Proteins Flashcards
Protein Domain
A portion of an amino acid sequence that can form a tertiary structure independent of the rest of the protein.
How many amino acids are typically found in a protein domain?
Around 40-350 amino acids.
Typically, hydrophobic residues are located in the core of the protein, while hydrophilic ones are located on the surface. However, hydrophilic residues can be located in the core if what condition is satisfied?
Hydrophilic residues are on the surface because they interact with water. Likewise, a hydrophilic residue in the interior would interact not with water, but other residues on the polypeptide.
What observation would lead you to believe that proteins fold into their conformation using only the information in the amino acid sequence?
Proteins spontaneously regain their conformation if a denaturing agent is removed.
What’s the role of a molecular chaperone in protein folding?
Molecular chaperones help a protein reach it’s final conformation, but they are not required for a protein to fold.
α-helix
A type of secondary structure stabalized by hydrogen bonds between the amino and carboyxl groups on a polypeptide backbone. Each hydrogen bond is seperated by four peptide bonds, resulting in a helical structure.
β-sheet
A type of sheet-like secondary structure where two regions of polypeptide are held together side-by-side through hydrogen bonding between the backbone.
Coiled-coil
A structural motif where two alpha helices are wrapped around each other like strands of rope. The structure is stabalized by repetitive hydrophobic residues located at the areas where the two strands merge.
There are many possible unstable conformations, and yet the majority of proteins in cells have stable conformations. Why?
Natural selection selects for proteins with stable conformations.
Protein familly
A group of proteins which share evoltionary homology.
Paralog
Structurally different proteins belonging to the same familly.
Ortholog
Different versions of the same protein found in different organisms.
Domain shuffling
An evolutionary process, in which new proteins are created through the shuffling, addition, or removal, of protein domains.
In-line protein
Proteins who have binding sites located on opposite poles of the molecule, allowing the protein to join together with itself or other proteins into long chains.
Plug-in type proteins
Proteins who have binding sites located on the same side of the molecule. These proteins are inserted into a loop region of another protein.
Binding site
A region of a protein that can interact with another molecule through non-covalent interactions.
Protein subunit
A polypeptide which has formed a non-covalent interaction with another polypeptide. The entire unit acts as one protein.
How do proteins form assemblies of rings and helices?
If a protein is capable of binding to itself, then it is capable of forming rings and helices.
Intrinsically disordered proteins
Proteins which contain regions that have no stable structure. These regions often change their structure when they bind to target molecules.
Large structures such as tubes, rings, and spheres are often assembled from protein subunits. What is the advantage of this approach?
It use less genetic material, its easier to assemble and dissasemble, and subunits are easier to repair.
What provides the information for the assembly of a large protein structure?
The subunits themselves in most cases. Sometimes certain assembly factors are required.
Assembly factor
A molecule used in the assembly of a large protein structure but not part of the structure itself.
Hydrolase
General term for enzymes which catalyze hydrolytic cleavage reactions.
Nuclease
Hydrolytically cleaves nucleic acids.
