Biochemistry Coenzymes and Proteases

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What type of reaction do aspartyl proteases primarily use to cleave peptide bonds?

Hydrolysis reactions

Addition reactions

Nucleophilic substitution

General acid-base catalysis (correct)

Which enzyme is NOT classified as an aspartyl protease?

Chymosin

Pepsin

HIV-protease

Trypsin (correct)

What is a common use of proteases in biotechnology?

Detoxifying heavy metals

Promoting plant growth

Preparing antibiotics

Cleaning agents in biological detergents (correct)

Which of the following statements is true about the molecular mechanism of action of serine proteases?

They involve a catalytic triad consisting of Ser, His, and Asp. Signup and view all the answers

Which role do cofactors play in enzymatic reactions?

They assist in the catalytic process for some enzymes. Signup and view all the answers

Which of the following proteases cleave peptide bonds based on specificity pockets?

Proteases in general Signup and view all the answers

What is the primary significance of protein engineering using proteases like TEV protease?

To cleave at specific sequences, removing tags. Signup and view all the answers

Which protease is involved in protein fingerprinting within proteomics?

Trypsin Signup and view all the answers

In which of the following biotechnological applications are proteases critical?

Meat tenderization Signup and view all the answers

How does the regulation of proteases typically occur?

Via the presence of inhibitors or activators. Signup and view all the answers

Which coenzyme is known for facilitating the transfer of carboxylate groups?

Biotin Signup and view all the answers

What is the main characteristic of serine proteases?

They have a catalytic triad that includes aspartate. Signup and view all the answers

Which of the following is NOT a type of protease based on its mechanism of action?

Alkaline proteases Signup and view all the answers

Which vitamin is associated with Pyridoxal phosphate (PLP)?

Vitamin B6 Signup and view all the answers

In the mechanism of serine proteases, what occurs first during the reaction?

Formation of an acyl-enzyme intermediate Signup and view all the answers

Which of the following statements about proteases is correct?

Proteases cleave peptide bonds through hydrolytic reactions. Signup and view all the answers

Which component is NOT part of the catalytic triad of serine proteases?

Tyrosine Signup and view all the answers

What role does the Ser residue play in serine proteases?

Serves as a nucleophile. Signup and view all the answers

What type of protease cleaves peptide bonds at the chain's ends?

Exopeptidase Signup and view all the answers

Which of the following best describes the overall reaction catalyzed by proteases?

Hydrolytic reaction Signup and view all the answers

What is the primary function of biotin in enzyme reactions?

Facilitates carboxylation and decarboxylation reactions. Signup and view all the answers

Which amino acid in the catalytic triad of serine proteases helps activate the serine residue?

Histidine Signup and view all the answers

Which mechanism describes how serine proteases cleave peptide bonds?

Two-step mechanism involving bond formation and breaking Signup and view all the answers

Which of the following is a key aspect of protease selectivity?

Proteases generally lack absolute substrate specificity. Signup and view all the answers

What structural feature allows polypeptides to bind effectively to serine proteases?

Main chain hydrogen bonding Signup and view all the answers

Which type of amino acid is preferred by trypsin in its selectivity pocket?

Positively charged amino acids Signup and view all the answers

What distinguishes cysteine proteases from serine proteases?

Cysteine proteases utilize an active cysteine residue Signup and view all the answers

Which amino acids stabilize the oxyanion hole in the mechanism of action of papain?

Cysteine and Gln Signup and view all the answers

What is a characteristic of most serine proteases in terms of substrate specificity?

They exhibit no absolute substrate specificity. Signup and view all the answers

In the catalytic mechanism of cysteine proteases, what role does His159 play?

General acid/base Signup and view all the answers

Which protease is known for having a preference for bulky amino acids in its selectivity pocket?

Chymotrypsin Signup and view all the answers

What mechanism does papain use for substrate binding?

Seven amino acids accommodated at the binding site Signup and view all the answers

What is the significance of the selectivity pocket in proteases?

It controls the enzymes' specificity for certain amino acids. Signup and view all the answers

What type of bond do the main chain atoms of polypeptides form with the enzyme in an antiparallel b-sheet structure?

Hydrogen bonds Signup and view all the answers

What characteristic feature do most serine proteases have regarding their interaction with peptides?

They often show preference for a side chain before the cleaved peptide bond. Signup and view all the answers

What defines the catalytic dyad of cysteine proteases, such as papain?

His and Cys interaction Signup and view all the answers

Which property of cysteine (Cys) side chain significantly influences its catalytic role in proteases?

It can act as a strong acid. Signup and view all the answers

Study Notes

Coenzymes

Biotin is Vitamin B7 and is involved in the transfer of carboxylates.
Pyridoxal phosphate (PLP) is Vitamin B6 and forms a Schiff base with amines, including enzyme active sites.
PLP is involved in amino transferases, eliminations, and isomerisations.

Proteases

Proteases are also known as peptidases.
Proteases cleave the peptide bond between amino acids in a hydrolytic reaction.
Protease families are classified by their mechanism of action: serine proteases, cysteine proteases, acid proteases, and metalloproteases.

Serine Proteases

They have a conserved serine residue in the active site that participates in the reaction mechanism.
The active site contains a catalytic triad: an Aspartate to align the Histidine and act as a general acid, a Histidine to activate the Serine and act as a base, and a Serine to act as a nucleophile.
Serine proteases cleave peptide bonds in two steps: the formation of an acyl-enzyme intermediate involving the reactive Ser residue and the subsequent hydrolysis of the acyl-enzyme intermediate.

Cysteine Proteases

They utilize an active cysteine residue in the active site, such as papain, ficin, and bromelain.
Cysteine proteases have a catalytic dyad of His and Cys because the pKa of Cys is much stronger than Ser, eliminating the need for an Asp.
The mechanism of action of papain involves a catalytic dyad of Cys25 and His159, and an oxyanion hole formed by Cys25 and Gln19.

Aspartyl Proteases

They use reactive Asp residues in the active site, such as pepsin, chymosin, and HIV-protease.
Cleaving in aspartyl proteases proceeds through general acid-base catalysis.

Biotechnology

Proteases have multiple applications in biotechnology, including cleaning agents, meat tenderizers, cheese making, protein engineering, and protein fingerprinting (proteomics).
TEV protease is used in protein engineering to cleave specific sequences and remove tags.
Proteases are used in protein fingerprinting to cleave at specific positions, based on their pocket’s specificity.

Learning Outcomes

Understand how coenzymes are involved in reactions.
Know the molecular mechanism of action of serine proteases.
Know how cysteine proteases cleave peptide bonds.
Know how acid proteases cleave peptide bonds.
Understand the uses of proteases.

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Description

This quiz covers essential concepts of coenzymes like Biotin and Pyridoxal phosphate, as well as the classification and mechanisms of proteases, including serine proteases. Test your knowledge on enzyme active sites and the roles of different protease families in biochemical reactions.