Ch 2 Text 5

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Ch 2 Text 5
2014-08-31 21:39:36
Test One
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  1. o   To determine the relation between the amino acid sequence and the conformation, __ planned to destroy the structure of ribonuclease and try to restore it
    §  Agents like __ disrupt __ because they do what?
    §  Most polypeptide chains devoid of __ take on a __ in 8 M urea or 6 M guanidinium chloride
    • Christian Anfinsen
    • urea
    • noncovalent bonds
    • replace water as the solvating molecule and disrupt bonds
    • cross-links
    • random-coil configuration
  2. §  These conditions promote __
    · For ribonuclease,  once freed from urea, what happened?
    §  This experiment showed that what? 
    • denaturation
    • it eventually regained an active form by having sulfhydryl groups being oxidized by airà refolded and the physical/chemical properties were restored
    • the information needed to specify the catalytically active structure of rionuclease is contained in its amino acid sequence· SEQUENCE SPECIFIES CONFORMATION
  3. §  A different result was obtained when reduced ribonuclease was reoxidized while in 8 M urea and the prep was dialyzed to remove the urea; what was the result?
    · Why? __
    it only had 1% enzymatic activity

    The wrong disulfides formed pairs in ureas
  4. o   Although there are __ different ways of pairing __cysteine molecules to form __, only one is __. The __ are termed__.
    • 105
    • eight 
    • four disulfides
    • enzymatically active
    • 104 wrong pairings
    •  “scrambled” ribonuclease
  5. What did Alfinsen find regarding the scrambled ribonuclease?
    it converted into fully active, native ribonuclease when trace amounts of beta-mercaptoethanol were added because it catalyzed the rearrangement of disulfide pairings until the native structure was regained in about 10 hours
  6. §  This process was driven by the __ as the scrambled conformations were converted into the stable, native conformation of the enzyme
    ·         The native __ of ribonuclease thus contribute to the stabilization of the thermodynamically preferred structure
    • decrease in free energy
    • disulfide pairings
  7. §  For many proteins, this same refolding is seen; others, the refolding process does not proceed efficiently. They become tangled and form aggregates.
    · Inside cells, proteins called __block such illicit interactions
  8. o   Amino acids have different propensities for forming __(3)
    §  What determines whether a particular sequence forms an alpha helix, a Beta strand, or a turn can be viewed in the __
    · Residues such as alanine, glutamate, and leucine tend to be present in __, whereas valine and isoleucine are present in __. Glycine, asparagine, and proline have a propensity for being present in __.
    • alpha helices, beta sheets, and beta turns
    • frequency of occurrence of particular amino acid residues in the secondary structures
    • alpha helices
    • Beta strands
    • turns
  9. Preferences are due to four things. 
    o   Alpha helix is the default conformation. And, branching at the beta-carbon atom, as in valine, threonine, and isoleucine, tends to destabilize alpha helices because of steric clashes; they fit better in beta strands
  10. Preferences are due to four things. 
    o   Serine, aspartate, and asparagine tend to disrupt alpha helices because the side chains contain hydrogen-bond donors or acceptors in close proximity to the main chain, where they compete for main-chain NH and CO groups
  11. Preferences are due to four things. 
    o   Proline disrupts both alpha helices and beta strands because it lacks an NH group and because its ring structure restricts its phi value to near 60 degrees
  12. Preferences are due to four things. 
    o   Glycine fits into all structures and does not favor helix formation
  13. §  It is hard to predict the preferences of secondary structure, especially since conformational preferences of amino acid residues are not __

    · Also, some peptide sequences have been found to do what? 
    • tipped all the way to one structure
    • adopt one structure in one protein and an entirely different structure in another
  14. · Hence, some amino acid sequences do not uniquely determine __.
    · Tertiary interactions may be decisive in __
    §  Protein structure has evolved to __
    • secondary structure
    • specifying the secondary structure of some segments
    • fit a particular environment
  15. o   For many proteins, a comparison of the degree of __ reveals a sharp transition from the folded to the unfolded form, suggesting that only these two conformational states are present to any significant extent
    unfolding as the concentration of denaturants increases
  16. §  The sharp transition suggests that protein folding and unfolding is an “__” process that results from a __
    · Conditions that lead to the disruption of any part of a protein structure are likely to do what?
    • all or none
    • cooperative transition
    • unravel the entire protein
  17. §  Cooperative folding can be illustrated by considering the contents of a protein solution under conditions corresponding to the middle of the transition between the folded and the unfolded forms, when the protein is “half folded." What is viewed at this point?
    Yet, no half folded proteins exist. Instead, there is a 50/50 mix of fully folded and fully unfolded
  18. o   Although it appears to exist in only two forms, the simple two-state existence is __at a molecular level. Even simple reactions go through __, and so a complex molecule like a protein cannot simply do what?
    o   __ must exist between the native and denatured state
    • impossible 
    • reaction intermediates
    • switch from a completely unfolded state to the native state in one step
    • Unstable, transient intermediate structures
  19. o   Proteins fold by __ rather than __
    §  The difference between calculated and actual folding times is called __, which reveals that __; instead, they must follow at least a __
    progressive stabilization of intermediates rather than by random search

    Levinthal’s paradox

    proteins do not fold by trying every possible conformation

    partly defined folding pathway consisting of intermediates between the fully denatured protein and its native structure
  20. §  Instead of this random idea, there is cumulative selectionExplain it.
    §  The essence of protein folding is the tendency to __
    the first try employs a completely random search, whereas, in the second, partly correct intermediates are retained

    retain partly correct intermediates
  21. · First, the criterion of correctness is not a residue-by-residue scrutiny of conformation by an omniscient observer but rather the __
    · Second, proteins are only __
    o   The interactions that lead to cooperative folding can __
    • total free energy of the transient species
    • marginally stable

    stabilize intermediates as structure builds up
  22. §  Thus, local regions that have significant structural preference, though not necessarily stable on their own, will tend to __ and, as they form, can interact with one other, leading to increasing stabilization
    ·         This conceptual framework is often referred to as the __
    o   A protein follows a __rather than a __pathway in its transition from an unfolded to the native state
    • adopt their favored structures
    • nucleation-condensation model
    • general 
    • precise
  23. What is the funnel analogy?
    The wide rim of the funnel represents all the combos that can occur. As the free energy of the protein molecules decreases, the proteins have fewer conformations. The bottom is the well-defined conformation
  24. o Predicting the 3D structure is challenging. There are two approaches right now. 

    What is the first?
    §  Ab initio prediction: predicts amino acid sequence folding without prior knowledge about similar sequences in protein structures. Computers are used to figure out the folding with the least free energy
  25. What is the difficulty with the first prediction method?
    · Difficulty: there’s a vast number of possible conformations; the marginal stability of proteins, and the subtle energetics of weak interactions in aqueous solution
  26. o Predicting the 3D structure is challenging. There are two approaches right now. 

    What is the second?
    • §  Knowledge-based methods: amino acid sequence of unknown structure is examined for compatibility with known protein structures or fragments therefrom
    • · Match= known structure used as initial model
  27. o   Some proteins are inherently __and can exist in __
    §  One may result in __; another from __
    §  Examples:
    · __: do not have a discrete 3D structure under physiological conditions. 50% of eukaryotic proteins have at least one unstructured region greater than 30 amino acids in length. 
    • unstructured 
    • multiple conformations
    • protein aggregation
    • pathological conditions
    • Intrinsically unstructured proteins (IUPs)
  28. o   These unstructured regions are rich in __ with few __--> assume a defined structure on interaction with other proteins
    §  One protein can assume different structures and interact with different partners, yielding different biological functions
    o   __are especially important in __ and __
    • polar and charged amino acids with few hydrophobic residues
    • IUPs 
    • signaling and regulatory pathways
  29. · __: exist in an ensemble of structures of approximately equal energy that are in equilibrium
    o   Small molecules or other proteins may bind to a particular member of the ensemble, resulting in a __
    Metamorphic proteins

    complex having a biochemical function that differs from that of another complex formed by the same metamorphic protein bound to a different partner
  30. §  Example: the __ are signal molecules in the immune system that bind to receptor proteins on the surface of immune-system cells, instigating an immunological response
    cytokine lymphotactin (cytokines)
  31. ·         __exists in two structures: one is characteristic of __(three-stranded beta sheet and a carboxyl-terminal helix), which binds to its receptor and activates it; the other is an __, which binds to glycosaminoglycan
    • Lymphotactin 
    • chemokines 
    • identical dimer of all Beta sheets
  32. o   Protein misfolding and aggregation are associated with some neurological diseases
    §  The diseases result in the __, called __ or __; and, the diseases are called __
    • deposition of protein aggregates
    • amyloid fibrils or plaques
    • amyloidosis
  33. · A characteristic feature of amyloidosis is that __. 
    What happens to teh correctly folded one?
    normally soluble proteins are converted into insoluble fibrils rich in beta sheets

    The correctly folded one gets pulled into the incorrect form by the incorrect form despite its slight marginal stability over the incorrect form
  34. §  The agents causing certain diseases and are similar to viruses but only containing proteins are called __, which are composed largely or completely of a __
    • prions
    • cellular protein called PrP, which is normally present in the brain
  35. o   The structure of normal PrP contains __
    o   In infected PrP, there is evidence that some parts that were __ have been converted into __
    §  The Beta-strands of largely planar monomers __on one another with their __ tightly interwoven; these fibrous protein aggregates are referred to as __forms 
    extensive regions of alpha helix and relatively little beta-strand structure

    alpha-helical or turn conformations

    Beta-strand conformations


    side chains

  36. §  With the realization that the infectious agent in prion diseases is an aggregated form of a protein that is already present in the brain, a model for disease transmission emerges
    · Protein aggregates built of abnormal forms of PrP act as __to which other PrP molecules attach and can thus be transferred among organisms

    §  __ are also seen in human diseases, such as Alzheimer’s 


    Amyloid plaques
  37. §  How do such aggregates lead to the death of the cells that harbor them? 
    · Theory: large aggregates themselves are not dangerous, but small may damage cell membranes
  38. o   Many proteins are covalently modified, through attachment of groups other than amino acids, to augment their functions

    Explain what addition of acetyl and hydroxyl groups does.
    • §  Acetyl groups: attached to the amino termini of many proteinsà more resistant to degradation
    • §  Addition of hydroxyl groups to proline residuesà stabilizes fibers of newly synthesized collagen
  39. Explain what addition of sugars and fatty acids do?
    • §  Addition of sugars makes the proteins more hydrophilic and able to participate in interactions with other proteins
    • §  Addition of a fatty acid: makes a more hydrophobic protein
  40. §  Hormones alter activities of enzymes by doing what?: __ and __ are the most ubiquitous modified amino acids in proteins
    stimulating the phosphorylation of the hydroxyl amino acids serine and threonine

    phosphoserine and phosphothreonine
  41. §  Growth factors like insulin act by triggering the __ of the __ of __ to form __
    · The __ on these three modified amino acids are readily removed; thus, the modified amino acids are able to act as __ in __
    phosphorylation of the hydroxyl group of tyrosine residues


    phosphoryl groups

    reversible switches in regulating cellular processes
  42. o   Other special groups are generated by chemical rearrangements of __ and sometimes the __

    o   Many proteins are __ and __ after synthesis
    • side chains
    • peptide backbone
    • cleaved and trimmed