Molecular Text 3.1

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Molecular Text 3.1
2015-01-20 12:08:30
Test One
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  1. a.       atoms behave almost as if they were __; the requirement that no two atoms overlap does what?
                                                                  i.      these constraints restrict __
    b.      the folding of a protein chain is also constrained by many different __
                                                                  i.      The three types of weak bonds are __, __, and __
    hard spheres with a definite radius (their van der Waals radius)

    limits greatly the possible bond angles in a polypeptide chain

    possible 3D arrangements of atoms (or conformations)

    weak noncovalent bonds that form between one part of the chain and another

    hydrogen, electrostatic attractions, and vdW attractions
  2.                                                               i.      Another weak force also plays a part in the shape of a protein: __, which causes hydrophobic molecules to __
    1.       Nonpolar amino acids __in the interior of the molecule, avoiding __
    2.       Polar groups are located near __; polar amino acids within the protein are usually __ to other polar amino acids or to the polypeptide backbone
    • hydrophobic interactions
    • clump together to minimize the disruptive effect on the hydrogen-bonded network of water molecules

    • cluster 
    • contact with water

    • the outside of the molecule
    • hydrogen-bonded
  3. a.       Most proteins have a specific __, determined by the __
                                                                  i.      Some chemicals disrupt __ holding the chain together, __the protein. When it is removed, the protein __, indicating that the __ contains all the information needed for specifying the 3D shape of a protein
    1.       There is __, but it may change slightly when the protein interacts with other molecules in the cell
    • 3D conformation
    • primary sequence of amino acids
    • noncovalent interactions
    • denaturing 
    • refolds (renatures) into its original conformation
    • amino acid sequence
    • one single conformation
  4.                                                               i.      Molecular chaperones __ and __, helping them reach their most energetically favorable folding pathway.
    1.       Chaperones prevent the __
    b.      Proteins have distinct protein domains,w hich are __
    assist in protein folding and bind to partly folded polypeptide chains

    hydrophobic regions from associating with each other

    structural units that fold more or less independently of each other
  5. i. There are many ways to view a protein:
    • 1.       A polypeptide backbone model
    • 2.       A ribbon model
    • 3.       A wire model with side chains
    • 4.       A space filling model
  6. a.       Two common folding patterns are the __ and the ___; and, they result from __ in the polypeptide backbone without involving __
                                                                  i.      Beta sheets can be __ or __, each section running in the direction opposite its immediate neigibor
    1.       Both are _, held together by __
    alpha helix and the beta sheet

    hydrogen bonding between NH ad C=O groups

    side chains

    parallel or antiparallel


    hydrogen bonds
  7.                                                               i.      Alpha helices are generated when __
    1.       Alpha helices are abundant in __ and __
    Some alpha helices wrap around each other to form __
    a single polypeptide chain twists around on itself to form a rigid cylinder; a hydrogen bond forms beween every fourth peptide bond, linking C=O and NH

    transport proteins and receptors

  8. a.       The four levels of organization of proteins: __
                                                                  i.      A protein domain is a __
    1.       A domain usually contains between __ and __ amino acids, and it is the molecular unit from which many larger proteins are constructed
    primary, secondary, tertiary (3D organization), and quaternary (complete structure)

    substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure

    40 and 350 amino acids
  9. 1.       Different domains have different functions
    a.       The smallest protien molecules contain only a __, whereas larger proteins can contain as many as several dozen
    b.      Only a small faction of conceivable polypeptide chains would adopt a __. Yet, a majority of proteins present in cells adopt __. __ is responsible
    single domain

    single, stable 3D conformation

    unique nd stable conformations

    Natural selection
  10.                                                               i.      A protein with an unpredictably variable structure and biochemical activity is __. Therefore, they’d be eliminated by __
                                                                ii.      Only one conformation is __; and, its chemical properties enable the protein to do what? 
    1.       Proteins are so precisely built that one change in amino acid can __ 
    unlikely to help the survival of a cell that contains it

    natural selection

    extremely stable

    perform a particular catalytic or structural function in the cell

    disrupt the structure of the whole molecule and its function
  11. a.       __ can be duplicated, allowing one gene copy to evolve independently to perform a new function. This led the classification of proteins into families
                                                                  i.      Example: serine proteases= __ enzymes that include the digestive enzymes __; similar in their __.
    1.       Despite their similarity, tey have different __ and __
    Functional genes


    chymotrypsin, trypsin, and elastase

    catalytic triad

    enzymatic activity 

    cleave different protiens
  12.  i.      Generally speaking, the structure of the different members of a protein family has been more __ than has the __.
    1.       The difference in family members were evolutionary because they resulted in __, giving the individual family members the __ they have today
    a.       Some changes are __
    b.      Some nutations were __and altered the 3D structure enough to harm them. These were lost 
    • highly conserved
    • amino acid sequence
    • useful changes in biological activity
    • different functional properties
    • neutral
    • deleterious
  13.  i.      Protein families are recognized when what?
    1.       __are most proteins in each family that have evolved to perform different functions
    a.       __are corresponding proteins in different organisms
                                                                ii.      To find protein sequences using databases, there must be a __ match
    • the genome of an organism is sequenced
    • Paralogs 
    • Orthologs 
    • 30%
  14. a.    Multidomain proteins are believed to have originated from their __, creating a new gene. Novel binding surfaces have often been created at the __, and many of the __ where proteins bind to small molecules are found to be located there.
                                                                  i.      In __, many large proteins have evolved through the joining of preexisting domains in new combinations

                                                                ii.      Some protein domains have been mobile; they are __
    accidental joining of the DNA sequences that encode each domain

    juxtaposition of domains

    functional sites

    domain shuffling

    protein modules
  15. a.       Loops that arise from the backbone are used to do what? 
    b.      Another feature of protein domains is their __. When the structure is duplicated, they can be linked to form __, which are common in __ and in __ 
    form binding sites for other molecules

    ease of integration into proteins

    extended structures

    ECM molecules and in extracellular portions of cell-surface receptor proteins
  16. a.       Our chromosomes contain only about 25,000 genes, which is no more complex than a mustard weed
                                                                  i.      __ has given rise to many novel combinations of protein domains, with the result that there are nearly twice as many combinations of domains found in human proteins as in worm or fly
    Domain shuffling
  17. a.       The same weak noncovalent bonds that enable a protein chain to fold into a specific conformation also allow proteins to__.

    What is a binding site?

     Each polypeptide chain in such a protein is called a __
    bind to each other to produce larger structures in the cell

    Any region of a protein’s surface that can interact with another molecule through sets of noncovalent bonds; It recognizes the surface of a second protein, the tight binding of two folded polypeptide chains at this site creates a larger protein molecule with a precisely defined geometry.

    protein subunit
  18. a.       In the simplest case, two identical folded polypeptide chains bind to each other in a head-to-head arrangementà __
    b.      Some proteins can form __that may span the entire length of the cell; a long chain of identical protein molecules can be constructed if each molecule has a __
    c.       Helices are so common bcause __
    • dimer
    • filaments 
    • binding site complementary to another region of the surface of the same molecule

    straight lines are very rare and helices allow a specific fit and twist
  19. a.       Other proteins are __and fold into a compact shape like a ball with an irregular surface
                                                                  i.      __are usually globular
                                                                ii.      Other proteins have roles in the cell that require each individual protein molecule to span a large distance, called __
    1.       __ are stable and are __ of two identical subunits with __, which is capped at each end by __ containing binding sties
    a.       This allows a __
    • globular 
    • Enzymes 
    • fibrous proteins
    • Keratin filaments
    • dimers
    • long alpha helices of each subunit forming a coiled-coil
    • globular domains
    • ropelike intermediate filament
  20. 1.       Fibrous proteins are usually in the __
    a.       Collagen is another example with __, each containing the __, allowing winding around one aother

    3 polypeptide chains

    nonpolar amino acid glycine at every third position
  21. a.       Many proteins can have large amounts of __
                                                                  i.      __is formed as a highly disordered polypeptide, which is essential to its function, which allows __that can be what?
                                                                ii.      These chains are frequent and have important functions ; these regions allow __, undergoing a structural transition to a __ when the other molecule is bound 
    • unstructured polypeptide chains
    • elastin
    • rubberlike elastic meshwork 
    • reversibly pulled from one conformation to another
    • interaction with other molecules
    • specific folded conformation
  22.                                                               i.      Unstructured regions of polypeptide chain are often used to do what?
    1.       Ex: large scaffold proteins use such flexible regions as __that concentrate sets of __, often confining them to particular sites in the cell
    connect the binding sites for proteins that function together to catalyze a biological reaction


    interacting proteins
  23. 1.       Unstructured regions have a biased amino acid composition: Why? 
    they contain few of the bulky hydrophobic amino acids that normally form the core of a folded protein, being composed instead of a high proportion of the amino acids Gln, Ser, Pro, Glu, and Lys.
  24. a.       To help maintain protein structure, the polypeptide chains in such protiens are often stabilized by __. These can __or __
                                                                  i.      __ are most common and they do not change the conformation of a protein. They just reinforce.
    covalent cross linkages

    tie two amino acids int eh same protein 

    connect different polypeptide chains in a multisubunit proein

    Disulfide bonds
  25. a.       The same principles that enable a protein molecule to associate with itself to form rings or filaments also operate to __—__
                                                                  i.      They are formed by __ of many separately manufactured moelcules
    • generate much larger structures in the cell
    • supramoelcular structures like ribosomes
    • noncovalent assembly
  26.                                                               i.      The advantages of using smaller subunits to build alrger ones are several 
    • 1.       A large structure built from one or a few repeating smaller subunits requires only a small amount of genetic information
    • 2.       Both assembly and disassembly can be readily controlled, reversible processes, because the subunits associate through multiple bonds of relatively low energy
    • 3.       Errors in the synthesis of the structure can be more easily avoided, since correction mechanisms can operate during the course of assembly to exclude malformed subunits 
  27. a.       Some protein subunits assemble into __ in which the subunits are arranged in __,a case occurring in __, which can be converted into a __ or __; this forms the __
    b.      The formation of closed structures, like rings, tubues, or spheres, provides __ because it does what?
                                                                  i.      Small changes in subunit interactions can cause __ or __ as is the case with capsids
    • flat sheets
    • hexagonal patterns
    • lipid bilayers
    • tube or hollow sphere
    • coats of viruses
    • additional stability
    • increases the number of bonds between the protein subunits
    • assembly or disassembly
  28. a.       The information for forming many of the complex assemblies of macromolecules in cells must be contained in the __. Why? Examples are TMV and bacterial ribosomes
    b.      In some proteins, regarding assembly, a long core protein or other macromolecule provides a __that determines the extent of the final assembly
    subunits themselves

    because purified subunits can spontaneously assemble into the final structure under the appropriate conditions

  29. a.       Not all cellular structures held together by noncovalent bonds __. Special enzymes and other proteins perform the function of __, guiding __but not taking part in the final assembled structure