Ch 2 Text 2

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Ch 2 Text 2
2014-08-31 17:06:50
Test One
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  1. o   Proteins are __ formed by linking the __ of one amino acid to the __ of another amino acid, called a __. __is also lost
    §  The equilibrium of this reaction lies to the side of __. Therefore, making peptide bonds requires __

    • linear polymers
    • alpha-carboxyl group
    • alpha-amino group
    • peptide bond or an amide bond
    • Water 
    • hydrolysis rather than synthesis
    • free energy
  2. · They are still quite stable kinetically because the __
    §  Several amino acids joined by peptide bondsà __chain (each amino acid unit in a polypeptide is called a __)
    o   A polypeptide chain has polarity due to the __ at one end and the __ at the other end
    §  The amino end= __
    • rate of hydrolysis is really slow
    • polypeptide 
    • residue
    • amino group
    • carboxyl group
    • beginning
  3. o   A polypeptide chain consists of a regularly repeating part, called the __, and a __, comprising the distinctive side chains
    §  Rich in __
    §  Each residue contains a __, which is a good hydrogen bond acceptor, and, with the exception of proline, an __, which is a good H-bond donor
    · These groups interact to stabilize structures
    • main chain  or backbone
    • variable part
    • hydrogen bonding potential
    • carbonyl group
    • NH group
  4. o   Most natural polypeptide chains have between 50 and 2000 amino acid residues and are referred to as __, __being the largest (27k amino acids)
    §  Peptides with small numbers of amino acids are __
    • proteins
    • titin 
    • oligopeptides (peptides)
  5. o   In some proteins, the linear polypeptide chain is __, the most common being __, formed by the oxidation of a pair of __. The resulting unit of two linked __ is called __
    §  Extracellular proteins often have several __bonds, whereas intracellular proteins usually lack them. Rarely are __ present in proteins 
    • cross-linked
    • disulfide bonds
    • cysteine residues
    • cysteines is called cystines
    • disulfide 
    • nondisulfide cross-links derived from other side chains
  6. Frederick Sanger

    - Sequences are determined by __
    • determined the sequence of amino acids of insulin 
    • o   only L amino acids linked by peptide bonds
    • nucleotide sequences of genes
  7. o   Knowing amino acids sequences is important:
    • §  Knowledge of the sequence of a protein is essential to elucidating its mechanism of action
    • §  Amino acid sequences determine the 3D structure of proteins (from DNAà 3D structure)
    • §  Sequence determination is a component of molecular pathology; alterations in the sequenceà abnormal function and disease
    • §  The sequence of a protein reveals much about its evolutionary history
    • · Molecular events in evolution can be traced from amino acid sequences
  8. o   Polypeptide chains are __ yet __, revealing important features in the backbone
    §  The peptide bond is essentially planar: explain this
    • flexible yet conformationally restricted
    • for a pair of amino acids linked by a peptide bond, six atoms lie in the same plane—the two alpha carbons and the CO group of the first amino acid and the NH of the second
  9. §  The nature of the chemical bonding within a peptide accounts for the bond’s __. The bond resonates between a single bond and a double bond giving it __ and thus __
    o   The peptide bond is __, allowing polymers of amino acids linked by peptide bonds to do what?
    • planarity
    • double-bond character and thus restricting rotation
    • uncharged
    • form tightly packed globular structures
  10. o   Two configurations: __(alpha carbons on opposite sides of peptide bond) and __(same side). Almost all peptide bonds in proteins are __due to __
    §  The most common cis peptide bonds are __, which show less preference for the trans configuration because what?

    • trans 
    • cis
    • trans 
    • elimination of steric clashes between groups
    • X—Pro linkages
    • the nitrogen of proline is bonded to two tetrahedral carbon atoms, limiting the steric differences between the trans and cis forms
  11. o   The bonds between the amino group and the alpha carbon and between the alpha carbon and the carbonyl group are pure __ and can rotate, taking on various orientations, as well as allowing proteins to fold in different ways
    §  The rotation about these bonds can be specified by __
    • single bonds
    • torsion angles
  12. §  The angle of rotation about the bond between the nitrogen and the alpha carbon atom is called __and the angle of rotation about the bond between the alpha carbon and the carbonyl carbon atoms is called __.
    §  Clockwise rotation as viewed from the N atoms or the carbonyl group towards the alpha carbon = __ value. The phi and the psi also determine the __
    • phi (Φ) 
    • psi (Ψ)
    • positive
    • paths of the polypeptide chain
  13. Gopalasamudram Ramachandran 
    • o   recognized several rotations are forbidden due to steric collisions and can be plotted on a Ramachandran diagram
    • §  Steric exclusion is a powerful organizing principle
  14. o   An unfolded protein can exists as a __; each copy of an unfolded polymer will have a different __, yielding a mix of possible forms
    §  The favorable entropy associated with a mixture of many possible conformations opposes __ and must be __
    • random coil
    • conformation
    • folding and must be overcome by interactions favoring the folded form
  15. §  The __ and the __ limits the number of structures accessible to the unfolded form sufficiently to allow __ to take place
    • rigidity of the peptide unit
    • restricted set of allowed Ψ and Φ angles
    • protein folding