Membranes: Integral Proteins

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Membranes: Integral Proteins
2013-09-21 13:49:25
Cell Bio

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  1. a.      can be __at the surface, __ or __ involved in movement, or __that transfer electrons during processes of __ and __
    • receptors 
    • channels or transporters
    • agents 
    • photosynthesis and respiration
  2. a.      amphipathic
                                                                  i.      those within bilayer: __
                                                                ii.      __ in __domains form__ with the __ of the bilayer, which seals the protein into the lipid “wall” of the membrane
    • hydrophobic
    • amino acid residues
    • transmembrane 
    •  van der Waals interactions
    • fatty acyl chains
  3. 1.      as a result, the __ of the membrane is preserved, the __is anchored within the bilayer, and the protein is brought into direct contact with surrounding __molecules
    • permeability barrier
    • protein 
    • lipid
  4. a.      most lipids that make contact with a __domain are __bystanders and rapidly __with other lipid molecules in the bilayer
    b.      certain sites on the membrane protein surfaces do form important __ with lipid molecules
    • transmembrane 
    • passive 
    • exchanged 
    • functional interactions
  5.                                                               i.      the portions that project into either the cytoplasm or extracellular space are like __
    1.      __surfaces that interact with __ substances at the edge of the membrane
    a.      in some, the __domains are devoid of __ molecules, whereas others allow __ to go deep into protein’s __regions
    • globular proteins
    • hydrophilic 
    • water-soluble
    • transmembrane 
    • water
    • aqueous solvent
    • membrane-embedded
  6. 1.      several large families of membrane proteins have __ for passage
    a.      lining= __
    • interior channel
    • hydrophilic residues
  7. a.      distribution
                                                                  i.      this concept of membrane penetration came from __. Explain that

    • freeze-fracture replication
    • tissue frozen and struck ith knife bladeà 2 piecesà metals deposited on surface to form shadowed replica
  8. What does replica of a freeze fracture look like?
    a.      replica resembles road strewn with pebbles, which are membrane-associated particles
  9. 1.      since the fracture plane is through center, __are seen that extend halfway
    a.      when it reaches a particle, it does what?
                                                                                                                                          i.      each protein __with __, leaving __ on other half
    • integral proteins 
    • goes around, not cracks it
    • separates 
    • one half of the membrane
    • a pit
  10. a.      Isolation
                                                                  i.      difficult due to __form
    1.      removal requires __, which are __, with a __ and __
    • soluble 
    • detergent
    • amphipathic
    • polar end
    • nonpolar hydrocarbon chain
  11. a.      __can sub for phospholipids in __ while rendering them __in aqueous solution
                                                                                                                                          i.      once proteins have been __by __, various analyses can be carried out to determine the protein’s __(3)__, etc. 
    • detergents 
    • stabilizing integral proteins
    • soluble 
    • solbilized 
    • detergent
    • amino acid composition, molecular mass, amino acid sequence
  12.                                                               i.      hard to isolate crystals for __, but one fo the first membrane proteins whose entire 3D structure was determined by__
    this protein—__—has __subunits with__
    • X-ray crystallography
    •  X-ray crystallography
    • bacterial photosynthetic reaction center
    • three 
    •  11 membrane-spanning alpha helices
  13. True or False:
    most membrane proteins have not been as amenable to crystallization as the photosynthetic reaction center
  14. 1.      among the obstacles, many membrane proteins __(4)__
    • a.      are present in low numbers per cell
    • b.      are unstable in detergent-containing solutions required for their extraction
    • c.       prone to aggregation
    • d.      heavily modified by glycosylation and can’t be expressed as recombinant proteins in other types of cells
  15.                                                               i.      some technical difficulties in __ overcome by new methodologies and laborious efforts
                                                                ii.      in some cases, __versions of a membrane protein are found to be better suited to forming the ordered arrays of molecules that make up a __
    • preparing membrane protein crystals
    • mutant 
    • crystal lattice
  16.                                                               i.      in other ways, __has been achieved by __linking the membrane protein to other molecules, often small __
    1.      these added elements __ and __
    • crystallization 
    • covalently 
    • soluble proteins
    • stabilize the structure of the target protein
    • increase the number of sites on the surface of the protein that can participate in intermolecular contacts required for lattice formation
  17.                                                               i.      Identifying Transmembrane Domains
    1.      __ of its __, which is readily deduced from the __ of an isolated gene
    a.      the segments within the membrane (transmembrane) have simple structure
    • computational analysis
    • amino acid sequence
    • nucleotide sequence
  18.                                                                                                                                       i.      string of about __ that span the core of the lipid bilayer as an __
    1.      chemical strcutre of a single transmembrane helix is __, the major integral protein of the erythrocyte plasma membrane
    • 20 nonpolar amino acids
    • alpha helix
    • 2D structure of glycophorin A
  19. a.      of the 20 amino acids that make up the lone __ of a __monomer, all but three have __
                                                                                                                                                                                                                  i.      exceptions: __(2))
    • alpha helix
    • glycophorin 
    • hydrophobic side chains
    • serine and threonine (noncharged, polar, residues)
  20. 1.      __ may also appear in transmembrane helices, but they tend to be near __ and to be accommodated in ways that allow them to fit into their __
    • fully charged residues
    • one of the ends of the helix
    • hydrophobic environment
  21. 1.      knowing the amino acid sequence of an integral membrane protein, we can usually identify the transmembrane segments using a __, in which each site along a polypeptide is assigned a value that provides a measure of the __of the amino acid at that site as well as that of its neighbors
    • hydropathy plot
    • hydrophobicity
  22. a.      this provides a “__” of the __of short sections of the polypeptide, and guarantees that one or a few polar amino acids in a sequence do not alter the profile of the entire stretch
    • running average
    • hydrophobicity
  23. hydrophobicity of amino acids can be determined using
    1) __
    2) __
    • 1.      lipid solubility 
    • 2.      energy required to transfer them from a nonpolar medium into an aqueous medium
  24. 1.      transmembrane segments are usually identified as a __ that extends well into the __side of the spectrum
    • jagged peak
    • hydrophobic
  25. a.      a reliable prediction concerning the orientation of the transmembrane segment within the bilayer can be made by examining the __
                                                                                                                                          i.      those parts of the polypeptide at the __ flank of a transmembrane segment tend to be more __ than those at the __ flank
    • flanking amino acid residues
    • cytoplasmic
    • positively charged
    • extracellular
  26. 1.      not all integral membrane proteins contain __
    a.      a number of membrane proteins contain a relatively large channel positioned within a circle of __ organized into a __ and have only been found in the outer membranes of __(3))__
    • transmembrane alpha helices
    • membrane-spanning beta strands
    • barrel
    • bacteria, mitochondria, and chloroplasts
  27. a.      Experimental Approaches to Identifying Conformational Changes within an Integral Membrane Protein
                                                                  i.      to determine which sites within transmembrane domains are accessible to aqueous environment and how this changes as the protein carries out is function, __ can be used by using specific changes into the gene that encodes the protein
    site-directed mutagenesis
  28. a.      determining __ between specific amino acids in a membrane protein is another approach to learning about dynamic events that occur as a protein carries out its function
    spatial relationships
  29.                                                               i.      one way to learn distance between selected residues in a protein is to introduce __ whose properties are sensitive to the distance that separate them
    chemical groups
  30. 1.      __are chemical groups that contain an __, which produces a characteristic spectrum when monitored by a technique called __
    • nitroxides 
    • unpaired electron
    • electron paramagnetic resonance spectroscopy
  31. a.      a __group can be introduced at any site in a protein by first __that site to a __and then attaching the __to the__ group of the __residue
                                                                                                                                          i.      this was used to discover the conformational changes that occur in a membrane protein as its channel is opened in response to changes int eh pH of the medium
    • nitroxide 
    • mutating 
    • cysteine 
    • nitroxide 
    •  –SH
    • cysteine
  32. a.      a technique called __can also be used to measure changes in the distance between labeled groups within a protein