BIOC 402 - Complete Final Exam Review || A+ Certified.
Side chain naming of amino acids correct answers A, B, G, D, E, Z, H
What are chi angles? correct answers Angles between side chain (R-group) atoms
What are the 3 peptide backbone angles? correct answers Phi (C-N-CA-C), psi (N-CA-C-N), and
omega (CA-C-N-CA)
What 4 atoms describe the phi angle? correct answers C-N-CA-C
What 4 atoms describe the psi angle? correct answers N-CA-C-N
What 4 atoms describe the omega angle? correct answers CA-N-C-CA
What is the trans:cis ratio of the peptide bond in a typical peptide bond (not X-Pro)? correct
answers 99:1
What is the trans:cis ratio of the peptide bond in an X-Pro peptide bond? correct answers 4:1
What are the four helices in proteins? correct answers 2.2_7 ribbon, 3_10 helix, alpha helix
(3.6_13), pi helix (4.4_16)
Why isn't a 2.2_7 ribbon seen in proteins? correct answers Unfavourable phi/psi angles and
distorted H-bonds
Why isn't a 3_10 helix as common as an alpha helix? correct answers Phi/psi angles are at the
edge of the allowable area, packing is too close, and H-bonds aren't as straight
Why isn't a 4.4_16 helix seen as a full helix in proteins? correct answers Unstable, open hole in
the centre, no favourable atom packing
What is a polypeptide II helix? correct answers Left-handed helix of mainly Pro and Gly, without
backbone H-bonds, stabilized by 3 helices twisted together
What are the characteristics of antiparallel beta sheets? correct answers H-bonds occur in pairs
on the same side of the sheet and are nicely aligned
What are the characteristics of parallel beta sheets? correct answers H-bonds are distributed
evenly and are not in straight lines
What is a beta turn? correct answers A four-residue turn, where the first residue H-bonds with
the fourth. Type I has the oxygen and R-group on opposite sides, whereas Type II have the
oxygen and R-group on the same side (only occurs w/ Gly in pos. 3)
,When is a coil formed? correct answers When phi/psi angles are not consecutively in the alpha
helix or beta sheet regions
What is a protein domain? correct answers Compact, locally folded region of tertiary structure
What are the levels of CATH? correct answers Domain class, architecture, topology,
homologous superfamily
How do hairpins and crossovers differ? correct answers Hairpins connect strands on the same
edge of a beta sheet, whereas crossovers connect a strand to the opposite side of the sheet
What does it mean for proteins to be homologous? correct answers Share a common evolutionary
ancestry
How are structural similarity and sequence identity related? correct answers High sequence
identity (> 30%) confers a high structural similarity (but NOT vice versa)
How are structural similarity, sequence identity, and protein function related? correct answers
High sequence or structure identity do not indicate similar function
What are the steps in homology modelling? (8 main steps) correct answers 1) Identify homologs
in a database, 2) align sequences, 3) find conserved sequence regions, 4) find variable sequence
regions, 5) generate coordinates of CSRs, 6) swap in different variable regions, 7) add side
chains, 8) minimize energy to find optimal structure
What are IDPs / intrinsically disordered polypeptide segments correct answers Segments > 30
amino acids long that lack a unique tertiary structure when alone in solution
What are characteristics of IPD amino acid sequence? correct answers Lack hydrophobics,
enriched in charged and polar residues, low complexity
How are IPDs and protein regulation related? correct answers IDPs can be easily accessed by
proteins that add/remove PTMs and by binding partners, allowing for regulation of different
interactions
What are SLiMs? correct answers Short sequences of specific residues that are recognized for
binding in IDPs (e.g. Pro-X-X-Pro is common IDPs and recognized by SH3 domains)
What are the main types of advantages of IDPs in binding? (2 key points) correct answers
Thermodynamic advantages: fold upon binding for high specificity and low affinity;
conformational advantage: able to adopt different conformations and have multiple binding
partners
What types of protein roles are IDPs enriched for, and what are they depleted in? correct answers
Enriched in signalling, regulation, assembly, and recognition; depleted in enzymes (metabolism,
catalysis)
, What are biomolecular condensates? correct answers Membraneless organelles formed from
lipid droplets of multivalent proteins
What are the characteristics of liquid droplets? correct answers Spherical, can drip, can fuse,
constituents are dynamic
How does FRAP demonstrate that liquid droplets are dynamic? correct answers Fluorescing
droplet > photobleach with laser > fluorescence increases back over time
What is an ideal solution and what comprises the free energy of mixing? correct answers A
solution in which components do not interact; the free energy of mixing is due the entropy of
mixing
How do you calculate the ratio of the enriched vs. depleted phase using the Lever rule? correct
answers Fraction of the solution that is in the depleted phase: ([overall]-[enriched])/([depleted]-
[enriched])
What are the requirements for proteins to phase separate? correct answers Low solvation
(interact w/ each other instead of H2O), multivalency, weak interactions (to remain dynamic)
How are bimolecular condensates regulated? correct answers Levels of expression and PTMs to
change valency, structure, concentration, and solubility
What are some functions of bimolecular condensates? (3) correct answers Increasing reaction
specificity, inhibition by sequestration, and clustering components together (e.g. TCRs)
What are the properties of amyloid fibrils? (4) correct answers Characteristic diffraction pattern,
negative stain EM, Congo red birefringence, nucleated growth pattern
How is protein aggregation likely prevented in liquid droplets? correct answers Condensates are
short-lived and chaperones and disaggregases may be present
What is the average free energy of a folded protein? correct answers -5 to -15 kcal/mol
What are the factors that drive protein folding? correct answers Hydrophobic effect, vdW,
internal H-bonds, electrostatic interactions, conformational entropy
How do you calculate conformational entropy using the Boltzmann formula? correct answers S =
k ln W
Why does the hydrophobic effect favour protein folding? correct answers The unfolded protein
has a significant loss of entropy due to the first layer of water molecules locked in a clathrate
What is the typical strength of an H-bond? correct answers 1 to 10 kcal/mol
Side chain naming of amino acids correct answers A, B, G, D, E, Z, H
What are chi angles? correct answers Angles between side chain (R-group) atoms
What are the 3 peptide backbone angles? correct answers Phi (C-N-CA-C), psi (N-CA-C-N), and
omega (CA-C-N-CA)
What 4 atoms describe the phi angle? correct answers C-N-CA-C
What 4 atoms describe the psi angle? correct answers N-CA-C-N
What 4 atoms describe the omega angle? correct answers CA-N-C-CA
What is the trans:cis ratio of the peptide bond in a typical peptide bond (not X-Pro)? correct
answers 99:1
What is the trans:cis ratio of the peptide bond in an X-Pro peptide bond? correct answers 4:1
What are the four helices in proteins? correct answers 2.2_7 ribbon, 3_10 helix, alpha helix
(3.6_13), pi helix (4.4_16)
Why isn't a 2.2_7 ribbon seen in proteins? correct answers Unfavourable phi/psi angles and
distorted H-bonds
Why isn't a 3_10 helix as common as an alpha helix? correct answers Phi/psi angles are at the
edge of the allowable area, packing is too close, and H-bonds aren't as straight
Why isn't a 4.4_16 helix seen as a full helix in proteins? correct answers Unstable, open hole in
the centre, no favourable atom packing
What is a polypeptide II helix? correct answers Left-handed helix of mainly Pro and Gly, without
backbone H-bonds, stabilized by 3 helices twisted together
What are the characteristics of antiparallel beta sheets? correct answers H-bonds occur in pairs
on the same side of the sheet and are nicely aligned
What are the characteristics of parallel beta sheets? correct answers H-bonds are distributed
evenly and are not in straight lines
What is a beta turn? correct answers A four-residue turn, where the first residue H-bonds with
the fourth. Type I has the oxygen and R-group on opposite sides, whereas Type II have the
oxygen and R-group on the same side (only occurs w/ Gly in pos. 3)
,When is a coil formed? correct answers When phi/psi angles are not consecutively in the alpha
helix or beta sheet regions
What is a protein domain? correct answers Compact, locally folded region of tertiary structure
What are the levels of CATH? correct answers Domain class, architecture, topology,
homologous superfamily
How do hairpins and crossovers differ? correct answers Hairpins connect strands on the same
edge of a beta sheet, whereas crossovers connect a strand to the opposite side of the sheet
What does it mean for proteins to be homologous? correct answers Share a common evolutionary
ancestry
How are structural similarity and sequence identity related? correct answers High sequence
identity (> 30%) confers a high structural similarity (but NOT vice versa)
How are structural similarity, sequence identity, and protein function related? correct answers
High sequence or structure identity do not indicate similar function
What are the steps in homology modelling? (8 main steps) correct answers 1) Identify homologs
in a database, 2) align sequences, 3) find conserved sequence regions, 4) find variable sequence
regions, 5) generate coordinates of CSRs, 6) swap in different variable regions, 7) add side
chains, 8) minimize energy to find optimal structure
What are IDPs / intrinsically disordered polypeptide segments correct answers Segments > 30
amino acids long that lack a unique tertiary structure when alone in solution
What are characteristics of IPD amino acid sequence? correct answers Lack hydrophobics,
enriched in charged and polar residues, low complexity
How are IPDs and protein regulation related? correct answers IDPs can be easily accessed by
proteins that add/remove PTMs and by binding partners, allowing for regulation of different
interactions
What are SLiMs? correct answers Short sequences of specific residues that are recognized for
binding in IDPs (e.g. Pro-X-X-Pro is common IDPs and recognized by SH3 domains)
What are the main types of advantages of IDPs in binding? (2 key points) correct answers
Thermodynamic advantages: fold upon binding for high specificity and low affinity;
conformational advantage: able to adopt different conformations and have multiple binding
partners
What types of protein roles are IDPs enriched for, and what are they depleted in? correct answers
Enriched in signalling, regulation, assembly, and recognition; depleted in enzymes (metabolism,
catalysis)
, What are biomolecular condensates? correct answers Membraneless organelles formed from
lipid droplets of multivalent proteins
What are the characteristics of liquid droplets? correct answers Spherical, can drip, can fuse,
constituents are dynamic
How does FRAP demonstrate that liquid droplets are dynamic? correct answers Fluorescing
droplet > photobleach with laser > fluorescence increases back over time
What is an ideal solution and what comprises the free energy of mixing? correct answers A
solution in which components do not interact; the free energy of mixing is due the entropy of
mixing
How do you calculate the ratio of the enriched vs. depleted phase using the Lever rule? correct
answers Fraction of the solution that is in the depleted phase: ([overall]-[enriched])/([depleted]-
[enriched])
What are the requirements for proteins to phase separate? correct answers Low solvation
(interact w/ each other instead of H2O), multivalency, weak interactions (to remain dynamic)
How are bimolecular condensates regulated? correct answers Levels of expression and PTMs to
change valency, structure, concentration, and solubility
What are some functions of bimolecular condensates? (3) correct answers Increasing reaction
specificity, inhibition by sequestration, and clustering components together (e.g. TCRs)
What are the properties of amyloid fibrils? (4) correct answers Characteristic diffraction pattern,
negative stain EM, Congo red birefringence, nucleated growth pattern
How is protein aggregation likely prevented in liquid droplets? correct answers Condensates are
short-lived and chaperones and disaggregases may be present
What is the average free energy of a folded protein? correct answers -5 to -15 kcal/mol
What are the factors that drive protein folding? correct answers Hydrophobic effect, vdW,
internal H-bonds, electrostatic interactions, conformational entropy
How do you calculate conformational entropy using the Boltzmann formula? correct answers S =
k ln W
Why does the hydrophobic effect favour protein folding? correct answers The unfolded protein
has a significant loss of entropy due to the first layer of water molecules locked in a clathrate
What is the typical strength of an H-bond? correct answers 1 to 10 kcal/mol
