Biochemistry Exam 1

  1. Primary Structure
    Linear sequence of amino acids
  2. Secondary Structure
    Spatial arrangement of amino acids due to backbone and H-bonding. Not R groups.
  3. Tertiary Structure
    The 3-D shape of the amino acids due to substituent interactions.
  4. Quaternary Structure
    Connection of different protein sub-units to create the overall shape.
  5. Consequences of the peptide group in amino acids (why?)
    • The peptide bond is very rigid, giving the bond a very planar structure. This is because the peptide bond has 40% double-bond character due to resonance.
    • -shorter than other bonds
    • -extra pi bond overlap
  6. Confirmation of peptide groups.
    • Typically trans configuration due to sterics (making it planar too)
    • -10% of Pro residues are cis
    • -8 kJ/mol less stable than trans
  7. Define Torsion Angles
    A way to describe the conformation of the peptide backbone:

    • Cα - N bond Φ (counterclock)
    • Cα - C bond ψ (clockwise)

    Notice peptide bond not included because it is very rigid.
  8. What is the conformational freedom of torsion angles?
    Angles are sterically constrained to avoid collisions with other adjacent residues.
  9. Ramachandran Diagram
    • Indicates angles that are sterically allowed for Ψ and Φ.
    • -smallest shows angles that are allowed sterically not including Gly and Pro
    • -medium shows angles with very limited movement
  10. Which secondary structure falls most within the fully allowed torsion angles in a Ramachandran diagram?
    α helix
  11. What is the most and least sterically hindered amino acid?
    Pro most confirmationally restricted amino acid.

    Gly least sterically hindered amino acid and capable of ore freedom.
  12. Define Regular Secondary Structures
    α helices and β sheets are named as such because they have repeating Φ and ψ values.
  13. How many residues occur per turn in the α helix (average length too)?
    3.6 turns in a right handed manner.

    Average length: 12 residues (3 turns)
  14. What is the core of the α helix like? What about the outside?
    It is tightly packed due to Van der Waals forces. 

    The outside has side chains projecting out to reduce steric hindrance.
  15. How is the backbone arranged in the α helix?
    The backbone hydrogen bonds with each other at a distance of  2.8 Α. The lone pairs of the carboxyl group are attracted to the H of the nitrogen.
  16. Two varieties of β sheets.
    Antiparrallel: the neighboring H-bonded chains run in opposite directions. It is better this way and causes less strain on the sheet.

    Parallel: H-bonded polypeptide chains run in the same direction but it does cause steric strain. They are rare and require extensive crossover of the β band.
  17. What is the range of strands in β sheets? What is the average number of strands? What is the average number of residues per strand?
    • Range: 2-22 strands
    • Average: 6 strands

    Average Residues: 15 residues

    This is for antiparallel strands. The numbers are much less in parallel strands.
  18. What is the geometry of the β sheet?
    It generally has a right handed twist to it.

    The twisting causes a weakening of the H-bonding. But the twisting is a consequence of the side chain residues.

    In conclusion, the twist is a compromise between optimizing conformational energies of polypeptide chain and H-bonding.
  19. Define Reverse Turns / β Bands (what are they stabilized by?)
    The stretch of amino acids that make sharp turns. They are what connects β sheets or α helices. It is most common in β sheets.

    They are stabilized by H bonding.
  20. What are the two types nof fibrous proteins?
    • Keratin: mechanically durable and unreactive protein
    • Collagen: major stress bearing component of connective tissues that is strong and insoluble
  21. The primary structure of keratin is derived from what?
    The left handed twisting of two α helices forming a coiled coil is because of the primary structure. It has a 7 amino acid repeat with nonpolar ends and 3.5 residues per turn.
  22. Whta is the difference between "hard" and "soft" α keratin?
    Hard α keratin is rich in Cys residues to form disulfide bonds within oxidative environments.

    Soft α keratin lacks many Cys residues.

    These disulfide bonds are cleaved reductively.
  23. Two classifications of keratins coiled coil
    • α keratin in humans
    • β keratin in birds and reptiles
  24. Structure of collagen
    • Composed of:
    • 1/3 Glycine
    • 1/5 Proline
    • The above amino acids are incapable of forming an α helix because there is a lack of H-bonds from Pro

    It has repeating triplets of Gly, Pro, Hyp (hydroxyprolyl). The Gly is in every 3rd turn because that is when the chain moves through center of the left turn helix where only Gly can fit and the N-H can H bond with Pro carbonyl.

    • Structure:
    • Left handed turn oppositely twisted with crosslinks at C and N termini at the ends that increase with age.
  25. Difference between irregular coiling and random coiling
    • Irregular Coiling: coiling that appears to be random BUT is ordered (just difficult to describe)
    • Random Coiling: denatured proteins, and rapidly fluctuating confirmations
  26. β bulge
    When the last amino acid of the α helix cannot hydrogen bond with another amino acid causing distortion.
  27. How does Pro affect the secondary structure?
    Causes a kink due to irregular shape and destabilize the structure
  28. Define Helix Capping
    The α helices are normally surrounded by Asn and Gln that form H bonds with α helix
  29. What affect do large residues have on the α helix?
    It destabilizes it.
  30. Amino acid side chains in globular proteins are spatially distributed according to what?
  31. Nonpolar Residues that occur on the interior of the protein
    • Val (Valine)
    • Leu (Leucine)
    • Ile (Isoleucine)
    • Met (Methionine)
    • Phe (Phenylalinine)
  32. Charged Polar Residues that occur on surface of the protein
    • Arg (Arginine)
    • His (Histidine)
    • Lys (Lsine)
    • Asp (Aspartic Acid)
    • Glu (Glutamic Acid)
  33. Uncharged Polar Residues that occur on surface but can also be on the interior of the protein
    • Ser (Serine)
    • Thr (Threonine)
    • Asn (Asparagine)
    • Gln (Glutamine)
    • Tyr (Tyrosine)
  34. What kind of confirmation is the interior of the protein typically?
  35. Where do the turns and loops of between secondary structures typically occur?
    Along the protein surface
  36. βαβ motif
    Image Upload 1
  37. β hairpin
    Image Upload 2
  38. αα motif
    Image Upload 3
  39. Greek Key Motif
    Image Upload 4
  40. α proteins
    β proteins
    α/β proteins
    • α proteins: primarily α helices
    • β proteins: primarily β sheets
    • α/β proteins: mix of α and β
  41. β Barrels
    β sheets that are plenty enough that they form a twisting barrel like structure
  42. Define Domains
    Portions of globular proteins that give it a multilobal appearance. These domains normally act as independent units. Layers of domains allow the protein to seal off the hydrophobic core of certain domains.

    They allow flexible interactions between proteins and small molecules.
  43. What is the most important evolutionary aspect of a protein?
    Structure and function more important than the residues.
  44. What is the benefit of a Quaternary structure composed of several different sub units?
    Allows for easier subunit repair rather than having the whole molecule go to waste when damaged.
  45. Define Oligiomers
    Proteins with more than one subunit.
  46. Define Protomers
    Identical subunits.
  47. How is the protomer stabilized in the oligiomer?
    They are stabilized by nonpolar side chains and backbone hydrogen bonding.
  48. How are protomers connected within the protein? What kind of symmetry does it have?
    It has cyclic symetry commonly named C2, C3... etc depending on how many are on the same plane. Those not on the same plane and spiral up are notified as D2... etc.
  49. What is the stability of amino acid residues and what does it mean for the protein itself?
    To denature an amino acid residue, 0.4 kJ/mol is required to break it. This is very easy to break meaning outside forces increase protein stability.
  50. Define Hydrophobic Effect
    Minimizing the the contact water has with nonpolar molecules. Having nonpolar side chains on the interior of the protein increases entropy.

    The higher the hydropathy (hydrophobic / hydrophhilic tendencies) the more the residue will be in the interior.
  51. What effect foes H-bonding have on the tertiary structure?
    It adds a bit of stabilizing energy by "selecting" the unique native structure of protein from among a relatively small number of hydrophobically stable conformations.
  52. How much does ion pairing contribute to the stability of the molecule?
    It contributes little to the stability of the molecule. The formation of the ion pair costs more entropically such that they do not compensate for their formation.
  53. How much do disulfide bonds contribute to the structure of the protein?
    Not too much because proteins can still function without them and they are rare intracellularly.
  54. What effect do metal ions have on small domains?
    They function to cross-link proteins.

    For example, zinc can can stabilize small polypetide chain stretches through tetrahedral coordination (especially Cys, His and sometimes Asp, Glu)
  55. What does it mean for polpeptide folding to occur cooperatively?
    It means that protein folding occurs all at once.
  56. What four things cause proteins to denature?
    • -heating
    • -pH change (changes charge distribution and H-bonding)
    • -detergents that associate with nonpolar residues
    • -chaotropic agents (ions or small molecules that increase solubility of nonpolar substances in water)
  57. What is the quality of an intrinsically disordered protein?
    One that is rich in charged amino acids and lacks nonpolar amino acids.

    But the good thing is they take up less space and become functional with transcription factors.
  58. What did Anfinsen's work demonstrate?
    Proteins can fold spontaneously into native conformation under physiological conditions implying that the primary structure is responsible for protein 3D structure.

    The probability of a disulfide bond reforming after RNase to proper link is around 1/105 if it was at random. This would mean that only 1% of proteins would be catalitically active.
  59. Define Protein Breathing
    The conformational flexibility of proteins. Proteins have more than one possible structure that can be changed by pH, oxidation state, or binding partner.
  60. Levinthal's Experiment
    Levinthal's paradox is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations.

    For example, a polypeptide of 100 residues will have 99peptide bonds, and therefore 198 different phi and psi bond angles. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3198 different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation.
Card Set
Biochemistry Exam 1
Amino Acids, Protein Folding, Enthalpy and Entropy