Cell Biology Exam 1-3

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Cell Biology Exam 1-3
2011-12-13 17:54:49
Cell Biology Exam

Cell Biology Exam 1-3
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  1. What are the macromolecules of cells?
    • 1)Carbohydrates
    • 2) Lipids
    • 3) Proteins
    • 4) NucleicAcid
  2. What is the most structurally diverse macromolecule?
  3. Levels of Protein Folding:
    • Primary: sequence of amino acids (polypeptide chain)
    • Secondary: Alpha helix and Beta sheet
    • Tertiary: additional folding and looping of the polypeptide chaind R-group interaction
    • Quantunary: more than 1 polypeptide interacting together to form a protein complex
  4. Alpha helix:
    • Helix is a regular structure that resembles a spiril staircase
    • generated by placing many similar subunits next to each other - repeating
  5. An alpha helix is created when a single polypeptide chain turns rigid and a hydrogen bond...
    is made every 4th amino acid, linking the C=O of one peptide bond to the N-H of another
  6. Protein Domain:
    Organizational unit, which is defined as any segment of a polypeptide chain tha can be fold independently into a compact, stable structure
  7. Proteins can be grouped into families because
    When 2 enzymes compare, portions of the amino acid sequence are foudn to be nearly the same
  8. Details about X-Ray Crystallography
    • - No limititaion to size
    • Must be a purified protein --> perfect crystal
    • --> Hit w/ narrow beam of x-ray --> that pattern which is defracted can be read on the computer which will tell you the paticular structure
  9. NMR Spectroscopy
    • 1) Purfied Protein
    • 2) Hit with Different radio frequencies which creates a pattern showing positions of hydrogen bonds
    • 3) Computer Program models it and we can read it and decipher what it all mean

    Size: 4,000 Daltons or less
  10. Enzyme substrate (lose a hyrogen) --> Enzyme product
    ... gain a hydrogen before the product
  11. Membrane proteins are classified as integral or peripheral - describe each
    Integral: strongly associated (embedded) with the membrane (Transmembrane/ membrane associated/ lipid-linked)

    Peripheral: loosely associated with membrane (protein-attached)
  12. Phospholipids are amphipathic which will spontaneously form a closed, spherical bilayer in water
    • Hydrophilic heads outside
    • this is most energerically favorable
  13. Physical Properties of membranes are affected by their fluidity - what three factor influence fluidity?
    • 1) Saturated (decrease in fluidity) and Unsaturation (increase in fluidity)
    • 2) Temperature (increase temperature = increase fluidity)
    • 3) Tail Length (fatty acid tail length) - increase shorter fatty acid --> increase fluidity
  14. The lipid bilayer is often called a fluid mosaic?
    The bilayer is very thin and a phospholipids, which are amphipathic (dual functional ends). This refers to the hydrophilic head (orients toward the water) and hydrophobic tail (orients toward the middle/each other) Bilayer also has proteins.
  15. Why are cell membranes asymmetrical?
    • Cell membranes are symmetrical: distinct "inside" and "outside" faces - different on each layer - not symetrical
    • Glcyolipid on outside (external)
    • Monolayer is seperate/different than another
    • Cholesterol equally in both up and bottom
  16. The plasma membrane is reinforced by the...
    cell cortex (inside)
  17. Disorder increases when useful energy that could be used to do work is used as heat

    Delta G measures...
    the amount of disorder created in the universe

    (2nd law)
  18. How to get an unfavorable reaction to proceed?
    Pair an unfavorable reaction with a favorable - as long as the total delta G is negative :)
  19. What is used in the metabolic pathway to drive unfavorable reactions?
  20. There is energy stored in the nucleoside triphophates used to make polymers...this means there is energy in the ....
    • energy in the phosphate bonds -->
    • assemble to make a polymer
    • Hydrolysis leads to breaking of water
  21. Proteins are made of what
    amino acids
  22. Proteins are made of amino acids and are the ______ to our DNA
    Instructions !

    Proteins contain specific sequences of nucleotides that serve as coding for direction for how to synthesize proteins

    = genes in the genome
  23. Two ends of a polypeptide chain:
    Amino (N) && Carboxyl (C)
  24. Proteins folding involves:
    A protein final 3D shape/configuration is stablized by ....
    • 1) Noncovelent forces/bonds
    • 2) Hydrophobic forces which help to fold proteins
    • - Membrane is filled with hydrocarbon so the outside is hydroPHOBIC
    • the inner core is hydroPHILIC
  25. Protein Domain invovles :
    an organizational unit, which is defined as any segment of a polypeptide chain that can fold independently into a compact, stable structure
  26. Proteins have the ablity to bind specifically to other molecules as well as...
    allowing proteins to as a catalyst, structural support, singal receptors
  27. Proteins bind to a molecule called the ____
    Proteins bind its ligand with high specify and high infinity
    Proteins function by binding other

    molecules: a ligand is the molecule a protein binds
  28. Mechanisms enzymes have to increase the rate of the
    • a)bring really close together (enzyme pulls the two substrates together)
    • b)creates a more favorable positive/negative
    • charged environment
    • c)straining bonds (force)
  29. Lysosome: the classic enzyme
    • Natural Antibodic
    • - helps protect mouth, eyes from bacteria
    • Reaction medicates hydrolsis of polysaccharide in the cell wall of bacteria
    • Cell wall helps prevent trigger pressure from too much pressure
  30. Feedback inhibition (you made enough, turns activity off)
    Phosphorlation/Dephosphoryalation (+/- a Pi group)
    Nucleotide Binding & Hydrolysis (GTP/ATP)
  31. Roles of the Plasma Membrane:
    • - Fight delta G by creating order
    • - Mediates contct with the enviorment
    • - Mediates movement
  32. Components of the Cell Membrane:
    • Lipids : phosolipid
    • sterols (cholesterol)
    • glycolipids (sugar fatty acid)
    • Protein
  33. Major component of the cell membrane is the phospholipid, which is amphipathic meaning...
    Amphipathic: hydrophilic head group orients toward the water, while hydrophobic tails orients toward each other
  34. Phosphatidyl choline the the most common?
  35. Integral proteins span the membrane with common motifs which are (name thee 2)
    • Alpha Helix: spiril
    • Beta Barrel: sheet wraps so much turns into tube
  36. Experiment that lipids and proteins diffuse freely:
    • Mouse cells and human cells in a glass - shaken together...Would the mix? Yes
    • Proteins are fluid and can move
    • - Mobility
  37. Describe the structure of a bilayer - why is it often called a fluid mosaic?
    • Different variety of components in the bilayer
    • Major component: phospholipids, which are amphipathic (dual fuctional ends)
    • Hydrophilic head (orients toward the water)
    • Hydrophobic tail (orients toward each other inside)
    • Bilayer also had proteins
  38. Cell Membrane is asymmetric which refers to the "inside" and "outside" layer are different.
    • The different groups/heads on each side give rise to different functions.
    • Hydrophilic outside/ Phobic internally
    • Bilayer = ampathetic refers to membrane philic/phobic
    • Glycolipids = external monolater, while cholesterol is distrubuted equally both top and bottom.
  39. Cell Membrane Truths:
    • 1) Phospholipid bilayer spontaneously close in on themselves to form sealed compartments
    • 2) Membranes serve as higly selective barriers in cells
    • 3) Lipid Bilayer is 2 dimentional fluid
    • 4)Membrane fluidity is essential for cells to live, grow, reproduce
  40. Patch Clamp: recording used to monitor channel activity
    Measure changes in electrical current – used to study ion movement and on channels measure how long current is open
  41. It is important for a cell to avoid being torn apart by having an equal amount of + and - charges
    What controls the concentration differences?
    • membrane transport proteins
    • lipid bilayer itself
  42. What are cells permeable to?
    Permeable: can move across – hydrophobic molecules – gas:CO2, O2

    • Hydrophobic molecules – small nonpolar
    • Steroid: hormones, gases (CO2,O2)
    • Small polar molecules (uncharged)
    • The interior of the lipid bilayer is hydrophobic, so that is what will diffuse the quickest and more readily.

    Ion concentrations inside the cell vary differently from those outside
  43. What are cells Impermeable to?
    • not able to pass through the lipid bilayer
    • Large polar molecules, glucose
    • Ions, charged molecules: H+, Na+, ATP, amino acid
    • Impermebles need/require transport proteins
  44. Different types of proteins used to transport molecules across cell membranes include:
    • Channel: faster, allows molecules to move through selective for: size, charge
    • When open, continuous channel as molecules run through -- gated/discriminates

    Carrier: slower, more specific, Highly specific, depends on bind sites
  45. What influences the movement of substances across the membrane?
    Size, Charge and polarity, specific roles
  46. What is membrane potential and how does it work?
    • most cells have a voltage (charge)
    • Difference in potential exerts a force on any molecules that holds a charge
    • Inside (cytoplasmic side) = negative-ish
    • outside: more positive ish
  47. Na and K in passive transport
    Na+ is higher in concentration outside the cell as it tends to enter the cell if given the opprotunity, while K+ is higher in concentraion inside the cell and will try to rush out
  48. Sodium- Potassium Pump is an example of Active Transport - How does it occur?
    • 1) ATP driven Na+ binds to protein which stiumlates phosphorylation
    • 2) Phosphorylation causes the protein concentration/shape to change
    • 3) Change in shape expels Na+ out, K+ binds in
    • 4) K+ binding in triggers release of a phosphate group
    • 4) Loss of Pi, restores orignal conformation
    • 5) K+ is released, Na+ sites are recycled
  49. three ways cells carry about active transport:
    • 1) Cotransporters: concentration gradient of one substance used to drive the active transport of another
    • 2) ATP: couple uphill transport to hydrolysis of ATP
    • 3) Light: energy uphill transport from light
  50. Describe the Na+/K+ pump
    • ATP-driven Na+ pump (in animals cells) hydrolyzes ATP to ADP to transport Na+ out of the cell.
    • Proteins couple outward transports of Na+ with the inward transport of K+
    • Burns 30% of energy in cells (3 Na+ and 2 K+)
  51. The Ca2+ pump :
    Movement of Ca2+ is crucial to the cell membrane as calicum is used as a signaling messenger to triger intracellular events --> contraction of muscle cells in the sacroplasmic reticulum
  52. Ca2+ levels have what affect, lead to what?
    Ca2+ is released in our skeleltal muscles/contractions - when a muscle cell is stimulated Ca2+ rapidly floods from the sarcoplasmic reticulum
  53. H+ pump (plants) vs. the Na+/K+ pump (animals)
    • electrochemical gradients of Na+ is generated by the Na+/K+ pump, used to drive active transport of solutes across the plasma membrane
    • ATP-driven Na+ pump in animals cells hyrdolized ATP to ADP to transport Na+ out of the cell
    • (Same Time) outward transport of Na+ and inward transport of K+

    PLANT: H+ symport brings nutrients into cells, helps keep the pH of cytosol neutral, & pH of interior organelle acidic
  54. Different types of proteins involved in vesicular transport?
    • Clathrin-coated vesicles transpot selected cargo from Golgi Apparatus to the outward secretary pathway
    • Clathrin assembles a basketlike network on the surface of membrane

    • Docking & Fusion invovles a class of proteins called SNAREs
    • v-snares interact with t-snares to force fusion of vesicles to target molecule, docking vesicle into place

    Force of SNAREs winding together squeezes out any water molecules that remain trapped between the 2 membranes, allowing their lipids to flow together to form a continous layer
  55. Describe the intermediate filaments of teh cytoskeleton:
    • - strong and dense stable ropelike
    • - good for dealing for mechinical stress
    • - non polar: end are not different
    • - keratin filaments: (skin/hair) epithelial cells - attach to desmosomes
    • - Nuclear Lamins: strengthen the nuclear envelope
  56. Microtubles of the cytoskeleton : breifly describe
    • dynamic instablity (2nm)
    • microtubles are hollow which provide road ways for celluar material to move, microtubles are critical for cells division
  57. Actin Filaments (thinest and most flexable)
    • Actine is a component of the cell cortex and allows cells to crawl as they pull forward
    • When myosin walks on actin = contraction
  58. What are the specalized function for each of the filaments of the Cytoskeleton

    is built on a framework of three types of proteins
    • Actin: cell movement
    • Microtubles: organize cytoplasm of cell; rail road track for motor proteins
    • Intermediate filaments: distrubute mechinacal strss across cells
  59. K+ is kept inside the cell, but there are these leak
    channels which randomly allow K+ to rush out.
    K is positive keeping the inside positive but when it rushes out (+) rushing out, the inside turns more negative (-) also when K+ leaves to the outside, the

    outside becomes more positive
  60. A chemical reaction that occurs spontaneously must have
    negative delta G
    • TRUE
  61. Hydroxyl groups decrease the solubility of sugars in water

  62. Antibodies are proteins produced by the immune system in
    response to foreign molecules

  63. A decrease in saturation of fatty acids tails in lipid
    bilayer would increase the fluidity of the membrane

  64. Glycolipids contain sugars as part of the hydrophilic head
    group of the molecule

  65. The hydrophobic amino acids of a transmembrane protein would
    be found largely in the interior of the folded proteins

  66. Intertwined alpha helices can form a coiled-coil

  67. Lipids in the lipid bilayer readily flip flop in the
    monolayer to the other

  68. A lipid-linked membrane protein would be considered a
    peripheral membrane protein
    FALSE it would be an integraL

  69. Both fatty acids and polysaccharides can be important energy
    stores in the cell

  70. Entropy of a system is a measure of the system’s disorder

  71. Protons and electrons are found in the atomic nucleus of an

  72. Hydrocarbon molecules are polar molecules

  73. Nucleotide hydrolysis allows motor proteins to produce large
    movements in the cells

  74. The distribution of elements in the earth’s crust is very
    similar to the tissue of an animal

  75. Robert Hooke first identified cells in a piece of cork in

  76. Competitive inhibition of protein function involves binding
    of another molecule at a separate site other then the active site

  77. Cholesterol fills spaces between neighboring phospholipids
    making the membrane more flexible

  78. Two atoms that engage in a polar covalent bond will equally
    share a pair of electrons

  79. Allosteric proteins have two or more conformational states

  80. Prokaryotic cells contain internal membrane bound
    compartments called organelles

    • Highly specific for the substrate they bind
    • Speed up the rate of the reaction by lowering AE of a
    • reaction
    • An enzyme’s Km value indicated how effectively the enzyme
    • binds to its substrate
    • Hydrolase is a general term for a group of enzymes that catalyze a hydrolytic
    • cleavage
    • Can be classified into families in which members share a 3D
    • shape/amino acid sequence
    • Two identical polypeptides that assemble together as a
    • larger protein complex would be considered a heterodimer
    • Many proteins are composed of separate functional domains

  83. Three types of bonds which stabilize the structure of
    cytosolic protein
    • Hydrogen bond
    • Ionic bond
    • Van der Waals Forces

  84. Proteins:
    • Proteins are held together by peptide bonds
    • Each type of protein has a unique amino acid sequence that
    • determines both its 3D shape and biological activity
    • Refolding of an unfolded polypeptide is termed renaturation
    • Binding site of a protein contains specific amino acids that
    • form a set of noncovalent bonds only with certain ligands

  85. Carbohydrates:
    • Contain C, H, and O = (CH2O)n
    • Disaccharides are two covalently linked sugar monomers
    • Long chains of sugar molecules called polysaccharides are
    • important storage forms of energy and serve as structural material in cells
    • Smaller oligosaccharides can be covalently linked to lipids
    • to form glycolipids

  86. Fatty Acids
    • Largely Hydrocarbon length 14-24
    • Addition of shorter fatty acid increases fluidity
    • Unsaturated fatty acids have one or more double bonds which
    • form by removal of hydrogen atoms

  87. ATP
    • Serves as energy carrier
    • ATP hydrolysis to ADP and Pi provides energy to drive
    • reactions
    • ATP formed through reaction that release energy such as
    • oxidative breakdown of foods

  88. Energy:
    • Living organism use energy to create order
    • 1st Law of Thermo, energy can only be transferred
    • not destroyed
    • Cells obtain energy by oxidation of organic molecules
    • The primary source of energy for most living organism is the
    • sun