Regulatory Strategies for Controlling Enzymes Flashcards Preview

Biomedical Sciences Core > Regulatory Strategies for Controlling Enzymes > Flashcards

Flashcards in Regulatory Strategies for Controlling Enzymes Deck (24)
Loading flashcards...
1

Allosteric Enzymes


•Binding at ____ site triggers _____ change that is _____ to the ____ ___. 

•Cooperativity - ___ at ___   ____ ____ ____ _____

•2 Models
1.
2.
 


•Binding at regulatory site triggers conformational change that is transmitted to active site.

•Cooperativity - action at 1 site affects other sites.

•2 Models
1.Concerted
2.Sequential
 

2

Allosteric Models of Regulation


1.Concerted - 
2.Sequential - 

 


1.Concerted - First binding changes binding in all sites
2.Sequential - Stepwise alteration of sites

 

3

Aspartate Transcarbamoylase (ACTase)
•Catalyzes the____step in the biosynthesis of____ giving rise to_____ nucleotides ____ ______(end product of the pathway)


•Catalyzes the first step in the biosynthesis of pyrimidines giving rise to pyrimidine nucleotides cytidine triphosphate (end product of the pathway)
 

4

ACTase Consists of Separable Catalytic and Regulatory Subunits

•ACTase consists of ___ ____ catalytic subunits and ___ ___regulatory subunits. (Quaternary structure)
•Each catalytic subunit consists of ___ chains, while the regulatory unit consists of ___ chains.
•The catalytic subunit and the regulatory subunits are held together by ____ _____ containing ___ ____residues bound to a ___ ion. 
 


•ACTase consists of 3 large catalytic subunits and 3 small regulatory subunits. (Quaternary structure)
•Each catalytic subunit consists of 3 chains, while the regulatory unit consists of 2 chains.
•The catalytic subunit and the regulatory subunits are held together by stabilization domains containing four cysteine residues bound to a Zinc ion. 
 

5

ATCase is Allosterically Inhibited and Activated
 


•At sufficiently high concentrations of CTP, ATCase is ____ by a end product feed back mechanism.
•The binding site for CTP is ___ from the ___ ____ of the enzyme. (____site). This site is found on the ____ subunit.
•High concentrations ATP acts as an allosteric ____.

 


•At sufficiently high concentrations of CTP, ATCase is inhibited by a end product feed back mechanism.
•The binding site for CTP is distinct from the active site of the enzyme. (allosteric site). This site is found on the regulatory subunit.
•High concentrations ATP acts as an allosteric activator.  

 

6

ATCase Exists as Two distinct Quaternary Forms
 


•One predominates in the ____ of the substrate, while other predominates in the ____ of the substrate.
•T ____and R _____states.
•T state has ___affinity for the substrate and ___ catalytic power compared to the R state. 
 


•One predominates in the absence of the substrate, while other predominates in the presence of the substrate.
•T (Tense) and R (Relaxed) states.
•T state has low affinity for the substrate and lower catalytic power compared to the R state. 
 

7

Allosteric Regulators Modulate the T-to-R Equilibrium

•In the absence of substrate the R and T state are ____, however, the ___ is favored.
•In the presence of the allosteric inhibitor CTP, the position of equilibrium between the T and R states is shifted more towards the ___ state.
•This is a _____ mechanism (___ or ____) where ___ the subunits are converted to the ___state resulting in enzyme being___ ___ ___
•The R state is favored by ___ ___ and stabilized by ___ binding.

 


•In the absence of substrate the R and T state are equilibrium, however, the T is favored.
•In the presence of the allosteric inhibitor CTP, the position of equilibrium between the T and R states is shifted more towards the T state.
•This is a concerted mechanism (all or nothing) where all the subunits are converted to the T state resulting in enzyme being completed turned off.
•The R state is favored by substrate binding and stabilized by ATP binding.

 

8

Isozymes


•Enzymes of ____ amino acids sequences catalyzing the ____ reaction.
•These enzymes differ in ________ and _____
•Helps fine tune metabolic pathways within ___ ____


•Enzymes of different amino acids sequences catalyzing the same reaction.
•These enzymes differ in kinetic parameters (Km) and regulatory properties.
•Helps fine tune metabolic pathways within specific tissues. 
 

9

Types of Covalent Modifications


______modification (______)
_______
_______
______
______ modifications (______)
______
_____
_______
-

 


•Regulatory modification (reversible)
–Phosphorylation
–ADP ribosylation
–Acetylation
•Structural modifications (mostly irreversible)
-Glycosylation
-Lipid modifications
-g-Carboxylation of amino acid residue
-

 

10

Covalent Modifications that Regulate Protein Activity
 

11

Phosphorylation 


•Addition of a____ group to a protein.
•Enzymes that catalyze these reactions are known as___
•Serine and threonine are phosphorylated  by _______________. (Example – Protein kinase A)
•Tyrosine is phosphorylated by_______
•Energy in the form of ___ is required.
•Dephosphorylation (removal of phosphate groups) is catalyzed by _____

 


•Addition of a phosphate group to a protein.
•Enzymes that catalyze these reactions are known as kinases.
•Serine and threonine are phosphorylated  by Serine/Threonine kinases. (Example – Protein kinase A)
•Tyrosine is phosphorylated by Tyrosine kinases.
•Energy in the form of ATP is required.
•Dephosphorylation (removal of phosphate groups) is catalyzed by Phosphatases.

 

12

Ribosylation


•The enzyme_________________ transfers the _______ group from __________ onto ______________ residues.
•Bacterial toxins such as ____ toxin, ____ toxin, ____ toxin are  ADP-ribosyltransferases.
•Diphtheria toxin catalyzes the ADP-ribosylation of _______ inactivating it and inhibiting protein synthesis.



 


•The enzyme ADP-ribosyltransferase transfers the ADP-ribose group from Nicotinamide Adenine Dinucleotide (NAD+) onto Arginine, Glutamate or Aspartate residues.
•Bacterial toxins such as cholera toxin, pertussis toxin, diphtheria toxin are  ADP-ribosyltransferases.
•Diphtheria toxin catalyzes the ADP-ribosylation of eukaryotic elongation factor-2 (eEF2), inactivating it and inhibiting protein synthesis.



 

13

Acetylation


•Histone proteins are components of the ___ ___ ____
•_____ residues of histones  are acetylated  by _____ The enzyme that catalyzes this reaction  is _______
•The process is reversed by _______
•Process regulates ___ ___

 


•Histone proteins are components of the nuclear chromatin structure.
•Lysine residues of histones  are acetylated  by Acetyl-CoA The enzyme that catalyzes this reaction  is histone acetyltransferase (HAT)
•The process is reversed by histone deacetylase (HDAC)
•Process regulates gene expression.

 

14

Lipid Modifications


•Lipid molecules covalently bound to the _______ residues of proteins.
•Generally _____ ____ (____ and ____) or ____ ____ [____or _____-____(____groups) moieties] bind to proteins.
 


•Lipid molecules covalently bound to the N and C termini residues of proteins.
•Generally fatty acids (palmitate and myristate) or unsaturated lipids [farnsyl or geranyl-geranyl (prenyl groups) moieties] bind to proteins.
 

15

γ-Carboxylation


•Carboxylation of ______side groups.
•Found in the protein _____. (First ___ _______residues in the ___-terminus of the protein are carboxylated)
•g-carboxyglutamate is a stronger ___ ____ than glutamate.
•Binding of Ca2+ promotes Prothrombin to interact with the ____ enabling to be ___ ___ _____to enzymes that catalyzes it to the ___ ___ (____)

 


•Carboxylation of glutamate side groups.
•Found in the protein Prothrombin. (First 10 glutamate residues in the N-terminus of the protein are carboxylated)
•g-carboxyglutamate is a stronger Ca2+ chelator than glutamate.
•Binding of Ca2+ promotes Prothrombin to interact with the membrane enabling to be in close proximity to enzymes that catalyzes it to the active form (Thrombin)

 

16

Zymogens


•Many enzymes are fully functional when they fold into their native structure.
•However, some enzymes are synthesized as ___ ____ known as zymogens (____).
•Zymogens are activated by ____ ____ of one or more peptide bonds.
•Examples; Enzymes secreted in the ____ ___, ___ ___ ___and ____.
 


•Many enzymes are fully functional when they fold into their native structure.
•However, some enzymes are synthesized as inactive precursors known as zymogens (proenzyme).
•Zymogens are activated by proteolytic cleavage of one or more peptide bonds.
•Examples; Enzymes secreted in the digestive system, blood clotting factors and hormones.
 

17

Activation of Chymotrypsinogen


•Synthesized as a ___ amino acid chain.
•Activated by the enzyme ___ (cleavage between ____ and _____).
•Cleavage results in the generation of ____
•π-chymotrypsin further catalyzes the cleavage of other ________molecules.
•Generates _____consisting of ___polypeptide chains held together by ___ ____ ____. Results in the ___ form of the enzyme.


 


•Synthesized as a 245 amino acid chain.
•Activated by the enzyme Trypsin (cleavage between arginine 15 and isoleucine 16).
•Cleavage results in the generation of π-chymotrypsin
•π-chymotrypsin further catalyzes the cleavage of other π-chymotrypsin molecules.
•Generates a-chymotrypsin consisting of 3 polypeptide chains held together by two disulfide bridges. Results in the active form of the enzyme.


 

18

Protein Degradation


•Cells continuously ____ and _____ proteins.
•Controlling protein degradation is important to the cell.
–To provide _____________
–To ___________
–____ OF _____
•Different proteins have life times that range from ______to____  or more. (half life of protein)
•Protein degradation takes place within ____ or ____ of ____


•Cells continuously synthesize and degrade proteins.
•Controlling protein degradation is important to the cell.
–To provide building blocks for energy and synthesis.
–To eliminate misfolded or damaged proteins.
–Regulation of pathways.
•Different proteins have life times that range from few minutes to weeks or more. (half life of protein)
•Protein degradation takes place within lysosomes or independent of lysosomes.
 

19

Ubiquitin


•Protein degradation occurs in the presence of ___, ____ of lysosomes.
•Involves the protein ubiquitin.
•Consist of __ amino acid residues.
•Proteins are marked for degradation by ____ _____ them to ____


 


•Protein degradation occurs in the presence of ATP, independent of lysosomes.
•Involves the protein ubiquitin.
•Consist of 76 amino acid residues.
•Proteins are marked for degradation by covalently linking them to ubiquitin.


 

20

Ubiquitination of Proteins


•The_____terminal _____ residue of ubiquitin (Ub) becomes covalently attached to the ____ ____ ____ of ____ ____residues on a protein for degradation.
•Forms an ____ bond which ____ ____
•Requires three enzymes-
–Ubiquitin____ ____ (E1)
–Ubiquitin _____ ____ (E2)
–Ubiquitin- ____ ____(E3)
 


•The carboxyl-terminal glycine residue of ubiquitin (Ub) becomes covalently attached to the ϵ-amino groups of several lysine residues on a protein for degradation.
•Forms an isopeptide bond which requires ATP.
•Requires three enzymes-
–Ubiquitin activation enzyme (E1)
–Ubiquitin conjugating enzyme (E2)
–Ubiquitin-protein ligase (E3)
 

21

Proteins are Marked for Degradation


•Ubiquitin is _____ in presence of____ by ___
•Ubiquitin is transferred to a _____ residue of___
•Followed by transfer to a ____ residue of ____
___ transfers ubiquitin to the ____ of the protein intended to be degraded. 
 


•Ubiquitin is adenylated in presence of ATP by E1.
•Ubiquitin is transfer to a cysteine residue of E1
•Followed by transfer to a cysteine residue of E2
•E3 transfers ubiquitin to the lysine of the protein intended to be degraded. 
 

22

Proteins are Marked for Degradation


•One ubiquitin molecule is ___ enough to signal degradation.
•___ or ___ ____ molecules in ____ mark a protein for degradation. (lysine residue ___ in ____serves as the site for the attachment of the subsequent ubiquitin molecule)


•One ubiquitin molecule is not enough to signal degradation.
•4 or more ubiquitin molecules in chains mark a protein for degradation. (lysine residue 48 in ubiquitin serves as the site for the attachment of the subsequent ubiquitin molecule)



 

23

26S Proteasome


•Ubiquitin marked proteins are degraded by the ____
•Resembles a___
•Consists of___proteins and a catalytic___ protein.
•Marked proteins are ____ and the____ ___ is ___ _____ ____before degradation.
•Requires___
____ is recycled. 
 


•Ubiquitin marked proteins are degraded by the proteasome.
•Resembles a barrel.
•Consists of cap proteins and a catalytic core protein.
•Marked proteins are unfolded and the isopeptide bond is broken releasing ubiquitin before degradation.
•Requires ATP.
•Ubiquitin is recycled. 
 

24

Summary


•The concerted and sequential models describe the allosteric mode of regulation for enzymes.
•Covalent modifications are also important modes of regulation of enzymes.
•Zymogens are inactive precursors of enzymes that are activated by proteolytic cleavage.
•Protein degradation that occurs independent of lysosomes require ubiquitin.