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186 Cards in this Set
- Front
- Back
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What is the basic unit of biology?
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The Cell
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What is the study of cellular structure and organization?
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BioImaging
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What is the study of chemical reactions of biomolecules (enzyme-catalyzed reactions, metabolic pathways)?
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Biochemistry
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What is the study of interactions and regulation between cellular systems involving DNA, RNA and protein synthesis?
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Molecular Biology
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Who first invented the light microscope?
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Robert Hooke
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Who coined the word cell?
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Robert Hooke
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Who improved on the microscope?
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Antonie van Leeuwenhoek
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What is one of the cell biologists most important tools?
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The Light Microscope
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What is the limit of resolution of light microscopy?
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0.2 um
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What is the advantage that the light microscope has?
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Live-Cell imaging
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What is the ability to discriminate two closely placed structures?
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Resolution
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What is a measure of the increase in the diameter of a structure?
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Magnification
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What is a contrast that involves light absorption?
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Amplitude Contrast
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What is a contrast that involves a change in wave phase?
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Phase Contrast
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What type of instrument utilizes a focused laser beam to provide an attractive or repulsive force?
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Optical Tweezers
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What type of microscopy is useful in detecting specific fluorescent labeled proteins or molecules?
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Fluorescence Microscopy
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What is a molecule that will emit a characteristic wave length of light when excited by a specific wave length?
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Fluorochrome
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What is the strategy for epifluorescence microscopy for dead cells?
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Indirect immuno-fluorescence
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How many antibodies are involved in Indirect Immuno-fluorescence?
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Two, a primary (binds to the protein) and a secondary (binds to the primary antibody)
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In indirect immuno-fluorescence where is the fluorescent molecule attached?
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To the secondary antibody
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What are the advantages of confocal microscopy?
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Increased clarity of images
Creation of Optical Sections Three Dimensional Information |
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What is the strategy for epifluorescence microscopy for living cells?
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Green Fluorescent Protein integration and dyes.
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What are the two types of electron microscopy?
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Scanning Electron Microscopy
Transmission Electron Microscopy |
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Who developed the electron microscope?
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Knoll and Ruska
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How much stronger (in fold) is the electron microscope as opposed to the light microscope?
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1000-fold
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How thick are cross sections in transmission microscopy?
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70nm
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What is the most widely used procedure to separate subcellular structures?
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Centrifugation
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What is repeated centrifugation at progressively higher speeds?
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Differential centrifugation
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What components of a solution require greater force to sediment during centrifugation?
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The smaller and less dense components
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Which type of centrifugation requires the use of a chemical gradient (sucrose or cesium chloride)?
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Equilibrium centrifugation
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What does an SDS-PAGE separate proteins by?
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Size
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Who developed the southern blot?
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Edwin Southern
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What method can be employed to separate cells of a particular type from a mixture (based on fluorescence)
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Flow Cytometery
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What are the four buildung blocks of the cell?
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Sugars
Fatty Acids Amino Acids Nucleotides |
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What are the simplest sugars?
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Monosaccharides
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What type of saccharide is glucose?
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Monosaccharide, a simple sugar
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What type of reaction occurs when two monosaccharides form a disaccharide?
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A condensation reaction
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What is the term for a reaction requiring energy?
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Anabolic
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What is the term for a reaction that releases energy?
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Catabolic
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What type of reaction is seen in the breakdown of polysaccharides?
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Hydrolysis
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Oligosaccharides constitute approximately how many monosaccharides?
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3-50
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What is an example of a polysaccharide made entirely of glucose units?
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Glycogen
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What are the three functions of sugars?
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Production and Storage of Energy
Mechanical Support (cellulose) Molecular Recognition (glycoproteins) |
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What are the two types of fatty acids?
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Saturated and Unsaturated
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Which type of fatty acid is often a liquid at room temperature?
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unsaturated
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Which type of fatty acid contains no double bonds?
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Saturated
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What do fatty acids form for energy storage?
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Triacylglycerols
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What cellular building block makes up a component of cell membranes?
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Fatty Acids (Phospholipids)
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What is the term for the carbon that links the carboxyl and amino group of an amino acid?
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The alpha carbon
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What are the four basic categories of amino acids?
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Acidic
Basic Uncharged Polar Nonpolar |
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What links amino acids?
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Peptide Bonds
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What type of reaction joins amino acids together?
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Condensation reaction
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How is a polypeptide sequence read?
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From the N terminus to the C terminus
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What links nucleic acids together?
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Phosphodiester bonds
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What links the three phosphate bonds in ATP?
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Phosphoanhydride Bonds
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What are the functions of nucleotides?
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Combine to form coenzymes (CoA)
Used in cellular signaling (cAMP) Used in DNA, RNA Carry Chemical Energy (ATP) |
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What two reactions constitute the cell's metabolism?
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Catabolism and Anabolism
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What type of chemical pathway is used in the breakdown of food and smaller molecules?
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Catabolic Pathways
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What type of pathway is used when harnessing energy to drive synthesis?
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Anabolic Pathways
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What organizes cell metabolism?
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Enzymes
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What law of thermodynamics states that the universe likes to be disordered?
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The Second Law
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What measures disorder in a system?
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Entropy
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How do living cells not defy the second law of thermodynamics?
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The amount of order inside the cells causes a decrease in order outside the cell.
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How do anabolic unfavorable reactions occur?
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They must be coupled to a second reaction with a larger negative gibbs free energy to cause the entire process to be negative.
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What does the cell use to store energy temporarily?
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Activated carrier molecules
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What are the two most important activated carrier molecules?
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ATP and NADH
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What gives amino acids its unique properties?
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The Side Chains
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What assists protein folding?
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Molecular Chaperones (proteins)
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What are three types of noncovalent bonds?
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Electrostatic Attractions
Hydrogen Bonds Van-Der-Waals Attractions |
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What type of force is produced by fluctuations in electron clouds of atoms?
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Van-Der-Waals Attractions
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What force often causes proteins to fold into compact conformations?
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Hydrophobic Forces
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When do disulfide bonds form?
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When proteins are exported from cell
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Can Denatured proteins recover their natural shape?
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Yes
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Who sequenced the first protein and what was it?
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Frederick Sanger
Insulin |
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What is used to determine the structure of large proteins?
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X-Ray Crystallography
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What is used to determine the structure of small protein molecules?
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NMR
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What is the resolution of X-Ray Crystallography?
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0.1nm
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What are the two common folding patterns of proteins?
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Alpha Helix and Beta Sheet
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What makes folding patterns common?
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The Hydrogen Bonds in the polypeptide backbone
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Are amino acid side chains involved when forming the folding pattern hydrogen bonding?
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No
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Keratin and Myosin are examples of what type of folding?
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Alpha Helix
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What are the two varieties of Beta Sheet folding?
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Antiparallel and Parallel
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Anti-Freeze Protein is an example of what type of folding?
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Beta Sheet
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What type of structure is only the amino acid sequence?
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Primary Structure
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What type of structure includes the folding patterns (alpha helices and beta sheets)?
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Secondary structure
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What type of structure is a fully three dimensional structure?
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Tertiary Structure
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What type of structure includes a complex of more than one polypeptide chain?
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Quaternary Structure
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What is the term for a segment of a polypeptide chain that can fold independently into a compact stable structure?
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Protein Domain
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About how many amino acids are found in a protein domain?
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100-250 Amino Acids
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What is the substance that is bound by a protein referred to?
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A ligand
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What is the term for the location where the protein associates with a ligand?
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A binding site
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Why does a protein have a high degree of specificity?
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The many weak noncovalent bonds allows for a lock-and-key type fit
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What are proteins produced by the immune system in response to foreign materials?
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Antibodies or Immunoglobulins
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What is the target of an antibody?
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Antigen
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What is an antibody made of?
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Two heavy and two light chains held by disulfide bonds
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What are proteins that utilize ligands in their first step for function?
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Enzymes
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What are the molecules that enzymes bind to called?
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Substrates
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What is the specific term for the binding site of an enzyme?
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Active Site
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What is the term for the inhibition of enzyme activity by the product of the reaction?
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Feedback Inhibition
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What is the regulation when a molecule binds to deactivate an enzyme?
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Allosteric Regulation
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What type of regulation utilizes protein kinases and protein phosphatases?
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Protein Phosphorylation
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What is an example of protein phosphorylation regulation?
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GTP-binding proteins
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What is the control center of the cell?
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Nucleus
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Who was the first to isolate the nucleus?
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Miescher
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Who identified the base, sugar, and phosphate nucleotide unit?
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Levene
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Who performed the experiment with smooth and rough streptococcus pneumoniae on mice?
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Griffith
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Who identified DNA as the transforming principle?
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Avery-MacLeod-McCarty
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Who showed that DNA is the genetic material of the T2 phage?
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Hershey and Chase
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Describe the Avery-MacLeod-McCarty experiment
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They separated out all of the molecules of the cell, and found that only DNA (not RNA, protein, lipid, nor carbohydrates) would transform a rough strain into a smooth strain
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Who first came up with the idea of molecular modeling without exact knowledge of coordinates?
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Pauling and Corey
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What are the two purines?
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Adenine and Guanine
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What are the two pyrimidines?
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Thymine and Cytosine
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What is the most important function of chromosomes?
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To carry genes
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What are the two phases of the cell cycle?
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Interphase and M-Phase
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What phase of the cell cycle does chromosome duplication occur?
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Interphase
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What types of bases are replication origins rich in?
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A=T base pairs
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What does DNA do when the cell hits M-Phase?
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Condenses to form mitotic chromosomes
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What is the DNA region required for orderly separation?
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Centromere
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What is the complex of proteins with nuclear DNA?
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Chromatin
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What are the packing proteins for DNA?
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Histones
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What is the first and most fundamental level of chromatin packing?
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The Nucleosome
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What does the packing of the nucleosome rely on?
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Histone H1 Protein
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What are the extended portions of interphase chromosomes called?
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Euchromatin
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What are the condensed portions of interphase chromosomes called?
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Heterochromatin
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How do packed genes get expressed?
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Chromatin remodeling complexes and chemical modification of histones
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At what speed does DNA replication occur?
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1000 nt/sec
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What is the central enzyme of the replication machine?
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DNA Polymerase
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About how many DNA polymerases are found in Eucaryotes?
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About 15
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What are the Y-shaped junctions during replication called?
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Replication Forks
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What enzyme cleaves mispared nucleotides?
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Nuclease
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Which direction does proofreading take place?
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3' - 5'
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About how many times does DNA polymerase make an error?
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About one error per 10^7 nt pairs
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What initializes the binding of DNA polymerase?
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an RNA Primer
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What is the enzyme that synthesizes the RNA primer?
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Primase
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What erases the old RNA primer from the okazaki fragments?
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RNA nuclease
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What seals the nicks of the Okazaki fragments?
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DNA ligase
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What molecule facilitates the opening of the DNA double helix?
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DNA Helicase
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What molecule stablizes the open DNA?
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Single Stranded Binding Proteins
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What keeps the polymerase attached to the template?
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Sliding Clamps
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What molecule hydrolyzes ATP each time it locks a sliding clamp around the DNA?
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Clamp Loader
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What allows the lagging strand to be completed by DNA polymerase?
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Telomerase
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What is the backup system to repair mistakes in DNA replication?
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DNA Mismatch Repair System
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What are permanent changes to DNA?
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Mutations
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What type of DNA damage results in the loss of purine bases (A,G)?
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Depurination
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What is the result of depurination?
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Results in gaps in the double helix
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What type of DNA damage is the loss of amino groups from cytosine?
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Deamination
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What is the result of deamination?
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The change of cytosine to uracil
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What is the result of ultraviolet DNA damage?
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The production of thymine dimers
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What is the most common mean of repairing double-strand breaks?
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Nonhomologous End-Joining
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What is the disadvantage to nonhomologous end-joining?
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It sacrafices information contained at the injury site
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When does homologous recombination occur?
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Shortly after DNA replication
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What is the repair mechanism utilized with genetic information provided by an entirely separate DNA duplex is used to repair a break accurately?
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Homologous Recombination
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What is the advantage of homologous recombination?
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It allows for the flawless repair of DNA strand breaks
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What are short sequences of DNA that can move from one position to another within the genome?
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Mobile Genetic Elements
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What do MGE's provide to the genome?
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Genetic Variation
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What are transposons, retrotransposons, insertion sequences, plasmids, and bactriophase elements?
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Mobile Genetic Elements
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Who discovered Mobile Genetic Elements?
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McClintock
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What type of transposons are unique to eucaryotes?
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Retrotransposons
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What are the most common transposons in bacteria?
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DNA-only transposons
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What is the process name when DNA -> RNA?
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transcription
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What is the process when RNA -> Protein?
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translation
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What does the extra OH group in RNA do to the molecule?
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It makes RNA less stable and more susceptible to hydrolysis
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What allows RNA to fold into a three dimensional molecule?
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The single stranded nature allows for base-pairing with complementary sequences
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What types of RNA are genes and not translated into a protein?
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non-coding RNA
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In what direction does transcription take place?
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5'-3'
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What are the enzymes that carry out transcription called?
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RNA polymerases
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What are the three stages of transcription?
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Initiation
Elongation Termination |
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What is the "start transcribing" signal in a nucleotide sequence called?
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Promoter
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What is a component of a promoter region?
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TATA box
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What recognizes the TATA box?
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Transcription Factors
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What TF is essential for elongation to occur after binding?
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TFIIH
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Does RNA polymerase require a primer?
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No
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Does RNA polymerase have proofreading capability?
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Sleight
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What stops the RNA synthesis and begins termination?
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A terminal Sequence
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What are the two RNA processing steps for mRNA?
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5' G Capping
Poly-A Tail Addition |
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What does the RNA processing do for the mRNA strand?
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It increases the stability of mRNA and helps transport it out of the nucleus
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What is added to the 5' end of mRNA?
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A guanine nucleotide with a methyl group
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About how many Adenine nucleotides are added to the poly-A tail of mRNA?
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150-200
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What is the process where introns are removed and exons are stitched together?
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RNA splicing
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When does RNA splicing take place?
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After capping
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How does the cell determine which parts of the mRNA are introns?
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Each intron has short nucleotide sequence cues
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What structure is formed when splicing machinery cuts out the introns?
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A lariat Structure
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What carries out RNA splicing?
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Spliceosome
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What forms the core of the spliceosome?
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small nuclear ribonucleoprotein particles (snRNPs)
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Where does transcription take place?
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Inside the nucleus
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Where does translation take place?
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In the cytoplasm
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