Principles of Biomolecular Structures Flashcards
Proteins play many roles in the body. What determines the role of a protein?
Its structure
What is the difference between primary, secondary, tertiary and quaternary structures?
Primary: sequence of amino acids
Secondary: Alpha helices and Beta sheets
Tertiary polypeptide chain, 3 dimensional folding
Quaternary: association of multiple of multiple folded chains
What is a property of all aliphatic amino acids?
Mostly just hydrocarbons
Which two AAs are found primarily in loops and why?
Glycine for its flexibility and Proline for its rigidity
Where are most hydrophobic AAs found?
In the hydrophobic core of proteins (away from water)
Which AA is prevalent in active sites?
Cysteine
Which proteins are nucleophilic and why?
Serine, Threonine Cysteine and Tyrosine, because of their electronegative atoms
What happens to ionizable groups in proteins at physiological pH of 7.4?
Depending on the pKa, the acid or base is favored
Why do helices have a strong dipole?
Because the dehydration synthesis of peptides create a dipole moment, a spiral of AAs cancel outwards pointing dipoles and add up the axial dipoles
Which conformation is favoured in a X-Z peptide bond?
What about for X-Pro?
X-Z - Trans (Cis has too much steric hindrance)
X-Pro - both configurations have equal repulsion and are found in equal populations
Which terminal group has the phi torsion? the psi torsion?
Amino - Phi
Carbonyl - Psi
Why are only certain combinations of phi and psi angles possible? How can you visualize these combinations?
Because of steric clashes between side chains
Combinations can be visualized in a Ramachandran plot
An alpha helical polipeptide has _____ phi and ______ psi torsion angles (positive/negative)
Both negative
An alpha helix formed by L-amino acids is said to be ____-handed, and is stabilized by H bonds between ______
right
the carbonyl oxygen of residue i and the amide group of i+4
A beta strand has ____ phi and ____ psi torsion angles (positive/negative)
negative
positive
How are beta strands sustained?
By cross-strand hydrogen bonds in both parallel and anti-parallel sheets
In convention, what is the difference between a turn and a loop?
Turn: less than 4 AA
Loop: greater than 4 AA
What dictates the protein fold?
The primary sequence
proteins fold in such a way to form a _____ core which tends to be very efficient and compact
Hydrophobic
What is the helical propensity of an amino acid?
Its tendency to form helices
Why arent S-S bonds found intracellularly?
Because of the reducing environment of the cytosol
What is a hydration shell?
A layer of water molecules surrounding the protein, stabilized by hydrogen bonds to the exposed polar groups
How is the loss of entropy compensated during formation of a hydration shell?
Hydrogen bond formation
How can drugs stabilize proteins?
By shifting the temperature stability map to the right
What can be added to water to denature proteins in solution?
Decreasing the entropy of water by adding eg a chaotropic agent (like urea)
How are chaperones useful?
To assist overcoming the entropic barrier of folding (and to avoid intermolecular contacts leading to amyloid fibrils)
How many post-translational modifications are there?
A lot
True/False? Proteins with the same function have similar structure
False
proteins can have the same function with completely different folds, or similar structure but different functions
What is molecular surface?
The VdW surface contact plus the re-entrant surface generated with a molecular probe such as water
What is buried surface area?
The difference between the sum of the individual subunits surface of the complex
True/False? Proteins are typically quite rigid
False, only some parts are very rigid but for the most part are floppy
