Enzymes Flashcards
1
Q
One method to increase the amount of CO2 in sodas would be to pump CO2 into the cans. What method do companies do instead?
A
Utilize the H2O + CO2 = H2CO3 (carbonic acid) method instead as this allows CO2 to be dissolved into the the liquid itself and therefore much more CO2 can be fit inside the can
2
Q
The fizz you see on the top of the soda can is due to CO2. However as you drink it, you notice the bubbles are dramatically more. What is causing this increase in bubbles?
A
Carbonic anhydrase found in the mouth causes an increase in CO2 through H2O + CO2 H2CO3 backwards reaction. The enzyme helps facilitate the reaction to occur much more quickly than it would naturally on its on (seen on/in the can)
3
Q
Enzymes have many mechanisms to function. Name them all.
A
Acid-Base Catalysis, Proximity-Orientation, Covalent Catalysis, Electrostatic Catalysis
Mnemonic: CAPE
4
Q
An enzyme facilitating the transfer of a hydrogen from one species to another. What type of mechanism of action is the enzyme committing to? A. Proximity - Orientation B. Electrostatic Catalysis C. Covalent Catalysis D. Acid - Base Catalysis
A
D. Acid-Base Catalysis
5
Q
A newly discovered protein is transferring an oxygen from a carbonyl to an inole. What mechanism of action is this protein committing to?
A
None of knowledge yet. The ones required to know are: Acid-Base Catalysis, Proximity-Orientation, Covalent Catalysis, Electrostatic Catalysis
6
Q
An enzyme facilitating the transfer of an electron from one species to another. What type of mechanism of action is the enzyme committing to? A. Proximity - Orientation B. Electrostatic Catalysis C. Covalent Catalysis D. Acid - Base Catalysis
A
B. Electrostatic Catalysis. It is acting like a carrier or an electron sink
7
Q
True or false: Electrostatic Catalysis is a mechanism of an enzyme in which the enzyme will act as a mediator to hold electrons temporarily and even transfer it from one molecule to another.
A
False. Electrostatic catalysis is a when a cofactor of an enzyme such as magnesium, functions in stabilizing the reactants. Ex: DNA Polymerase uses Mg2+ to stabilize the negatively charged DNA in order to replicate it
8
Q
What is the purpose of an enzyme utilizing the proximity and orientation mechanism of action?
A
These enzymes bring the needed molecules closer together to increase collision, and orient molecules in appropriate angles to allow a reaction to occur.
9
Q
What are the requirements from reactants in order for a reaction to occur?
A
In order for molecules to react, they need to collide at the right angles
10
Q
Carbonic Anhydrase catalyzes a reaction involving which molecules to form carbonic acid? A. H2O and CO2 B. H2 and CO2 C. H2O and CO D. H2 and CO
A
H2O and CO2
11
Q
CO2 is not as readily carried by hemoglobin or any protein in the body. How does this increase the importance of carbonic anhydrase?
A
This enzyme allows the addition of CO2 and H2O into a soluble form (bicarbonate in blood). This process is important to allow the excretion of CO2 in the lungs, which can’t be done in the tissues.
12
Q
True or False: CO2 is 10 times as soluble as O2 in water.
A
False, CO2 is 20 times as soluble than water, therefore CO2 can be carried in the blood stream while O2 needs a special carrier. CO2 is soluble because water molecules are attracted to these polar areas. The bond between carbon and oxygen is not as polar as the bond between hydrogen and oxygen, but it is polar enough that carbon dioxide can dissolve in water. In blood, 85% of CO2 is carried as HCO3-
middleschoolchemistry.com
13
Q
The production of carbonic acid from carbon dioxide and H2O occurs… A. In the tissues B. In the bloodstream C. In the blood cells D. In the lungs
A
C. Occurs in the blood cells, and diffuses out to dissolve into the bloodstream as bicarbonate. At the lungs, catabolize carbonic acid into H2O and CO2
14
Q
True or false: After the generation of carbonic acid, another enzyme catalyzes the acid into bicarbonate and acid
A
False. This is a spontaneous event that occurs very quickly after the formation of carbonic acid. Therefore once it is shuttled out, the molecule is a bicarbonate already
15
Q
Bicarbonate ends up in the bloodstream once it is produced. Describe the mechanism of its travel there. What is the importance of this mechanism
A
It binds onto a chlorine/bicarb shuttle at the membrane of the RBC. As Cl- from the ECM is taken into the cell, bicarbonate is shuttled out. This mechanism preserves the electrical charge both in the plasma and the red blood cell.
16
Q
While the acid buffer system of bicarbonate anabolism is seen in RBC, where else in the body is this system also seen in?
A
In the kidneys as well as the lungs
Media.lanecc.edu
17
Q
HCO3- is used to adjust the H+ concentrations in the blood. What happens to the pH at the lungs when CO2 is exhaled?
A
Some HCO3–, which helps to adjust H+ concentrations, is lost from the body when CO2 is expelled from the lungs. As a result the H+ concentration also decreases as well because it is converted into H2O and the pH increases. [Note: Lung pH is around 7.4]
Media.lanecc.edu
18
Q
The efficiency of carbonic anhydrase’s conversion of CO2 to H2CO2 is A. 100,000 CO2/ min B. 1,000,000 CO2/ min C. 100,000 CO2/sec D. 1,000,000 CO2/sec
A
D. 1,000,000 CO2/sec. Therefore this enzyme is very good at its job in lowering the toxic CO2 levels in the blood
19
Q
Of the following, which is not a fact about enzymes:
A. They have the ability to transform energies
B. Apoenzymes are dependent on cofactors for function
C. Enzymes limit the number of unwanted products
D. All enzymes are proteins
A
D. Not all enzymes are proteins, some are RNA molecules that have the ability to catalyze reactions as well.
B. Enzymes without their cofactors are called apoenzymes, and with interaction between the two, these are called holoenzymes
C. Enzymes limit the number of unwanted products by having a high specificity for substrates and conducting only one or related sets of reactions
20
Q
Enzymes bound to their cofactors are called: A. Apoenzymes, B. Vitamins C. Coenzymes D. Holoenzymes
A
D. Holoenzymes are produced when apoenzymes bind their cofactors.
B and C: Vitamins tend to be the composition of coenzymes (which are organic cofactors)
21
Q
Compare and contrast metal ions and coenzymes
A
Metal ions and coenzymes are both cofactors to an enzyme to allow efficient and effective function. However, both differ as metal ions are metals, or metal compounds while coenzymes are made organic molecules usually made of vitamins
22
Q
Compare and contrast prosthetic groups and coenzymes
A
Prosthetic groups are a specific class under coenzymes. While coenzymes refer to all organic cofactors, prosthetic groups are cofactors that are tightly/covalently bound to the protein itself which means that this group is essential for the function of the enzyme
23
Q
Two molecules, CO2 and H2O are bound by carbonic anhydrase and are converted into H2CO3. What prevents a CO2 and H2O from converting into other types of substrates such as glucose?
A
The enzymes innate property of commiTting to one or related sets of reactions (it’s specificity) leads to specific orientation and combination of molecules
24
Q
Trypsin, an protease cleaves carboxyl groups of…
A
(1) cleaves peptide bonds on the carboxyl side of lysine (2) binds and cleaves the carboxyl side of arginine amino acid. [demonstrates its specificity for related reactions
25
In an experiment, you throw in an unknown enzyme into its substrates. After a reaction, you momentarily see change to its structure. You conclude this is not an enzyme. Is your conclusion correct?
Maybe not, if this is a true enzyme, the structure and shape may change, however, it will assume its original shape and structure once the reaction is completely over.
26
Identify the correct definition
A. Enzymes lower the standard free energy of a reaction
B. Enzymes consume the substrate to produce product
C. Enzymes lower the free energy of activation
D. Enzymes lower the E_rcn
C. Enzymes lower the free energy of activation aka the reaction’s activation energy (ΔG‡). They don’t change the standard free energy of a reaction (E_rcn/ΔG°) and don’t change the products or reactants. They simply change the pathway from reactant to product.
27
Compare and contrast the two catalytic strategies enzymes can take on: Covalent and electrostatic.
Both are strategies by enzymes. However, covalent catalysis is the covalent bond of an enzyme to the substrate, while the electrostatic catalysis is the enzyme using molecules such as metal cofactors to stabilize big positive or negative charges
28
While conducting an experiment, you analyze a reaction from a reaction coordinate diagram. The graph shows the substrate with a higher energy state compared to the product and the free energy of activation, to be bigger compared to the standard free energy. Which molecule is more stable?
The product is more stable compared to the reactants as it has a decreased energy state. Molecules with increased energies are more reactive and unstable.
29
Where on a reaction coordinate graph can you find the transition state?
This will be the highest peak along the pathway of a substrate’s conversion to its product.
30
Compare and contrast free energy of activation and the standard free energy.
Delta G Double Dagger - (ΔG‡) - this is the free energy of activation - amount of energy substrate needs to have in order to break the reaction barrier to get to point B. Standard Free Energy (ΔG°) the net change between our reactant and product. This is the energy released into the environment once the reaction is over. This includes ΔG‡ in its equation as well
31
What will determine how fast a reaction occurs?
Its innate free energy of activation (the energy difference from substrate to transition state)
32
You are working on a biochem problem and the calculate that the reaction has a negative Gibbs free energy. Is this reaction in equilibrium?
No, negative Gibbs free (Energy of products - energy of reactants) demonstrates a spontaneous, exergonic reaction and therefore is still taking place. When Gibbs free energy (ΔG) has reached 0, the reaction is said to have reached equilibrium
33
Describe what Gibbs free energy is.
Gibbs free energy is how much energy is inputted or released into the chemical reaction. It relies only on the energy of the product - reactant. The pathway in which it takes to achieve this, does not matter.
34
During your attempt to combust an ATP, you discover the standard free energy of your reaction is positive. What has gone wrong with your experiment?
You have created ATP rather than combust. Creating this high energy molecule requires energy (endergonic reaction/nonspontaneous reaction). OR your math could be wrong
35
Your intern is calculating how much energy is released as you force a GTP molecule to release a phosphate by calculating the transition state energy and the substrate energy level. What should you tell him?
Gibbs free energy is the energy released/inputted into a reaction and does not rely on the pathway of a reaction.
36
K1 = K2. What does this mean in terms of G?
Q represents a quantity of a species of a reaction. When Q changes to K, this entails that the substrate/product has reached equilibrium, therefore K is the numerical values of Q at the end of the reaction. Therefore when K1 = K2, equilibrium has been reached. And therefore Gibbs is 0 (also mean equilibrium)
37
Compare and contrast activation energy and gibbs free energy
Activation energy = the free energy of activation. This is the required energy needed for a substrate to enter into its transition state. Changing the pathway in which the substrate gets converted into its product, such as addition of an enzyme, will lower this value.
Gibbs free energy is the standard free energy, or the energy released with a substrate changing into its product. Changes to the pathway will ont change this value
38
Describe the role of an enzyme and the transition state of a substrate.
As the substrate enters into its transition state (the most unstable state) the enzyme stabilizes it to allow it to enter this stage much more quickly. In the active site, there exists and environment which allows the stability of the bonds creating and forming, decreasing the activation energy. Remember, a reaction is dependent on the activation energy.
39
The x axis of a reaction coordinate diagram of a chemical reaction is …
The reaction progress of the chemical reaction. This is not time!!! Time cannot be determined by the reaction progress
40
You are comparing two scenarios of the same reaction: One with a catalysis and another without. They both reach equilibrium. What key things do both share at this point?
Both scenarios should have the same quantity of products and reactants and they should have the same amount of gibbs free energy released/consumed.
41
You have 10 enzymes and add 3 substrates into the mixture. What is its activity?
The enzymes are functioning at 30% of its maximum velocity. Activity of enzymes are measured based on all the same enzymes's activity. When all enzymes of the same type are functioning (meaning all substrates have binded to the active site), then it has reached its max capacity.
42
You are solving a problem and you read that the enzyme has reached its max velocity with 100 mg of bicarbonate. What does max velocity represent?
The maximum velocity of the enzyme represents the activity of the active site. Keep in mind that enzymes will never reach this, but simply an estimation
43
Compare and contrast the binding of a substrate to an enzyme when it is done initially, and when it is in its induced fit.
The Initial binding of an enzyme and a substrate occurs when theses two molecules first interact. This binding leads to strong interactions, however the fit of another is not the strongest quite yet. As the substrate and enzyme conform to one another’s shape, they develop the strongest interaction - this process is called induced fit. This interaction is the point in which the substrates enter into their transition state in order to be cleaved into their products.
44
Once the molecules have exited the transition state when it is bound by an enzyme, what happens to it?
The interactions between the molecule/product and the enzyme weakens (mirroring the same interactions seen during initial binding site) and eventually the product is released by the enzyme while the enzyme returns back to its normal state.
45
True or false: Enzymes have one active site and are specific in binding one substrate only, leading to increased specificity in chemical reactions.
False. Some enzymes can have more than one active site. However, only one substrate can bind to one active site at a time. For example, lactic dehydrogenase has two active sites, but one can either bind to NADH or pyruvate. The rest of the statement is true.
46
Describe the relationship of allosteric regulators to enzymes.
Allosteric regulators are chemicals that can alter the activity of the enzymes by either upregulating or downregulating the enzyme. (Note: These regulators bind to other sites outside of the active site and not directly to the active site)
47
There are many residues within the active site of an enzyme. What are the two important roles of these amino acids?
(1) Stabilize the substrate to lower the energy of it in order to undergo its reaction and (2) Catalyze the substrate itself
48
Compare the active site’s size to the enzyme as whole.
The functional portion of the enzyme is the active site, yet this is the smallest portion of the enzyme. This is because in order to properly allow residues responsible for stabilizing and catalyzing the substrates to be in the active site, the primary structure needs to be folded and manipulated in lots of different methods. This foldings and scaffolds are much bigger in size compared to the active site, but they allows stability and support the active site
49
How does the enzyme create a microenvironment for the substrate to catalyze?
Once the substrate binds, the enzyme closes and semi isolates the substrate from the interstitial. (remember, the environment tends to be partially nonpolar)
50
What is one important feature the microenvironment contributes to to prevent other products from forming?
As the enzyme closes and conforms around the substrate, the enzyme orients the substrate in a fashion that prevents other collisions between the two substrates from colliding
51
Water is never really found within the active site of a biological enzyme. Why is this the case?
Active sites tend to be nonpolar in order to carry out chemical reactions. Water is only found there when it plays a role or is a by product of the chemical reactions(s).
52
What can other portions of the enzyme commit to?
It has the ability to interact with other things outside of the subunit and is important for things like adherence to cell membrane or binding to the other subunits
53
What interactions seen in the enzyme - substrate interactions allows the for the substrate to bind strongly enough for catalysis but not be irreversible?
Weak interactions all functioning at once - hydrogen bonds, hydrophobic interactions, and van der waals forces
54
What is the requirement for weak interactions to exist between substrates in the active site? How is this achieved?
Short distances are required for weak interactions such as hydrogen and london dispersion interactions to exist. The enzyme achieves this by conforming around the substrate. As it does so, it decreases the substrate distance as well as creates a microenvironment for them and orient them as well.
55
Compare and Contrast the lock and key model to the induced fit model
Both are models entailing how the substrates and enzymes interact with one another. The older model - lock and key model, elaborates how the substrate and enzyme are innately the same shape, in which the substrate is the key that perfectly fits in the lock. The more accepted model - induced fit model - entails how they do have similar structure, but after initial binding, the enzyme will conform to the shape of the substrate in order to better thoroughly interact (stabilize and catalyze) with the substrate.
56
You’re staring at an unknown protein that appears to have some enzymatic activities. When introduced to a strand of mRNA, it brings in new amino acids. What type of enzyme category does this protein fall under?
Transferases. The enzyme is able to move portions of one molecule to another. This protein is peptidyl transferase, which plays a role in transferring amino acid tRNA onto a growing polypeptide chain
57
In passing electrons from NADH or Lactic Acid to Pyruvate, lactate dehydrogenase is an example of what type of enzyme?
Oxidoreductase - has two different types of reaction that involve transfer of electrons from one species to another. These are called both because typically they can catalyze a forward and backwards reaction
Oxidase - involved in oxidizing electrons from a molecule AKA taking electrons away from a molecule
Reductase - involved in removing an electron away from a molecule
58
Define an isomerase.
Isomerase - groups are typically involved in reactions where a molecule is converted into one of its isomers. For instance. Glycolysis - Conversion of glucose 6 phosphate to fructose 6 phosphate. This is catalyzed by a phosphoglucose isomerase. Therefore it creates an isomer of the substrate it just phosphorylated
59
Serine Proteases functions in breaking peptide bonds. For instance, Lys-Ala + H2O -> Lys + Ala. What kind of enzyme is Serine Protease?
A Hydrolase - uses a water to cleave a molecule into two other molecules
60
Compare and contrast ligases and lyases.
Ligases catalyze reaction between two molecules and combine to form a complex between the two meanwhile lyases catalyze the dissociation of a molecule into two different molecules without the use of water or oxidation or reduction. Therefore this means the products they produce tend to be a double bond or a ring structure to preserve electrons
61
From the urea cycle, a protein catalyzes the reaction of Argininosuccinate -> Arginine + Succinate. What category does this molecule fall under? What is the name of this protein?
Argininosuccinate lyase is a lyase, which means, catalyze the dissociation of a molecule into two different molecules without the use of water or oxidation or reduction. Therefore this means the products they produce tend to be a double bond or a ring structure to preserve electrons.
62
```
NADH is an example of
A. Cofactor
B. Ligase
C. Transferases
D. Coenzyme
```
D. Coenzymes - organic carrier molecules. This means the coenzymes are “holding” something for the enzyme in order to function smoothly. NADH acts as a great electron carrier. It can dissociate into its oxidized form. Therefore NAD+ can accept electrons and carry electrons for an enzyme.
Not C because in order to be classified as a transferase, it has to be an enzyme and NAD is not an enzyme, but functions as a component for enzymes
63
```
CoA is a
A. Coenzyme
B. Ligase
C. Transferases
D. Cofactor
```
A. Coenzyme. Coenzyme A - acts like NADH carrier molecule, but CoA carriers acyl groups instead of an electron
COASCOO + H2O = COOH + COA-SH
64
What is seen in cofactors that are not seen in coenzymes?
Cofactors tend to participate in catalysis (not seen in coenzymes which carry things for other reactions) such as Stabilizing the enzyme, Stabilizing the substrates, and Aiding in converting substrates from one form to another
65
Mg2+ is seen very often in the use of DNA synthesis. What is the role of Mg2+ in this process?
DNA molecules (a very negatively charged molecule because of the PO4 surrounding it). Enzyme uses Mg2+ cofactor to minimize the very negative charge seen on the outside of DNA
66
Compare and contrast vitamins and minerals.
These are often dietary cofactors and coenzymes!!! Body can’t produce this directly and many people need to consume this to stay healthy
Vitamins - organic cofactors and coenzymes. Vitamin B3 AKA Niacin (this is a precursor for NAD. Vitamin B5 is a precursor for COA
Minerals - usually Inorganic cofactors in our bodies. Ex Magnesium. Not all minerals are cofactors. Some minerals, like calcium, can act as a cofactor, but is also an important building block for bone and teeth
67
True or false: Enzymes function best at particular environments.
True. They require specific pH, temperature, salinity, etc in order to exist in a particular structure in order to function properly.
68
α - amylase only functions where in the body? Why?
This enzyme functions best at neutral pH, therefore it is found in the mouth and in the small intestine where the pH are close to normal. This enzyme functions in breaking complex carbs into smaller indv sugar molecules
69
Is α - amylase able to function in the stomach? Why?
This enzyme is unable to function in the stomach because the pH in the stomach is closer to 2 and α - amylase requires a closer to neutral pH to function properly.
70
Explain why pepsin is able to digest food in the stomach.
Pepsin requires a low pH and because the stomach has a low pH of 2, it can properly digest food there.
71
What temperature is required of most enzymes in the body?
In general, most enzymes need a temperature of 37C to function properly
72
Under normal pH, how does DNA polymerase hold onto the Mg2+ cofactor?
Under normal pH of 7, the enzyme will hold onto the Mg2+ ion through an electrostatic interaction between the Mg2+ and aspartate residue within the enzyme (-ly charge residue at normal pH)
73
DNA polymerase is submerged into the stomach. What is the expected result of its hold onto its cofactor?
Reduced pH, the aspartate residue of enzyme will become protonated. The mg is released and this means DNA polymerase can’t function properly
74
What occurs to an enzyme when the temperature in your body changes, such as when you have a fever.
Changes in temperature significantly can disrupt a protein’s folded geometry and cause it to lose its functionality.
75
Juan is having a fever tonight and every time you feed him, he experiences emesis. How can you explain this with the temperature change he is experiencing
A fever will lead to increase in body temperature and this will cause the digestive enzymes to be misfolded. Maybe why he may have a harder time eating when he’s sick with a fever
76
Contrast Non Enzymatic proteins from enzymatic proteins.
These proteins have the ability to bind to other things, but have no ability to speed up/catalyze a reaction
77
ame categories of non-enzymatic proteins.
Receptors, ion channels, transport proteins, motor pro -, antibodies
78
True or False - Proteins are either enzymatic or non-enzymatic proteins
False. Not all proteins are either an enzyme or non-enzyme. Oftentimes they have noth characteristics.
79
What is the ultimate result when a cell of the liver binds to insulin? Which portion of this example acts as the receptor?
Binding of insulin causes an influx of glucose taken up by the cell to undergo metabolism. The receptor here is the liver cell/its membrane molecule.
80
How is an ion channel different from a receptor?
Both are non-enzymatic receptors, however, they differ because a receptor merely binds onto its ligand to cause a chemical reaction within the cell. However, ion channels allow an influx of molecule/ion. The mechanism at which both opens/functions differ based on particular ones
81
What is a requirement a protein must have in order to be a transport protein?
These proteins need to have a high affinity when their ligand is present in high concentration. At low concentrations, these molecules need to have low affinity for their ligands
82
Elaborate how hemoglobin exemplifies the requirement of a transport protein.
Hemoglobin present in RBC, is able to pick up O2 in the lungs, and delivers O2 to the tissues where O2 is present (transport proteins need to have a high affinity when their ligand is present in high concentration. At low concentrations, these molecules need to have low affinity for their ligands)
83
Juan and you are squatting. What is the active protein allowing for this contraction?
Myosin - responsible for generating the forces exerted by contracting muscles. Every time flex muscle, myosin is contracting to create the movement
84
A patient arrives at the hospital and as you check her charts, you see a pattern of chronic pneumonia and bronchitis. You start to suspect some form of dyskinesia. What protein dysfunction could potentially create this sort of problem?
Dysfunction or mutations to a particular dynein (an important motor protein) of the respiratory tract, could result in problems with cilia motion. This would lead to decreased mucus clearance from the lungs and result in increased chronic infections.
85
Contrast how kinesin and dynein are different from myosin
While all play a role in motor, myosin is involved with muscle fiber contraction, while kinesin and dynein are involved in intracellular transport. All are forms of motor, they differ on cellular and molecular motor.
86
on-enzymatic proteins are known to have the ability to bind other molecules. Does antibodies fit this category?
Yes, antibodies are proteins of the adaptive immune system and bind to their ligands (antigens). Antigens, while they can be proteins of other foreign substances, are the ligands as well.
87
What is a requirement for the efficiency of antibodies?
They need to have very high affinity and tight binding to their antigens
88
Proteins tend to require modification after it has been translated. What modifications exist?
Cotranslational and Post translational - Changes to the polypeptide while it is translated from mRNA to Pro and modification after the polypeptide chain has been translated.
89
As a protein is translated, its first amino acid, methionine, is removed and replaced with a COCH3 group. What is this process? What does this type of modification fall under?
This is acetylation, a process under co-translational protein modification. [Note: Much of the purpose of this process is unknown, but is seen in 80 - 90% of eukaryotic proteins]
90
Where does the post translational modification occur?
In the ER and the Golgi Apparatus
91
After all day at the blood drive, you sit down to analyze some samples for viability. What portion of the RBC are you looking for identification of blood type? What process in the body allows this identification?
You should be looking for the carbohydrate attachments on the red blood cell, called glycoproteins. These glycoproteins are produced by a process called glycosylation done in the ER or the Golgi where the carbohydrates are added onto proteins after they have been translated.
92
After being in the field all day, you’ve collected a new plant you’ve never seen before. Its cell membrane appears to have proteins anchored to it. What is responsible for this anchorage of a protein into a membrane? What process allows?
Lipid proteins such as GPI anchors, allow a normal hydrophilic exterior proteins to attach to tightly within the membrane. This is achieved through lipdation, a process done in the ER or Golgi where a lipid is attached onto the newly translated protein
93
In the process of a Na/K exchange seen in the Na/K ATPAse, when is dephosphorylation and phosphorylation achieved?
Phosphorylation is seen when 3 Na from the ICM attaches onto the ATPase. ATP dissociates a PO4 and phosphorylates the enzyme. This causes the enzyme to conformationally change and rotate 180 degrees to release them into the ECM.
Dephosphorylation of the enzyme is seen when PO4 is released after 2 K+ from the ECM as attached onto the receptor. This deattachement, causes conformational change where the receptor rotates 180 again, allowing the K+ to be released into the ICM.
94
```
Phosphorylation is
A. Co-translation Modification
B. Acetylation
C. Post translational modification
D. Lipidation
```
C. This is a type of post translational modification. They are used to regulate reactions, rather than to allow the protein to function properly (the commonly thought definition of post translation).
95
```
Na+/K+ pump exchanges
A. 2 Na in - 3 K out
B. 2 Na in - 1 K out
C. 3 Na out - 2 K in
D. 2 Na out - 1 K in
```
C. 3 Na out - 2 K in
96
What is the Sodium Potassium pump attempting to achieve?
When this enzyme/pump is active, it is attempting to increase the concentration of K+ in the cell and decrease the membrane potential, while increasing the concentration of Na+ in the ECM
97
How are histones regulated?
Histones are regulated by methylation, which helps upregulate or downregulate the gene transcription. Methylation of some lysine and arginine residues of histones results in transcriptional activation. Modification of certain amino acids in a histone protein by the addition of one, two, or three methyl groups [science direct.com]
98
Proteolysis is often seen in digestion when a protease degrades a big protein into absorbable molecules. How can it be used as regulation in other parts of the body?
Protein breakdown/cleavage. Can activate protein by cutting. Ex: Insulin needs to be cut 2 times in order for it to be in its active form. In this manner, proteolysis can be used as a post translational modification of a protein
99
You’re analyzing a sample from a patient who is suffering from alcohol poisoning. He is a chronic alcoholic for 35 years and severe issues in his lower abdomen. The sample shows his alcohol dehydrogenases are all tagged with ubiquitin. What does this mean?
Addition of ubiquitin marks the protein for degradation, a process of post translational modification. As these enzymes are destroyed while he is consuming alcohol, this will raise the concentration of alcohol, thus explaining his alcohol poisoning at a very fast rate when he has been a long time drinker.
100
Enzymes are:
I. Proteins
II. Proteins and RNA
III. Proteins, RNA, and Small Inorganic Molecules
IV. Proteins, RNA, Small Inorganic Molecules, and Metals
IV. Proteins, RNA, Small Inorganic Molecules, and Metals. While many molecules are enzymes, the main focus in enzymes are proteins
101
Trypsinogen is released as an inactive protein from the pancreas into the small intestines. How does this enzyme exemplify the perfect zymogen? What is the purpose of its inactive form?
Trypsinogen is a zymogen (inactive protein) that requires covalent modification by the enzyme, enterokinase. Once it is modified, it becomes active and is able to cleave proteins. This mechanism prevents digestion of proteins of the pancreas and the pathway connecting the pancreas to the duodenum
102
After some work in the field Africa, you find a species of toad newly discovered that has been affecting some villagers. Upon closer analysis, you find a new toxin that functions similarly to suicide inhibitor. What are the requirements to classify the molecule as a suicide inhibitor.
Suicide inhibitors have covalently bind to enzymes and prevent them from catalyzing reactions. Due to the strong bind, inhibitors rarely unbind and this usually means enzyme death. This can lead to build up of toxic molecules in this case and explain the high poison levels seen in the villagers
103
```
Sulfonation and Methylation are
A. Co-translational modification
B. Post translational modification
C. Enzyme inhibition
D. Covalent modification
```
D. Covalent modification. Though covalent modification are post translational modification, covalent modification is a more precise term of description. Covalent modifications include methylation, acetylation, sulfonation, and phosphorylation
104
Addition of lipid to a protein is to lipidation as Phosphorylation is to …
Covalent modification! Covalent modifications include methylation, acetylation, sulfonation, and phosphorylation
105
Phosphorylation is a very common method used in eukaryotic cells as a post translational modification. Why might this be the case?
This covalent modification is commonly used to regulate protein activities because it is a very efficient and convenient method. ATP concentration is most abundant in the cell therefore regulation within cells would be very efficient
106
After studying your patient’s blood sample you find that a kinase of hemoglobin is dysfunctional. What results could this produce?
Failure for a kinase to properly function means the hemoglobin is not properly regulated (either unable to dePO4 or PO4) Without proper function means that this protein is unable to properly bind to 02 or release 02 which can lead to blood disorders.
107
What particular amino acids have the ability to accept PO4 functional groups from ATP. Why might this be the case?
Serine, Threonine, and Tyrosine Their OH side chains makes them exceptional acceptors of PO4 as PO4 is able to act as a good nucleophile and bind with O. These amino acid residues then are important in incoporation of the protein’s primary sequence.
108
Explain the limitations of regulation of enzymes outside the cell by phosphorylation.
Enzymes outside of the cell are unable to undergo this process because there is a limited supply of ATP. Therefore cells outside of the cell are not regulated in this method/process
