7 Protein Structure

  1. What are the components of amino acids (5)
    • 1. Alpha carbon (chiral except in glycine [R=H])
    • 2. Hydrogen
    • 3. R group (gives AA its properties)
    • 4. Amine group (NH3+ at neutral pH)
    • 5. Carboxylate acid group (COO- at neutral pH)

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  2. Hydrophobic R Groups
    rich in hydrocarbons

    hydrophobic interactions are on the INSIDE of a water-soluble protein
  3. Hydrophilic R Groups
    have oxygens, nitrogens & ESPECIALLY charged groups
  4. Protein Backbone
    linear chain formed by N & 2 C atoms

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    proteins adopt particular shapes to maximize favorable atomic interactions to make a shape with a function
  5. What forces dictate protein folding & stability?
    the sum of weak, non-covalent (low energy) bonds [1-7 kcal/mol v. covalent forces: > 50 kcal/mol]

    • some proteins don’t fold easily on their own & to do so require the assistance of chaperones

    • destabilizing amino acid mutations disrupt fold(ing)

    • unfolded proteins can aggregate & be improperly trafficked
  6. How can you predict the function of a protein who’s role is unknown?
    by looking at its AA sequence & seeing if it’s homologous to other proteins’
  7. Specific Activity
    the amount of activity per amount of purified protein
  8. How can one measure the amount of purified protein?
    • insert a sample of protein in a spectrophotometer calibrated to detect absorbance of the sample at a wavelength of 280nm

    • tryptophan & tyrosine absorb UV light at 280 nm

    • amount of light produced ~ amount of protein?
  9. Alpha Helix
    secondary protein structure held together via hydrogen bonds that occur between the oxygen of a carbonyl group & the HN of an amino acid that is 4 residues down the polypeptide chain

    • protein with charged residues (eg. Lys Lys) adjacent to each other in sequence can’t exist in a helix because the shape of it puts them too near each other

    • CAN be AMPHIPATHIC (having both hydrophilic & phobic parts)
  10. Which amino acid cannot fit in an alpha-helix?
    Proline: has a five-member ring & is referred to as the “helix breaker”
  11. Beta Sheet
    secondary protein structure held together via hydrogen bonds that occur between backbone atoms within stretches of amino acid residues

    • at least 2 (usually more) extended polypeptide chains are involved

    • prolines can exist in beta sheets

    • adjacent R groups can be 180° apart so it’s a favorable conformation for AAs that have the same charge & exist next to each other in the peptide chain
  12. CFTR protein
    transmembrane protein of the ATP Binding Cassette family with 5 domains

    • activation allows passage of Cl- ions through the PM via 2 methods (phosphorylation of the R domain & ATP binding + hydrolysis by NBD domains)

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  13. What are the 5 domains of the CFTR protein?
    • • TM1, TM2: 2 transmembrane domains that are groups of 6 alpha helices that form a chloride channel
    • - these helices are amphipathic: hydrophilic on the inside conducive to Cl- & hydrophobic on the outside conducive to placement in the PM

    • • NBD1, NBD2: 2 cytoplasmic nucleotide binding domains that bind & hydrolyze ATP
    • - a lot of mutations occur in the nucleotide binding domain

    • R domain: a regulatory domain modified by phosphorylation
  14. Describe how CFTR is activated:
    • R domain phosphorylation activates the channel

    • ATP hydrolysis by NBD domains changes channel conformation & allows passage of Cl- ions through the PM
  15. Kalydeco
    a treatment for CF patients with the G551D mutation

    • fixes CFTR protein misfolding → allows it to fold properly

    • only assists 4-5% of people with CF (75% have the deltaF508 mutation)
  16. Glycine
    • has the smallest amino acid side chain (R = Hydrogen)

    • allows for sharp bends in chains & for chains to come close to each other (eg. hairpin bend in p53 protein)

    • can be hydrophilic or hydrophobic due to its minimal H side chain

    • the CF G551 mutation is one that changes a Glycine to another AA → disrupting CFTR function
  17. Name 2 Fibrous Proteins:
    1. Elastin

    2. Keratin

    are relatively insoluble in water & are ELONGATED instead of being compact
  18. Elastin
    • fibrous protein found in elastic tissue (eg. Lungs)
    • the major kind of protein found in elastic tissue
    • has no regular 2ndary structure
    • is relatively water insoluble & elongated
  19. Desmosine Residue
    a polypeptide connection involving four Lysines found only in elastin (springy connective tissue protein)

    [connects spaghetti noodles that make up elastin]
  20. Keratin
    • tough fibers rich in Cysteine
    • contains tightly wound alpha-helices that are difficult to digested
    • protein of hair, nails & skin
  21. Hereditary Acidosis
    • disease in which there is increased acidity in the blood & other body tissue

    • can result in growth defects, eg. bone formation issues, cognitive problems

    • treatment is often ingesting bicarbonate

    • causes problems in protein function because if protein isn’t at the right pH, it’s side chains will have wrong charge & may not function
  22. pH
    • the negative log of the hydrogen ion concentration
    • when [H+]=10-7 M → pH = 7
  23. pKa
    the pH at which you have 50% of the conjugate acid & 50% of the conjugate base

    • when the pH of a solution equals a molecule’s pKa, that solution can best absorb changes in pH (addition of other basic or acidic molecules)

    • [pKa is when the concentration of the acid form of a molecule = the concentration of the base form of the same molecule]
  24. At what pH will a buffered solution be most resistant to changes in the pH after the addition of acid or base?
    when pH ~ pKa

    • this is when the pH is most resistant to change upon addition of OH- or H+

    • relatively large additions in the amount of base (or acid) produce only small changes in pH → maximal buffering capacity
  25. What form of a molecule predominates when the pH value is lower or higher than the pKa?
    pH < pKa → acid form of the molecule predominates

    pH > pKa → base predominates

    [base is form of molecule with fewer hydrogens]
  26. What is a major buffer inside cells?
    phosphate (pKa ~ 7)

    H2PO4- ↔ H+ + HPO42-
  27. What is a major buffer in the blood?
    Carbonic acid/Bicarbonate

    H2CO3 ↔ H+ + HCO3-
  28. Proteins make a significant contribution to the buffering capacity in cells and plasma. What part of proteins allows them to act as buffers?
    • titratable groups on the amino acid side chains

    • lots of amino groups & carboxyl groups (the AAs cyteine & histidine are especially good buffers)

    • pKa of these groups differ depending on the side chain

    • proteins have a considerable buffering capacity because the protein concentration in cells & plasma is quite high
  29. In terms of breathing, what causes the pH of blood to rise or fall?
    • taking deep breaths → ↑ pH (CO2 is released)

    • pulmonary obstruction/holding one’s breath → ↓ pH (CO2 builds up)
  30. How Aspirin Gets Absorbed
    • • upon entering the stomach, Aspirin will be uncharged
    • - stomach pH = 1.5
    • - pKa of Aspirin = 3.5 [it’s a weak acid]
    • - at a pH < pKa → Aspirin will exist in it’s acid form (more protons)
    • - because of the acidic environment, Aspirin will be protonated (-COOH) & therefore uncharged

    • as an uncharged molecule it can passively cross membranes
  31. Same Q: Aspirin is a weak acid at low pH and has a pKa of 3.5. Will more aspirin be absorbed in the stomach (pH 1.5) or in the intestine (pH 6.5)?
    • when pH < pKa, molecule exists in its acidic form (RCOOH)

    • when pH > pKa, molecule exists in its basic form (RCOO-)

    • non-ionized molecules cross cell membranes passively whereas ionized molecules do not, more aspirin will be absorbed in the stomach than in the intestine
  32. Isoelectric Point (pI)
    the pH at which a compound is electrically neutral, aka the net charge is zero

    to find, average the 2 pKa's surrounding the isoelectric species
  33. Proline
    contains a ring that limits its flexibility & makes it incompatible with alpha helix formation (called the PRO helix breaker)
  34. Tyrosine & Tryptophan
    • both absorb UV light (280 nm) and makes protein detection easy

    • tryptophan has a non-polar R group

    • tyrosine has a polar R group
  35. Cysteine
    can form disulfide bonds between S's at the end of their R group
  36. Which amino acid is capable of forming disulfide bonds?
    Cysteine: disulfide bonds are most often found in oxidizing environments such as outside of the cell
  37. Which amino acids are positively charged at neutral pH?
    arginine, lysine, histidine
  38. Which amino acids are negatively charged at neutral pH?
    aspartate & glutamate (ate = negatively charged)
  39. Which of the 20 standard amino acids are aromatic?
    phenylalanine, tryptophan, and tyrosine (all have benzene rings)
  40. Regions of proteins that interact with DNA are usually __________ charged:
    Positively charged, because DNA carries a negative charge
Card Set
7 Protein Structure
Biochemistry Exam 1