Biochemistry enzyme kinetics lab report

Siavosh Naji-Talakar

siavosh@outlook.com

TITLE: Enzyme Kinetics

INTRODUCTION

Alkaline phosphatases are enzymes that are typically membrane-bound glycoproteins that catalyze the hydrolytic cleavage of monoesters at basic pH levels2. This enzyme is found in most advanced level eukaryotes and prokaryotes. When the hydrolysis of the monophosphate ester takes place at the basic pH levels an inorganic phosphate is released2. The enzyme can remove phosphate groups from several different types of molecules such as alkaloids, proteins, or nucleotides. In humans’ alkaline phosphatases play critical roles in the growth and development of teeth and bones, however, it can be found it other parts of the body such as in the liver and kidneys3. The phosphatases are essential for mineralization in humans to allow calcium and phosphorus to be deposited in bones and teeth3. The enzyme was reacted with 4-nitrophenyl phosphate as the substrate1. 4-nitrophenyl phosphate does not resemble a protein and is a non-specific substrate commonly used to assay alkaline phosphatases4. When the alkaline phosphatase performs hydrolysis on 4-nitrophenyl phosphate a highly colored phosphate free product is given1,4. This reaction releases the phosphate group on 4-nitrophenyl phosphate to give the product 4-nitrophenolate which has a molar absorptivity at 405nm under basic conditions with an extinction co-efficient of 18.8x103 M-1cm-1 1,4.

To experiment the effects of inhibition on the enzyme the inhibitor phenylalanine at 75mM and Na2HPO4 at 15mM was also used. Inhibition of enzymes may be carried out via irreversible pathways that work through covalent bonds or through reversible pathways. Reversible pathways include a competitive inhibition where the inhibitor binds to the active site of the enzyme or through a noncompetitive pathway where the enzyme binds to a side other than the active site, which may subsequently change the shape or conformation of the active site6. When a phosphate group PO43- is removed by hydrolysis from an organic compound it is referred to as dephosphorylation. This is the reaction in which the phosphatases operate. The reaction is important in a physiological setting because it enables the activation or deactivation of enzymes by removal of phosphoric esters; a prime example is the conversation of adenosine triphosphate to adenosine diphosphate through phosphorylation7.

The Michaelis-Menten kinetics model is used in biochemistry as a model for enzyme kinetics. The model uses an equation to explain the rate of the enzymatic reactions that occur . It does this by relating the reaction rate, Velocity or Vmax, to the substrate concentration, [S]. Vmax describes the constant values for each enzyme-substrate complex with the theoretical maximum velocity of the enzyme to turn over products at maximum saturation of the substrate concentration6. The Km value, known as the Michaelis constant, is the dissociation constant of the enzyme-substrate complex and measures the enzyme-substrate affinity6. Low Km values equate to a higher affinity of the enzyme-substrate6. The Michalis constant equal to the substrate concentration at half of the Vmax value6. The model best describes single substrate single substrate kinetics with an assumption that the back reaction of enzyme plus product being negligible6.

Inhibitors effect both the Vmax and Km values according to the type of inhibition produced on the enzyme or enzyme-substrate. Irreversible inhibitors create permanent inhibition through covalent bonds6. Reversible inhibitors work through intermolecular forces. Competitive inhibition prevents the substrate from binding active site of the enzyme, the Km appears to increase, and the Vmax does not change6. Noncompetitive inhibitors bind to any site other than the active site allowing for the enzyme-substrate complex to still form, no change to the Km, a decrease to the Vmax, with the enzyme conformational change restricting activity6. For each of these models a disassociation constant value of Ki can be calculated and is analogous to the Km for a substrate6. The Beer-Lambert Law, , is applied to determine what the concentration is in these biomolecules after samples have been prepared and analyzed through a platereader by measuring the attenuation of light8. The absorbance, or attenuation of light, is reliant on two assumptions, the value ‘A’ is directly proportional to the concentration ‘C’ and is also directly proportional to the light path ‘L’8. ‘E’ is a constant that is referred to as the molar extinction coefficient and is used to measure the probability of the electron transition8.

The Michaelis-Menten equation requires deeper calculations that need computer software to process in a timely manner1. Prior to the availability of computers or non-linear regression software the Lineweaver-Burk plot was used to determine the critical points in the enzyme kinetics such as Km and Vmax6,9. The Lineweaver-Burk equation, , linearizes the Michaelis-Menten equation and allows the Km and Vmax to be determined more accurately1,6,9. It is a the double reciprocal setup of the plot that allows for the y-intercept of the graph to be equal to the inverse of Vmax and the x intercept representing -1/Km9. The plot gives a visual impression of how enzymes are inhibited9.

Enzymes are the catalysts in living creatures and are a critical component in all chemical reactions that maintain homeostasis. This key role in life sustaining processing lends credence to the need to understand their behavior and chemical mechanisms. Pharmacological and medical understanding of enzyme kinetics are important in diagnostic assays or therapeutics such as medicines10. Enzymes are found throughout the human body and come in various forms. Oxidoreductases help in redox reactions, transferases transfer functional groups, hydrolases add water, lyases remove atoms to form double bonds or add atoms to double bonds, isomerases help in intramolecular rearrangement, and ligases help catalyze bond formations6. The plethora of different enzymes with varying functions impresses the importance of understanding how each work and the kinetics associated with them.

METHODS

Part 1: Effect of Enzyme Concentration upon Reaction Rate

Enzyme concentration’s effect on the reaction rate was analyzed using a 96-well microplate. The well B1-B6 and C1-C6 were filled with 240 µl of substrate solution. The substrate solution was 5mM 4-nitrophenyl phosphate in buffer. The multichannel pipette was used for ease of loading the substrate. After the substrate was loaded care was taken to ensure no air bubbles were present in the wells since that may lead to erroneous readings.

Enzyme dilutions were prepared on the same microplate. The dilutions were made in wells A1-A5 of the microplate. Alkaline phosphatase, stock concentration of 1mg/ml, was used to make 100 to 200 µl of each of the prescribed concentrations. The concentrations ranged from 250 µg/ml, 125 µg/ml, 50 µg/ml, 25 µg/ml and 10 µg/ml. The dilutions were done in the form of serial dilutions; taking the larger dilution to make the next and using that smaller dilution to make the following in subsequent order. Water was used as the diluting agent for each of the enzyme solutions. Well A6 held 200 µl of water and was used as a blank control with 0 µg/ml concentration.

Care was taken to ensure the enzyme was not added to the substrate solutions until the microplate was placed on the platereader and ready to be processed. The platereader was set up to read at λ = 405nm. Using the multichannel pipette tool 10 µl of the enzymes from row A1-6 were added to row B1-6. The solution was gently stirred with the tip of the pipette and the process repeated for row C1-C6. The platereader was initiated quickly thereafter. The data was collected and exported to Excel for further processing. The data was collected for 2 minutes and the actual increase in absorbance for each well was calculated by subtracting the time zero absorbance value from the reading. The change in absorbance per minute was translated to change in product concentration per minute using the extinction coefficient. The data was plotted on a graph of initial velocity vs. enzyme concentration. From the graph the optimal concentration of enzyme was determined that gave a linear plot of absorbance vs. time.

Part 2: Effect of Substrate Concentration and an Inhibitor

Part 2 was carried out very similar to part 1 with the difference being the enzyme concentration was held constant and the substrate concentration was varied. The best constant amount of enzyme derived from part 1 was used. Using the 96-well plate 36 wells were used. A1-12, B1-12, and C1-12 will be the only wells read by the platereader instrument. The substrate, 5 mM 4-nitrophenyl phosphate in buffer, was prepared to the final concentrations of 2.5 mM, 1.0 mM, 0.5 mM, 0.1 mM, and 0.05 mM. The total volume of each prepared substrate was about 1.5 ml and diluted using stock 0.05M amidol buffer. The instrument was programmed to scan row A to measure spontaneous hydrolysis of the sample, row B for the effect of the substrate concentrations, and row C for the effect of an inhibitor1. Table 1, Table 2, and Table 3 describe the setup of each well and row on the microplate. All samples were run in duplicate with column 1+2, 3+4, 5+6, 7+8, 9+10, and 11+12 being doubles of one another. The multichannel pipette was used to add the amounts of water or inhibitor. Stock concentration of the inhibitor phenylalanine was 75mM and Na2HPO4 was 15mM. The plate was taken to the microplate reader prior to the enzyme being added.