Chapter 7
Learning Objectives
1. What occurs in amloidosis? /AL variant?
 Amyloidosis is a term for diseases that exhibit extracellular deposition of insoluble proteins
called amyloid. Amyloidosis/AL has amyloid derived from immunoglobin light chains, which
deposits most frequently in the kidney and heart
2. What AAs tend to form alpha helices? What amino acid is a “helix breaker?”
 Since the R groups face outwards, only hydrophilic AAs form alpha helices
 Because its nitrogen is part of its cyclic structure, proline is a helix breaker
3. Describe the attraction pattern in beta-pleated sheets. How is the structure different in parallel
and antiparallel arrangements?
 The carbonyl oxygen of one peptide backbone is hydrogen-bound to the nitrogen of another
peptide backbone (same for alpha helices)
 In parallel orientations the bonds are slightlly skewed, whereas in antiparallel orientations
the bonds are at “right” angles to each other
4. ATP is bound by which type of protein fold? How about NAD+ or NADP+?
 ATP binds in the cleft of an actin fold, such as that belonging to actin, hsp70, or hexokinase
 NAD+ or NADP+ are bound by nucleotide-binding folds
5. Where would you find Ser, Thr, Asn, Gln, Tyr, or Trp in a protein?
 You could find them on the exterior, or in the interior, with their R groups hydrogen bonded
to other chains.
6. How are the subunits of globular proteins held together?
 Subunits of globular proteins are held together usually by hydrogen or ionic bonds, very
rarely by interchain disulfide bonds, and never by covalent bonds
7. Protein MagickBanana binds its ligand tighter than another. How will its Ka differ?
 Protein MagicBanana will have a higher association constant, or larger Ka
8. Why does urine turn red after muscle injury?
 Myoglobin leaks from damaged muscle cells and passes into the urine. It is red because the
heme group remains covalently attached to the protein.
9. How does sickle cell’s hemoglobin polymerization occur?
 The valine substitution of glutamate in the mutant beta2 chain creates a “valine knob” on
the surface of deoxygenated hemoglobin that fits into a hydrophobic binding pocket of a
beta1 subunit. If this beta1 subunit is deoxygenated and its connected beta2 also has the
valine knob, the process continues.
“You can B 2 Mutant”
10. How is the process of oxygen binding different between hemoglobin and myoglobin?

When hemoglobin binds O2, the O2 molecule pulls a proximal histidine (his-92) residue
towards the porphyrin ring, changing the comformation of all other subunits to more easily
accept O2
11. What conditions are necessary for spontaneous refolding after urea exposure?
 We must have a single-subunit protein, and we have to carefully return it to physiologic
conditions. Urea disrupts hydrogen bonding.
12. Which are the most abundant class of immunoglobins?
 Out of the five major classes, gamma globulins are the most abundant.
13. What does a cis-trans isomerase do?
 Converts a trans bond preceding a proline into the cis formation, creating a hairpin turn
14. Name a condition in which the rate of glycosylation increases. Does it affect hemoglobin?
 Glycosylation is a nonenzymatic reaction with a rate of reaction proportionate to the
concentration of glucose present, therefore hyperglycemia will increase glycosylation
 Glycosylated hemoglobin—HbA1c is diagnostically useful but functionally no different from
normal hemoglobin
15. The PrPSc conformer is enriched in which structure? How is this structure harmful?
 The abnormal form of a prion protein has more Beta-sheets, which favor aggregation of the
protein into multimeric complexes. The structure also acts as a template for further
misfoldings