Biochem set 2

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  1. Chiral type of amino acids found in proteins
    L-amino acids
  2. Another name for dipolar molecules.
  3. Disulfide bonds are formed by pairs of which amino acid?
  4. The amino acid with a pKa near neutral pH.
  5. When a peptide bond is formed, what molecule is also made?
  6. Where are proteins with extensive disulfide links likely to be found?
  7. This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.
  8. The overall structure of a protein is referred to as
    tertiary structure
  9. Name of the plot that allows one to investigate the likely orientation of certain amino acid pairs.
  10. The type of structure to which α  helices, β sheets, and turns are referred.
    secondary structure
  11. The amino acid that contains a weakly acidic “phenolic” group is
  12. is a fibrous protein and is the primary component of wool and hair.
    Α keratin
  13. Every third residue in the protein collagen is
  14. Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such
    β mecaptoethanol
  15. A protein is considered to be __________________ when it is converted into a randomly coiled structure without its normal activity.
  16. is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.
  17. Collagen contains _____________________, a modified amino acid.
  18. Agents such as ______________________ and guanidine hydrochloride denature proteins by disrupting the noncovalent interactions.
  19. refers to the spatial arrangement of subunits and the nature of their interactions
    Quaternary structure
  20. The ________________________ β-sheet structure occurs when the two strands are oriented in opposite directions (N → C).
  21. What determines a protein’s function?
  22. Key properties of proteins include
    • A)    a wide range of functional groups.
    • B)    an ability to possess either rigid or flexible structures as dictated by functional requirements.
    • C)    the ability to interact with other proteins.
  23. What charged group(s) are present in glycine at a pH of 7?
    A) –NH3+     B) –COO
  24. At a pH of 12, what charged group(s) are present in glycine?
  25. In what pH range is zwitterionic Alanine the predominate structure?
  26. Which amino acids contain reactive aliphatic hydroxyl groups?
    serine and threonine
  27. Name three amino acids that are positively charged at a neutral pH.
    lys, arg, and his
  28. In the following peptide, which amino acid is the N-terminus?
  29. What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other protein modifications.)
  30. Which individual won a Nobel Prize for his landmark work in sequencing the protein insulin?
  31. Why is the peptide bond planar?
    It contains partial double-bond character, preventing rotation.
  32. The configuration of most α-carbon atoms of amino acids linked in a peptide bond is
  33. What structure(s) did Pauling and Corey predict in 1951?
    A) α helix     B) β sheet
  34. Which of the following protein(s) contain examples of α helical character?
    A) keratin     B) ferritin     C) myosin     D) tropomyosin
  35. Where are Ω and β turns and loops often found?
    on the surface of proteins
  36. What are some of the modifications that proteins acquire?
    • A)    cleavage and trimming of the protein    
    • B)    addition of carbohydrate groups    
    • C)    phosphorylation of certain groups
  37. Which of the following amino acid residues would most likely be buried in the interior of a water soluble, globular protein?
  38. How does a protein’s amino acid sequence influence the tertiary structure?
    A protein will spontaneously fold into a three-dimensional structure determined by the amino acid sequence.
  39. What is the advantage of having 20 different amino acids available to form proteins?
    The amino acids provide a rich diversity of functional groups, which can independently contribute to protein structure and function. In addition, many can be modified, increasing the diversity of functional groups
  40. What is the advantage of protein interaction and assembly with other proteins?
    When proteins interact or assemble, new functions and specificity become available. Protein interactions allow new binding sites at the assembly interface, as well as providing multifunctional activity and specificity, such as found in polymerases and signal transduction.
  41. What are the three aromatic amino acids?
    phenylalanine, tyrosine, and tryptophan
  42. Which amino acid side chains are capable of ionization?
    The amino acids are: Asp, Glu, His, Cys, Tyr, Lys, and Arg.
  43. How does the protein backbone add to structural stability?
    The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.
  44. Why are all the theoretical combinations of phi and psi not possible?
    Steric hindrances of the side chains make certain combinations and angles impossible.
  45. Describe some of the features of an α helix.
    The α helix is coil stabilized by intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away. There are 3.6 amino acids per turn. The hydrogen bonds are between amino acid residues that have two intervening residues.  Thus, these amino acid residues are found on the same side of the coil.  The helix is almost always right-handed, although left-handed helices are, in theory, possible.
  46. What is the “hydrophobic effect” as it relates to protein structure?
    The three-dimensional structure of a water soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule.
  47. What is a protein domain?
    A domain is a defined region of a protein. Often, a domain is defined by a particular function.
  48. What are prions?
    Prions are proteins that can assume (after infection or by other causes) a new protein structure, which is self-propagating. The disease has several variants, and at least one is fatal to humans.
  49. In the ribonuclease experiments performed by Anfinson, what was the significance of the presence of the reducing agent β mercaptoethanol?
    The reducing agent reduced incorrectly paired disulfide bonds allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.
  50. What is the advantage of having certain regions of partially correct folded regions?
    If some regions interact preferentially, lending stability to certain conformations as the protein folds, they can impact the overall structure of the protein.
Card Set:
Biochem set 2
2014-10-05 21:00:44
Biochem set

Biochem set 2
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