Protein Structure and Function Flashcards
What is a cofactor?
A cofactor is a non-protein chemical compound or metallic ion that is required for a protein’s biological activity to happen
What is a binding pocket?
Binding pockets- as the binding sites for ligands involve residues from different parts of the poly peptide chain and as the protein folds, it brings all these binding sites together to form the binding pockets
What is meant by “concerted switch”? (Hint: haemoglobin oxygen binding).
As one oxygen binds it changes the shape and this pulls and changes the shape of the other sub units of the tetramer which causes their affinity for oxygen to increase
Why do globular proteins tend to be more soluble?
Globular proteins tend to be more soluble because it is much easier to have the hydrophobic structures on the inside and the hydrophilic structures on the outside
What type of cross links are formed in collagen and keratin matrices? (Hint: which residues are involved in cross link formation)?
Collagen- cross links involving lysine residues
Keratin- cross links involving cysteine residues.
What is the structure and function of collagen?
- Extracellular matrice
- Connective tissue, skin and tendons
- Triple helix
What is the structure of keratin?
Double helix
Describe the structure of spider silk?
-Beta sheets joined by irregular structured regions
What are the two proteins in spider silk? Which parts of the silk do they form?
- Sericin-sticky material surrounding structural centre
- Fibroin-structural centre
What are the structures that extrude the spider silk?
Spigots.
How does gel filtration chromatography separate proteins by size?
Gel beads can retain small proteins but not large ones. Large ones pass through column more quickly.
How does ion exchange chromatography separate proteins by charge?
- Charged beads
- Charged proteins interact with oppositely charged beads
- Use different concentrations of salt solutions to liberate protein
- How much salt it takes to remove them =how strong their charge is.
What are the two storage proteins in wheat? Why do they allow wheat to be a storage protein?
-Gliadin and glutenin
What is a prosthetic group on an enzyme?
Non removable coenzyme which is bound tightly (usually)
What are apoenzymes and holoenzymes?
- Apoenzyme-Enzyme lacking cofactor (inactive)
* Holoenzyme- Enzyme with bound cofactor (active)
What is the transition state?
Transition state- energy you need to put in is the activation energy (the increase on a reaction pathway graph)
How does a catalyst decrease the activation energy?
By selectively stabilising the substrate transition state, the activation energy can be lowered and the reaction can occur faster. Stabilisation usually occurs through covalent interactions.
What type of curve does the Michaelis Menten equation give (to model ES complexes)?
Hyperbola
What are the effects on Km (substrate conc at 1/2 Vmax) and Vmax for competitive and non competitive inhibitors?
Competitive:
- Increase Km as less substrate can bind
- No effect on Vmax
Non-competitive:
- Does not affect Km
- Decrease in Vmax
Why do small rings often make good inhibitors?
Small rings (e.g. 4 membered rings) tend to be reactive as they are strained- this makes them good inhibitors as they easily bind to the enzyme
How does penicillin kill bacteria? (Hint: talk about the specific ring structure in penicillin).
Penicillin’s 4 membered beta-lactam ring binds to the enzyme DD-transpeptidase which therefore cannot catalyse the formation of the peptidoglycan crosslinks in the cell wall so therefore the bacteria burst from osmotic shock
How does phosphorylation increase protein interaction?
-Gives it a negative charge and allows charge charge interactions to form
How can cleavage of specific peptide bonds cause activation of a protein?
Cleavage of specific peptide bonds in a precursor forms of a protein can lead to a conformational change which activates the function of the protein
How does urea prevent aggregate formation?
Urea is a denaturant and prevents aggregate formation by preventing H bonds forming
