Protein Structure and Function

Question 1

What is a cofactor?

Answer 1

A cofactor is a non-protein chemical compound or metallic ion that is required for a protein’s biological activity to happen

Question 2

What is a binding pocket?

Answer 2

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

Question 3

What is meant by “concerted switch”? (Hint: haemoglobin oxygen binding).

Answer 3

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

Question 4

Why do globular proteins tend to be more soluble?

Answer 4

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

Question 5

What type of cross links are formed in collagen and keratin matrices? (Hint: which residues are involved in cross link formation)?

Answer 5

Collagen- cross links involving lysine residues

Keratin- cross links involving cysteine residues.

Question 6

What is the structure and function of collagen?

Answer 6

• Extracellular matrice
• Connective tissue, skin and tendons
• Triple helix

Question 7

What is the structure of keratin?

Answer 7

Double helix

Question 8

Describe the structure of spider silk?

Answer 8

-Beta sheets joined by irregular structured regions

Question 9

What are the two proteins in spider silk? Which parts of the silk do they form?

Answer 9

• Sericin-sticky material surrounding structural centre

- Fibroin-structural centre

Question 10

What are the structures that extrude the spider silk?

Answer 10

Spigots.

Question 11

How does gel filtration chromatography separate proteins by size?

Answer 11

Gel beads can retain small proteins but not large ones. Large ones pass through column more quickly.

Question 12

How does ion exchange chromatography separate proteins by charge?

Answer 12

• 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.

Question 13

What are the two storage proteins in wheat? Why do they allow wheat to be a storage protein?

Answer 13

-Gliadin and glutenin

Question 14

What is a prosthetic group on an enzyme?

Answer 14

Non removable coenzyme which is bound tightly (usually)

Question 15

What are apoenzymes and holoenzymes?

Answer 15

• Apoenzyme-Enzyme lacking cofactor (inactive)

* Holoenzyme- Enzyme with bound cofactor (active)

Question 16

What is the transition state?

Answer 16

Transition state- energy you need to put in is the activation energy (the increase on a reaction pathway graph)

Question 17

How does a catalyst decrease the activation energy?

Answer 17

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.

Question 18

What type of curve does the Michaelis Menten equation give (to model ES complexes)?

Answer 18

Hyperbola

Question 19

What are the effects on Km (substrate conc at 1/2 Vmax) and Vmax for competitive and non competitive inhibitors?

Answer 19

Competitive:

• Increase Km as less substrate can bind
• No effect on Vmax

Non-competitive:

• Does not affect Km
• Decrease in Vmax

Question 20

Why do small rings often make good inhibitors?

Answer 20

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

Question 21

How does penicillin kill bacteria? (Hint: talk about the specific ring structure in penicillin).

Answer 21

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

Question 22

How does phosphorylation increase protein interaction?

Answer 22

-Gives it a negative charge and allows charge charge interactions to form

Question 23

How can cleavage of specific peptide bonds cause activation of a protein?

Answer 23

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

Question 24

How does urea prevent aggregate formation?

Answer 24

Urea is a denaturant and prevents aggregate formation by preventing H bonds forming

Question 25

Are disulphide bridges essential for protein folding?

Answer 25

No. Only useful in maintaining stability, does not influence folding.

Question 26

How may residues per turn does an alpha helix have?

Answer 26

3.6

Question 27

Why are glycine and proline often found in ‘loops’ (are tight loops where there is a change in direction of the polypeptide backbone)?

Answer 27

• Glycine because its the smallest amino acid

- Proline because it has a kink in its side chain

Question 28

What are loops?

Answer 28

More flexible structures corresponding to extended turns

Question 29

What are random coils?

Answer 29

Proteins contain regions that do not correspond to any secondary structure types- are called random coils and they give the whole protein flexibility.

Question 30

What is a motif?

Answer 30

A pattern in a protein associated with a particular function.

Question 31

What is a protein domain?

Answer 31

A 3D region which can be independently folded and stable.

Domains have specific functional roles.

Question 32

What is a salt bridge?

Answer 32

Charge charge interactions between ionised side chains are a strong non covalent force that affects tertiary structure.It many be pH dependent.

Question 33

What is the difference between a peptide and a protein?

Answer 33

The difference between a peptide and a protein is that a peptide is a chain of amino acids whereas a protein is a (group of) peptide(s) that have been folded into a specific shape.

Question 34

What is N terminal sequencing? What is the process?

Answer 34

Finding out a protein’s sequence directly rather than through genetics (Sanger sequencing).

> Protein is broken into fragments
Chemical reactions remove successive N terminal residues
Fragments are assembled into their complete sequence
Each fragment that has been taken off can be identified using chromatography
However, usually only between 10-30 cycles can be run before there is overlap between cycles

Question 35

What is meant by orthologue, homologue and paralogue?

Answer 35

Orthologue- genes in different species that have the same function

Homologue- similar sequence

Prologue- different function, same organism

Question 36

What is convergent and divergent evolution?

Answer 36

> Divergent evolution = accumulation of differences between groups which can result in the formation of a new species.
Convergent evolution = where organisms evolve analogous structures or functions despite having unrelated or dissimilar evolutionary ancestors.

Question 37

Why is urea a denaturant?

Answer 37

Forms H bonds which disrupts the internal H bonds

Question 38

Why is urea a denaturant?

Answer 38

Forms H bonds which disrupts the internal H bonds of the protein so thereby denatures it.