Lecture 1 Flashcards
(19 cards)
How are protein 3D structures determined?
X-ray crystallography (crystals), Cayo-electron microscopy(Frozen) and NMR spectroscopy ( Solution)
What protein was used for the first folding experiment?
RNaseA 124 aa
Biological interest of Urea
Denature agent, degrades H bonds
Biological interest of Mercaptoethanol
Denature agent, degrades S bonds
Why was Anfinsens Experiment important
The primary sequence of amino acids contains all the
information required for the polypeptide chain to fold
into its biologically active, three dimensional structure
Why is it important for proteins to be dinamic
-Must be able to degrade and create proteins easily -Some enzymes need structural flexibility -Controlling their own availability and those of other proteins -Precise timing of cellular events such as signalling, transport -Fast turnover
What is the hydrophobic effect
The tendency of water to
self-associate and exclude non-polar molecules
What is the folding process?
The transition from the unfolded to the folded state
What is a molten globule
A protein intermediate that possess some secondary structure,
but have very little well-formed tertiary structure
protein states that are more or less compact (hence the “globule”), but are lacking the specific tight packing of amino acid residues which creates the solid state-like tertiary structure of completely folded proteins.
What are the classical mechanism for describing folding?
- The framework model
- The hydrophobic collapse model
- The nucleation-condensate mechanism
What is a protein ensemble?
A protein’s ‘state’
What are protein funnels used for?
Folding funnels can be used to describe how folding takes places on these dynamic molecules
How are protein funnels studied?
Protein folding is studied using biophysical, biochemical, structural and computational approaches
in vitro using isolated proteins, in-cell and also, more recently, as it occurs on the ribosome
How is protein folding assisted?
Folding of many proteins is facilitated by a specialized class of proteins called Chaperones.
What are chaperones?
A specialized class of proteins that assist with protein folding
What does thermodynamic says about systems at constant temperature and pressure?
They will seek equilibrium stages at low energgy and high entropy
Does thermodynamics favour protein folding
Energetically wise yes, Entropy wise not.
That is why inter-residue attractiveness interactions must be made in order for the protein to fold.
How is protein folding related to an increase entropy
By blurring hydrophobic amino acids in the core, entropy is increased as it increases the number of their configurations.
Aliphatic Compounds
any chemical compound belonging to the organic class in which the atoms are connected by single, double, or triple bonds to form nonaromatic structures.
