Lecture 7 DA Flashcards
What determines the function of a protein?
Its structure.
What determines the conformation of a protein’s active site?
The conformation of the side chains of the protein’s non-active site regions.
Are non-active site region residues crucial to a protein’s function?
Yes, because they help correctly form the active site.
What are the aliphatic/polar amino acids?
Glycine Alanine Valine Leucine Methionine Isoleucine
Where are aliphatic/polar amino acids generally found, and why?
Typically inside the protein, usually not on the surface. Stabilises the protein’s structure by hydrophobic interactions, reducing free energy.
What are the aromatic amino acids? Which are hydrophobic/polar/non-polar?
Tyrosine - polar
Tryptophan - non-polar
Phenylalanine - very hydrophobic
Which amino acids strongly absorb UV light?
Aromatic
What are the polar/hydrophilic amino acids?
Serine Threonine Cysteine Proline Asparagine Glutamine
Where are polar/hydrophilic amino acids typically found?
On the surface.
Which amino acid is the only one able to form disulphide bridges?
Cysteine
What are the acidic amino acids? What charge do they have?
Aspartate
Glutamate
Both negative
What are the basic amino acids? What charge do they have?
Lysine
Asparagine
Histidine
All positive
Do peptide bonds have any degrees of freedom, or are they rigid? Do they contribute to 3D structure?
They are planar, with no degrees of freedom. Doesnt contribute to 3D structure, the phi and psi angles do.
Do all proteins form secondary structures?
Most, but not all.
What bonds are responsible for hydrogen bonds?
Hydrogen
Can the secondary structure of proteins be predicted by the primary structure?
Some regions, but not all.
What is the central paradigm?
Amino acid sequence of a protein determines its structure and function.
How can we tell if the primary sequence determines structure?
Protein can be denatured in urea, then allowed to renature. Some, but not all of the proteins will fold to its native state again.
What are three approaches to determining the structure-function relationship of a protein?
Predictive
Experimental
Protein peptide arrays - synthetic/expressed
What are two methods in the predictive approach to determining the structure-function relationship of a protein?
Sequence analysis
Modelling
What are two methods in the experimental approach to determining the structure-function relationship of a protein?
Site directed mutagenesis
Synthetic peptide analogues
What is looked for in a new protein sequence when determining function?
- Similar sequences (ie. BLAST)
- Distinctive patterns or domains with associated functions
- Secondary/tertiary structure predictions
- Motifs/residues important for function
- Physical properties - MW, pI, solubility etc
Describe the levels of protein structure/function relationship (6).
Superfamily Family Domain Motif Site Residue
Which levels of the protein structure/function relationship is associated with the secondary structure (3)?
Superfamily, family, and domain
