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Biochemistry > Catalytic Strategies > Flashcards

Catalytic Strategies Flashcards

1
Q

EC1 - Oxiodoreductase

A

Oxidation/Reduction reaction catalyst - always will require an electron carrier such as NAD+

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2
Q

EC2 - Transferases

A

Transfer a functional group - commonly uses methyl or phosphate

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3
Q

EC3 - Hydrolases

A

hydrolysis of bonds - uses water to break bonds - all proteases

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4
Q

EC4 - Lysases

A

Non-hydrolytic non-oxidative breaking of bonds - easiest to think of as splitting a molecule into two pieces

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5
Q

EC5 - Isomerases

A

Catalyze isomerization changes w/in a single molecule - rearrange the inside of one molecule to a different structure

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6
Q

EC6 - Ligases

A

Join two molecules by covalent bonds - example if argininosuccinate synthetase

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7
Q

What are enzymes for?

A

Speed up reactions

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8
Q

Proteases

A

Enzymes that break peptide bones

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9
Q

Serine Protease contain what?

A

A residue essential for catalysis

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10
Q

Serine Proteases do what

A

Cleave peptide bonds at specific sites for cutting. They recognize specific amino acids and cut adjacent to them.

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11
Q

What is the burst phase?

A

It is when a peptide becomes broken and we see a color reaction

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12
Q

What happens during the long phase?

A

That is when the other part of the polypeptide chain becomes attached to the enzyme to carry out the remainder of the reaction.

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13
Q

catalytic triad

A

Three parts- in serine proteases - serine, histidine and aspartic acid. important to remember as it is folded together to create the active site.

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14
Q

What are the steps of the serine protease mechanism - Part 1

A

Binding of substrate to the S1 pocket - leads to structural change and brings the triad closer together to start reaction

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15
Q

S1 Pocket

A

region of enzyme that determine what substrate the enzymes binds to

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16
Q

What are the steps of the serine protease mechanism - Part 2

A

Formation of alkyoxide ion - Histidine moves away from aspartic acid due to electron sink (lots of electrons that are same charge) and pushes towards the serine. This then pulls the proton on serine away and towards the N-group on the Histidine. Once Proton is on N of histidine, this is the alkyoxide

17
Q

What are the steps of the serine protease mechanism - Part 3

A

Nucleophilic attack occurs on the carbonyl carbon of the peptide bond, allowing for the oxyanion hole to provide stability to the unstable intermediate.

18
Q

oxyanion hole

A

provides environment for unstable intermediate to fall apart. Stabilizes unstable intermediate

19
Q

What are the steps of the serine protease mechanism - Part 4/5

A

Breakage and release of the peptide bond and half of the polypeptide chain falls off. This signifies the burst phase on the graph. Other half is covalently linked to the Serine

20
Q

What are the steps of the serine protease mechanism - Part 6

A

Water then enters the active site and Nitrogen will attack the proton of water, and Hydrogen will attack the carbonyl carbon. This will create another unstable intermediate which oxyanion hole will stabilize.

The Oxygen attracts the H on the N-ground, breaking the bond on the serine

21
Q

What are the steps of the serine protease mechanism - Part 7

A

Release of peptide 2 from the enzymes - end of the long phase

22
Q

S1 Pocket specificity

A

Nature of the S1 pocket will determine specificity of the enzyme

23
Q

Chymotrypsin

A

Broad, nonpolar - likes phenylalanine, tryptophan and tyrosine

24
Q

Trypsin

A

Negatively charged bottom - likes lysin and arginine

25
Q

Elastase

A

Narrow, nonpolar - likes glycine, alanine and valine

26
Q

If we alter the site we see what?

A

We see that Serine and Histidine are the most important pieces to the reaction. We also see that with no enzyme, there is no feasible reaction time.

27
Q

Cleavage Agents - Subtilisin

A

Cuts at C-Terminal of large uncharged side chains

28
Q

Cleavage Agents - Chemotrypsin

A

Cuts at C-Terminal side of aromatics (Phe,Tyr,Trp)

29
Q

Cleavage Agents - Trypsin

A

Cuts at C-Terminal side of Lysin and Arginines

30
Q

Cleavage Agents - Carboxypeptidase

A

Cuts at N-Terminal of C-terminal amino acid

31
Q

Cleavage Agents - Elastase

A

hydrolyzes C-side of small AA’s (Gly, Ala)

32
Q

Cleavage Agents - Cyanogen Bromide

A

Chemical - Hydrolyzes C-side of Met

33
Q

Serpins

A

Serine Protease Inhibitors - polypeptides that block access to active site to prevent other binding from occurring - important for medicine

34
Q

alpha-1-antitrypsin

A

inhibits elastase - made by body to protect lungs - w/o this this leads to emphysema.

35
Q

Reactive Oxygen Species

A

Oxygen byproduct

36
Q

alkyoxide ion

A

This is very reactive and responsible for the reaction that occurred

Biochemistry (12 decks)

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