Chapter 2 Enzymes Flashcards
What are enzymes?
Enzymes are biological catalysts that are unchanged by the reactions they catalyze and are reusable.
Each enzyme catalyzes a single reaction or type of reaction with high
specificity.
What is an Oxidoreductases?
Oxidoreductases catalyze oxidation–reduction reactions that involve the transfer of electrons.
What is a Transferases?
Transferases move a functional group from one molecule to another molecule.
Transferases are enzymes that catalyze the transfer of functional groups from one molecule to another. A common example is aminotransferases, which transfer amino groups between amino acids and α-keto acids in protein metabolism. Kinases, a type of transferase, specifically transfer phosphate groups, often from ATP to other molecules.
Questions may focus on the role of transferases in cellular processes like protein metabolism and phosphorylation, particularly the action of kinases in signal transduction and energy transfer.
What is a Hydrolase?
Hydrolases catalyze cleavage with the addition of water.
Common hydrolases include phosphatases (which remove phosphate groups), peptidases (which break down proteins), nucleases (which break down nucleic acids), and lipases (which break down lipids).
Questions may focus on the role of hydrolases in breaking down biomolecules, especially in processes like protein degradation, DNA/RNA cleavage, and lipid metabolism, all of which are vital to cellular function and energy production.
What is a Lyase?
Lyase catalyze cleavage without the addition of water and without the transfer of electrons.
The reverse reaction (synthesis) is often more important biologically
Lyases are important for the MCAT in enzyme function and metabolic pathways. Questions may focus on the role of lyases in reactions like the formation or breakdown of molecules in metabolic cycles (e.g., the citric acid cycle), and their unique mechanism of action that differs from hydrolases and oxidoreductases.
Mnemonic for Major enzyme classifications
LIL HOT
Major Enzyme Classifications: LIL HOT
Ligase
Isomerase
Lyase
Hydrolase
Oxidoreductase
Transferase
What is an isomerase?
Isomerases catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers
Isomerases are important for the MCAT in enzyme function and stereochemistry. Questions may explore their role in metabolic pathways, such as glycolysis or the citric acid cycle, where they help rearrange molecules for further reactions. Understanding isomerases is key for topics involving structural changes in molecules and their biological implications.
What is a Ligase?
Ligases are responsible for joining two large biomolecules, often of the same type requiring ATP as an energy source.
MCAT Relevance:
Ligases are crucial for the MCAT in topics related to DNA replication, recombination, and enzyme function. Questions may cover how ligases facilitate the joining of biomolecules in processes such as genetic repair, replication, and synthesis, emphasizing their role in energy-dependent bond formation.
What is Thermodynamics and Enzyme Catalysis?
Thermodynamics describes the energy changes in reactions, where endergonic reactions require energy input (ΔG > 0) and exergonic reactions release energy (ΔG < 0). Enzymes do not change the free energy (ΔG) or equilibrium of a reaction; instead, they speed up the reaction by lowering the activation energy, allowing reactions to reach equilibrium faster. Since enzymes are not consumed in the reaction, a small amount of enzyme can act on many substrates over time. Catalysts make it easier for substrates to reach their transition state, like lowering the height of a hill to make it easier to climb.
What is Exergonic Reaction
Exergonic reactions release energy; ΔG is negative
Do Enzymes raise or lower activation energy?
Enzymes lower the activation energy necessary for biological reactions
Do enzymes effect free energy (ΔG) or enthalpy (ΔH) ?
Enzymes do not alter the free energy (ΔG) or enthalpy (ΔH) change that
accompanies the reaction nor the final equilibrium position; rather,
** they change the rate (kinetics) at which equilibrium is reached.**
What is An Active Site?
Enzymes act by stabilizing the transition state, providing a favorable microenvironment, or bonding with the substrate molecules.
Enzymes have an active site, which is the site of catalysis.
(Catalysis is the process of increasing the rate of a chemical reaction by using a catalyst. A catalyst lowers the activation energy required for the reaction to occur, making it easier for reactants to convert into products. Importantly, the catalyst itself is not consumed or permanently altered during the reaction, allowing it to be reused multiple times. Catalysis is essential in both biological systems (e.g., enzymes) and industrial processes.)
What is the Lock and Key theory?
The lock and key theory hypothesizes that the enzyme and
substrate are exactly complementary.
What is the induced fit model?
The induced fit model hypothesizes that the enzyme and substrate
undergo conformational changes to interact fully
Some enzymes require metal cation called _______ or small organic
_______ to be active.
Some enzymes require metal cation cofactors or small organic
coenzymes to be active.
What is Saturation Kinetics?
Enzymes experience saturation kinetics:
as substrate concentration increases, the reaction rate does as well until a maximum value is reached.
What are cooperative enzymes?
Cooperative enzymes display a sigmoidal curve because of the
change in activity with substrate binding.
How do Temperature and pH affect enzyme activity
Temperature and pH affect an enzyme’s activity in vivo;
changes in temperature and pH can result in denaturing of the enzyme and loss
of activity due to loss of secondary, tertiary, or, if present, quaternary structure.
In vitro, salinity can impact the action of enzymes
What is feedback inhibition?
Feedback inhibition is a regulatory mechanism whereby the catalytic
activity of an enzyme is inhibited by the presence of high levels of a
product later in the same pathway
Example:
Feedback inhibition is like when your body says, “I’ve had enough, stop making more!” Imagine you’re building a toy tower, and every time you put a block on, a helper gives you more blocks. But when the tower gets tall enough, the helper stops giving you blocks because you don’t need any more.
In your body, feedback inhibition works the same way: when enough of something (like a chemical or protein) has been made, it tells the process to stop making more, so you don’t waste energy or resources.
What is reversible inhibition?
Reversible inhibition is characterized by the ability to replace the
inhibitor with a compound of greater affinity or to remove it using
mild laboratory treatment.
Example:
Reversible inhibition is like when someone presses the “pause” button. Imagine you’re playing a game, and your friend stops you by holding your hand. You’re not done playing, but you just need to wait until they let go.
In your body, reversible inhibition works the same way: something temporarily stops an enzyme from doing its job, but once the “block” is removed, the enzyme can start working again. It’s not permanent, just a short pause!
What is competitive inhibition?
Competitive inhibition results when the inhibitor is similar to the
substrate and binds at the active site. Competitive inhibition can be
overcome by adding more substrate. vmax
is unchanged, Km
increases
Example:
Competitive inhibition is like two kids trying to sit in the same chair. Only one can sit down at a time, so they compete for the spot. In your body, competitive inhibition happens when a molecule (the “inhibitor”) competes with the real substance (the “substrate”) to bind to an enzyme. The enzyme can only work if the real substance sits in the spot, so if the inhibitor gets there first, the enzyme can’t do its job until the spot is free again!
In competitive inhibition, the inhibitor competes with the substrate for the enzyme’s active site. Here’s how it affects Vmax and Km:
Vmax (maximum reaction rate): This stays the same because if you add enough substrate, it will outcompete the inhibitor, and the enzyme can still reach its full speed.
Km (substrate concentration at half Vmax): This increases because you need more substrate to outcompete the inhibitor and reach half of the enzyme’s maximum speed.
So, with competitive inhibition, it takes more substrate to get the enzyme working at its usual speed, but the maximum possible speed (Vmax) doesn’t change.
What is noncompetitive inhibition?
Noncompetitive inhibition results when the inhibitor binds with equal affinity to the enzyme and the enzyme–substrate complex.
vmax is decreased, Km
is unchanged
Example:
Noncompetitive inhibition is like someone turning off the power while you’re playing a video game. No matter how hard you press the buttons, the game won’t work properly because the power is off.
In your body, noncompetitive inhibition happens when an inhibitor binds to an enzyme at a different spot (not the active site). This changes the enzyme’s shape so it can’t work well, even if the real substance (the substrate) is still there. Adding more substrate won’t help because the enzyme’s “power” is already turned off!
In noncompetitive inhibition, the inhibitor binds to the enzyme at a site other than the active site, changing the enzyme’s shape so it can’t function properly. Here’s how it affects Vmax and Km:
Vmax (maximum reaction rate): Decreases because no matter how much substrate you add, the enzyme can’t reach its full speed due to the inhibitor altering its function.
Km (substrate concentration at half Vmax): Stays the same because the inhibitor doesn’t compete with the substrate for the active site. The enzyme’s affinity for the substrate doesn’t change, but its overall efficiency is reduced.
So, with noncompetitive inhibition, the enzyme can’t work as fast, but the amount of substrate needed to bind remains the same.
What is mixed inhibition?
Mixed inhibition results when the inhibitor binds with unequal affinity to the enzyme and the enzyme–substrate complex. vmax
is decreased, Km is increased or decreased depending on if the
inhibitor has higher affinity for the enzyme or enzyme–substrate complex.
Mixed inhibition is like trying to ride a bike, but someone either messes with the pedals or tightens the brakes. It makes it harder to ride, and the bike doesn’t go as fast, no matter how hard you try.
In mixed inhibition, the inhibitor can bind to the enzyme either before or after the substrate attaches, but in both cases, it slows down the enzyme’s ability to work.
Vmax (maximum reaction rate): Decreases because the enzyme can’t work as fast, even if you add more substrate.
Km (substrate concentration at half Vmax): It can either increase or decrease depending on where the inhibitor binds:
If the inhibitor binds to the enzyme before the substrate, it increases Km (makes it harder for the substrate to bind).
If the inhibitor binds after the substrate, it decreases Km (makes it easier for the substrate to bind).
In mixed inhibition, the enzyme’s speed is always reduced, but how much substrate is needed depends on how the inhibitor works.
What is uncompetitive Inhibition?
Uncompetitive inhibition results when the inhibitor binds only with the enzyme–substrate complex. Km
and vmax both decrease.
Uncompetitive inhibition is like someone locking the pedals on your bike after you’ve already started riding. Even though you can still sit on the bike, you can’t pedal anymore because it’s stuck.
In uncompetitive inhibition, the inhibitor only binds to the enzyme after the substrate has attached, preventing the enzyme from doing its job.
Vmax (maximum reaction rate): Decreases because the enzyme-substrate complex gets “stuck,” and no matter how much substrate you add, the enzyme can’t work at full speed.
Km (substrate concentration at half Vmax): Decreases too because the inhibitor stabilizes the enzyme-substrate complex, making it seem like the enzyme binds the substrate more easily (lower concentration needed to reach half-speed).
So, in uncompetitive inhibition, both Vmax and Km decrease because the enzyme is stuck and can’t work as efficiently.
What is irreversible inhibition?
Irreversible inhibition alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently; new enzyme molecules must be synthesized for the reaction to occur again.
Irreversible inhibition is like someone breaking your bike pedals—once they’re broken, you can’t pedal anymore, no matter what you do.
In irreversible inhibition, the inhibitor permanently binds to the enzyme, often by forming a strong bond. This stops the enzyme from working completely and can’t be undone.
Vmax (maximum reaction rate): Decreases because the enzyme is permanently disabled, so the maximum speed of the reaction can never be reached again.
Km: Stays the same for the remaining active enzymes because the inhibitor doesn’t affect how the enzyme binds to the substrate, but the overall amount of working enzymes is reduced.
In irreversible inhibition, the enzyme is permanently “turned off,” lowering the overall reaction rate, while the remaining enzymes still function normally.
What is kM and Vmax?
Km (Michaelis constant) represents the substrate concentration at which an enzyme works at half its maximum speed, reflecting the enzyme’s affinity for the substrate. A low Km means high affinity, while a high Km indicates low affinity. Vmax is the maximum reaction rate when all enzyme active sites are saturated with substrate. Both values are important for understanding enzyme efficiency and regulation, often tested on the MCAT.
Like You’re 5:
Km is like how hungry you need to be before you eat half of a big sandwich. If you eat half of it quickly, you’re really hungry (low Km). Vmax is how fast you can eat the whole sandwich when you’re super hungry and nothing is stopping you!
What is the Michaelis-Menten Equation?
Use it to:
Determine how the reaction rate changes with varying substrate concentrations.
Calculate enzyme activity if you have Vmax and Km values.
Example:
If you’re given substrate concentration and need to find the reaction rate, use this equation.
v= Vmax [S] / Km =S
v: Reaction rate (velocity)
Vmax: Maximum reaction rate
Km: Michaelis constant (substrate concentration at half Vmax)
[S]: Substrate concentration
This equation describes how the reaction rate depends on substrate concentration.
What is the Lineweaver-Burk Equation
Use it to:
Analyze enzyme kinetics by plotting data on a double-reciprocal graph.
Identify types of inhibition (competitive, non-competitive, etc.) by looking at changes in the slope and intercepts of the plot.
Example:
If the problem provides a graph or asks you to interpret a Lineweaver-Burk plot, use this equation to understand enzyme behavior and inhibition.
1/v = Km/Vmax[S] + 1/Vmax
A linear form of the Michaelis-Menten equation used to plot enzyme kinetics.
what is Catalytic Efficiency?
Use it to:
Evaluate how effectively an enzyme converts substrate into product.
Compare the efficiency of different enzymes.
Example:
If comparing two enzymes to determine which one is more efficient, use this equation to calculate and compare their catalytic efficiencies.
CatalyticEfficiency= Kcat/Km
kcat: Turnover number (how many substrate molecules one enzyme converts to product per second)
Reflects how efficiently an enzyme converts substrate into product. High efficiency = high kcat and low Km.
What is Vmax and Enzyme Concentration
Vmax = kcat E
Shows that Vmax depends on the enzyme concentration and how fast it can catalyze the reaction.
Use it to:
Relate the maximum reaction rate to the total enzyme concentration and the enzyme’s turnover number.
Calculate Vmax if you know the enzyme concentration and kcat.
Example: If the problem gives enzyme concentration and kcat but not Vmax, use this equation to find Vmax.
Each equation helps in understanding different aspects of enzyme function, kinetics, and inhibition, so be familiar with when to apply them based on the type of information provided or required.
What are allosteric sites?
Allosteric sites can be occupied by activators, which increase either
affinity or enzymatic turnover.
Allosteric sites are like extra buttons on a toy that can change how it works. Imagine your toy has a special button that, when pressed, changes the way it moves or sounds.
In your body, an allosteric site is a special spot on an enzyme where something can attach and change how the enzyme works, even if it’s not the main place where the enzyme does its job. So, just like that special button changes your toy, an allosteric site changes how the enzyme functions!
Explain Phosphorylation and glycosylation?
Phosphorylation (covalent modification with phosphate) or
glycosylation (covalent modification with carbohydrate) can alter
the activity or selectivity of enzymes.
Phosphorylation is like putting a special sticker on a toy to change how it works. When you add the sticker, the toy might move faster or change colors. In your body, phosphorylation is when a phosphate group is added to a protein, which can turn the protein’s activity on or off.
Glycosylation is like adding a colorful tag to your toy. This tag helps the toy do special tricks or makes it recognizable. In your body, glycosylation is when sugar molecules are added to a protein, which helps the protein function properly or signals it to go to a certain place.
What are zymogens?
Zymogens are secreted in an inactive form and are activated by cleavage.
Zymogens are like toys that are packed up and need to be unpacked before they can be played with. The toy is ready, but it’s in a special box that needs to be opened first.
In your body, zymogens are inactive forms of enzymes. They need to be “unpacked” or activated before they can start doing their job. This is done to make sure they don’t start working too early or in the wrong place.
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. ey are also regenerated at the end of the reaction to
their original form.
What is enzyme specificity?
Enzyme specificity refers to the idea that a given enzyme will only
catalyze a given reaction or type of reaction. For example,
serine/threonine-specific protein kinases will only place a phosphate
group onto the hydroxyl group of a serine or threonine residue.
What are the names and main functions of the six different classes of enzymes?
Ligase: Addition or synthesis reactions, generally between large molecules, often require ATP
Isomerase: Rearrangement of bonds within a compound
Lyase: Cleavage of a single molecule into two products, or synthesis of small
organic molecules
Hydrolase: Breaking of a compound into two molecules using the addition of water
Oxidoreductase: Oxidation–reduction reactions (transferring electrons)
Transferase: Movement of a functional group from one molecule to another
In what ways do enzymes affect the thermodynamics vs. the kinetics of a reaction?
enzymes have no effect on the overall thermodynamics of the reaction;
they have no effect on the ΔG or ΔH of the reaction, although they do lower the energy of the transition state, thus lowering the activation energy.
However, enzymes have a profound effect on the kinetics of a reaction. By lowering activation energy, equilibrium can be achieved
faster (although the equilibrium position does not change).
Name the B vitamins (B1 - B12)
B1 : thiamine
B2: riboflavin
B3: niacin
B5: pantothenic acid
B6: pyridoxal phosphate
B7: biotin
B9: folic acid
B12: cyanocobalamin
