Protein Primary Structure Flashcards
(26 cards)
What is a peptide bond?
A bond formed between the a-carboxyl of one amino acid and the a-amino of another, with the removal of water
What are the phi (ɸ) and psi (Ѱ) angles?
Angles around the N-Cα and Cα-C bonds of amino acids that determine protein conformation
What does the Ramachandran plot represent?
Plots degrees of freedom of phi and psi angles on x (phi) and y (psi) axes
What do the red and yellow regions on a Ramachandran plot indicate?
Red region = conformations with no steric clashes; Yellow region = allowed regions with slight steric clashes
Why is glycine special in the context of the Ramachandran plot?
Glycine has a hydrogen R-group, allowing it to exist in any of the four quadrants of the plot
What are the main types of physiochemical interactions in proteins?
- Hydrogen bonds
- Hydrophobic interactions
- Ionic interactions
- Covalent bonds
- Disulfide bridges
- Van der Waals forces
What is the characteristic structure of an alpha-helix?
A spiral conformation where every backbone carbonyl oxygen forms a hydrogen bond with an amide group of an amino acid 4 residues ahead
How many amino acids are typically in one turn of an alpha-helix?
Approximately 3.6 amino acids
What defines a beta-strand?
A segment of 5-10 amino acids that rarely exists alone and usually aligns with other strands to form a sheet
What are loops in protein structure?
Flexible regions present on the surface of proteins, rich in polarity, and form hydrogen bonds with surrounding water molecules
What are domains in protein structure?
Tightly folded sub-regions of a polypeptide, often serving independent functions and comprised of structural motifs
What are the three categories of protein domains?
- α-domain
- β-domain
- αβ-domain
What experimental approaches are used to determine tertiary structure?
- X-ray crystallography
- NMR
- Cryo-EM
What is X-ray crystallography?
A technique that bombards protein crystals with electrons to amplify and detect/diffract the protein structure
What are the steps involved in crystallography?
- Protein expression
- Purification
- Precipitation
- Sample preparation
What factors affect protein solubility during crystallization?
- Concentration
- pH
- Salts
- Polar solvents
- Temperature
What are the two methods of crystallization?
- Vapour diffusion
- Dialysis method
What is Bragg’s Law?
λ = 2dSinΘ, where λ is the wavelength, d is the Bragg plane separation distance, and Θ is the angle of incidence
What is the purpose of AlphaFold?
To predict protein structure de novo using deep neural networks trained on specific properties
What are the three overlapping problems of the protein folding problem?
- The Folding code
- Computational problem
- Kinetic question
What is the primary driving force behind protein evolution?
Gene duplications
What is the role of divergence in protein evolution?
Further modifies existing paralogs, leading to more diversity between protein families
What is phylogenetics?
The study of evolutionary history of species through construction and analysis of phylogenetic trees
What are the two main tree building methods in phylogenetics?
- Distance methods
- Character-based methods
