Proteolysis

Proteolysis is the breakdown of  into
amino acids by the action of enzymes

Proteases cleave proteins by catalyzing peptide bond   (type of rxn)

Polypeptides can be cleaved either  
or 

Proteins can be broken down to eliminate  

Environmental toxins, translation errors, and genetic mutations can damage proteins
• Sickle cell is a genetic mutation that causes a misfolded  

Misfolded proteins are   to the cell ‐> they can form non‐physiological interactions with other
proteins
•   disease is caused by misfolded proteins

Proteins can be broken down for regulation of  

Regulation of cellular metabolism
• Increase or decrease the number of  molecules and   substances

Proteins can be broken down to generate  
• The proteolytic cleavage of the precursor generates an active enzyme –  ,  
•   and   of the proteasome are expressed as precursors that are proteolytically
processed to yield catalytically active subunits

Proteins can be broken down for recycling of amino acids via the  

If a damaged protein is not repaired, it is degraded in specialized organelles such as the   and by
the   pathway.

TEST QUESTION
Serine proteases have serine residue at the 
• Involved in  activity
• example enzymes:  ,  ,  

TEST QUESTION
Serine is involved in  (i.e.   or  )

Metalloproteases (  proteases) needs a  at active site
• example enzymes:  ,  

Cysteine proteases (  proteases) have   residue at the active site
• example enzyme:  

TEST QUESTION
  proteases ( proteases) have aspartic acid residue at the active site
• example enzymes:  ,  ,  

Proteases are categorized by their   structures

Serine and cysteine proteases
• the ser or cys residue is paired with
a   to
promote   on the
peptide bond ( )

Aspartyl proteases and metalloproteases
• activate a   to serve
as the nucleophile, rather than
using a   of the
enzyme itself

In mammals, serine proteases perform many
important functions, especially in ,  , and the  

Despite their similarities, serine proteases have
different 

  are Serine Protease Inhibitors ‐> use a
conformational change to inhibit target enzymes

The catalytic triad consists of  , , and 

Normally, a  group does not carry out a nucleophilic
attack on a peptide bond, but in this triad it can!

Histidine abstracts the H+ from the  allowing
the   to attack the peptide bond

The  is stabilized by binding to Asp‐

  proteases catalyze peptide bond hydrolysis in two sequential steps

SERINE PROTEO
In the first ( ) reaction (steps 1‐3)
1. the nucleophilic serine attacks the substrate
  bond ‐> forming first a  
2. Then a  releases the N‐
terminal fragment.

SERINE PROTEO
In the second ( ) reaction (Steps 4‐7)
1. A water molecule attacks the  ‐>
leading to a second  
2. followed by release of the  fragment.

Coagulation ‐>   hemostasis
• Circulating coagulation factors undergo a cascade of
reactions that ultimately generate  .
•   forms a mesh that stabilizes platelets in the clot.
• The clot remains until the underlying damage gets repaired.
• Blood clotting factors are activated by 

At the end blood clotting, when you need to dissolve the  

Clot retraction and Fibrinolysis:
• Happens after   and  hemostasis
• Helps the clot to contract and degrade to restore .
• Must activate at least   to degrade 
• But also can activate 

Fibrin degradation stimulated by...
• ‐> activated by fibrin binding
•   ‐> found in urine and cells lining renal
tubes to lyse fibrin deposits there
• Factor  ,  ,  

Inhibit fibrin degradation
•  
•  
•  

  therapy ‐> is the use of drugs to break up or dissolve blood clots

The three thrombolytic agents currently approved by the FDA for
use in patients with acute   are:
•  
•  
•  

Streptokinase ‐> not a  
• Forms a 1:1 complex with   exposing the active
site (activating  )

Thrombolytic therapies are not an  . The clot has to be there for this drug to work on it.

TEST QUESTION
Zymogens are   (usually proteins) that
are activated by a   cleaving off a repressing
subunit.

• Most common examples of zymogens are found in the
  and   used for digestion

The stomach zygmogen is called  

Pancreatic zymogens include  ,  ,  , and 

TEST QUESTION
 formation is the most important initiating step for zymgogen activation in the pancrease

TEST QUESTION
Trypsin activates  ,  ,  , and   by protease activity

Trypsin is activated by  enzyme that is
secreted in the duodenum
• it cleaves off the  terminal animo acid to covert
 to  .

 is the protease of choice for mass spectrometry (MS)‐based proteomics.
• Technique use to identify   in a sample.

Trypsin cleaves   end of   and   residues, resulting in a positive charge at the peptide  ‐
terminus

TEST QUESTION
In the stomach,   gets activated by exposure to   and cleaves itself to the active pepsin form

In the stomach, the   pH breaks between positively charged residues  and   and negatively charged
 and   residues

Pepsinogen is classified as a   protease

TEST QUESTION
Attachment of   to a proteins, marks it for degradation via 

In the cytoplasm, proteasomes associate with the , and the outer
surface of the  

Ubiquitination: the processes of adding   to a target protein

Ubiquitin undergoes an   requiring reaction
with a  ,  , forming a
 bond to E1.

The ubiquitin is then transferred to a   on the  ,  .

Finally, a  ,  , transfers the
ubiquitin to the target protein a  residue

The polyubiquitinated protein is then transported
to the   proteosome.

In the cylinder structure the protein is lysed to give  and  

These proteolytic actives of Protesosomes include
•  
•  
•  

Proteins that are rich in   are rapidly degraded by ubquinin

PEST is rapidly degraded because they often
contain sites that are  ,
targeting these proteins for ubiquitination

  hours: Met, Gly, Ala, Ser, Thr, Val
  mins: Iso, Glu
 mins: Tyr, Gln
  mins: Pro
 mins: Leu, Phe, Asp, Lys, Arg

TEST QUESTION
Proteolysis is necessary for   and  to
take place.

Test QUESTION
Use of   that can reduce the invasive and  capabilities of tumor cells

TEST QUESTION
Proteases are important for   and development of  

HIV protease releases enzymes and proteins for   packaging.
• Protease inhibitor drugs block the action of   enzymes

Protease inhibitors don't  HIV ‐> they lower the body's viral load
and slows the progression of HIV.

TEST QUESTION
Proteolysis of   is necessary for infected cells to spread virions