Extra Notes of Exam II

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Extra Notes of Exam II
2012-10-23 13:23:09

Exam II
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  1. What are the major similarities among phagocytosis, pinocytosis, and receptor-mediated endocytosis?
    •Membrane-bound vesicles

    •Take in large molecules/particles  or   take in groups of molecules

    •Require cellular energy (ATP)
  2. What are the major differences
    among these 3 processes ?
    • Phagocytosis:
    • •Pseudopodia
    • •Takes in large particles

    • Pinocytosis:
    • •No pseudopodia
    • •Takes in fluid
    • •Not specific
    • •Depression forms “naked” vesicle

    • Receptor- Mediated Endocytosis
    • •No pseudopodia
    • •Very specific:  receptors on membrane
    • •Coat protein on inner side of membrane
  3. What are the RNA subunits?
  4. What is the RNA sugar?
    ribose (OH attached to C #2)
  5. Explain RNA shape.
    • variable, depending on type
    • eg: straight or folded
    • no alpha-helix
    • when folded, the shape is maintained by base-pairing
  6. Length of RNA in relation to DNA
    smaller in length
  7. Types of RNA
    • mRNA
    • rRNA
    • tRNA
    • small nuclear RNA
    • heterogeneous nuclear (hnRNA)
  8. General function of RNA:
    protein synthesis
  9. metabolism
    collectively, all of the biochemical reactions occurring in an organism
  10. Biochemical reaction
    a chemical reaction that occurs in an organism
  11. Energy
    the capacity to do work and cause change; exists in different forms and can be converted from one to another
  12. Types of energy
    • heat
    • light
    • mechanical
    • chemical
    • nuclear 
    • electrical
  13. 1st Law of Thermodynamics
    • The total energy in the universe is constant; energy can be neither created or destroye, only transformed from one form to another
    • - In a chemical (or biochemical reaction), the reactants and products rarely contain the same amount of energy, but the amount of energy on both sides of the reaction must be the same
  14. 2 classes of reactions:
    • exergonic: reactants contain more energy than the products (spontaneous/ downhill)
    • A + B --> C + D + energy

    • endergonic: reactants contain less energy than the products
    • energy + A + B --> C + D
  15. Free energy
    • the energy available in any particular system to do useful work; in cells, the energy released in an exergonic reaction is never all free energy
    • e.g. A + B --> C + D + free energy + heat
  16. 2nd Law of Thermodynamics
    • All physical and chemical change proceeds to that the total entropy of the universe increases to the maximum possible; entropy of the universe never decreases, which means that free energy decreases
    • Althoiugh the universe is disorganized, the system may be organized. The part that supplies the energy (sun) is getting more disordered.
  17. Energy that is supplied from exergonic reaction does what?
    couples the exergonic and endergonic reactions so energy from exergonic drives endergonic
  18. Write out the structure of ATP.
    phosphate-phosphate- phosphate- ribose- adenine
  19. Hydrolysis of ATP:
    ATP + H2O --> ADP + phosphate + energy
  20. Activation Energy
    the initial investment of energy for starting a reaction; the energy required to break bonds
  21. How do catalysts work?
    • work by lowering activation energy needed for reaction to occur
    • almost all biochemical reactions are catalyzed
    • most catalysts in organisms are enzymes (proteins)
    • RNA may act as a catalyst for a few biochemical reactions (ribozyme)
  22. Although exergonic reactions are spontaneous, they need a little push. What is this push?
    energy that supplies this push in Gibb's free energy
  23. What is the connection between EA and energy released.
    • no connection
    • only connection is if EA is high, its a slow reaction
  24. Points of enzymes.
    • Globular
    • Simple or conjugated
    • May/ may not have quaternary structure
    • May or may not have cofactor
    • ends in -ase
    • can, in most cases, catalyze a reaction in either direction depending on relative concentrations; does not determine which direction
    • reactants in enzyme catalyzed reactions= substrates
    • enzymes differ in specificity
  25. In cells, a vast majority of catalysts are __, but some can be __.
    • proteins
    • inorganic
  26. Explain enzyme specificity.
    can be very specific, such as urease, which only catalyzes urease; or can have small specificity, for example, ligase, which catalyzees several lipid- involving reactions
  27. Two ways active site and substrate might fit
    • lock and key model (perfect fit/ match exactly)
    • induced-fit model (most common)
  28. Types of bond between enzymes and substrate
    due to speed of reaction, it may form H bonds or ionic bonds
  29. Some ways that an enzyme might help speed a reaction:
    • bring substrates close together
    • orient substrates correctly for a reaction to occur
    • strain/ weaken bonds in substrates so ehtey are more likely to break
  30. Inhibitors
    • competitive: similar to substrate's structure; compete for active site, but does not change shape of active site; may/ may not permanently bind
    • non-competitive: don't resembe substrate structure; bind to place other than active site and change shape of enzyme
  31. Enzymes exhibit a property called __
    saturation kinetics
  32. Biochemical pathways
    a series of biochemical reactions that are linked together with the products becoming reactions
  33. Characteristics of control mechanisms
    • 1) must control rates of enzyme-catalzyzed reactions
    • 2) should prevent waste of energy and materials
    • 3) must function efficiently and without interruption
  34. Control or regulation by allosteric enzymes
    allosteric enzyme: enzyme usually composed of 2 or more polypeptide chains that exists in two phsyical shapes with one or mroe allosteric sites (active/ inactive)
  35. Chemicals that affect allosteric enzyme activity
    • activator (modulator, effector [positive])
    • inhibitor
  36. The binding between an activator or inhibitor and its allosteric enzyme is usually __.
  37. What is the modern cell theory?
    • 1) all organisms are composed of cells
    • 2) the cells come from pre-existing other cells
    • 3) the structure of cells is related to their function
  38. Resolution
    a physical measure of how close two objects can be and still be seen as distinct objects; measured in units, such as mm, um, nm
  39. Multicellular organisms= __
    cell specialization
  40. Resolution of __ is better than in __.
    The __ the # of resolution, the __ the resolution.
    - eye: __
    - LM: __
    TEM: __
    • EM
    • LM
    • smaller
    • greater
    • 100 um
    • .2 um
    • 0.002 um (best res)
  41. Size
    • not all cells are the same size
    • largest cell: ostrich egg
  42. Reason for smallness of cells
    • surface area/ volume ratio
    • nuclear control over cell metabolism: nucleus sends out chemicals/ molecules to carry out functions and its advantageous if the molecules/ chemicals don't have to travel as far to leave the nucleus
    • lower limit to cell size
  43. Protoplasm
    • the living material or substance of a cell (cell wall not included)
    • Divided into nucleus and cytoplasm
  44. Cytoplasm can be defined in two ways: __
    • - all parts of the protoplasm except the nucleus: sub-cellular organelles and cytosol [equivalent to cytosol]
    • - physical nature of the cytosol
  45. True or False:
    Only some cells, no matter what kind, have a membrane on the surface of the protoplasm; eukaryotic cells and some prokaryotic cells also have internal membranes
    • False: 
    • Only some cells, no matter what kind, have a membrane on the surface of the protoplasm; eukaryotic cells and some prokaryotic cells also have internal membranes
    • True: 
    • All cells, no matter what kind, have a membrane on the surface of the protoplasm; eukaryotic cells and some prokaryotic cells also have internal membranes
  46. Proteins within the membrane are __.
  47. What is the function of carbs (oligosaccharides) on the membrane?
    • cell-cell recognition 
    • adhesion
  48. Why do phospholipids rarely flip-flop?
    • hydrophobic tails will be exposed oto the aqueous solution
    • hydrophilic has to go through hydrophobic
  49. Membrane functions
    • compartmentalization: forms boundary around cell; barrier; separates environment from inside membrane; 
    • detects outside info
    • controls movement of csubstances inside/ outside cell
  50. What moves via facilitated diffusion?
    polar substances, amino acids, sugars, H2O
  51. Explain cotransport.
    • movement of ORGANIC molecule AGAINST concentration gradient
    • no energy required due to potential energy of particle diffusing down
  52. Due to __, anything above __  moves.
    Its vibration movement is the __.
    • heat (thermal energy)
    • absolute zero
    • Brownian motion
  53. membrane potential
    difference in voltage on opposite sides of membrane (electrochemical gradient)
  54. Why do fruites ripen? What is done?
    • action of enzymes
    • prseervation techniques that have been developed to half the action of natural enzymes and prevent spoilage
    • involves freezing, drying, or blanching
  55. How are enzymes used in food processing?
    • fermenting beer and wine
    • making bread dough
    • creating flavors and products
    • preserve quality