Biochemistry Chapter 2: Enzymes
What is the Michaelis-Menten equation?
v = (vmax [S])/(Km + [S])
When does noncompetitive inhibition occur? How can it be overcome and what does it alter?
-It occurs when the inhibitor binds to the allosteric site - so it is not competing for the active site. Once inhibitor binds to allosteric site, it changes confirmation of enzyme so substrate can't bind. -It has equal affinity for the allosteric site of the enzyme as it does for the enzyme-substrate complex. -Increasing inhibitor concentration decreases the Vmax because less enzyme is available for reaction. -Does not alter Km value because the active enzyme still has the same affinity for the substrate.
What are apoenzymes and haloenzymes? What are prosthetic groups? Example?
Apoenzymes are enzymes without their cofactors Holoenzymes are enzymes with their cofactors Prosthetic groups are tightly bound cofactors or coenzymes that are needed in order for an enzyme to function Example - Thiamine is an important coenzyme and is therefore a prosthetic group - without thiamine, you have nerve issues, balance problems, cant keep new memories, etc Lack of thiamine is cause of wernicke-korsakoff syndrome.
What are the water-soluble vitamins?
B-complex vitamins and ascorbic acid (vitamin C)
Why are the amino acid residues that make up a protein's active site closer together in its teritary or quaternary structure than in its primary structure?
Because Amino acids that are far apart in primary structure are brought together once the protein has folded.
How do Enzymes function as biological catalysts?
Catalysts are characterized by two main properties: they reduce the activation energy of a reaction, thus speeding up the reaction, and they are not used up in the course of the reaction. Enzymes improve the environment in which a particular reaction takes place, which lowers its activation energy. They are also regenerated at the end of the reaction to their original form.
What do cofactors and coenzymes do? How do they differ?
Cofactors and Coenzymes are both small, nonprotein molecules that bind to the active site of the enzyme so that the enzyme can function. Cofactors are often metal ions and inorganic molecules - ingested as dietary materials Where as coenzymes are often organic compounds in the form of vitamins - watersoluble are B-vitamins and ascetic acid (vitamin C), where as fat-soluble are vitamins A, E, D, K.
Of the four types of reversible inhibitors, which could potentially increase Km?
Competitve inhibitors increas Km because more substrate is needed to outcompete the inhibitors. Mixed inhibitors can only increase Km when they prefer binding to enzymes, because more substrate is needed to outcompete inhibitors.
Why are some enzymes released as zymogens?
Enzymes need to be released as zymogens because they need to be tightly regulated otherwise they are deadly - so in zymogens, you need to change the regulatory site in order for the active site to be available Zymogens are precursors of active enzymes
What is the functional consequence of the fact that enzymes are unchanged by a reaction?
Fewer copies of the enzyme are required , so one enzyme can act on many many molecules of substrate.
What is the ideal temperature for most enzymes in the body? The ideal pH?
Ideal temperature is 37 degrees C (98.6 F and 310 K) Ideal pH most enzymes (7.4); gastric enzymes (2); pancreatic enzymes (8.5)
WHat is competitive inhibition and how can it be overcome?
In competitive inhibition, the inhibitor competes with the substrate to bind to the active site of the enzyme. In this case, when the inhibitor binds, it doesn't do anything, it just keeps the space occupied so nothing else can bind. This can be overcome by increasing the concentration of the substrate, so that the substrate floods the active site more than the inhibitor does. The Km value is higher because you need more substrate to reach 1/2 Vmax because you have inhibitors taking enzymes also. The Vmax value does not change.
In what ways do enzymes affect the thermodynamics vs. the kinetics of a reaction?
In terms of kinetics, they speed it up by lowering the activation energy, but they don't affect the thermodynamics
When does uncompetitive inhibition occur and what does it alter?
In uncompetitive inhibition, the inhibitor binds to the allosteric site on the enzyme-substrate complex, locking the enzyme-substrate in place, preventing the enzyme from releasing the substrate. Increasing inhibitor concentration lwoers both Vmax and Km.
What are the effects of increasing [S] on enzyme kinetics? What about increasing [E]?
Increasing [S] prior to Km (when substrate concentration is low), it largely affects the reaction rate of the enzyme, but once it exceeds Km (when substrate concentration is high), it affects the reaction rate of the enzyme a lot less, up until it reaches Vmax, in which it is fully saturated and no amount of [s] would affect it.\ Increasing [E] - well if you have a large [E] and a small [S] - you have a higher reaction rate because there are a lot of stress balls available for the hands, so increasing [E] would increase reaction rate, aka increase Vmax.
What occurs during mixed inhibition?
Inhibitor has binding affinity preference to either the enzyme or the enzyme-substrate complex. If its is preferentially to enzyme, then it increases Km. If enzyme-substrate complex, decreases Km.
What is irreversible inhibition?
Irreversible inhibition is when the active site is made unavailable for a prolonged period of time or enzyme is altered, making it unavailable.
What is Enzyme specificity?
Just the fact that enzymes are picky - enzymes only act on specific substrates
What does Km represent? What would an increase in Km signify?
Km represents the concentration of substrate ([S]) needed to reach 1/2Vmax (when number of active sites are 50% full). A high Km means a low affinity because there are a lot of substrate that is needed to reach 1/2vmax, meaning theres less love of enzyme on that substrate. A low Km means a high affinity, because small amount of substrate needed to reach ½ vmax, so enzymes can't keep it in their pants. An increase in Km signifies an increase in [S] required to reach 1/2 Vmax signifying a lower affinity.
What is enzyme cooperativity?
Sometimes enzymes need subunits to help them be activated/function. It is interactions between subunits in a multisubunit enzyme or protein. Binding of substrate to one subunit can induce a change of that subunit from a T state (low affinity high tense state), to and R state (high affinity, relaxed state).
What are the effects of temperature, pH, and salinity on the function of enzymes?
Temperature: Enzyme activity doubles every 10 degree increase in C up until optimal temperature is reached, once optimal temp is passed, enzyme activity decreases rapidly because enzymes can denature at high temps because of the increased molecular motion caused by adding heat. pH: Affects ionization of the active site and changes in pH can denature enzymes. Enzymes function best at optimal pH - in humans this is 7.4 - before 7.4 is acidemia. Exception - pepsin- in stomach - digestion- optimal pH is 2; pancreatic - small intestine - optimal pH is 8.5. It functions best at 7.4 because changing the pH can protonate or deprotonate the enzyme, affecting hydrogen bonding between amino acids in the enzyme - this alters the active site and the entire enzyme structure. Salinity: Changes in salt can disrupt hydrogen and ionic bonds, which cause partial changes in enzyme which cause denaturation of enzyme and conformation in enzyme. Increasing IN VITRO salt concentrations can cause denaturation.
List the B-vitamins from B1 to B12:
Then: B1 - Thiamine Roland: B2 - riboflavin N: B3 - niacin Peter: B5: pantothenic acid Played: B6: pyridoxal phosphate Bowling: B7: Biotin For: B9: folic acid Chester: B12: cyanocobalamin
How are the Michaelis- Menten and Lineweaver- Burk plots similar? Different?
They both display Vmax and Km graphically M-M: Compares velocity and [S] - creates hyperbolic curve - aka parabola L-B: 1/v vs /1[S] - straight line
What are the fat-soluble vitamins?
Vitamins A, D, E, K - regulated by partition coefficients - determine how much a molecule can dissolve in a polar vs nonpolar environment.
What is feedback inhibition?
When products further down a metabolic process (past the enzyme) have a regulatory effect on the enzyme, inhibiting enzyme activity, Basically, the more product made, the less product being made or whatever.
What do the x- and y-intercepts in a Lineweaver- Burk plot represent?
X-intercept: -1/km; Y-intercept: 1/vmax
What is Hill's coefficient and what happens if it is bigger than 1, less than 1, or = 1?
bigger than 1, positively cooperative binding is occurring - binding increases affinity of enzyme for other subunits-Less than 1 - negatively cooperative binding -after one ligand is bound - affinity of enzyme for other subunits decreases-=1 - no cooperative binding
WHat are the names and main functions of the six different classes of enzymes? Give an example of each and show/draw a diagram displaying how each works. (LIL'HOT)
1) Ligase - Addition or synthesis reactions for large molecules - turns two molecules into one ( A + B = AB). 2) Isomerase: Rearrangement of bonds within a molecule: A becomes B. 3) Lyase: cleaves a single molecule without using water or oxidoreductase: A becomes B + C 4) Hydrolase: Cleaves a molecule using water: A + H2O = B + C. 5) Oxidoreductase: Transfers electrons from one molecule to another: Oxidizing agent gains electrons causing it to be reduced, and a reducing agent loses electrons causing it to be oxidized. 6) Transferase: Transfers a functional group from one molecule to another.
What are the 6 definitions of an enzyme/catalyst?
1) Lower the activation energy 2) Increase the rate of a reaction 3) Does not alter the equilibrium constant 4) Enzymes are not changed or consumed in the reaction - they appear in both reactants and products 5) Enzymes are pH and temperature-sensitive, with optional activity and specific pH ranges and temperatures 6) Do not affect overall change in gibbs free energy for the reaction
What are the four mechanisms in which enzymes reduce the activation energy?
1) Transition state stabilization - the transition state in which the action gets to go forward exhists for longer - seen in SN2 reactions - enzyme binds to substrate via an SN2 reaction - creating a transition state that can be favorable by removing obstacles to stability like torsional strain. 2) Microenvironment adjustments - making environment more favorable like adjusting pH or keeping water away from molecule, preventing negative water molecules (oxygen) from interfering with forward reaction. 3) Adjust substrate proximity to make sure more of the necessary reactants get close enough to eachother. 4) Transient covalent bonding - substrate binds to residues inside the enzyme instead of just one - substrate is vulnerable to nucleophilic attack which binds substrate to the active site so the reaction can proceed. 5) Reactant destabilization - Making reactants uncomfortable by introducing torsional strain or introducing hydrophobic/hydrophilic reaction that makes favorable because molecules are in wrong hydrophobic state.
What are some examples of transient and covalent enzyme modifications?
Covalent enzyme modifications - phosphorylation/dephosphorylation Transient - allosteric activation or inhibition
How do the lock and key theory and induced fit model differ?
Lock and key model: There is no change in conformation - the enzyme's active site is the lock, and the substrate that binds to it is the key and they fit perfectly like a puzzle, rigid with no changes. Less accurate model. No changes in tertiary or quaternary structure. Induced fit model: The enzyme's active site is like a stress ball, and the substrate is like the hand, the substrate binding to the enzyme's active site induces conformational change on both of them, and they both conform until they fit perfectly - this part requires energy so it is endergonic. Then the substrate is released because it is now happy and enzyme goes back to original - this part is exergonic. Main difference is lock and key has no conformational change, and induced fit model they both have conformational change.
