36 Questions
The F1 component of the ATP synthase enzyme has 3 β subunits with each adopting a different ______ at a given time (loose, open, and tight conformations).
conformation
The hydrophobic effect stabilizes ______ structure.
protein
Aromatic R Groups can contribute to the ______ effect.
hydrophobic
Cys can form ______ bonds.
disulfide
Cys has a positive hydropathy index, classified as polar due to its SH group's ability to act as a weak acid and be involved in weak ______ bonds.
hydrogen
Amphitropic Proteins have a reversible lipid attachment process, where the lipid attachment is __________
covalently
B-strands never occur singly, but always as part of a ________
sheet
In a b-strand, each residue extends ________ Å
3.5
β-barrel proteins have no unpaired hydrogen bonding main chain groups, making them suitable as __________ proteins
membrane
All b-barrel membrane proteins have an even number of b-strands, reflecting the requirement that they be inserted ________
pairwise
Since side chains in a beta strand project alternately on either side, all hydrophobic residues fall on one side and the hydrophilic residues fall on the other side of the ________ strand
beta
The hydrophobic side faces the __________ and the hydrophilic side faces the interior of the barrel.
exterior
Even number of strands in OMP structures results in strands that do not ______ each other.
cross
Periplasmic loops in OMP structures are often very ______, sometimes forming β-turns.
short
Barrels with 8-10 strands in OMP structures have a solid core filled with ______ residues.
hydrophilic
Intermediate-sized b-barrels with 16-18 strands in OMP structures have aqueous pores generally with inserted ______.
loops
Large barrels with 22–26 b-strands in OMP structures generally have a plug domain that ______ into and closes most of the channel.
inserts
Match the OMP structure characteristics with their corresponding descriptions:
Even number of strands = Results in strands that do not cross each other Antiparallel β sheet = All b-strands in OMP structures are arranged in this manner Extracellular loops are often long = Characteristic feature of OMP structures with 16-18 strands Periplasmic loops are very short = Common in OMP structures such as OmpX with 8 strands
Match the OMP examples with their respective number of beta strands:
OmpX = 8 strands OmpF = 18 strands FepA = 22 strands VDAC = Odd number of beta strands
Match the OMP structure sizes with their corresponding features:
Barrels with 8-10 strands = Have a solid core filled with hydrophilic residues Intermediate sized b-barrels with 16-18 strands = Have aqueous pores generally with inserted loops Large barrels with 22–26 b-strands = Generally have a plug domain that inserts into and closes most of the channel VDAC - voltage-dependent anion channel = Made up of an odd number of beta strands
Match the location descriptions to the corresponding termini in OMP structures:
N and C-termini always periplasmic and next to each other = Characteristic positioning in OMP structures Helix at N-terminus inserts into pore = Specific feature observed in certain OMP structures Most abundant OM protein in eukaryotic mitochondria = VDAC - voltage-dependent anion channel Acts as an ion channel; also plays a role in apoptosis = VDAC - voltage-dependent anion channel
Match the residue types to their location in the beta-barrel structure:
Hydrophobic residues = Found on the side facing the exterior of the barrel Hydrophilic residues = Found on the side facing the interior of the barrel Interior residues = Residues within the beta-barrel structure Bilayer facing residues = Residues facing the lipid bilayer
Match the amino acid property with its corresponding description:
Negatively Charged R Groups = Can form ionic bonds Aromatic R Groups = Can contribute to the hydrophobic effect Polar, Uncharged R Groups = R groups can form hydrogen bonds Nonpolar, aliphatic R groups = Contribute to hydrophobic effect
Match the protein symmetry with its example:
Quasi-symmetry = F1 component of the ATP synthase enzyme Anti-parallel symmetry = VDAC protein
Match the number of beta strands with the corresponding OMP structure size:
8-10 strands = Small barrels with a solid core filled with hydrophobic residues 22–26 strands = Large barrels generally with a plug domain that closes most of the channel
Match the location in a beta strand with its characteristic feature:
Hydrophobic side = Faces the lipid bilayer Hydrophilic side = Faces the interior of the barrel
Match the residue type with its specific location in a beta-barrel structure:
Cys = Located in positions where disulfide bonds can form Aromatic R Groups = Located to contribute to the hydrophobic effect
Match the effect with its role in stabilizing protein structure:
The hydrophobic effect = Stabilizes protein structure
Match the amino acid classification with its rationale:
Cys classified as polar = Due to its SH group's involvement in weak hydrogen bonds
Match the termini description with its corresponding location in OMP structures:
Periplasmic loops = Often forming beta-turns
Match the number of subunits with their conformations in a protein complex:
3 beta subunits = Adopting different conformations (loose, open, tight) at a given time
Match the lipid attachment process with its characteristic for Amphitropic Proteins:
Reversible lipid attachment process = Where lipid attachment can occur
Match the following terms related to protein structure with their corresponding descriptions:
Anti-parallel beta strands = Side chains project alternately on either side Hydrophobic effect = Stabilizes protein structure Polar, Uncharged R Groups = Can form hydrogen bonds Cys = Can form disulfide bonds
Match the following characteristics of VDAC (Voltage-Dependent Anion Channel) with their functions:
Solid core filled with hydrophobic residues = Forms the interior of the barrel Aqueous pores in OMP structures = Generally have inserted proteins Plug domain in large barrels = Inserts into and closes most of the channel Reversible lipid attachment process = Characteristic of Amphitropic Proteins
Match the residue types with their specific locations in beta-barrel structures:
Aromatic R Groups = Contribute to the hydrophobic effect Negatively Charged R Groups = Located on the hydrophilic side Positively Charged R Groups = Located on the hydrophilic side Cys = Classified as polar due to its weak acid ability
Match the following amino acid properties with their corresponding descriptions:
Hydropathy index of Cys = Positive due to SH group's weak acid ability 20 naturally occurring amino acids = Include nonpolar, aliphatic R groups Quasi-symmetry proteins = Have multiple copies with different conformations F1 component of ATP synthase enzyme = Has 3 β subunits with different conformations
Explore the characteristics of beta-strands in proteins, including their conformation, hydrogen bonds, arrangement in sheets, and side chain orientation. Learn about the reversible lipid attachment process for some lipid-linked proteins.
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