Protein Structure Flashcards
What are the characteristics of a peptide bond?
A peptide bond is rigid and planar. This will constrain the protein to certain, allowed conformations. Contain both phi and psi bonds around the R group.
Define native fold.
Protein molecules adopt a specific three-dimensional conformation. The structure of the protein is able to fulfill a specific biological function. This is when the protein is considered properly folded and functional conformation. The protein will contain a large number of favorable interactions (non-covalent and disulfide do the work).
Describe what primary structure is.
Defines all other structures which means it defines function. It is an amino acid sequence that includes covalent bonds. There is a clear distinction between the proteins. Amino acid sequence is determined by the gene in the DNA.
Describe what secondary structure is.
Regular recurring arrangements in space of adjacent amino acid residues in a polypeptide chain. Most prominent structure is alpha helix and beta sheets.
What are the four levels of protein structure?
Amino acid residues (sequence) –> alpha helix (repeating hydrogen bonding) –> polypeptide chain –> assembled subunits
Describe an alpha helix.
Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n+4 amino acids. Right handed helix contains 3.6 residues.
Describe what a beta sheet is.
The planarity of the peptide bond and tetrahedral geometry of the alpha-carbon create a pleated sheet-like structure (zigzag). Sheet like arrangement of backbone is held together by hydrogen bonds between the backbone amides in different strands. Side chains protrude from the sheet alternating in up and down direction.
Describe what a beta turn is.
Beta turns occur frequently when strands in beta sheets change direction. The 180 degree turn is accomplished over four amino acids. The turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence.
Describe what a tertiary structure is.
Overall 3D arrangement of all atoms in a protein. This structure is stabilized by numerous weak interactions between amino acid side chains (Large hydrophobic, polar interactions, and disulfide bonds). Increase entropy when taking up their shape.
What is a fibrous protein?
Proteins that contain high proportions of alpha helices and beta pleated sheets. Contains repeating units of 2nd structure. Often have structural rather than dynamic roles and are water insoluble. (ex. keratin and collagen)
What is a globular protein?
Have an arrangement of different secondary structural elements. Have more dynamic roles. (ex. enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins, hemoglobin)
What is a motif?
Specific arrangement of two or more secondary structure elements. They can be found as reoccurring structures in numerous proteins. They typically do not have independent function. (Think of your finger)
What is a domain?
It is a relatively stable, independently folded region within the tertiary structure of a globular protein. Each one may encompass one or more motifs, and each has a specific function.
Describe what quaternary structure is.
Results from the aggregation of two or more polypeptide subunits into a larger functional cluster.
