Week 3 Flashcards
In what ways are enzyme-catalyzed reactions are controlled by regulatory enzymes?
- When a particular substance is needed, reaction increases
2. When a substance is not needed, reactions rate decreases
What is the benefit of controlling the rate of metabolic pathways?
Allows cells to adapt to its changing needs
Why does an enzyme rate depend on substrate concentration?
The higher the concentration, the faster the reaction until active sites are fully saturated.
What controls the rate of a metabolic pathway at the right place and time?
Regulation enzymes
What are the two mechanisms of regulating enzyme activity?
- Control of catalytic efficiency through protein modification
- Bioavailability
What are 5 ways enzymes are regulated?
- Allosteric control (non-covalent)
- By having multiple forms of enzymes (isozymes)
- Reversible covalent modification (transfer of phosphoryl groups)
- Proteolytic Activation (zymogens)
- Controlling amount of enzyme present (transcriptional level)
How is enzyme activity controlled?
Inhibition by enzyme inhibitors
Differentiate between allosteric activators and inhibitors
Activators increase the affinity of the enzyme for a substrate by binding to the T state and conformational changes the enzyme to an R state.
Inhibitors bind more tightly to the T state making it difficult for subunits to be in a more active conformation
What are examples of allosteric activators?
AMP and ADP indicate low energy state and the need to turn on enzymes to generate ATP
It is a rapid process
How do you overcome the effects of the allosteric inhibitor?
- Increase in substrate concentration
2. Increase in activator concentration
What is the purpose for allosteric site?
Apart from the active site, it causes conformational change that affects enzymes affinity for the substrate
What is a homotropic effectors?
- Presence of substrate in one active site enhances the catalytic properties at other binding sites (positive cooperativity)
- Most function as allosteric activators
- When an enzyme’s substrate serves as an effector
What are heterotropic effectors?
- Different from the enzyme substrate
- Ligand binding to the allosteric site has a different purpose than a ligand binding to the active site
- Most function as allosteric inhibitors
- Important to feedback mechanisms where products from downstream reactions feedback and affect allosteric enzyme activity
Explain positive cooperatively
When the binding of a substrate to one subunit facilitates the binding of a substrate to another subunit
What is the “T” conformation?
Low affinity for substrate (inactive state)
What is the “R” state
High affinity for substrate (active state)
What is the purpose for allosteric enzymes?
- Rate limiting enzymes in metabolic pathways
2. Junctions between different pathways that use the same substrate
What are isozymes?
Enzymes that catalyze the same reactions but have different physical properties
What is the difference between glucokinase and hexokinase?
- Glucokinase has low affinity for glucose and found in the liver
- Hexokinase has high affinity for glucose and found in RBCs, skeletal muscles, and most tissues
What is lactate dehydrogenase and does it express isozymes?
- Utilized for pyruvate to lactate reactions (anaerobic) and lactate to pyruvate (aerobic)
- Has 5 isozymes revealing tissue specificity differing in structure and kinetic properties
What mechanism regulates most enzymes?
Phosphorylation
What enzyme carries out phosphorylation?
Protein kinase
What enzyme carries out dephosphorylation?
Protein phosphatase
What enzyme transfers a phosphate group from ATP to OH group of serine on target enzyme?
Serine/threonine kinases
What enzyme transfers a phosphate group to the hydroxyl group of a specific tyrosine residue?
Tyrosine kinases
What are the key features of phosphorylation?
- The addition of the phosphoryl group alters electrostatic interactions
- A phosphoryl group can form H-bonds
- Phosphorylation and dephosphorylation occurs rapidly
- Phosphorylation can be used to amplify signals
- Kinases use ATP as the source of phosphate groups
Explain glycogen phosphorylase
- Rate limiting enzyme in glycogen degradation (glycogen to G1P)
- Activated by phosphorylation of Ser side chain
- Inactivated by dephosphorylation of Ser residues
Explain Proteolytic Activation-Zymogens
An irreversible regulation where zymogens most undergo proteolytic cleavage to become fully functional does not require energy to cleave
What is a zymogen?
An inactive precursors of enzymes
Describe the process of activating chymotrypsinogen?
- Chymotrypsinogen is stored in the pancreatic cell and secreted into the intestinal lumen
- By proteolytic enzyme trypsin, chymotrypsinogen converts to a-Chymotrypsin
- Enzyme cleaves primary structure cause tertiary structure to cleave as well
- a-chymotrypsin actives
Give a brief explanation of the blood clotting cascade
- Fibrinogen and prothrombin circulate in the blood in the inactive form
- They are cleaved by proteases to active form
- Proteases are activated by their attachment to a damaged region in the vessel wall
- Keeps clot formation to site of injury and not in circulation
What factors effect maximal capacity of a tissue change?
- Increased protein synthesis
2. Increased protein degradation
How would you increase the velocity of a reaction?
Increase the amount of enzyme present to convert substrate to product
What is the difference between induction and repression?
Induction is the increase in rate, repression is the decrease in rate of gene transcription
Is regulated enzyme synthesis a slow or rapid process?
Slow – hrs to days
What is an example of induction?
Cytochrome P450-2EI oxidizes ethanol in alcohol. Increased in the liver with increased ingestion of alcohol relaying to the induction of gene transcription.
Explain what protein degradation is in regards to fasting
Protein degradation in skeletal muscles are activated to increase amino acid levels in blood
Explain what protein degradation is in regards to infection
Degradation is used to liberate amino acids to produce antibodies and other proteins for the immune response
What enzymes are involved with lysosomal degradation?
Acidic proteases and hydrolases
What is a ubiquitin-proteasome system?
Attachment of a ubiquitin polypeptide to proteins targeted for degradation by proteasome
What are the principles of pathway regulation?
- Metabolic pathways are a series of sequential reactions
- Product of one reaction is the substrate for another
- Pathways have branch points where intermediates become precursors for another pathway
Explain rate limiting step
- Pathways are regulated by one key enzyme-regulatory enzyme
- Slowest step and not easily reversible
- 1st committed step of a pathway
- Changes in this step can influence the rest of the pathway
What happens when there is high end product?
Product binds to regulatory enzyme and of pathway and inhibits the formation of intermediate substrates in pathway
What happens when there is low end product?
The allosteric inhibitor dissociates from the allosteric site allowing the regulatory enzyme to become active again
Why do cells compartmentalize enzymes?
- Provide unique conditions
- Limit access of enzymes to substrates
- Separates anabolic pathways from catabolic ones
Define inhibitors
Substances that decrease the rate of an enzyme-catalyzed reaction by binding to the enzyme
Describe reversible inhibitors
Substance non-covalently bind to E or ES are subsequently released
Explain competitive inhibition
Competes with substrate for binding in the active site by binding to the active site
How is competitive inhibition overcome?
Increasing concentration of substrate
Why is Statin drugs considered competitive inhibitors?
Inhibits the rate-limiting step of cholesterol synthesis
Statin binds to HMG CoA reductase inhibiting the formation of cholestrol
Why are Saquinavir and Indinavir considered competitive?
Mimics the natural Phe-Pro substrate cleaving viral protein from active sites
Explain uncompetitive inhibition
Does not compete with substrate because it only binds to ES complex
Why can’t you overcome inhibition by increasing substrate concentration?
An increase in [S], increases ES complexes leading to more inhibitor binding
Explain noncompetitive inhibition
Can bind to both E or ES complex
Causes conformational change of the enzyme affecting the affinity of the E for the substrate reducing overall functionality of enzymes
Describe irreversible inhibitors
Substances cause covalent alterations of enzyme causing it to permanently shut down
They are unreactive until bound to an active site
What are important roles of lipids?
- Energy storage
- Cell membranes
- Endocrine signaling
What does amphopathic mean?
Molecule that has one end with a polar water-soluable group and another end with a nonpolar hydrocarbon group