Ch 2 Text 1

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  1. Functions of proteins

    transport and store molecules like oxygen

    mechanical support and immune protection

    generate movement

    transmit nerve impulses

    control growth and differentiation
  2. Several key properties enable proteins to participate in a wide range of functions. 

    What are the first two?
    • o   Proteins are linear polymers built of monomers called amino acids, which are linked end to end
    • o   Proteins contain a wide range of functional groups, most of which are chemically reactive and determine protein function
  3. Several key properties enable proteins to participate in a wide range of functions. 

    What are the last two?
    • o   Proteins can interact with one another and with other biological macromolecules to form complex assemblies that can produce functions that individual proteins may not perform on their own
    • o   Some proteins are rigid and can function as structural elements in the cytoskeleton or in connective tissue; others are flexible and can act as hinges, springs, or levers that are crucial to the function, assembly of proteins with one another, etc. 
  4. Structural levels?
    • §  The primary structure is the sequence of amino acids and determines the 3D structure
    • §  Secondary structure is the 3D structure formed by hydrogen bonds between amino acids in the vicinity
    • §  Tertiary structure is the long-range interactions between amino acids
  5. Explain the composition of an amino acid

    How does nature prefer them?
    • o   An alpha-amino acid consists of a central carbon (the alpha carbon), linked to an amino group, a –COOH group, a H atom, and a distinctive R group (side chain). Since there are four different groups bonded, the amino acid can exist as an L- or D- isomer
    • §  Only L amino acids are constituents of proteins with an S absolute configuration.
    • ·  L isomers are slightly more soluble than is a racemic mixture of D and L
  6. o   Amino acids in solution at neutral pH exist predominantly as __

    §  In the __form, what? 
    dipolar ions (zwitterions)


    the amino group is protonated and the carboxyl group is deprotonated
  7.  The __ of an amino acid varies with pH. In acid, how does it appear? 
    ionization state

    the amino group is protonated and the carboxyl group is not dissociated
  8. o Increase in pH results in what?
    the –COOH group giving up a proton as low as pKa near 2. The dipolar form persists until about a pH of nine, at which point both the amino and –COOH group are deprotonated
  9. o   Twenty side chains varying in _(6)_ are found in proteins
    §  The functions of proteins results from the diversity and versatility of the 20 building blocks (amino acids) 
    size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity
  10. How are amino acids classified?
    • o   acids on the basis of:
    • §  Hydrophobic amino acids with nonpolar R groups
    • §  Polar amino acids with neutral R groups but the charge is not evenly distributed
    • §  Positively charged amino acids with R groups that have a positive charge at physiological pH
    • §  Negatively charged amino acids with R groups that have a negative charge at physiological pH
  11. Hydrophobic amino acids

    What are the nine?
    glycine (simplest, achiral)







    phenylalnine (purely hydrophobic)

    tryptophan (less hydrophobic due to --NH)
  12. §  The larger __side chains are especially __; that is, they tend to cluster together rather than contact water
    §  The 3D structures of water soluble proteins are stabilized by what; and, what enables them to pack together to form compact structures with little empty space


    the tendency of hydrophobic groups to come together, called the hydrophobic effect

    the different sizes and shapes of these hydrocarbon side chains
  13. Proline's ring structure makes it more __ than other amino acids.
    conformationally restricted than the other amino acids
  14. Polar Amino Acids: ___

    Name them.
    six amino acids are polar but uncharged

    Serine, threonine, and tyrosine (have --OH groups attached to hydrophobic side chain)



  15. Explain serine

    Explain threonine
    • · Serine: version of alanine with a hydroxyl group attached
    • · Threonine: resembles valine with a hydroxyl group in place of one of valine’s methyl groups
    • o   Like isoleucine, it contains an additional asymmetric center
  16. Explain tyrosine
    · Tyrosine: version of phenylalanine with the hydroxyl group replacing a hydrogen atom on the aromatic ring
  17. §  The –OH makes the amino acids more __ and __
    §  This group also contains __ and __, uncharged derivatives of __
    · Each of these two amino acids contains a __ in place of the __

    hydrophilic and reactive

    asparagine and glutamine

    the acidic amino acids aspartate and glutamate

    terminal carboxamide in place of the carboxylic acid
  18. What is the difference between asparagine and glutamine? 

    §  __is similar to __but has a __ in place of the __, which is much more reactive
    · Pairs of __ may come together to form __ bonds, which are particularly important in stabilizing proteins 
    o The side chain of glutamine is one –CH2— loner than that of asparagine



    thiol (sulfhydryl) group

    –OH group

    sulfhydryl groups

  19. o   Positively charged amino acids
    §  Highly __
    §  Explain lysine
    Explain arginine

    They have long side chains that terminate with groups that are positively charged at neutral pH

    Lysine is capped by a primary amino group and arginine by a guanidinium group
  20. o   Positively charged amino acids
    §  Explain histidine
    Histidine is found in active sites of enzymes, where the imidazole ring can bind and release proteins during enzymatic reactions
  21. o   Negatively charged amino acids
    §  Contains two acidic side chains: __ and __, which are often called __ and __ to show that their side chains usually __
    · In some proteins, these side chains do __, which can be important
    • aspartic acid and glutamic acid
    • aspartate and glutamate
    • lack a proton that is present in the acid form
    • and is negatively charged
    • accept protons
  22. o   Seven of the 20 amino acids have readily __; and, they can __ or __ to __ as well as to __
    §  Two other groups in proteins—the __—can be ionized
    Amino acids have __ and __ abbreviations 
    • ionizable side chains
    • donate or accept protons
    • facilitate reactions as well as to form ionic bonds
    • terminal alpha-amino group and the terminal alpha—carboxyl group
    • three and one letter
  23. o   How did this particular set of amino acids become the building blocks of proteins? 
    • §  They are diverse; their structural and chemical properties vary, allowing versatility
    • §  Many were probably available from prebiotic reactions, from reactions that took place before the origin of life
    • §  Other possible amino acids may have been too reactive 

Card Set Information

Ch 2 Text 1
2014-09-01 19:21:06
Test One
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