Lecture 7: Enzyme Regulatory Mechanisms Flashcards
General ways to regulate enzyme activity
- allosteric control
- multiple forms of enzymes
- reversible covalent modification
- proetolytic activation
- controlling the amount of enzyme present
allosteric control
- linked to noncompetitiv einhibition
- allosteric proteins contain distinct regulatory sites and multiple functional sites
–> binding of smal molecules at regulatory sites
- cooperativity
–> activity of one functional site affects the activity at others (information is transduced)
ex: aspartate transcarbamyolase
cooperativity
- allosteric control
- activity at one functional site affects activity at others
multiple forms of enzymes
- isozymes or isoenzymes
- isozymes provide an avenue for varying regulation of the same reaction at distinct locations or times to meet specific physiological needs
- homologous enzymes with a single organism that catalyze the same reaction but differ slightly in structure and kinetic properties
ex: lactate dehydrogenase - usually slightly different structure and different kinetics
- arise through genetics, duplications and mutations
reversible covalent modification
- catalytic enzymes are markedly altered by the (reversible) covalent attachment of a modifying group
- usually phorphoryl group
- modification by a phosphoryl group = phosphorylation
–> ATP is the phosphoryl donor of the reactions, catalyzed by protein kinases
–> removal of phosphoryl groups by hydrolysis is carried out by protein phosphatases
–> ex: glycogen phosphorylase
- phosphorylation cascade
proteolytic activation
- enzymes can be irreversibly converted from an inactive state into an active one by proteolytic cleavage
- wait to activate them until they are needed, otherwise they would act on the wrong things
–> activation occurs via hydrolysis of at least one peptide bond in inactive precursors called zymoens or proenzymes
–> regulatory mechanism generates many active digestive and (blood) clotting enzynes
–> ex: chymotripsinogen/chymotrypsin
Controlling the amount of enzyme rpesent
enzyme activity can be regulated by adjusting the amount of enzyme present
- enhanced/upregulated or diminished/downgraded by a cell at the transcriptional, posttranscriptional or translational level in response to a change in cellular environment
- depend on the rate of enzyme degradation - post translational regulation strategy
- ex: ubiquitin proteasome pathway
labeled and recognized by a protein “shredder” because:
- dont need it anymore
- recycle ieces
Ex: allosteric enzyme aspartate transcarbamyolase
- ATCase catalyzes the first step in biosynthesis of pyrimidines
- condensation of aspartate and carbamoyl phosphate to form N-carbamoylaspartate and orthophosphare
- committed step in the metabolic pathway that will ultimately yield pyrimidine mucleotides such as cytidine triphosphaste (CTP)
How is ATCase inhibited by CTP?
- ATCase is inhibited by CTP, the final product of the pyrimidine synthesis pathway (feedback inhibition)
- CTP is structurally quite different from the substrates of the reaction
- it binds the allosteric or regulatory sites and acts as an allosteric inhibitor
(as CTP is increase, rate of N-carbamoylaspartate decreases)
Feedback inhibition
- final product of a metabolic pathway shuts down the pathway
- prevents a cell from wasting chemical resources by synthesizing more product than is needed
ATCase structure
- dodecamer with 12 subunits
- 2 catalytic trimers
- 3 regulatory dimers
(C3)2(r2)3
Interaction of PALA with ATCase
- PALA is a competitive inhibitor that binds to the active site
- it can only bind to it when it is in the r/reactive state
Conformations of ATCase
- compact, relatively inactive form called the tense (T or low substrate affinity state)
- expanded form called Relaxed (R or high subs affinity) state
T to R trantision
CTP holds ATCase in the T state
- it moves into that conformation itself, and CTP keeps it there
Kinetics and ATCase
- do not display michaelis-menten kinetics
–> binding of substrate to one active site of the enzyme increases the activity at the other active sites (cooperativity)
- not a steady increase, instead is an on/off switch
Homotropic and heterotropic regulation
Homotropic = 1 at a time
- concerted: all are in R state and bind substrate one at a time
- sequential: all begin in T state, convert to R one at a time and bind substrate one at a time
heterotropic = all at once
- either all in R with effector
- all in T with effector
*see diagram
Homotropic regulation
heterotropic regulation
ATP and CTP effects on ATCase?
- ATP activates ATCase
- CTP inhibits
- both are allosteric EFFECTORS
ATP is a purine, in DNA synthesis equal amounts of purine and pyrimidine are needed, so if ATP is produced it will trigger pyrimidine production
Example of izosymes - Lactate dehydrogenase
- humans have two isozymes of lactate dehydrogenase (LDH) an enzyme catalyzing a step in anaerobic glucose metabolism and glucose synthesis
1. the H isozymes is highly expressed in heart muscle, has high affinity for substrate, and is allosterically inhibited by high levels of pyruvate
2. M isozyme is highly epxressed in skeletal muscles, has low affinity for substrate, and is not regulated by pyruvate - tetramer of various various H and M isozyme combinations
* different abundances of combinations in diff tissues
Examples of phosphorylation
- adenylation
- acetylation
Adenylylaiton mechanism
(tyrosine)
proteins use it to make g proteins last forever
acetylation mechanism
(lys)
DNA is normally condensed with histones and cannot be replication or transcribed
- acetylation removes the histones
myristoylation
no example given
ADP-ribosylation
influences signal transduction pathways in bacteria
ubiquitination
ubiquitin helps to remove proteins
methylation
activates proteins
Protein phosphorylation mechanism
cAMP and protein kinase A
Protein phosphatases
- reverse the effects of protein kinases, protein phosphatases turn off phosphorylation-dependent signaling pathways
Things activated by proteolysis
apoptosis and hormones
- cysteine proteases involved in programmed cell death or apoptosis (procaspases to capsases)
- hormones (proinsulin to insulin)
- blood clotting enzymes (proteolytic cascade)
- digative enzymes (chymotrypsinogen to chymotrypsin)
- fibrous proteins (procollagen to collagen)
what is apoptosis
- apoptosis is a series of morphological changes in a cell that are triggered by DNA damage, viral infection, oxidative stress and other events –> ultimately lead to ell death
–> changes include a decrease in cell volume, damage to the plasma membrane, swelling of mitochondria, and fragmentation of chromatin
- apoptosis is a major physiological route by which damaged, unwanted, or harmful cells are eliminated
what happens at the end of apoptosis?
- vesicles containing cellular sontents form and are engulfed by neighboring cells
–> some of these contents (such as certain proteins) can be saved and reused
- all eukaryotes have a similar set of endogenous enzymes responsible for cell death and these enzymes include proteases called capsases (cysteine proteases that cleave next to aspartic acid residues within a consensus sequence of target proteins)
–> initiator caspases cleave inactive pro-forms of executioner caspases, while activate executioner caspases in turn cleave other proteins within the cell
- mitochondria swell, trigger factors are released, apoptosis ocurs
procaspase activation by cleavage
2 pieces are each cleaved in 2 spots
- becomes a dimer, each side with a small and large subunit
- only active in dimer form
caspase cascade
- one molecule of active caspase activates many others
Preproinsulin to insulin
- insulin is small protein hormone activated in two steps
- synthesized by pancreatic b-cells as single chain ER signal sequence-containing precursor (preproinsulin)
- in ER the singal seauence is removed and 3 disulfide bonds are formed (between A and B components), generating proinsulin
- further proteolysis removes an internal sequence (C peptide) to produce mature insulin, composed of A and B chains
Releas eof insulin
- stored in secretory vessels/granules in pancreatic b-cells
- elevation of blood glucose above certain threshold level causes insulin-containing granules to fuse with the plasma membrane, relesing insulin into the blood
–> called glucose-stimulated insulin secretion and involves a glucose-dependent intracellular uptake of STP, which causes an ATP-sensitive K+ channels to close. the closure of this channel alters the charge across the membrane and causes a Ca2+ channel to open. Ca2+ influx results in insulin release
Insulin release mechanism
Ubiquitin mediated protein degradation
- turnover of ellular proteins is a regulated process requiring a complex enzyme meachinery
- proteins to be degraded are conjugated with ubiquitin via an isopeptide bond
Enzymes in the ubiquitin conjugation process
- performed by three distinct enzymes and driven by ATP hydrolysis
- Activator
- Carrier
- Ligase
- AMP gets attached
- E1 removes AMP and attaches itself
- E2 replaces E1
- E2 and Ubiq go to E3 that serves like a bowl for ubiq to attach to the target protein
-
- ubiquitin is the Id that proteins should be degraded
hydrolysis of ubiquitinated proteins via proteasome
proteasome recognizes ubiquitin tagged proteins
releases peptide fragments and ubiquitin
peptide fragments can be further broken down into amino acids
processes regulated by protein degradation
- gene transcription
- cell-cycle progression
- organ formatino
- circadian rhythms
- inflammatory response
- tumor suppression
- cholesterol metabolism
- antigen processing
Half life of a protein is determined by…
- the N terminus of its chain
Most stable: Met, ser, Ala, Thr, Val, Gly
Destabilizing:
- Ile, Glu, Tyr, Gln
Highly destabilizing:
- Phe, Leu, Asp, Lys, Arg
