BIC Lecture 3

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BIC Lecture 3
2014-09-06 21:38:19
Test One
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  1. Description of hydrophobic side chains
    Don't like water and attempt to get away from it. Found inside of proteins, interacting with each other via van der Waals interactions

    aliphatic: long, branched, or straight side chains
  2. Name the nine hydrophobic side chains.








  3. Glycine

    side chain: hydrogen

    Use: fits in tight spaces
  4. Alanine, Valine, Leucine, Isoleucine
    you just keep adding --CH2--
  5. Methionine
    1st S- containing amino acid; sulfur doesn't react with anything

    --> first amino acid when protein is synthesized
  6. Tryptophan
    Largest side chain incorporated into protein 

    good for filling large places

    If introduced into the wrong places, a negative interaction can occur
  7. Phenylalanine
    all hydrocarbon ring structure; contains a benzene ring
  8. Proline
    its side chain loops around and binds to --NH2-- of the backbone

    unique because it is very rigid to side chain

    when incorporated, it forms kinks in the amino acid backbone
  9. What are the polar amino acids?
    • serine 
    • threonine
    • tyrosine
    • asparagine
    • glutamine
    • cysteine
  10. Describe the polar amino acids.
    - Have --OH groups and have Hydrogen bond donors

    - Important in proteins involved in signaling, which is done in a series of steps and hydrogen of --OH is replaced by a phosphate, changing size and charge dramatically 

    Causes protein to change its shape--> regulatory switches

    Good for pathways

    • Kinases add the phosphate group and stick it on the side chaine
    • --> serine and threonine kinases

    --> different set of tyrosine kinases
  11. Cysteine
    usually involved in disulfide bonds

    two cysteines will dump hydrogen and form covalent bonds between the sulfurs, stabilizing factor (sometimes activating)

    Once in a while, it is found in active sites
  12. Serine and threonine are _
  13. Tyrosine is __
    hydrophobic with the exception of --OH in benzene
  14. Positively Charged at Physiological pH


  15. Explain lysine and arginine.
    ionic bonds outside

    If inside, they are doing something important like a reaction mechanism
  16. Explain histidine
    Unique; can go either way depending on its microenvironment

    can be positive or deprotonated and neutral
  17. Negatively Charged at Physiological pH
    Glutamic acid (or glutamate)

    aspartic acid (aspartate)
  18. Glutamate and aspartate do what?
    lose their proton at pH of 7
  19. For the amino acids that are ionizable, what are their pKas?
    depends on the temperature, ionic strength, and the microenvironment
  20. Why are there twenty amino acids in our genetic code?
    1) evolution: molecules that assembled to put them together chose them. The others probably led to bad interactions
  21. What is the most important amino acid?
    They are all important
  22. How many different combinations of amino acids can there be?
    There are numerous ways, but combos are limited
  23. What are the limitations to protein combinations
    1) the most important is the genome, which limits the number of combinations. If it is not coded, that sequence will not occur

    2) steric hindrance due to side chains

    3) angle of rotation about the phi and psi bonds

    4) rigidity because the backbone is planar

    5) trans and cis
  24. What is the functional unit that tells you the order of amino acids?
  25. How many genes do you have?
    about 25,000
  26. How do we connect two amino acids?
    the carboxyl group of one is connected to the NH3 of the other. Water is lost
  27. Where is this polypeptide production occurring?
  28. Two amino acids= __

    alot= __

  29. What is the directionality of the amino acid sequence?
    Amino (N) terminus------> Carboxy (C) terminus
  30. What is the backbone?
  31. Two cysteine residues do what?
    combine to make cystine
  32. __ is a two polypeptide chain protein. How do the chains fold?

  33. Characteristic of a peptide bond?

    How many ways are there to fold amino acid chains?
    • rigid and planar
    • -- 6 atoms lie in the same plane --> there is no free rotation about the peptide bond
    • there's only one
  34. Why is there only one folding conformation?
    It is conformationally stable; the rest have higher energy

    --> if they are folded more than one way, it may not have enzymatic activity
  35. Why is there no rotation about the peptide bond?
    around the peptide bond, some electrons on nitrogen go to oxygen, giving it double bond character and leading to no free rotation
  36. Discuss trans and cis.
    trans tends to be used because there is less steric hindrance (you can't occuy the same space at the same time).

    The only exception is proline because there is not much diference between cis and trans
  37. Can you rotate about the phi and psi bonds?
    No, Ramachandran made a chart. Rotating about both bonds in 180 degrees

    What he found: amino acids have acceptable angles they can take on when folding 

    Limiting angles as well due to steric hindrance
  38. The shapes of polypeptides are called __.

    What are the shapes?

    alpha helix, beta pleated sheets, beta turns
  39. Explain the alpha helix.
    right-handed (common in nature)

    • Side chains stick out from the alpha helix
    • What holds the alpha helix together are intramolecular hydrogen bonds

    Alpha helix forms naturally after it is translated

    Four amino acids downstream is where the hydrogen bond occurs

    there is no cavity running down the middle because the electron clouds occupy that space

    there are specific bond angles

    proteins can be all alpha-helix (only secondary localized structure)
  40. Beta strands
    stretched out backbone piled on top or next to one another

    side chains are seven angstroms apart

    2 types of beta sheets: antiparallel or parallel

    held together by hydrogen bonds (intermolecular); different portions of polypeptides can bind
  41. What is the difference between parallel and antiparallel>
    They have different orientations.

    The cNH and CO group of each amino acid are hydrogen bonded to the CO group and NH group of the partner on the adjaent hain. 

    In parallel: the NH group is bonded to the CO group of one amino acid on the adjacent strand, whereas the CO gorup is hydrogen bonded to teh NH group two residues farther along the chain
  42. How do we connect different strands of secondary structure?
    beta turns

    stabilized by hydrogen bonds

    i binds to the amino acid in the position i + 3 (3 further down)
  43. Amino acids can't do all the work. Some require __. Explain them.
    prosthetic groups

    small molecules that bind to proteins to help it perform its structure

    --> organic or inorganic
  44. Explain what a prosthetic group does.
    • binds after protein takes on native conformation
    • generally doesn't form covalent bonds but it can
  45. Typical pKa of: 

    terminal alpha-carboxyl groups
  46. Typical pKa of: 

    aspartic acid/ glutamic acid
  47. Typical pKa of: 

  48. Typical pKa of: 

    terminal alpha-amino group
  49. Typical pKa of: 

  50. Typical pKa of: 

  51. Typical pKa of: 

  52. Typical pKa of: 

  53. When speaking of frequencies in relation to secondary structures, what does a frequency above 1 mean?
    the polypeptide is most likely to take on that structure
  54. Why is the frequency of proline predominately reverse turns?
    it is the kinky protein and very disruptive to alpha helices and beta sheets. It'll be located in reverse turns
  55. When alpha-helices form bonds around each other, what is it called?
    alpha helical coiled helix
  56. Secondary structure is __.
    localized sequence
  57. Explain the leucine zipper structure.
    leuicine is hydrophobic and hides away. It holds the helix together because usually one and four are inside and they line up and face the interior
  58. What does hydroxyproline do?
    gives hydrogen bonding ability--> better
  59. Collagen looks __. Why? What do we do with collagen?

    What is in the center of the three alpha helices?
    • helical
    • proline makes it very rigid

    we take three strands and make it structurally stronger

    glycine is in the center of the alpha helices
  60. With myoglobin, what can't the protein do by itself?
    it can't bind oxygen, but with heme, it can
  61. Explain porins.
    forms pores in the membranes with a reverse orientation: hydrophilic are inside, facing the interior where water is going through. Hydrophobic are exterior
  62. Explain domains?

    when the structure that is seen copies itself into genes, causing it to exist exactly the sme in numerous proteins

    subportion of a polpeptide that exists in many proteins (tertiary structure of polypeptide/ fold individually of teh rest of the protein with individual function that is unique from the rest of the rest of the protein
  63. Helix turn helix
    made of three motifs: two helices and one turn; localed alot in proteins that regulate genes; binds to dna
  64. Quaternary structure has __
    numerous subunits

    (when talking about quaternary like hemoglobin, which has four subunits, each subunit has its heme
  65. What do conditions such as urea and guanidium chloride do?
    cause unfolding of the molecule
  66. What does beta-mercaptoethanol do?
    reduces S-S bonds
  67. What do cystines do?
    bind disulfide bond to hold protein together

    bovine (cow) ribonuclease (has enzymatic activity and chops up RNA)
  68. If we dilute the elements (urea, etc) away, what can happen?
    scrambled ribonuclease refolds into the same structure as its native form
  69. What is the general connection we are getting?
    one protein, one shape