Cell Bio -Ch. 6 Enzymes
Draw a diagram and explain how and why feedback inhibition is used to regulate various biochemical pathways.
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Draw the graph that is predicted by the Michaelis-Menton equation. Label the axes, and the critical points on the curve.
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in addition to inhibition, allosteric interactions can be used to activate enzymes. Draw a diagram, label and describe enzyme domains, and explain how allosteric activator work.
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What are the three most common ways in which an enzyme interacts with its substrate within its active site?
1. Bond distortion 2. Proton transfer 3. Electron transfer
List 3 features of an active site that are important in enzyme function
1. Substrate specificity 2. Group Specificity 3. Prosthetic groups
What is activation energy and what does it have to do with enzyme function?
Activation energy is the minimum amount of energy needed to start a chemical reaction. Enzymes reduce the activation energy, to increase the rate of reaction.
Under a given set of experimental variables, an enzyme is functioning at its Vmax. What can you do to increase its Vmax?
Adding more enzymes
Compare and contrast reversible and irreversible inhibition.
Both reduce catalytic activity of an enzyme. Irreversible enzyme inhibitors: -slow dissociation of enzyme-inhibitor complex -classified in 3 categories; group-specific reagents, substrate analogs, and suicide inhibitors -substrate analogs imitate enzyme substrate and irreversibly modify active site Reversible enzyme inhibitors: -rapid dissociation of enzyme-inhibitor complex -classified in 2 categories; competitive, and non-competitive inhibitors -competitive inhibition can be reversed. by increasing substrate concentration
Compare and contrast competitive and noncompetitive enzyme inhibition.
Both reduce enzyme activity, but competitive inhibition binds to the active site while noncompetitive binds to another site on enzyme.
Suggest two properties of catalase that make it a more suitable intracellular catalyst than platinum.
Catalase is better catalyst than platanium because: 1) It lowers the activation energy more than the platanium and increase the rate of reaction without being consumed. 2) It doesnt affect the chemical equillibrium
How can an enzyme recognize and bind one specific substrate in a cell containing thousands of different molecules? How will extremes of temperature and pH affect this specificity?
Each enzyme has a unique shaped active site into which only one specific substrate will fit. Low temperature will have little effect on substrate binding, but extremely high temperatures can cause enzyme to denature, destroying active site. In contrast, having very low or very high pH will change ionization state of key residues in the active site and alter ionic bonding.
Why do enzymes need to be regulated? By what different mechanisms can this regulation be achieved?
Enzymes need to be regulated to ensure that they are active only when the cell is in need of the product of the reaction. Regulation is also important to ensure the appropriate rate of each reaction. Regulation can be achieved by substrate-level regulation, feedback regulation, or covalent modification such as phosphorylation/dephosphorylation or methylation/demethylation
Organic chemists often use inorganic catalysts such as nickel, platinum, or cations in their reactions, whereas cells use proteins called enzymes. What advantages can you see to the use of enzymes? Can you think of any disadvantages?
Enzymes= more exacting control, specificity inorganic catalysts= much energy needs to be expended to synthesize the catalyst, broad temperature range of action, broad pH range of action
Gasoline is highly combustible yet does not burst into flame spontaneously in the presence of oxygen. Why not? How is the action of a match to promote this combustion reaction different from the action of a catalyst.
Gasoline is a high energy compound, but it is in a metastable state. A lit match provides energy to allow some molecules to reach higher-energy transition state and undergo combustion. In contrast, a catalyst allows molecules to reach the transition state by lowering the activation energy.
An alternative solution is to lower the activation energy barrier. What does it mean in molecular terms to say that a catalyst lowers the activation energy barrier of a reaction?
Interaction of molecules is facilitated.
Many reactions that are thermodynamically possible do not occur at an appreciable rate because of the activation energy required for the reactants to achieve the transition state. In molecular terms, what does this mean?
It means that the molecules that ought to react would RELEASE energy if they were to do so, BUT THEY DO NOT POSSESS enough energy to collide in a way that allows the reaction to be INITIATED.
What is the difference between Km and Kcat?
Kcat is the turnover number, the amount of times each enzyme site converts substrate to products per unit time. Km is the substrate concentration needed to achieve half the maximum velocity
What is Km? What is important/special about it?
Km is the substrate concentration at which the reaction is going at half the maximum velocity. This is important because it allows to estimate where in the plot an enzyme is functioning in a cell.
How can the Lineweaver-Burke plot be used to diagnose various types of inhibition?
Km value increases when there is competitive inhibition, while Km value remains unchanged when there is noncompetitive inhibition.
Compare and contrast the lock and key model and the induced fit model of enzyme function.
Lock and key model - substrate fits into active site like a key into a lock Induced fit - the active site changes to fit the substrate, like a hand into a glove
What is the difference between phosphorylase a and phosphorylase b?
Phosphorylase b is inactive, while phosphorylase a is fully active.
What feature of a particular enzyme's active site would allow it to be more resistant than most enzymes to change in pH?
Presence of one or more charged amino acids
What does a protein kinase do? What does a protein phosphatase do?
Protein kinase catalyses the transfer of phosphate from ATP to its protein substrates Protein phosphatase catalyses the transfer of phosphate from a phosphoprotein to a water molecule
Hexokinase is an important enzyme in energy metabolism because it catalyzes the first step in the exothermic degradation of glucose. Understanding the kinetics of this reaction will help us to better understand its role in energy production in the cell. But how do scientists experimentally determine the kinetic parameters of Km and Vmax for an enzyme such as this?
Researchers can determine Km and Vmax by performing an experiment in which the enzyme concentration and all other variables are held constant as the substrate concentration is varied in a series of enzyme assays (individual measurements). By measuring the velocity (v ) at each substrate concentration [S] and graphing the results, we can find the numerical values of Km and Vmax.
Enzymes are said to be stereospecific. What does this mean in terms of their substrates and products?
They are able to discriminate or differentiate similar molecules
Why are enzymes sensitive to temperature and pH?
They will denature if either of them are too high and reaction will not occur
Some enzymes can transfer a hydrogen atom without lowering the activation energy barrier. How is this possible?
This is possible by means of a mechanism known as quantum tunneling.
One way to meet this requirement is by an input of heat, which in some cases need only be an initial, transient input. Give an example, and explain what this accomplishes in molecular terms.
Touching a match to a sheet of paper is an example. Thermal activation imparts sufficient kinetic energy to the molecules such that the porportion of them that possesses adequate energy to collide and react increases. The reaction is self sustaining because reacting molecules release sufficient energy to energize and activate neighboring molecules
Suggest yet another way that the rate of hydrogen peroxide decomposition can be accelerated. Is this a suitable means of increasing reaction rates within cells? Why or why not?
We can use the inorganic catalyst like magnese oxide in place of catalase enzyme in order to accelerate the rate of reaction. But magenese is not good for cells as it cause various harmful effects.
Describe how glycogenolysis is regulated.
When level of blood glucose fall, α cells of pancreases secretes the glucagon. Glucagon stimulates glycogenolysis inside the liver. Glycogenolysis releases glucose into the bloodstream to improve blood glucose levels again.
To maximize production of anti-cancer compounds, how would you want to manipulate Vmax and Km, and Kcat?
You want to increase Vmax is possible to ensure highest possible reaction rate at saturating substrate concentrations. Kcat should also be as high as possible to produce maximum amount of product molecules per minute. In contrast, you want to lower Km, so that a lower [S] would achieve half maximum velocity
What does phosphorylase a do?
adds an inorganic phosphate onto substrate without using ATP
Carboxypeptidase A, an example of a hydrolase, also exhibits group specificity. Why is group specificity logical for this enzyme?
because it degrades dietary polypeptide chains by removing the C-terminal amino acid
An enzyme with the unusual name "rubisco" has a very low Kcat. It turns out that rubisco does really important work, such that its low Kcat could be a problem for life as we know it. What does rubisco do and how does it overcome the problem of low Kcat?
carbon fixation during photosynthesis
Describe the properties of an enzyme that qualify it as a "catalyst."
increases rate of reaction without being consumed or altered, nor altering the equilibrium between reactants and products
Describe the catalytic cycle of an enzyme.
substrate enters site, induced fit, held in active site by weak interactions, active site speeds reaction, substrates converted to products, released.
Explain how peptidases are activated in the small intestine. Why does this form of activation make sense here, whereas it doesn't for metabolic enzymes inside cells?
they are activated by a cascade initiated by enterokinase.
What is the difference between trypsinogen and trypsin?
trypsin is a digestive enzyme that cleaves peptide bonds while trypsinogen is an inactive precursor of trypsin.