bio.txt

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bio.txt
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  1. What are lipids (definition)? Explain why this is a �catch all� definition.
    Lipid is a catch-all term for carbon containing compounds that are found in organisms and are largely nonpolar and hydrophobic (don�t dissolve in water, but in liquids with nonpolar organic compounds)
  2. Saturated
    hydrocarbon chains without double bonds. (max number of hydrogen,more chemical energy, higher melting point)
  3. Unsaturated
    contain double bond, fewer than max number of hydrogen atoms attached.
  4. Steroids
    family of lipids distinguished by the bulky four ring structure. Differ by functional groups
  5. Fats
    composed of three fatty acids that are linked to a three carbon molecule(glycerol) ( also called triglycerols, triglcerides) not polymers
  6. Phospholipids
    consist of a glycerol that is linked to a phosphate group, and to either two chains of isoprene or two fatty acids. Phosphate also bonded to small organic molecule that is charged or polar.
  7. Phospholipids and steroids are amphipathic molecules. What does that mean?
    Contain both hydrophilic and hydrophobic elements
  8. What is membrane permeability?
    The tendency of a structure to allow a given substance to pass across
  9. How do different molecules move through membranes? Can you look at a molecule and know its likely permeability?
    • �Small nonpolar molecules move across bilayers quickly.
    • �Large molecules and charge substances cross the membrane slowly.
    • �Sometimes they don�t cross at all.
    • � Large molecules and charge molecules can�t pass through the
    • Non polar hydrophobic tails of the lipid bilayer.
  10. How does the saturation level and tail length of the fatty acids and the amount ofcholesterol affect the permeability of a membrane?
    • �In a lipid bilayer membrane with unsaturated phospholipids the hydrophobic part is less tight
    • �Hydrophobic interactions become stronger as saturated hydrocarbon tails increase in length.
    • �Membranes compose of phospholipids with long saturated tails are more stiffer and less permeable.
    • �The reason is that the interaction between the tails are stronger.
  11. Solute
    dissolved molecules or ions
  12. Concentration gradient
    difference across space in the concentration of a dissolved substance
  13. Solvent
    liquid in which one or more solids can dissolve
  14. Diffusion
    spontaneous movement of a substance from a region of high concentration to one of low concentration (down gradient)
  15. Osmosis
    - diffusion of water across a selectively permeable membrane from a region of high water concentration (low solute) to region of low water [] (high solute)
  16. Facilitated diffusion
    movement of a substance across a plasma membrane down its concentration gradient with the assistance of transmembrane carrier proteins of channel protteins
  17. Active transport
    movement of ions or molecules across a plasma membrane against an electrochemical gradient. Requires energy (hydrolysis of atp) and assistance of transport protein
  18. tonicity
    measure of the osmotic pressure (as defined by the water potential of the two solutions) of two solutions separated by a semipermeable membrane.
  19. Hypotonic
    solution that has a lower solute concentration, therefore higher water concentration. Water flows into cell,cell swells or burts
  20. Isotonic
    solution that has the same solute concentration and water concentration. No change
  21. Hypertonic
    solution that has a greater solute concentration, lower water concentration. Water flows out of cell, cell shrinks
  22. Passive diffusion
    diffusion of a substance across a plasma membrane or organelle membrane. When this occurs with the assistance of a membrane protein, facilitated diffusion.
  23. Channel proteins
    selective, each protein has a structure that allows it to admit a particular type of ion or small molecule. (pore like)
  24. Carrier protein
    transporter) membrane protein that facilitiates diffusion of a small molecule (glucose) across the plasma membrane by a process involving a reversible change in the shape of the protein
  25. Pumps
    membrane protein that can hydrolyze ATP to power active transport of a specific ion or small molecule across a plasma membrane against its electrochemical gradient
  26. Eukaryotic Cells
    complex, composes animal, plants, fungi, protists. either single or multi-celled. Has nucleus, DNA, membrane bound organelles
  27. Prokaryotic Cells
    composes all bacteria and Archaea, lack membrane bound nucleus. Only has one membrane (plasma membrane) genetic material naked, ribosomes only organelle, always single celled
  28. Nucleoid region
    Only in prokaryotes. Where chromosomes are found, center of cell, not separated by membrane
  29. Golgi apparatus
    In eukaryotic, plant and animal cells. Consists of flattened, membranous sacs called cisternaw, has distinct polarity.. Functions in processing and sorting proteins and lipids destined to be secreted or directed to other organelles
  30. Lumen
    In eukaryotic cells. Interior of the rough ER. Where newly manufactured proteins undergo folding and other types of processing
  31. Plasmid
    In prokaryotic cells. Usually circular, supercoiled DNA molecules. Contain genes but are physically independent of the main, cellular chromosome. Help cells adapt to unusual circumstances (auxiliary geetic elements)
  32. Mitochondria
    In eukaryotic cells. Has two membranes, outer and inner with cristae. Solution inside mitochondrial matrix. Site of aerobic respiration, where most ATP is produced
  33. Nuclear envelope
    • In eukaryotic cells
    • Complex double embrane, encloses nucleus and is studded with pore like openings, inside surface linked to nuclear lamina
  34. Flagella (flagellum)
    In eukaryotes- long cellular projection that undulates. In prokaryotes- rotates To move the cell through an aqueous environment
  35. Chloroplast
    In plant cells. Chlorophyll containing organelle, bounded by double membrane. Where photosynthesis occurs
  36. Cell wall
    Prokaryotic and In plant cells, fibrous layer found outside plasma membrane of most bacter and archaea annd eukaryotes. defines shape f a plant cell.
  37. Nucleolus
    Specific site in nucleus where gene products are processed. Where RNA molecules found in ribosome�s are manufactured and the large and small ribosomal subunits are assembled
  38. Lysosome
    Animal cells. Function as digestive centers. Interior acidic, has enzymes that catalyze hydrolyss reactions and can digest large molecules
  39. Smooth er
    eukaryotic. Free of ribosome�s Contains enzymes that catalyze reactions involving lipids. ( lipids may be needed by organism or break down lipids that are poisonous.. Manufacturing site for phospholipids used In plasma membrane. Resevoir for calcium ions that act as a signal
  40. Rough er
    eukaryotic. Has ribosome�s attached to membrane. Protein manufacturing center
  41. Super coiled dna
    In prokaryotic cells. To fit in cell, DNA double helix coils on itself with the aid of enzymes to form supercoiled structure
  42. Vesicle
    Transport, eukaryotic
  43. Chromatin
    Complex of DNA and protiens, that compose eukaryotic chromosomes. Can be highly compact or loosely coiled
  44. Peroxisome
    Found in most eukaryotic cells. Contain enzymes for oxidizing fatty acids and other copounds including may toxins, rendering them harmless
  45. Vacuole
    In plant and fungal cells. Usually is used for bulk storage of water, pigments, oils, or other substances. Some contain enzymes that have digesive function similar to lysosomes in animal cells
  46. Ribosome
    SYNTHESIZES PROTEINS BY USING GENETIC INFORMATION ENCODED IN MRNA STRANDS. TWO SUBUNITS. both
  47. chromosome
    both. gene carrying structure consisting of single long molecule of DNA and associated proteins. Prokaryotic contain single, circular Eukaryotic contain multiple linear located in nuclues
  48. Cytoplasm
    Both All of the content of a cell, excluding nucleus bounded by the plasma membrane
  49. Centrioles
    in eukaryotic cells, one of two small cylindrical structurs, found together within the centrosome near the nucleus
  50. Cytoskeleton
    Eukaryotic cells. Network of protein fibers in the cytoplasm that are involved in cell shape, support, locomotion, and transport of materials withincell. Prokaryotic cells have similar but much less extensive netowrk
  51. Microfilaments
    long fiber, one of three types of cytoskeletal fibers. involved in cell movement
  52. Intermediate filaments
    long fiber, one of three types of cytokeletal fibers. help maintain cell shape and hold nucleus in place
  53. Microtubules
    involved in cell movement and transport of materials within the cell
  54. Myosin
    Any one of a class of motor proteins that use ATP to move along microfilaments in muscle contraction, cytokinesis, and vesicle transport
  55. Kinesis
    type of motor protein, uses ATP to transport vesicles, particles, or chromosomes along microtubules
  56. the signal recognition hypothesis
    proteins bound for the endomembrane system have a molecular zip code analogous to the nuclear localization signal.
  57. cis side of golgi apparatus
    receives products from the rough ER carried by vesicles
  58. trans side of golgi apparatus
    ships products out toward the cell surface
  59. Autophagy
    damaged organelle is surrounded by a membrane, delved to the lysosome, and digested and recycled into cytosol
  60. Phagocytosis
    plasma membrane of a cell surrounds a smaller cell or food particle and engulfs it, forming a structure called a phago some. Delivered to a lysosome and digested
  61. pinocytosis
    uptake by a cell of extracellular fluid by pinching off the plasma membrane to form small membrane bound vesicles, type of endocytosis
  62. exocitosis
    secretion of intracellular molecules contained within membrane-bound vesicles, to the outside of the cell by fusion of vesicles, to the outside of the cell by fusion of vesicles to the plasma membrane
  63. endocytosis
    general term for any pinching off of the plasma membrane that results in the uptake of material from outside the cell. Includes phagocuosis, pinocytosis, receptor-mediated endocytosis
  64. nuclear pore
    opening in the nuclear envelope that contains the inside of the nucleus with the cytoplasm and through which molecules such as mRNA and some proteins can pass
  65. How are the peptines and cellulose microfibril building blocks of a cell wall synthesized?
    • microfibril synthesized by a complex of enzymes in the plasma membrane, forming a crisscrossed network. Peptines are synthesize in the rough ER and Golgi apparatus
    • and secreted into the extracellular space.
  66. Animal's extracellular matrix
    structural support. animal ECM contains much more protein that a cel wall. structure correlates with the cell's function.
  67. plasmodesmata
    where gaps in cel walls create direct connections between cytoplasm of adjacent cells in plant cells. plasma membrane and cytoplasm of two cell continuous, smooth er runs through the hole.
  68. What do actin, integrin, and fibronectin have to do animal cell connection and attachment?
    The actin filaments in the cytoskeleton are connected to transmembrane proteins (integrins.) The integrins bind to nearby proteins in the ECM, including fibronectins, which in turn bind to collagen fibers. Helps adjacent cells adhere to each other via their common connection to the ECM, keep individual cells in place
  69. Tight Junction
    cell-cell attachment composed of specialized proteins in the plasma membrane of adjacent animal cells. (water tight seal, common in cells that form barrier)
  70. desmosomes
    cell-cell attachments common in animal epithelial cells and certain muscle cells. consist of proteins that bind the cytoskeletons of adjacent animal cells together. found where cells are strongly attached to each other
  71. gap junctions
    cell-cell attachment that directly connects the cytoplasms of adjacent animal cells, allowing the passage of water, ions, and small molecules between the cellos.
  72. hormones
    small information carrying molecules that are secreted from a plant or animal cell, circulate in the body, and act on target cells far from the original cell that sent the signal
  73. signal transduction
    hormone binds to a receptor in the plasma membrane, which is coupled to a peripheral G preen on the membrane's inner surface. The receptor changes shapes. TThe shape change activates the G protein,releasing GDP that kept in an inactive state and binds to GTP. When GTP is attached, the G protein splits into two parts. One part activates a nearby enzyme that is embedded in the plasma membrane, which catalyzed the production of a second messenger.
  74. The plant cell is _____ with the environment
    hypertonic
  75. Hydrophilic hormone
    They will be recognized by receptors in the cell membrane. lipids and hydrophilic hormones have two general qualities; Receptor are dynamic. Receptor can be blocked.
  76. second messenger
    intracellular signals that spread the message carried by the hormone. concentration increases as a result of the signal trigger by the first messenger (hormone) effective because small and diffuse the signaling rapidly inside the cell. No t proteinsNot restricted to a signal role/ activate protein kinases.
  77. What are chemical reactions? What factors can affect their rate?
    making and breaking of chemical bonds, leading to changes in the composition of matter. Affected by if the reactants collide in a precise orientation and if enough kinetic energy is involved in the reaction to overcome the repulsion between electrons that come into contact as bonds form
  78. How do enzymes accelerate the rate of chemical reactions? (Explain mechanism).
    bring the reactant molecules together in a precise orientation, allowing the electrons to interact. Also affect amount of kinetic energy that reactant must have for a reaction to proceed.
  79. substrate
    reactant on which an enzyme works
  80. transition state
    combination of old and new bonds that are formed when reactants collide
  81. activation energy
    amount of energy reactant must absorb before a chemical reaction will start
  82. catalyst
    substance that lowers the activation energy of a reaction and increases the rate of the reaction
  83. active site
    portion of an enzyme where substrates bind and react
  84. induced fit
    changes in shape of the active site of an enzyme, result of the initial weak binding of a substrate so that it binds more tightly
  85. Enzymes use a general 3 step process to accelerate reactions. Explain.
    initiation (enzymes orient the reactants precisely as they bind specific location in the active site) transitional state facilitations (binding of a substrate in the active site facilitate the transition state) and termination (the reaction product have less affinity for the active site)
  86. co-factors
    a metal ion that is required for an enzyme to function normally. may be bound tightly to an enzyme or associate wih it transiently during catalysis
  87. co-enzyme
    small organic molecule that is a required cofactor for an enzyme-catalyzed reaction. Often donates or receives electrons or functional groups during the reaction
  88. competitive inhibition
    occurs when a molecule that is similar in size and shape to the substrate binds to the active site (competes with the substrate for the active site
  89. allosteric regulation
    regulation of a proteins function by binding of a regulatory molecule, usually to a specific site distinct from the active site, causing a change in the proteins shape
  90. Explain how substrate concentration, pH, and temperature can affect enzyme function
    • and the rate of reaction.
    • as concentration of the substrate increase the increase in speed reaction slows, will plateau at a max speed, active site cannot accept substrate any faster temperature affects the movement of enzymes and substrate (only work at optimum temperature) pH affects makeupand charge of amino acids side chain that contain carboxyl groups or amino acids, also affects active site ability to participate in proton transfer or electron transfer reaction (have optimum pH)
  91. What is the goal of cellular respiration?
  92. Where does ATP get its potential energy?
    the amount of potential energy that an electron has is based on its position relative to other electrons and to the rtonselectron close to negative charges and far from positive, has high potential energy
  93. Why does sticking a phosphate group from an ATP onto a protein often cause that protein to do something? (usually change shape)
    ewr
  94. Explain energy coupling. Why is it so important in a cell�s metabolic reactions?
    exergonic and endergonic reactions are coupled. allows the endergonic reaction to become eexrgonic when the substrate or enzyme are phosphorylated
  95. Explain in detail an oxidation-reduction reaction (redox), including which atom(s) are
    • �oxidized� and �reduced.�
    • redox- class of chemical reaction that involve loss or gain of an electron. atom that loses electron iodized, atone that gains are reduced
  96. Describe glycolysis in your own words.
    breakdown of a glucose molecule. breakes into molecules of pyruvate, the cell must pen 2 ATP to start and 4 ATP are gnerated(2 net ATP gain) and two molecules of NAD+ enter pathways and become NADH
  97. What is the net energy gain of glycolysis?
    2 ATP
  98. kerns cycle
    the pyruvate molecule (which is a three carbon molecules) enter the pathway and subsecuently it gets transform into a six carbon molecules called citrate. As the cycle continues, the carbon atoms get rearrange and decarboxylated (which means that carbon is removed in the form of carbon dioxide). The Kreb cycles produces 1 ATP, 4 NADH, 1 FADH2 and 3 CO2. Notice that because two molecules of pyruvate were created these amounts should be multiply by two to get the total amounts of these molecules per molecule of glucose. At this point in cellular respiration the entire molecule of glucose has been catabolised
  99. Cellular respiration produces ATP in two ways. Compare and contrast.
  100. Why not oxidize glucose in one BIG step, get it over with already, instead of all those
    annoying little steps?
  101. When is ATP vs NADH made?
  102. Identify where the different reactions take place (use mitochondria for comparison �
    • inside mito lumen, outside in cytoplasm, etc.)
    • Glycolisis which occurs in the cytoplasm of the cell. Krebs Cycle- which occurs in the matrix of the mitochondria. electron transfer system which occurs in the mitochondria innermembranes.
  103. Where is the energy in a glucose molecule? How does respiration tap that energy?
    The energy in glucose is stored in the covalent bonds between the molecules, and most importantly, in the hydrogen electrons. T
  104. Explain the function of the NAD+ and FAD molecules in cellar respiration.
    NAD+ when reacted with 2 H produces NADH plus 1 H, FAD when reacted with 2 H produces FADH@. Molecules are important because they are carrying electrons that will transfer to the next metabolic reaction known as the electron transport system
  105. Explain how the electron transport chain works.
    set of membrane bound protein complexes and smaller soluble electron carriers involved in a coordinated series of reduce reactions in which potential energy of electrons transferred from reduced donors is successively decreased and used to pump protons from one side of a membrane to the other protein
  106. Describe the characteristics of the ETC molecules. How do their characteristics affect their position in the chain?
    Most molecules in the electron transport chain are proteins that contain distinctive chemical groups where the redox events take place. arranged in a sequence according to elecronegativity, lower to higher
  107. What does it mean that electrons flow through them? How does that help make ATP?
    • electrons will pass from molecules of lower electronegativity to molecules of higher electronegativity via a redox reaction.
    • A small amount of energy will be release in each step and the potential energy in each successive step will be lessen.
  108. Explain chemiosmosis and how it helps ATP synthase do its job.
    energetic coupling mechanism where energy stored in an electrochemical proton gradient is used to drive an energy-requiring process such as production of ATPfavor the movement of protons back into the matrix.
  109. When would you expect fermentation instead of cellular respiration?
    organism that use oxygen as their final electron acceptor, fermentation is use as a way of obtaining energy when the oxygen supply temporary ran out.
  110. What is the goal of fermentation? Is it similar in yeast and multicellular eukaryotes? Explain.
    metabolic pathway that regenerate NAD+ molecules from stock piles of of NADH allows glycolysis to continue
  111. Is sugar the only useful fuel for respiration? Explain.
  112. Can intermediate molecules obtained during cellular respiration be used for other metabolical pathways? Explain.
    jkj

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