Lecture 6: Cofactors

Question 1

What is a cofactor?

Answer 1

Any non-proteinaceous piece of an enzyme used for biological catalysis.

Can be covalently linked to protein or can bind similar to substrate

Question 2

Why does a protein need a cofactor?

Answer 2

Certain functions are required in biology, but cannot be completed with the amino acids available

• Easier to use cofactor
• Able to stabilize structure

Question 3

What is an apoenzyme and holoenzyme

Answer 3

Apoenzyme: no cofactor

Holoenzyme: cofactor

Question 4

What are advantages and uses of metal ions

Answer 4

Advantages

• no assembly
• small size
• versatile

Use

• ligand binding
• electron transfer
• folding

Question 5

How are copper ions used as coenzymes?

Answer 5

Multiple type of ligations and oxidation states allow for multiple chemical reactions

In Tyrosinase
In Hemocyanin
In Cytochrome Oxidase

Question 6

How are copper ions used in the tyrosinase enzyme

Answer 6

Tyrosinase enzyme able to toxidaize tyrosine using a di-copper center

Question 7

How are Iron metals used as cofactors

Answer 7

Fe can go between 2+ and 3 + charge states

Used in Nitric Oxide Reductase, converts nitric oxide to nitrous oxide

Question 8

How are Zinc ions used?

Answer 8

Used for both structural and functional reasons

• gives structure to Zinc finger protein
• binds and activates CO2 in carbonic anhydrase
• Normally in 2+ state

Question 9

What are metal clusters

Answer 9

1. Two more more metal ions linked through metal or covalent bonds
2. Sulfur (AA), Nitrogen (AA), and Oxygen often used to connect atoms and anchor cluster into protein
3. Advantages: can perform more advanced chemistry than single ion and more binding places
4. Disadvantages: need to be assembled and not stable

Question 10

What is an Fe- S cluster?

Answer 10

Used for electron transport

Come in Fe2S2 and Fe4S4

Question 11

What is an FeMoCo cluster?

Answer 11

Used in Nitrogenase proteins for N fixation

Able to convert N2 to NH3

Assembled by the Nif protein family

Question 12

What is an NiFe cluster

Answer 12

Used in hydrogenase enzyme

able to convert H+ to H2 and reverse

Constructed by the Hyp family of proteins

Question 13

What is Heme B

Answer 13

1. Fe-protoporphyrin IX
2. Found in all cells, seen in P450 enzyme, Globins, Electron transporters
3. Iron center is Fe2+ or Fe3+
4. Primary 1 electron carrier in biology

Question 14

What is Cytochrome P450?

Answer 14

• Major waste processing tool in nature
• Uses heme cofactor to activate oxygen radical
• Very reactive

Question 15

What is Heme C

Answer 15

Vinyl groups on heme are used to covalently ligate it to protein at CXXCH sequence