BIOC 212 - Midterm

• Where are positioned the side chains in an alpha helix?

  Point outwards
• Why can't beta strands/sheets be completely straight?

  Because of the rigid peptide bonds.
• Where are located the side chains in beta sheets/strands?

  alternate pointing on either side of the backbone.
• What holds different secondary structures together in a tertiary structure?

  Hydrogen bonds between the side chains of the secondary structure elements.

  Can also be some long-range contacts between residues of a secondary structure.
• Are the interactions between the different subunits of a quaternary structure stable?

  Yes, very stable. They are often non-reversible (permanent)
• What length are usually human polypeptides?

  100 to 800 amino acids or 12kDa to 90 kDa.
• What length are domains usually?

  50 to 200 amino acids
• What does sequence similarity (homology) indicate?

  Evolutionary conservation, a common structure or function.
• What are protein families?

  sets of proteins which have a similarity or homology in their sequences
• Can proteins with divergent sequences still have comparable functions?

  Yes, even if they have no similarity and different structures.
• What are modular domains?

  Conserved domains, they can be found in many different proteins and often in combination with other domains.
• Can the polypeptide backbone do hydrophobic interactions?

  No, because the polypeptide backbone itself is polar. It can do hydrogen bonds and Van der Walls
• What amino acids can be phosphorylated?

  Serine (S), Threonine (T) and Tyrosine (Y)
• What is the consequence of phosphorylation conserning the phosphorylated amino acid's properties?

  It adds a charge (-) from the phosphate group and increases the size of the initial amino acid.
• What is responsible for adding the phosphate to an amino acid during phosphorylation?

  Kinases, they transfer a phosphate group from ATP.
• Are Kinases selective for certain amino acids?

  yes, they are specific to an amino acid and to the surrounding polypeptide sequence.
• What is responsible for removing the phosphate from a phosphorylated amino acid?

  Phosphatases, they remove the phosphate and bring back the hydroxyl group.
• What are the different Kinase families?

  Ser/Thr kinases

  Tyr kinases

  Dual specificity (Ser/Thr and Tyr) they are able to modify both families
• What are the different phosphatase families?

  Ser/Thr phosphatases

  Protein Tyr phosphatases

  Dual specificity phosphatases (Ser/Thr and Tyr)
• In phosphopeptide binding, what do phosphate groups most interact with? What other interaction can be seen and where?

  Positively charged amino acids, because the phosphate group is negatively charged. There are also hydrophobic interactions with the sequence surrounding the phosphorylated amino acid.
• What amino acid can be acetylated?

  Lysine
• What amino acid can be methylated?

  Lysine and arginine.
• What are the results of lysine methylation?

  The creation of an isopeptide bond, and changes the polarity of the amino acid, which was at first positively charged, and now uncharged.
• What are the consequences of methylation of a lysine residue?

  It does not change the charge of the lysine but it adds in size.
• What is the consequence of methylation of arginine residues?

  It does not change the charge of the lysine but it adds in size.
• What is the family of enzymes responsible for methylation of lysine and arginine residues?

  Methyltransferases
• What is the family of enzymes responsible for acetylation of lysine residues?

  Acetyltransferase
• What is the family of enzymes responsible for reversing the methylation of lysine and arginine residues?

  Demethylases
• What is the family of enzymes responsible for reversing the acetylation of lysine residues?

  deacetylases
• What is the native state?

  is the completely folded structure, and generally the most stable conformation of the protein
• What are the different genetic mutations that lead to changes in the polypeptide sequence?

  Substitution, insertion, deletion.
• What is an allelic variation?

  change in amino acids in a polypeptide sequence sometimes causing genetic disease (pathogenic)
• What proceeds the native state?

  Folding intermediates.
• When does protein misfolding occur?

  Incompletely folded proteins:

  o Immediately after synthesis

  o Required ligand not available

  o Previously native but unfolded by stress (eg. heat)

  o Genetic mutations
• What are the functions of chaperones?

  promote protein folding and can change protein structure. assist folding and prevent aggregation, without being part of the native state. They are transient and are not considered in the quaternary structure.
• What do chaperones often recognize?

  Hydrophobic regions of the folding intermediates.
• What is the link between chaperones and HSP?

  Many chaperones are heat shock proteins (HSP), they are highly expressed after stress.
• What are the two types of chaperones?

  ATP-dependent chaperones: actively promote folding

  ATP-independent chaperones: prevent aggregation and can catalyze some folding steps.
• What are the families of ATP-dependent chaperones?

  Chaperonins (HSP60 family)

  HSP70 family

  HSP90 family
• Where are HSP70 chaperones found?

  In eukaryotes: Cytosol, ER lumen, mitochondria

  In bacteria