Enzyme Classifications and Enzyme Catalytic Mechanisms Flashcards

Question

What is the S1 pocket of an enzyme responsible for?

Answer 1

S1 pocket is what determines the specificity of the enzyme

Answer 2

``` No mutation- activity= 100 Serine to alanine- activity =0.00001 Histidine to alanine- activity 0.00001 Aspartic acid to alanine- activity= 0.001 All three to alanine- activity= 0.00001 No enzyme- activity- 0.0000000001 ```

Answer 3

Substilisin: C-terminal side of large uncharged side chains Chymotrypson: C terminal side of aromatics (Phe, Tyr, Trp) Trypson: C terminal side of lysine and arginines ( not next to proline) Carboxypeptidase: N-terminal side of C terminal amino acid Elastase: Hydrolyzes C-side of small AAs (Gly, Ala) Cyanogen Bromide (chemical) Hydrolyzes C-side of Met

Answer 4

So these are inhibitors that stop the action of proteases that block access to active site by other polypeptides

Answer 5

Serpins= Serine Protease Inhibitors Ex. Alpha-1-antitrypsin It inhibits elastase in your lungs, that allow you to break down proteins in bacteria, if you have too much elastase you get emphazema so if you have too much elastase your body produces Alpha-1-antitrypsin Polypeptide chains that block the active site.

Answer 6

Smokers produce a lot of hydroxyl radical. They are very reactive, that will attack the sulfur of a methionine (creates sulfoxide), and there is a critical sulfur in Alpha-1-antitrypsin that allows it to bind to elastase, when sulfur gets oxidize, it stops Alpha-1-antitrypsin from attaching to elastase and that is why smokers get emphysema, because the elastase attacks the lungs.

Answer 7

They have 2 side chains of aspartic acid. No catalytic triad. One of the carboxyl groups becomes ionized and one does not. Why would one ionize and the other does not? The electronic environment is not the same as an aqueous environment, so basically things behave differently inside of a protein than they do outside of a protein. Aspartic acid grabs a proton off water.

Answer 8

Don’t have catalytic triad, only have 2 amino acids involved. Have a Cysteine and a Histidine Similar to serine protease. Why? Binding of proper substrate, causes the histidine to move closer to the cysteine.

Answer 9

Has common themes as other proteases. They have a side chain that is electron rich (amino acid), it helps in the activation of water. This is seen in serine proteases. They also have a Metal. The metal helps hold the water, so that it can be activated.

Answer 10

Cathepsin D Cathepsin E • All involved in signaling. Pepsin • Digestive enzyme, in your stomach that is active at pH of 1-1.2.

Answer 11

Carboxypeptidase A • Digestive enzyme, very digestive, it starts at the carboxyl end and starts to chew up amino acids away, one at a time. • Trypsin breaks a peptide into fragments, and those fragments are broken down into individual amino acids by Carboxypeptidase A. Collagenases Enzymes that break down collagen, in digestion. When you eat food, you need to break up the connective tissue of the food you are eating.

Answer 12

Enzymes that use cysteine in their active site Process: Substrate binding by SH- of cysteine to Histidine. Sulfur anion • The proton is removed from SH- just like the OH is removed in serine. Nucleophilic attack • -S attacks the carbonyl carbon. Peptide bond breakage • We have a tetrahedral intermediate, and the peptide bond falls apart. Movement of proton, release of first peptide • Proton moves from the histidine hydrogen to the amine group of the released peptide COMPLETION OF FAST CYCLE Entry of water • The second peptide is attached to the sulfur just like in the serine protease. • Water is activated by the histidine, activation requires removal of proton. Nucleophilic attack • This causes the hydroxyl to attack the sulfur- carbon bond. • This forms the tetrahedral intermediate • The peptide bond breaks.

Answer 13

o Substrate is bound to the enzyme o Aspartate side chains (projecting upwards) There is a water that fits between the aspartate side chains. Process: Activation of water • Common step! Carboxyl pulls a proton off water and the hydroxyl created Reactive hydroxyl does the nucleophilic attack • You don’t have 2 steps, because the water attacks and not an amino acids The attack creates a tetrahedral intermediate. • The bond breaks into two peptides, and you’re DONE What’s the difference here? • There isn’t a covalent bond because water is doing the attacking, the water gets attached, but its not physically attached. • The peptide gets broken into two and that is it, so you have ONE STEP • This is a simpler mechanism.

Answer 14

This is an enzyme that works incredibly fast, it is responsible for dissolving carbon dioxide in your blood. Carbon dioxide can get attached to hemoglobin, it displaces protons and it goes back to the lungs where it gets released. THIS IS A MINOR WAY TO RELEASE CO2 THE MAJOR WAY TO RELEASE CO2 o The major way that CO2 gets moved is by HCO3- o CO2 + H2O H2CO3 HCO3- + H+ CO2 is a poisonous gas! o pH matters for this enzyme, max cap at pH 9. It has the highest activity rate at this pH Process: You have Zn holding on to water. Zn is held by 3 different histidines. Loss of H+ • Water needs to ionized, so increasing the pH helps the mechanism. O- attacks the CO2 • O- attacks the CO2 because it is electron poor. Water enters and HCO3- released

Answer 15

``` Enzymes cut DNA at specific sequences. The enzyme stops at a specific sequence and it stops there and bends it. Mechanism: -Looks for specific sequence -Bends DNA at specific DNA ```

Answer 16

Hind III (Restriction Enzyme) o Cuts out 5’-AAGC-3’ o Cuts out 3’- CGAA- 5’ This leaves a staggered end. o Has a lot of Glu and Asp so its very negative o Bending of DNA allows for reaction to occur. It only occurs at the proper sequence. Similar mechanism, you have activation of water.

Answer 17

Only in bacteria

Answer 18

Bacterial defense Viruses attack bacteria, the bacteria uses these restriction enzymes to cut the DNA that comes in.

Answer 19

Action of DNA methylase It’s a restriction enzyme that protects the cell The Methylase recognizes AAGC and adds Methyl groups so now the cellular DNA is protected. It’s a race between what enzyme gets there first