous with the ER membrane
    • Some regions have embedded ribosomes.
    • Is contiuous with the nuclear envelope
    • Two types: Rough and Smooth
  21. Rough ER
    • Heavily studded with ribosomes- protein synthesis. Proteins have signal sequences which direct to a docking site on the surface of the ER.
    • Both secrete finished products in transport vesicles
    • Has ribosomes that stud the outer surface of the membrane
    • Many types of specialized cells secrete proteins produced by ribosomes attached to rough ER; membrane factory for the cell
    • Most secretory proteins are glycoproteins, proteins that have carbohydrates covalently bonded to them; the carbohydrate is attached to the protein in the ER by specialized molecules built into the ER membrane; once secretory proteins are formed, the ER membrane keeps them separate from the proteins, produced by free ribosomes, that will remain in the cytosol; secretory proteins depart from the ER wrapped in the membrane of vesicles that bud like bubbles from a specialized region called transitional ER; vesicles in transit from one part of the cell to another are called transport vesicles; grows in place by adding membrane proteins and phospholipids to its own membrane; as polypeptides destined to be membrane proteins grow from the ribosomes, they are inserted into the ER membrane itself and are anchored there by their hydrophobic portions; the rough ER also makes its own membrane phospholipids; enzymes built into the ER membrane assemble phospholipids from precursors in the cytosol; the ER membrane expands and is transferred in the form of transport vesicles to other components of the endomembrane system
    • Animal and Plant
  22. Smooth ER
    • Lack ribosomes; have enzymes embedded in membrane for carbohydrate and lipid synthesis.
    • Both secrete finished products in transport vesicles.
    • Synthesizes lipids
    • Metabolizes carbohydrates
    • Stores calcium
    • Detoxifies poison
    • Outer surface lacks ribosomes
    • Synthesizes lipids; metabolizes carbohydrates; detoxifies drugs and poisons
    • The cells that synthesize and secrete sex hormones of vertebras and the various steroid hormones secreted by the adrenal glands are rich in smooth ER, a structural feature that fits the functions of these cells; other enzymes help detoxify drugs and poisons by adding hydroxyl groups to drugs, making them more soluble and easier to flush from the body; stores calcium ions which allows different responses to be triggered (i.e. muscle contraction)
  23. Golgi Complex/Apparatus
    • Flattened stacks of membranes in the cytoplasm-cisternae
    • Collection, packaging and distribution of proteins and lipids
    • Transport vesicles from RER and SER fuse with the Golgi membrane.
    • 1.Vesicles move from ER to Golgi
    • 2. Vesicles coalesce to form new cis Golgi cisternae
    • 3. Cisternal maturation:Golgi cisternae move in a cis-to-trans direction
    • 4. Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma mem-brane for secretion
    • 5. Vesicles transport  backward to newer Golgi cisternae
    • 6. Vesicles also transport certain proteins back to ER
    • Proteins (from RER) may have short sugar chains added--> glycoproteins
    • Lipids (from SER) may have short sugar chains added-->glycolipids
    • Both collect at flattened ends-cisternae
    • Cisternae membranes pinch off the glycoproteins and glycolipids into secretory vesicles (liposomes)
    • Liposomes may fuse with plasma membane or organelle membranes.
    • Consists of flattened membranous sacs (cisternae); the membrane of each cisternae in a stack separates its internal space from the cytosol
    • Products of the ER are modified here and stored and then sent to other destination; manufactures certain macromolecules by itself
    • Especially extensive in cells specialized for secretion; has a distinctive polarity (the membranes of cisternae on opposite sides of the stack differ in thickness in molecular composition; the two poles are referred to as the cis face and the trans face; this act, respectively, as the receiving and shipping departments); products of the ER are usually modified during their transit from the cis region to the trans region (proteins and phospholipids of membranes may be altered); manufactures and refines its products in stages with different cisternae between the cis and trans regions containing unique terms of enzymes; before a Golgi stack dispatches its products by budding vesicles from the tans face, it sorts these products and targets them for various parts of the cell; molecular identification tags aid in organizing the products; transport vesicles budded from the Golgi may have external molecules on their membranes that recognize “docking sites” on the surface of specific organelles or on the plasma membrane, thus targeting them appropriately
  24. Lysosomes
    • Carry out intracellular digestion by phagocytosis
    • Membrane-bound organelle with digestive enzymes
    • Breakdown protein, nucleic acid, carbos, lipids
    • Digest old organelles and invading bacterial cells
    • Digestive enzymes only active at low pH
    • Inactive lysosomes-Primary Lysosomes, high pH, enzymes are inactive
    • Once fused with food vacuole- pump H+ into compartment- active, Secondary Lysosomes
    • Involved in normal cell death and programmed cell death (apoptosis)
    • Ex. Tadpole tail tissue; webbing between human fingers.
    • Hydrolytic enzyme; a membrane bounded sac that buds from the Golgi Apparatus
    • Digests all kinds of macromolecules; carry out intracellular digestion in a variety of circumstances; autophagy
    • A membranous sac of hydrolytic enzymes that an animal cell uses to digest all kinds of macromolecules; lysosomal enzymes work best in the acidic environment found in lysosomes; phagocytosis forms a food vacuole which fuses with a lysosome, whose enzymes digest the food; digestion products pass into the cytosol and become nutrients for the cell; use their hydrolytic enzymes to recycle the cell’s own organic material (autophagy)
    • Animal only
  25. Peroxisomes
    • Oxidation 
    • Produce hydrogen peroxide and convert it to water
  26. Relationships among organelles of the endomembrane system
    • 1. Nuclear envelope is connected to rough ER, which is also continuous with smooth ER
    • 2. Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golg
    • 3. Golgi pinches off transport Vesicles and other vesicles that give rise to lysosomes and Vacuoles
    • 4. Lysosome available for fusion with another vesicle for digestion
    • 5. Transport vesicle carries proteins to plasma membrane for secretion
    • 6. Plasma membrane expands by fusion of vesicles; proteins are secreted from cell
  27. Mitochondrion (ia)
    • Rod-shaped organelle, 1-3 micrometers long
    • Bounded by two membranes- outer is smooth; inner is folded into continuous layers-cristae
    • Two compartments- matrix-inside the inner membrane and intermembrane space between the two membranes
    • Enzymes for oxidative metabolism are embedded in the inner membrane
    • Enclosed by two membranes: A smooth outer membrane and an inner membrane folded into cristae
    • Contain a circular piece of DNA for many of the proteins in oxidative metabolism
    • Also has its own rRNA and ribosomal proteins--> own protein synthesis.Involved in its own replication.
    • Enclosed by membranes but are not part of the endomembrane system; contain ribosomes; contain DNA; semiautonomous organelles that grow and reproduce within the cell; enclosed by two membranes , each a phospholipid bilayer with a unique collection of embedded proteins; the outer membrane is smooth; the inner membrane is convoluted, with infoldings called cristae; the inner membrane divides the mitochondrion into two internal components; the first internal component is the intermembrane space, the narrow region between the inner and outer membranes; the second compartment, the mitochondrial matrix, is enclosed by the inner membrane; the mitochondrial matrix contains many different enzymes as well as the mitochondrial DNA and ribosomes
    • Sites of cellular respiration
    • Cellular respiration is the metabolic process that generates ATP by extracting energy from sugars, fats, and other fuels; the DNA programs the synthesis of the proteins made on the organelle’s own ribosomes; the number of mitochondria a cell has is correlated with the cell’s level of metabolic activity; some of the metabolic steps of cellular respiration are catalyzed by enzymes in the mitochondrial matrix; other proteins that function in respiration are built into the inner membrane as highly folded surfaces, the cristae give the inner mitochondrial membrane a large surface area for these proteins, thus enhancing the productivity of cellular respiration
    • Animal and Plant
  28. Plastids
    • Chloroplasts
    • Leucoplasts
    • Amyloplasts
    • Chromoplasts
  29. Chloroplasts
    • Are found in leaves and other green organs of plants and in algae.
    • Algae and plants have organelles for photosynthesis
    • Two membranes- outer and inner membranes
    • A closed, stacked network of membranes-granum (a)
    • Fluid-filled space around grana-stroma
    • Disc-shaped structures-thylakoids
    • Light-capturing enzymes are embedded on thylakoids
    • Have DNA which encode many enzymes necessary for photosynthesis
    • May lose internal structure-leucoplasts
    • A leucoplast that stores starch-amyloplast. Found in root cells
    • A leucoplast that stores other pigments-chromoplasts.
    • Enclosed by membranes but are not part of the endomembrane system; contain ribosomes; contain DNA; semiautonomous organelles that grow and reproduce within the cell; type of plastid; contents are partitioned from the cytosol by an envelope consisting of at least two membranes separated by a very narrow intermembrane space; Inside the chloroplast is another membranous system in the form of flattened, interconnected sac called thylakoids; a stack of thylakoids are called a granum; the fluid inside the thylakoids is the stroma; the membranes of the chloroplast divide it into three compartments: the intermembrane space, the stroma, and the thylakoid space
    • Sites of photosynthesis 
    • Convert solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds;  the DNA programs the synthesis of the proteins made on the organelle’s own ribosomes; contain the green pigment chlorophyll, along with enzymes and other molecules that function in the photosynthetic production of sugar; the stroma contains the chloroplast DNA and ribosomes as well as many enzymes
    • Animal and Plant
  30. Centriole
    • Barrel-shaped organelles in animals and protists, NOT plants
    • Usually found in pairs around the nuclear membrane
    • Hollow cylinders made of microtubules (protein)
    • Have their own DNA
    • Help move chromosome during cell division.
  31. Central Vacuole or Tonoplast
    • In plants, for protein, water, and waste storage.
    • Are found in plant cells
    • Hold reserves of important organic compounds and water
  32. Vesicles
    In animals, usually smaller sacs used for storage and transport of materials.
  33. Cytoskeleton
    • Is a network of fibers extending throughout the cytoplasm
    • Three main types of fibes that make up the cytoskeleton: Microtubules, Microfilaments. and Intermediate Filaments
  34. Microfilaments (Actin Filaments)
    • Made of globular protein monomers- actin
    • Actin monomers polymerize to form actin filaments
    • Filaments are connected to proteins within the plasma membrane
    • Actin filaments are thinner, cause cellular movements like ameboid movements, cell pinching during division
    • Provide shape for the cell
    • Actin that function in cellular motility contain the protein myosin in addition to actin
    • Built from actin molecules
    • Linear filaments that may form structural support; help support the shape of the cell from inside the plasma membrane; allow cell motility 
    • Contraction of cells is caused by actin-myosin aggregated which causes a cell to crawl along a surface by extending and flowing into cellular extensions called pseudopodia
    • Animal and Plant
  35. Amoeboid Movement
    Involves the contraction of actin and myosin filaments
  36. Cytoplasmic Streaming
    Another form of locomotion created by microfilaments
  37. Microtubules
    • 2 globular monomers- a tubulin and B tubulin polymerize to form 13 protofilaments
    • Filaments form wide, hollow tubes- microtubules
    • Form from nucleation centers (near nucleus) and radiate out.
    • Constantly polymerize and depolymerize- GTP-binding at ends
    • Ends are + (away from center) or - (toward center)
    • Cellular movements and intracellular movement of materials and organelles.
    • Use specialized motor proteins to move organelles along the microtubule
    • Kinesins- move organelles toward the + end (toward cell periphery)
    • Dyneins- move them toward the - end (toward the center of cell)
    • Microtubules and Motor Proteins Rearrange Organelles
    • Microtubules are important in camouflage.  They move melanophores in fish epidermis.
    • Found in the cytoplasm of all eukaryotic cells; made from tubulin and grow out from a centrosome which contains a pair of centrioles
    • Shape and support the cell wall and also serve as tracks along which organelles equipped with motor proteins can move; Compression-resisting girders of the cytoskeleton
    • Animal and Plant
  38. Intermediate Filaments
    • Most durable protein filament- tough fibrous filaments of overlapping tetramers of protein (rope-like)
    • Between actin and microtubules in size. Stable
    • Ex. of Fibers- vimentin and keratin
    • Anchored to proteins embedded into plasma membrane
    • Provide mechanical support to cell.
    • Made up of proteins that include the keratins
    • Reinforces cell shape and the fixed position of specific organelles ; make up the nuclear lamina that lines the interior of the nuclear envelope
    • In cases where the shape of the entire cell is correlated with function, intermediate filaments support the shape
    • Animal and Plant
  39. Plasmodesmata
    • Plant
    • Are channels that perforate plant cell walls
  40. The Extracellular Matrix (ECM) of Animal Cells
    • Animal cells: Lack cell walls. Are covered by an elaborate matrix, the ECM
    • Made up of glycoproteins and other macromolecules
  41. Types of Intercellular Junctions in animals
    • Tight Junction
    • Desmosomes
    • Gap Junctions
  42. Ribosomes
    • Made of ribosomal RNA and protein; not enclosed in membrane; build proteins in two cytoplasmic locales; free ribosomes are suspended in the cytosol; bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope; bound and free ribosomes are structurally identical
    • Carries out protein synthesis
    • Most of the proteins made on free ribosomes function within the cytosol; bound ribosomes generally make proteins that are destined either for insertion into membranes, for packaging within certain organelles such as lysosomes, or for export from the cell (secretion); bound and free ribosomes can alternate between the two roles (the cell adjusts the relative numbers of each as metabolic changes alter the types of proteins that must the synthesized)
    • Animal and Plant
  43. Transport Vesicles
    • Membrane-bound and selected proteins are made on ribosomes found in the rough ER
    • Can move molecules between locations inside the cell
    • Proteins mature in the Golgi Apparatus then travel within the cell inside transport vesicles
    • Animal and Plant
  44. Secretory Vesicles
    • Contain materials that are to excreted from the cells
    • Excrete materials
    • Within a larger organism some cells are specialized to produce certain chemicals which are stored in secretory vesicles and released when needed
    • Animal and Plant
  45. Contractile Vacuoles
    • A membrane-bound organelle
    • Carry out hydrolysis; Pump excess water out of the cell
    • Maintains the appropriate concentration of salts and other molecules by pumping excess water out of the cell
    • Animal and Plant
  46. Central Vacuole
    • Enclosed by a membrane called the tonoplast
    • Versatile compartment; plant cell’s main repository of inorganic ions; disposal sites for metabolic by-products; contain pigments that color the cells; protection; growth
    • Develops by the coalescence of smaller vacuoles, themselves derived from the endoplasmic reticulum and Golgi Apparatus (makes this vacuole an integral part of a plant cell’s endomembrane system); the tonoplast is selective in transporting solutes which causes the solution inside the vacuole (cell sap) to differ in composition from the cytosol; protect the plant against predators by containing compounds that are poisonous or unpalatable to animals; major role in plant cell growth, which enlarge as their vacuoles absorb water
    • Plant only
  47. Peroxisome
    • Oxidative organelle that is not part of the endomembrane system; imports its proteins primarily from the cytosol; a specialized metabolic compartment bound by a single membrane
    • Break fatty acids down into smaller molecules; detoxify; initiate the conversion of fatty acids to sugar 
    • Contain enzymes that transfer hydrogen from various substrates to oxygen, producing hydrogen peroxide; use oxygen to break fatty acids down into smaller molecules that can then be transported to the mitochondria, where they can be used as fuel for cellular respiration; glyoxysomes, specialized peroxisomes, are found in the fat-storing tissues of plant seeds and contain enzymes that initiate the conversion of fatty acids to sugar 
    • Animal and Plant
  48. Plastids
    • Contain pigments;  possess a double-stranded DNA molecule; large cytoplasmic organelles
    • Site of manufacture and storage of important chemical compounds used by the cell;
    • responsible for photosynthesis
    • Contain pigments used in photosynthesis; once formed, certain kinds of plastids can be
    • converted into other types
    • Plant only
  49. Centrosome
    • A region often located near the nucleus
    • Considered to be a “microtubule -organizing center”
    • Containsa pair of centrioles (in an animal cell) which are each composed of nine sets of triplet microtubules arranged in a ring; centrioles may help organized microtubule assembly 
    • Animal and Plant
  50. Flagella of Prokaryotes (Bacteria)
    • Composed of a flagellin subunit
    • Usually sheathed (covered)
    • Rotates by way of a basal body in the bacterial cell
    • Unique to bacteria.
  51. Eukaryotic Flagella
    • Completely different than bacteria
    • Circle of 9 fused pairs of microtubules that make a cyclinder
    • 2 unfused microtubules in the center of cylinder
    • Called the 9 + 2 structure.
    • Whip-like appendage, used in movement and longer than cilia
    • Is an outward projection of cytoplasm.
    • Are found in microvilli
  52. Cilia
    • More numerous than flagella
    • Cilia of unicellular eukaryotes = movement of cell
    • Ex. Paramecium
    • Cilia of multicellular eukaryotes = movement of debris, sensory cells of vertebrate ear, epithelia of respiratory and reproductive tracts
    • Have similar microtubule structure of 9 + 2 as eukaryotic flagella.
    • Are found in microvilli
  53. Protein Dynein
    Is responsible for the bending movement of cilia and flagella
  54. Endosymbiotic Theory
    • Lynn Margulis (1970’s) 
    • Eukaryotic cells arose from symbioses and genetic exchanges between prokaryotes
    • Proposes that mitochondria and some other organelles were formerly small prokaryotes living within larger host cells.
    • The prokaryotic ancestors of mitochondria and plastids: Probably gained entry to the host cell as undigested prey or internal parasites
    • In the process of becoming more interdependent: The host and endosymbionts would have become a single organism.
    • The evidence supporting an endosymbiotic origin of mitochondria and plastids (chloroplatsts) includes: Similarities in inner membrane structures and functions. Both have their own circular DNA. DNA encodes genes for rRNA and can perform most of its own protein synthesis. Divides by splitting, “binary fission.”
    • Some investigators have speculated that eukaryotic flagella and cilia: Evolved from symbiotic bacteria, based on symbiotic relationships between some bacteria and protozoans. Also have circular DNA.
  55. Pelomyxa
    • A single-celled amoeboid protist.
    • Has a true nucleus but divides the nucleus more like a prokaryote, with no microtubules and spindle fibers.
    • Has no mitochondria.
    • Symbiotic bacteria that live within it that help produce energy for it.