Ch. 2: structure of proteins

  1. Slide 2: Primary structure
    sequence of AA's
  2. Secondary structure
    Regular alements: Short-range
  3. Tertiary structure
    complete 3D structure
  4. Quaternary structure
    Proteins (like hemoglobin) have more than one polypeptide chain- non covalent bonds
  5. Slide 1: Peptide bond
    • AA are joined together covalently by peptide bonds.
    • Free amino end
    • free carboxyl end 
    • partial double bond
    • rigid and planar
    • trans config.
    • uncharged but polar
    • Pg13: long exposure to strong acid or base at high temps is required to hydrolyze (break apart with water) these bonds.
  6. slide4: Edman Degradation
    • N terminus to C terminus
    • Begining in N terminal, Phenylisothiocynate is used to label the amino terminal residue.
    • substance made anyhydrous(without water) and acid, and residue comes up.
    • The identity of the AA derivative can then be determined by mass spectrometry or gas chromatography.
    • Most powerful method
    • Yield drops off fast
  7. pg 16: 2nd structure: Alpha-Helix
    • Spiral structure
    • tightly packed, coiled polypeptide backbone core.
    • carbonyl oxygen is H bonded to the 4th AA
    • Helix is right handed, and the most stable with L-AA's.
    • H bonds stabilize
    • viewed as peptide planes, attached to Alpha-carbons and parallel to helix.
    • H bonds are between chains.
  8. P16 Hydrogen bond
    • Intrachain hydrogen bond
    • all but except 1st and last peptide bond are linked to each other through intrachain
    • hydrogen bonding between carbonyl oxygens and amide hydrogens - part of backbone.
    • Hydrogen bonds extend up and parallel to the spiral and NH group
    • weak but work together to stabilize.
  9. p16: 2nd structure folding
    • each turn has 3.6 AA's.
    • AA are have 3 to 4 residues apart in primary sequence, so they are close together when folded.
  10. -pg16: disrupts Alpha-helix because it's 2ndary Amino group doesn't have the right shape that gets along with the right handed spiral of the Alpha helix.
    -Puts a kink in the chain
    -AA that disrupt and form ionic bond to repell.
    -AA with bulky side chains, if present in large amount enterfere.

    These  Destabilizing helix
    • -charge interactions
    • -proline
    • -bulky sidechains
    • -b turns

    • Proline: The AA that causes a "kink" in the chain.
    • charged amino acids(glu,asp,hist,lys,arg)
    • bulky (tryptophan,valine,isoleucine)
  11. pg 17. 2nd structure: B-pleated sheets
    • all peptide bonds with H
    • have 2 or more peptide chains or segments.

    • H bonds are perpendicular to the backbone.(alpha is parallel)
    • Slide 17: B sheet chains or segments can be parallel (less stable) or antiparallel (more stable) to each other.
  12. structures provide for maximal H bonding for peptide bonds
    Alpha-helix and B-sheet
  13. *** slide 22 ***
    H bond between carbonyl oxygen and amide H is located
    3 positions down.
  14. AA with the smallest R-group found in B-bends
  15. slide 7: Acid hydrolysis
    peptide (protein) is placed in HCL and heated at 110C. It will by hydrolyzed to a ______.
    What's the drawback?
    • Free amino acids.
    • problem: tryptophan is destroyed.
  16. slide 9: an anzyme that when digested, free's the amino acid from the C terminal
  17. Allow you to identify the kinds and amount of AA's in a mixture
  18. S10: Chemical reacts with the AA to show the color purlpe.
    spray shows if protein is present.
    (used in homocides)
    • Ninhydrin.
    • Shows the amount of AA's
  19. S11:
    > a endopeptidase
    >Enzyme made in the pancreas and found in the small inestines that spilts chians on the C(right) side of Arg and Lys.
  20. »a digestive enzyme
    »splits polypeptide chains on the C side of Phe, Trp, Tyr.
    • Chymotrypsin
    • not reliable as trypsin
  21. Agent that cuts carboxyl of Met
    • Cyanogen bromide, CNBr
    • Met is converted to O-homoseryllactone
  22. Tertiary structure
    Primary determines tertiary

    compact and High density (close packing of atoms in molecule)

    Hydrophobic chains are in interior of globular protein with nonpolar side chains and stabilize structure.

    Hydrophilic chains are on surface of molecule.

    Formation of disulfide bond by 2 cysteines produce 1 cystine
  23. slide 25
    Tertiary structure: SHAPE  classifaction
    • Fibrous
    • globular
    • membrane
  24. slide 25
    proteins that are water insoluble
    Fibrous proteins
  25. slide 25
    Proteins that are water soluble
    Globular proteins
  26. slide 29:
    Proteins that assist in protein folding.
    Notes: help stabilize the structural configuration of other proteins
    Molecular Chaperones
  27. Slide 29:
    Protein folding disorders
    • Amyloidoses
    • Prion disease
  28. PG 20: protein folding
    • interactions on side chains of AA determine how long a polypeptide chian folds.
    • pos & neg charged side chains attract each other.
    • similar charged side chains repel each other
  29. Single Polypeptide chain
  30. Quaternary Structure of proteins
    The arrangement subunits of 2 or more polypeptide chains.


    salting in/out:

    dialysis: slide 32

    Chromatography (cation/anion exchangers): slide 34

    Gel electrophorosis:
  31. Held together by non covalent interactions. (ex. H bonds, ionic bonds, hydrophobic interactions)
  32. Slide 30:
    ↳ A tetramer with chains that are non covalent.
    ↳Has 2 Alpha and 2 Beta chains.
    ↳binding of O2 to one subunit of tetramer increases affinity of the other subunits for oxygen.
    Quat structure: Adult hemoglobin (HbA)
  33. Protein separation techniques
    • 1. salt solution
    • 2. Gel Filtration or Molecular Exclusion Chromatography
    • 3. Gel Electrophoresis
  34. 1 Notes: Adding salt like Ammonium Sulfate to a protein solution to ppt the protein of interest on a salt concentration.
    Salting Out
  35. 1 Notes: proteins requiring Inorganic ions for H2O solubility. When protein needs to be dissolved, you can use a particular ion.
    Salting In
  36. 2 notes: based on the pore size of the gel material to capture particular proteins

    ⇒ slide 33: Small molecules enter aqueous space within beads, large molecules cannot enter beads.
    Gel filtration or molecular exclusion chromatography
  37. separates proteins based on charge and MW in an electric field.
    -Higher MW stays at the top of gel, lower MW stays at bottom of gel
    -direction is down
    Gel electrophoresis
  38. Notes: Denaturing proteins by agents to break down tertiary structure
    • extreme ph (high or low)
    • ionic detergents (sds-sodium dodedcyl sulfate)
    • heavy metals Hg++
    • organic solvents - acetone
    • high temp
  39. slide 34: + charged Protein binds to - bead and flows through.

    Negative Protein flows through.
    Chromatography (cation/anion)
  40. Slide 41:
    →Extracellular material
    →7.5nm thick seen in microscopy
    →stains with congo red, apple green color under polarized light.
    →Beta pleated sheet by radiographic crystallography
    • Amyloid
    • Can be AA, AL, or other forms amyloid.
  41. Made in liver and taken into heart or kidney
    • Amyloid AA from
    • Serum Amylod A (SAA) - in Liver
  42. AA or AL amyloid in different organs like liver, kidney, adrenals, spleen, or heart
    systemic amyloidosis
  43. specific amyloid deposits - Alzeime's disease in the brain.
    Localized organ
  44. In alzeimer's patient
    • ApoE4 promote the formation of abnormal Amyloid protein plaques
    • Amyloid forms Amyloid Precursor Protein (APP)
    • Enzymes break APP into short fragments
    • The fragments clump together to form plaques.
    • Once plaque forms, Tau starts to break down. Tau protein stabilizes a neuron's arms
    • When tau no longer supports the axons, the neuron weakens and dies, leaving a tangled carcass.
    • Treatment is to prevent death of neurons, so researchers aim for amyloid and tau targets.
  45. Prion protein (PrP)
    • Alpha helix is the non infectious PrP
    • B- sheets is the infectious PrP.
    • 2 infectious PrP multiply by 2 and increase.
    • Bovine spong encephalopathy- Can be from cattle (mad cow disease)
    • Creutzfelt-jakob disease in humans
  46. Treatment of prion disease (PrP)
    1 M NaOH for 1 hour deactivates the prion in the B-Sheets
  47. protein particle produced by Gene mutation
    Mad cow disease prion
    altered folding ⇒ Prions⇒ leads to
    Creutzfeldt-jakob disease
  48. Good prion
  49. Bad prion
  50. Altered folding ⇒ Amyloid proteins ⇒leads to
    Alzheimer disease
  51. 2ndary structure consists of
    • Alpha helix
    • B-sheet
    • B-bends
    • non repetitive structures
    • supersecondary structures
  52. tertiary structure is stabilized by
    • Hydrophobic interactions
    • hydrogen bonds
    • electrostatic interactions
    • disulfide bonds
  53. 2.1 Has a partial double-bond character

    51-60 cards are from pg 24, back of ch. questions.
    Peptide bond
  54. do not accept or give off protons
    A-amino and A-carboxyl
  55. 2.2  B-bends often contain
    proline: provides a kink
  56. involves the coiling of a single polypeptide chain
  57. occurs in parallel and antiparallel forms
  58. domains are elements of
    tertiary structure
  59. 2.3 Info required for the correct folding of a protein is located in
    the specific sequence of AA's along the polypeptide chain
  60. react to form Disulfide bond may be long distance apart in primary structure or on seperate polypeptides, but are brought closer by the 3diminsional folding of polypeptide chain.
    2 cysteine residues
  61. 2.4
    80y/o has impairment of higher intellectual function and alterations in mood/behavior. progressive disorientation and memory loss over 6 months. no family hx. was recently diagnosed with alzheimer disease. which best describes this disease?
    associated with the deposition of neurotoxic amyloid peptide aggregates.
  62. associated with long, fibrillar protein of B-pleasted sheets found in the brain. B-bleated sheet config. is neurotoxic. AB amyloid that's deposited in brain in alz is from proteolytic cleavages from a larger amyloid precursor protein - a single transmembrane protein on the cell surface of brain.
    alzheimer disease
  63. ch. summary pg 23
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Ch. 2: structure of proteins