KH5

Question 1

What’s the most important common activity to all protein functions?

Answer 1

Binding (between them, to ions, to molecules, etc.)

Question 2

What’s a ligand?

Answer 2

The molecule which binds to a protein

Question 3

What two properties govern ligand-binding?

Answer 3

Specificity: binds specific ligand
Affinity: strength (expressed as Kd, dissociation constant)

Question 4

Name an effect of ligand-binding on the protein

Answer 4

Conformational change

Question 5

True or False? “Binding occurs between any surfaces”

Answer 5

False. Binding comes from the addition of individually weak interactions (polarity, H-bonds) and complementary 3D shape.

Question 6

How are specificity and affinity important for antibodies?

Answer 6

Contain a CDR (antigen-binding surface) that involve segments from both light and heavy chains of the antibody. Every antibody has its own sequence of amino acids at CDR (binding to specific antigen)

Question 7

True or False? “Substrate binding and reaction catalysis occurs at the enzyme’s active site”

Answer 7

True

Question 8

Does specificity play a role in enzyme activity?

Answer 8

Yes. Active site only binds target ligand (complementary molecular surfaces).

Question 9

True or False? “Catalytic and substrate binding sites are found at the same place”

Answer 9

False. Both in the active site but separate defined regions.

Question 10

What determines the maximum rate of catalysis in enzyme activity (Vmax)?

Answer 10

The number of available enzymes and how fast they function.

Question 11

What’s “Km” in a Michaelis-Menten graph?

Answer 11

The enzyme concentration at which the speed is half of its maximum.

Question 12

True or False? “If enzyme concentration is increased 6 times, an equivalent increase is seen in Vmax and Km.”

Answer 12

False. It’s true for Vmax but Km remains the same. It depends on the chemical properties of the enzyme and substrate (intrinsic property).

Question 13

What allows trypsin to cleave peptide bonds without having the substrate float away?

Answer 13

The pocket ionically binds to large basic side chains (Arg/Lys) which retains the protein long enough for the catalytic site to break the adjacent bond.

Question 14

Is the “binding-pocket” mechanism unique to trypsin?

Answer 14

No. Other enzymes use it too and for different substrates (uncharged or small). Might even lead to faster plastic degradation (esterase)

Question 14

True or False? “The side chains used in the catalytic side of trypsin are closely positioned in the primary structure”

Answer 14

False. They’re close thanks to the protein folding (tertiary structure)

Question 15

True or False? “Enzyme activity is very little affected by pH changes”

Answer 15

False. Enzymes work best at an optimal pH range. Depends on the active site’s chemistry (i.e. catalytic mechanism) and the sensitivity of the overall structure.

Question 16

True or False? “Enzymes in a common pathway are physically associated”

Answer 16

True. Either through direct binding or binding to a common “scaffold” protein.

Question 17

Give a hypothesis for the existence of multiple active sites on certain polypeptides.

Answer 17

Evolution combined different (closely related) enzymes together.

Question 18

True or False? “Each binding site is always independent of the others”

Answer 18

False. The activity at one binding site may affect that of the other through conformational changes: allosteric regulation.

Question 19

Name two molecules widely used in allosteric switches.

Answer 19

Ca(2+): changes calmodulin structure, allowing binding.

GTP/GDP: binds to G-proteins which can be on (GEF) or off (GAP).

Question 20

True or False? “Phosphorylation leads to conformation and activity changes”

Answer 20

True. Phosphate group comes from ATP through protein kinases.

Question 20

What do we mean by “cascade” effect when talking about phosphorylation?

Answer 20

Often, a kinase or phosphatase will target another enzyme like them which in turn targets another and so on. A change early on will have ripples all the way to the end. One change leads to many more.