Biokjemi quizziiiii
Of the elements below, two are much more abundant in the earth's crust than in living organisms. Mark the two elements.
Iron
Oxygen
Silicon
Hydrogen
Nitrogen
To how many different atoms does a carbon atom bond if it is in the following hybridization state : sp3
1
2
3
4
To how many different atoms does a carbon atom bond if it is in the following hybridization state : sp2
1
2
3
4
To how many different atoms does a carbon atom bond if it is in the following hybridization state : sp
1
2
3
4
Which of the bonds depicted below has the highest EN?
O-H
N-H
C-C
C-H
What is the most appropriate definition of conformation?
The chemical formula of a molecule
The fixed arrangement of atoms dictated by the bonds of a molecule
The spatial arrangement of atoms around fixed bonds in a molecule
The three-dimensional structure a molecule is most likely to adopt
What is the most appropriate definition of configuration?
The chemical formula of a molecule
The fixed arrangement of atoms dictated by the bonds of a molecule
The spatial arrangement of atoms around fixed bonds in a molecule
The three-dimensional structure a molecule is most likely to adopt
The molecule drawn out is:
Chiral
Achiral
Determine the stereochemical orientation of the central carbon
S
R
The molecule of cholesterol is:
Chiral
Achiral
Do these two molecules above have a different configuration?
No
Yes
The notation as R/S is used for?
a stereo-genic center
the whole molecule
absolute assignment in stereochemistry
relative to Glyceraldehyde
The notation as D/L is used for?
a stereo-genic center
the whole molecule
absolute assignment in stereochemistry
relative to Glyceraldehyde
Humans use food for energy and as a source of carbon backbones to build organic molecules. How would they be classified?
Chemoautotroph
Photoautotroph
Chemoheterotroph
Photoheterotroph
You isolate an unusual bacterium that uses sunlight as an energy source but cannot fix CO2. Instead, it breaks down organic molecules from its environment and incorporates these carbon backbones into new molecules. How would this organism be classified?
Chemoautotroph
Photoautotroph
Chemoheterotroph
Photoheterotroph
What is the meaning of the term S in the equation G = H - TS?
The total amount of energy in the system
The temperature of the system in degrees Kelvin
The amount of energy available to do work in the system
The disorder of the system, the amount of energy that can not do work
What is the meaning of the term G in the equation G = H - TS?
. The total amount of energy in the system
The temperature of the system in degrees Kelvin
The amount of energy available to do work in the system
The disorder of the system, the amount of energy that cannot do work
The reaction S to P has a ΔG of -10 kJ/mol. The reaction is:
Spontaneous
Non-spontaneous
At equilibrium
The reaction S to P has a ΔH of -10 kJ/mol, and the product of TΔS is 15 kJ/ mol. The reaction is:
Spontaneous
Non-spontaneous
At equilibrium
In the reaction S to P, the enthalpy is negative, and the product of Temperature and Entropy is positive. What is the most appropriate description of the spontaneity of the reaction?
Spontaneous
Non-spontaneous
At equilibrium
If the concentration P, [P], is 10M, and the concentration of S, [S], is 1M, the forward reaction is:
Spontaneous
Non-spontaneous
At equilibrium
The products and reactants are at equilibrium when suddenly some products are removed. In what direction will the reaction proceed?
Forward
Reverse
Neither
The Keq of a reaction under standard conditions equals 1. What is the standard free energy of this reaction?
4×10^(-12)
0
98
69 ;)
The Keq of a reaction under standard conditions equals 1. Under standard conditions, this reaction is:
Spontaneous
Non-spontaneous
At equilibrium
Which of the molecules represent naturally occurring amino acids? (Select ALL that apply.)
0%
0
0%
0
0%
0
0%
0
0%
0
The non-covalent intermolecular forces described in this lecture behave differently. How are the forces ranked in terms of their energy?
Van Der Waals > Ionic > Hydrogen bonds
Ionic > Hydrogen bonds > Van Der Waals
Ionic > Van Der Waals > Hydrogen bonds
Hydrogen bonds > Ionic > Van Der Waals
Which labels list the curve showing the relationship between energy and distance for different types of non-covalent bonds in the order A, B, C? A, trough at -1 kJ/mol and 2.75 angstroms B, trough at -30 kJ/ mol and 2.5 angstroms C, trough at -5 kJ/mol and 2.6 angstroms
Van Der Waals , Ionic , Hydrogen bonds
Ionic , Hydrogen bonds , Van Der Waals
Ionic , Van Der Waals , Hydrogen bonds
Hydrogen bonds , Ionic , Van Der Waals
Which molecules likely represent the appropriate charge of aspartic acid at physiological pH (7.4)?
0%
0
0%
0
0%
0
0%
0
Which amino acids should have the largest conformational flexibility of their side chain?
Lysine
Alanine
Proline
Cysteine
Select the most appropriate classification for the amino acid shown.
Negatively charged, polar
Positively charged, polar
Non-polar, aliphatic, small
Non-polar, aliphatic
Which of the above atoms is a carbon with trigonal bonding geometry?
A
B
C
D
Which of the above atoms has tetrahedral geometry?
A
B
C
D
Which of the bonds represents a peptide bond?
A
B
C
D
The measurements of two bond angles are depicted on a Ramachandran plot. Select the letters that mark the bonds representing these TWO angles in the peptide sequence.
A
B
C
D
You solve the crystal structure of a peptide (~15 amino acids). When you measure the phi and psi angles, they all fall in the green region of the plot. What is the likely structure of this peptide?
Alpha helix
Beta sheet
Loop
Not enough information provided
In a Ramachandran plot (see Q3), what do all shaded areas represent?
Areas of a steric clash between the R groups of adjacent amino acids
Angles that cause the formation of alpha helices
Angles that cause the formation of beta-sheets
The most common combinations of bond angles in proteins
Thousands of protein structures have been solved by x-ray crystallography to date. Where do the phi and psi angles of loop regions tend to plot according to the analysis introduced by Ramachandran
The area labeled in green
The area labeled in blue
The area labeled in grey
Why are the yellow residues in the image clustered on one side of an alpha helix?
They are aliphatic. This pattern stabilizes alpha helices, and it is necessary for their structure.
They are aliphatic, forming a side of the helix that can interact with hydrophobic molecules.
The yellow residues all have long, flexible side chains that can interact with other proteins.
The yellow residues form a hydrogen bonding network with other proteins.
Why are prolines often claimed to “break” an alpha helix?
They provide no free hydrogen to bond with a carbonyl because of the imino ring.
It cannot adopt the psi and phi angles required to form an alpha helix.
It often adopts the trans conformation, unlike the other amino acids
It flips between the cis and trans conformations frequently.
What is the definition of a protein fold?
An independently folding unit of a protein
An arrangement of secondary structure elements of a protein fold
A commonly repeating arrangement of a few secondary structure elements
The complete tertiary structure of a protein
What is the definition of a domain?
An independently folding unit of a protein
An arrangement of secondary structure elements of a protein fold
A commonly repeating arrangement of a few secondary structure elements
The complete tertiary structure of a protein
What is the definition of a secondary structure motif?
An independently folding unit of a protein
An arrangement of secondary structure elements of a protein fold
A commonly repeating arrangement of a few secondary structure elements
The complete tertiary structure of a protein
Why have no new protein folds been discovered in the past few years?
Almost all protein structures have now been solved, so there are fewer new proteins yearly.
There is a limited number of folds in nature, although many have already been solved.
Although many complex protein folds are unsolved, it is not currently computationally possible to obtain crystal structures of very complex protein folds.
Many protein folds remain unsolved because the proteins exist in extraordinary biochemical conditions they are difficult to crystallize.
Why are there a limited number of protein folds in nature? (Select ALL that apply.)
Proteins are modular; different folds combine to generate many proteins.
Proteins of highly divergent sequences can still adopt the same fold.
Evolution has only sampled a narrow space of the possible arrangements of the 20 amino acids.
Because proteins are linear, they have very limited possible sequence diversity.
, It is likely that there are a limited number of stable, functional protein folds; however, nature utilizes most of them
Why is an aqueous solvent so crucial for protein folding?
It is the primary determinant in chain conformational entropy.
Water primarily contributes to the enthalpic effect that favors folding.
The dissolved salts form many contacts with the protein to stabilize its native conformation.
It is entropically favorable to mask hydrophobic residues from water.
What are the TWO main changes in the energy state that promote a protein adopting a folded conformation?
The hydrophobic effect
Decreased chain conformational entropy
Increased chain conformational entropy
Decreased entropy of the solvent due to folding
Enthalpy
What is the primary energy change that opposes protein folding?
Enthalpy
The hydrophobic effect
Chain conformational entropy
Increased entropy of water
What major force contributes to the stabilization of secondary structure?
Hydrogen bonding networks
The hydrophobic effect
van der Waals interactions
Salt bridges
Several changes in the system's energetic state contribute to protein folding. Consider an average protein of ~100 amino acids. Regardless of the sign, which contributor between the folded and unfolded state is most significant?
Chain conformational entropy
Enthalpy
The hydrophobic effect
van der Waals forces
What statement most accurately describes the thermodynamic hypothesis?
Proteins have numerous equally thermodynamically stable conformations, including unfolded and folded forms.
A protein's most thermodynamically stable conformation is its native fold.
An advanced understanding of thermodynamics allows us to accurately predict any protein's folded structure
A combination of thermodynamic and kinetic parameters determines the native fold of a protein.
From Anfinsen's experiment, the result of each step is shown, but the reagents or lab techniques used in each step still need to be included. Mark the appropriate molecules with label A
8M Urea
Beta-Mercaptoethanol
Dialyze
Reoxidize in Urea
From Anfinsen's experiment, the result of each step is shown, but the reagents or lab techniques used in each step still need to be included. Mark the appropriate molecules with label B
8M Urea
Beta-Mercaptoethanol
Dialyze
Reoxidize in Urea
From Anfinsen's experiment, the result of each step is shown, but the reagents or lab techniques used in each step still need to be included. Mark the appropriate molecules with labels C
8M Urea
Beta-Mercaptoethanol
Dialyze
Reoxidize in Urea
From Anfinsen's experiment, the result of each step is shown, but the reagents or lab techniques used in each step still need to be included. Mark the appropriate molecules with label D
8M Urea
Beta-Mercaptoethanol
Dialyze
Reoxidize in Urea
Which of the following labels A to D represents the native fold of the protein,
A
B
C
D
Which of the following labels A to D represents a semi-stable folding intermediate.
A
B
C
D
What of the below statements most accurately summarizes Levinthal's paradox?
With our current understanding of the laws of physics, we cannot explain protein folding.
There are trillions of possible conformations of proteins, yet they typically only adopt one conformation.
A protein would never find its native fold by sampling all possible conformations.
Protein folding in nature occurs at a time scale many orders of magnitude longer than the universe's age.
What is one reason that proteins are able to adopt their native conformation rapidly?
It is the most thermodynamically stable conformation.
There is a high degree of cooperativity in protein folding
Chaperones 'bend' proteins into their native conformation.
Strong ionic interactions between side chains drive the initial collapse of the protein core.
The thermodynamic hypothesis states that a protein's most thermodynamically stable conformation is its native fold. Additionally, Anfinsen's experiments and many others have shown that many different proteins tend to adopt their native folds in solution. So why are proteins at a high risk of aggregation in the cytosol?
The cytosol has a much higher salt concentration than is typically used in biochemistry experiments.
The cytosol is a much more crowded environment than is typical for an in vitro experiment.
We do not know why proteins are at risk of aggregation in the cytosol
Proteins in the cytosol are mainly hydrophobic. Thus, they tend to aggregate.
What types of interactions commonly lead to protein aggregation?
Ionic
Hydrogen bonds
Hydrophobic interactions
Covalent bonds
What statement best describes how chaperones perform their function?
They prevent intermolecular hydrophobic interactions while the protein folds.
They prevent the premature aggregation of secondary structure so the protein's hydrophobic core can form first.
Chaperones are proteases that digest and disrupt protein aggregates when they form.
They hydrolyze ATP to manipulate proteins into the appropriate shape physically.
Complete the statement below that describes the function of HSP70. HSP70 does not bind to its substrate in this state
ATP
ADP
Complete the statement below that describes the function of HSP70. HSP70 is bound to a substrate in state A or B. States:
ATP
ADP
Which statement most accurately characterizes the effect of high temperatures (above 37 celsius) on protein folding?
High temperature increases the rate of protein folding, so proteins adopt their native fold faster.
There is no effect of high temperature on protein folding.
Proteins are denatured, then re-fold into their native state upon cooling
Proteins are denatured and at risk of forming intermolecular aggregates.
A reaction is at equilibrium when...
the reaction proceeds in the forward and reverse direction at the same time.
the product concentration is equal to the substrate concentration.
there is no net change in the concentration of the reactants.
all of the substrates have been converted to product.
A reaction is spontaneous if...
the transition state has higher free energy than the substrate.
the product has lower free energy than the substrate.
it proceeds rapidly and without a catalyst.
it can proceed in only one direction.
Graphs A and B depict a spontaneous reaction. If all other conditions are equal, which of the graphs describes a reaction that likely proceeds more rapidly?
Graph A
Graph B
Both graphs
To reduce the activation energy of a reaction, do catalysts need to ............. constant?
increase the free energy of the substrate
decrease the respective transition state energy
or hold product free energy
An enzyme increases the rate of a reaction by stabilizing the...
Transition state
Substrate
Product
Catalyst
Which TWO factors can contribute to enzyme catalysis?
Weak non-covalent interactions between enzyme and substrate
Permanent covalent bonds between substrate and product
Transient covalent bonds between enzyme and substrate
The binding energy between enzyme and product
Solvation of the enzyme
In the diagram several changes in the free energy state are noted. Which of the 'change in free energy' arrows in the diagram above represents 'binding energy'?
A
B
C
D
In the diagram several changes in the free energy state are noted.Which of the 'change in free energy' arrows in the diagram above represents the activation energy for the enzyme-catalyzed reaction?
A
B
C
D
Binding energy is a broad term that includes which TWO of the following concepts?
The difference in free energy of the substrate between the enzyme-bound and unbound states
Transient covalent interactions that position the substrate in the active site
Weak non-covalent interactions between substrate and enzyme
Weak non-covalent interaThe diversity of substrates that any enzyme can bind
The diversity Energy from the desolvation of the substrate
Desolvation replaces bonds (select a first letter from A - F) with bonds (select a second letter from A - F).
A, enzyme-substrate
B, enzyme-transition state- substrate
C, enzyme-product
D, substrate-environment
E, enzyme-environment
F, product-environment
All except two of the following are reasons that enzymes are larger than their active sites. Which TWO of the following are NOT a reason?
To regulate enzyme activity with modifications such as phosphorylation.
To position catalytic residues for multiple substrate orientations.
To enable induced fit of one or more substrates
To allow the formation of multi-enzyme complexes.
. To increase the substrate-enzyme binding energy.
Why will a short peptide chain that contains all the necessary active site amino acids still be unable to catalyze a reaction?
The constrained folding of the short peptide chain prevents the catalytic residues from being correctly positioned.
The binding energy of the short peptide will not sufficiently reduce the activation energy of the reaction
Many residues in the full-length protein, besides those of the active site, participate in catalysis.
The short polypeptide chain will bind the substrate but not the transition state.
The alcohol dehydrogenase enzyme (ADH) catalyzes the reaction above. If the reaction were stochastic, we would expect the two hydrogens (in green) on the hydroxyl group carbon to have an equal probability of being transferred to NAD+, to form NADH. In contrast, we observe that it is always the same hydrogen that is transferred experimentally. How does this observation support the three-point attachment model?
. The NADH product, ethanol substrate, and ADH enzyme remain attached through hydrogen bonding.
It suggests that the orientation of ethanol is always the same in the active site relative to NAD+.
In total, three hydrogens of ethanol are involved in the ADH-catalyzed reaction.
ADH catalysis occurs in three hydrogen-transfer steps that occur sequentially.
The diagram represents the citrate synthase enzyme binding its two substrates, acetyl Co-A, and oxaloacetate, to form two products, Co-A, and citrate. What statement correctly describes this reaction?
. Oxaloacetate binding triggers a conformational change to promote acetyl-Co A binding.
Sequential binding of acetyl-Co A and then oxaloacetate ensures efficiency.
Each change in enzyme conformation corresponds to a catalytic event.
Three induced fit events are required for catalysis.
The diagram represents the citrate synthase enzyme binding its two substrates, acetyl Co-A, and oxaloacetate, to form two products, Co-A, and citrate. From the sequence of binding of the two substrates, we can hypothesize that acetyl-coA is (select option from A-D to complete the sentence correctly) than oxaloacetate.
A, more abundant
B, less abundant
C, more stable
D, less stable
Why are the amino acids tyrosine, serine, and threonine essential in eukaryotic enzymes?
These residues position a substrate within the active site.
These residues can be phosphorylated to regulate enzyme activity.
These residues can be interchanged.
These residues can be catalytically active.
What is a zymogen? Select the best answer from the list below.
A protein that changes conformation after phosphorylation of a side chain
An alternatively spliced isoform of a single gene
An inactive precursor of an enzyme that can be hydrolyzed into an active enzyme
None of the above
What is the benefit of post-translational modification? Select the best answer from the list below:
Allows for proteins activity to be turned on and off at specific times
Allow proteins to be turned on or off in specific cellular locations
Increases the functional diversity of the proteome
All of the above
From the list below, select the best description of a signaling sequence.
A sequence that is phosphorylated by a protein kinase
A sequence that is phoA sequence for secretion of a protein found in a leader peptide at the N-terminal of a protein
A sequence that changes the way the protein is translated in the ribosome
None of the above
The inactive form of chymotrypsin is called trypsin (A), or trypsinogen (B), or chymotrypsin (C), chymotrypsinogen (D). This inactive form is stored in the liver (E), or pancreas (F).
A
B
C
D
E
F
Ile16 faces towards the exterior (A), or interior (B), of the protein in chymotrypsinogen. When chymotrypsinogen is cleaved at Ile16 by trypsin, Ile16 turns inward (C), or outward (D), and forms ionic (E), or van der Waals (F) bonding with Asp194 inducing a conformational rearrangement that activates the enzyme.
A
B
C
D
E
F
From the list below, select the best description of proinsulin.
Proinsulin is the inactive precursor of insulin
Proinsulin is an alternative form of insulin
Proinsulin is a precursor of chymotrypsin
None of the above
Below is the insulin processing pathway broken down into a few images. Match image 1 with the correct label.
C-peptide cleaved
Signal peptide cleaved
Proinsulin folded
Insulin and C-peptide excreted
Below is the insulin processing pathway broken down into a few images. Match image 2 with the correct label.
C-peptide cleaved
Signal peptide cleaved
Proinsulin folded
Insulin and C-peptide excreted
Below is the insulin processing pathway broken down into a few images. Match image 3 with the correct label.
C-peptide cleaved
Signal peptide cleaved
Proinsulin folded
Insulin and C-peptide excreted
Below is the insulin processing pathway broken down into a few images. Match image 4 with the correct label.
C-peptide cleaved
Signal peptide cleaved
Proinsulin folded
Insulin and C-peptide excreted
From the options below, select which protein cleaves prothrombin.
Factor VII
Factor IX
Factor X
factor XI
None of the above
For the protein Factor XII , select the appropriate pathway
Extrinsic
Intrinsic
For the protein Factor VII , select the appropriate pathway (extrinsic (A) or intrinsic (B)).
Extrinsic
Intrinsic
For the protein Tissue Factor , select the appropriate pathway (extrinsic (A) or intrinsic (B)).
Extrinsic
Intrinsic
Select from the options below the reason(s) why the extrinsic pathway is not always activated.
Factor VII in the blood needs to be exposed to the outside air to activate and trigger the extrinsic pathway.
The endothelium forms a barrier between tissue factor and blood so that it cannot bind to its ligand, factor VII.
. A physical force from the vascular injury (cut) is needed to activate factor VII.
All of the above.
In which phase does the protein vWF bind collagen and unfold due to shear stress to recruit additonal platelets to the cut site?
initiation
extension
stabilization
none of the above
From the options below select which protein(s) inhibit(s) tissue factor activity.
AT
TFPI
Thrombomodulin
All of the above
Analysis of a sample from a patient with hemophilia reveals the individual does not form fibrin fibers but has high levels of fibrinogen protein expression and factor X activity. Select from the options below which protein most likely has a loss-of-function mutation.
Factor VII
Factor IX
Factor XIII
Thrombin
Not enough information
There is a mutation in fibrinogen that prevents it from being cleaved by thrombin. Given this mutation, select from the options below whether the individual will be at risk for developing hemophilia, thrombosis, neither, or both.
Hemophilia
Thrombosis
Neither
Both
How do enzymes achieve their maximum velocity?
The excess enzyme is self-inhibitory, blocking catalysis.
When the rate of catalysis matches the rate of ES complex formation, the enzyme reaches its maximum velocity.
At high substrate concentrations, the enzyme is saturated and cannot catalyze any faster.
There is no maximum velocity for an enzyme.
The equation represents an intermediate in the derivation of the Michaelis-Menten equation. In a typical experimental setting, which parameter is the simplest to determine?
S
E
km
ES
What is the reaction's initial velocity when the substrate concentration, [S], is set equal to km?
Initial velocity is equal to Vmax.
Initial velocity is equal to one-half Vmax.
The substrate concentration is so low that the initial velocity is negligible.
More information needs to be added to determine the substrate's initial velocity.
Replace A indicated in grey in the image below, to make the first key substitution in the Michaelis-Menten derivation.
[E][S]
[ES](k-1+k2)
[ET] -[ES]
k1[E]x[S]
km
km+ [S]
Vmax/Vo
Replace B indicated in grey in the image below, to make the first key substitution in the Michaelis-Menten derivation.
[E][S]
[ES](k-1+k2)
[ET] -[ES]
k1[E]x[S]
km
km+ [S]
Vmax/Vo
This schematic represents the derivation of the Lineweaver-Burk equation from the Michaelis-Menten equation. Select the appropriate equation piece fitting into the 2 and 3 grey area.
0%
0
0%
0
0%
0
0%
0
0%
0
This schematic represents the derivation of the Lineweaver-Burk equation from the Michaelis-Menten equation. Select the appropriate equation piece fitting into the 4, 5, 6 and 7. grey area.
0%
0
0%
0
0%
0
0%
0
0%
0
This schematic represents the derivation of the Lineweaver-Burk equation from the Michaelis-Menten equation. Select the appropriate equation piece fitting into the 1. grey area.
0%
0
0%
0
0%
0
0%
0
0%
0
Why is it preferable to use the Lineweaver-Burk equation rather than the Michaelis Menten equation when studying the kinetics of an enzyme? Select the TWO most appropriate explanations.
To directly visualize km and Vmax on the plot.
To get more accurate estimates of km and Vmax
To plot kinetic data as a line instead of a hyperbolic curve.
To collect fewer data points to calculate kinetic parameters accurately.
Remove terms that cannot be calculated in a typical enzyme kinetics experiment.
This schematic represents the Lineweaver-Burk equation derived from the Michaelis-Menten equation. Write the appropriate term provided below into the 1. blank fields.
0%
0
0%
0
0%
0
0%
0
This schematic represents the Lineweaver-Burk equation derived from the Michaelis-Menten equation. Write the appropriate term provided below into the 2. blank fields.
0%
0
0%
0
0%
0
0%
0
This schematic represents the Lineweaver-Burk equation derived from the Michaelis-Menten equation. Write the appropriate term provided below into the 3. blank fields.
0%
0
0%
0
0%
0
0%
0
This schematic represents the Lineweaver-Burk equation derived from the Michaelis-Menten equation. Write the appropriate term provided below into the 4. blank fields.
0%
0
0%
0
0%
0
0%
0
You test the activity of an enzyme at several different substrate concentrations without (red points), and with (blue points) an inhibitor added to the reaction. You then plot the results of this experiment on a Lineweaver-Burk plot, shown. What type of inhibitor is this? Please select the option that BEST describes its mode of action.
Noncompetitive
Competitive
C. Uncompetitive
Mixed
You test the activity of an enzyme at several different substrate concentrations without (red points), and with (purple points) an inhibitor added to the reaction. You then plot the results of this experiment on a Lineweaver-Burk plot, shown. What type of inhibitor is this? Select the option that BEST describes its mode of action.
Noncompetitive
Competitive
Uncompetitive
Mixed
An enzyme is modulated by a competitive inhibitor. What TWO statements below most accurately describe this inhibitor?
It increases the apparent Km of the enzyme
It decreases the apparent Km of the enzyme
It increases the Vmax of the enzyme.
It binds the enzyme-substrate complex
It binds the enzyme in its active site.
An enzyme is modulated by an uncompetitive inhibitor. What TWO statements below most accurately describe this inhibitor?
It increases the apparent Km of the enzyme.
It decreases the apparent Km of the enzyme.
It increases the Vmax of the enzyme.
It binds the enzyme-substrate complex
It binds the enzyme in its active site.
The above equation represents the LineweaverBurk equation for an enzyme with what type of inhibitor?
Competitive
Mixed
Noncompetetive
Uncompetitive
The above equation represents the LineweaverBurk equation for an enzyme with what type of inhibitor?
Competitive
Mixed
Noncompetetive
uncompetetive
Select which enzyme (A, B, C, or D) would be the best candidate for directed evolution.
Enzyme A
Enzyme B
Enzyme C
Enzyme D
For a protein with four sites (A, B, C, and D) to be subjected to ISM, after the first round you have the data as shown in the graph. From which library (A, B, C, or D) should a mutant serve as template for the next round of ISM be chosen?
Library A
Library B
Library C
Library D
For Protein Z, you would like to use ISM to saturate a given site with 8 amino acids. You use the NNK degeneracy method described. Calculate how many combinations are possible for each codon position.
16
32
10
30
You want to carry out ISM on the catalytic residues of Enzyme A. Its secondary structure map is shown below. Of the five residues highlighted, one is present in the catalytic site. Select which amino acid is found in the catalytic site
Amino acid A
Amino acid B
Amino acid C
Amino acid D
Not enough information
After round 1 of ISM, you have four individual mutants with the following single amino acid substitutions in the active site. Select which mutant is most likely to have the greatest change in protein activity.
Mutant A
Mutant B
Mutant C
Mutant D
If an individual is type O, what blood type can this individual receive during a transfusion?
Blood Type A
Blood Type B
Blood Type AB
Blood Type O
Can receive all blood types
When the enzyme activity of halohydrin dehydrogenase increases, no (A), more (B), or less (C) protons (H+) are released in the catalyzed reaction.
A, no
B, more
C, less
At a high pH, a solution of phenol red appears red. However, at a lower pH, a solution of phenol red appears yellow. You use a colorimetric approach to measure the yellow color of various solutions containing the halo hydrin dehydrogenase (wild type or ISM mutant), all the reaction components, and phenol red. The amount of yellow color is shown for the wild-type enzyme (WT) and each ISM mutant A, B, C, and D. Given this data, select which ISM mutant has the highest catalytic activity.
A.Mutant A
B.Mutant B
C.Mutant C
D.Mutant D
You have two ISM mutants (A and B) for the enzyme glucose oxidase. The bar graphs below show the mediator and oxygen activities of wild type (WT) and of each ISM mutant. Given this data, select which ISM mutant (A or B) is the best option.
Mutant A
Mutant B
In a colorimetric assay like the one used to assay the activity of halohydrin dehydrogenase, consider the pH change and its effect on the yellow signal if the enzyme has increased activity. Would you expect an increase or a decrease in the yellow signal?
Decrease
Increase
Which statement correctly describes the structure of lipids?
Lipids enclose the aqueous cytosol of an animal cell in a monolayer.
Lipids are formed by addition of repeating subunits into a polymer.
Lipids all have a large hydrophobic region.
Most lipids contain peptide bonds.
Which two statements correctly describe sphingosine?
Sphingosine has a nitrogen group that forms peptide bonds.
The hydrocarbon chain of sphingosine is fully saturated.
Sphingosine already contains one hydrocarbon 'tail'
Sphingosine serves as a backbone, like glycerol.
. Sphingosine is an energy-storage lipid.
Glycerol can form triacylglycerol when...
...three glycerol molecules react with one another.
...the acyl groups cyclize to form a multi-ring structure.
. ...each ester linkage is replaced with a phosphodiester linkage.
...a fatty acid is esterified to each hydroxyl group of glycerol.
Will molecule A or B have more van der Waals interactions with its neighboring lipids?
A
B
If present in a large number, will molecules A or B be more likely liquid at room temperature?
A
B
What is the main function of triacylglycerol in animal cells?
Maintain plasma membrane fluidity
Store energy for the short term
Store energy for the long term
Compartmentalize organelles
Which TWO of the following statements accurately describe the surface of a lipid droplet?
A monolayer of phospholipids
A bilayer of phospholipids
A network of perilipin protein
A structured layer of triacylglycerol
A chaotic hydrophobic/hydrophilic interface
Phospholipids are excellent for storing triacylglycerol because their .... face the aqueous environment
Hydrophilic head groups
Hydrophobic tails
High-energy phosphate groups
Phospholipids are excellent for storing triacylglycerol because their Hydrophilic head groups face the aqueous environment, while their .... face the densely packed triacylglycerol.
Hydrophilic head groups
Hydrophobic tails
High-energy phosphate groups
How does sub-cellular localization regulate lipolysis in a stimulated adipocyte?
A chaperone carries triacylglycerol from a lipid droplet to the first lipase.
The first and second lipase must be recruited to the lipid droplet to be active
The third lipase is sequestered on the surface of the lipid droplet while active
The perilipin network is degraded to release triacylglycerol into the cytosol.
Match the lipase of triacylglycerol metabolism with their modes of regulation. ......... is constitutively active in the cytosol.
the first lipase (ATGL)
the second lipase (HSL)
the third lipase (MGL)
Match the lipase of triacylglycerol metabolism with their modes of regulation. .......... is recruited to the lipid droplet based on a binding partner in the perilipin network.
the first lipase (ATGL)
the second lipase (HSL)
the third lipase (MGL)
Match the lipase of triacylglycerol metabolism with their modes of regulation. ....... is phosphorylated by PKA to facilitate recruitment to the lipid droplet.
the first lipase (ATGL)
the second lipase (HSL)
the third lipase (MGL)
Which TWO steps describe hormone regulation of triacylglycerol metabolism?
Adrenaline signals an adipocyte to degrade its lipases.
Hormones bind a transmembrane receptor on the surface of the lipid droplet.
Catecholamines trigger a signaling cascade that activates a key kinase.
The sphingolipid monolayer of a lipid droplet is phosphorylated to form phospholipids.
The perilipin network rearranges to promote recruitment of lipases.
Triacylglycerol has a structure adapted to its energy storage function. The .....properties of triacylglycerol allow for
repeating subunit
hydrophobic
hydrophilic
Triacylglycerol has a structure adapted to its energy storage function. The hydrophobic properties of triacylglycerol allow for ......
dense packing
spontaneous diffusion
rapid oxidation of carbons.
Triacylglycerol has a structure adapted to its energy storage function. The carbons of triacylglycerol are in an activated form. Meanwhile, the carbons of glycogen are in a ..... form
charged
highly reduced,
partially oxidised, activated form.
Gram for gram, triacylglycerol has ......... energy density as compared to glycogen
greater
equal
less
Gram for gram, triacylglycerol has greater energy density as compared to glycogen; however, glycogen is broken down .........
more slowly
more rapidly
in an unregulated manner
Of the phospholipids shown above, those with a ........ shape are more likely to be found in the outer leaflet of the membrane
Cylindrical
Conical
Spherical
Of the phospholipids shown above, those with a cylidrical shape are more likely to be found in the outer leaflet of the membrane, while lipids with a ....... shape are more likely to be found in the inner leaflet.
Cylindrical
Conical
Spherical
Match the protein to its activity. ....... moves lipids down their concentration gradient in either direction
Flippase
Floppase
Scramblase
Match the protein to its activity. ............. moves lipids against their concentration gradient from the inner to the outer membrane
Flippase
Floppase
Scramblase
Match the protein to its activity. .......... moves lipids against their concentration gradient from the outer to the inner membrane
Flippase
Floppase
Scramblase
Match the protein to its activity. ............. activity promotes membrane compositional symmetry.
Flippase
Floppase
Scramblase
In what cellular compartment are most phospholipids synthesized?
In the endoplasmic reticulum
In the nucleus
In the golgi apparatus
In the cysotol
Sphingomyelin is synthesized in the lumen of the golgi apparatus and is transported to the plasma membrane by vesicles. Sphingomyelin will first be incorporated into the ...... of the plasma membrane.
inner leaflet
outer leaflet
The figure above is from a Fluorescence Recovery After Photobleaching (FRAP) experiment. What is the hazy grey signal in the panel "pre"?
The fluorescently-labeled lipids
The bleached membrane of a cell
The lipid bilayer before diffusion begins
The recovered signal of a laser
The figure above is from a Fluorescence Recovery After Photobleaching (FRAP) experiment. What is the dark spot in panel "t=0s"?
The laser has bleached the lipid dye at this spot.
The lipids have diffused away from the spot.
. The laser has poked a hole in the membrane.
The fluorescent intensity is saturated at this spot.
The figure above is from a Fluorescence Recovery After Photobleaching (FRAP) experiment. Why is the dark spot nearly gone in panel "t=100s"?
The cell synthesized new lipids to fill in the spot.
The lateral diffusion of bleached and fluorescent lipids caused the dark spot to be mixed in
The laser light diffused among the lipids, so the dark spot has 'recovered'.
The diffusion coefficient of these lipids is about 100s.
After the membrane of a cell type or organelle type is isolated and dried, the percent mass of lipid versus protein will...
Correlate directly with the volume of the cell or organelle.
Reveal the abundance of protein in Schwann cells.
Vary according to the function of the cell or organelle.
. Generate the same ratio, regardless of cell or organelle type.
The protein composition of a membrane reflects its function. For example, while red blood cells and photoreceptors both have a .......... of protein in their plasma membranes,
high density
low density
The protein composition of a membrane reflects its function.For example, while red blood cells and photoreceptors both have a high density of protein in their plasma membranes, red blood cells have ..... of protein
a greater diversity
essentially one type
The protein composition of a membrane reflects its function. Photoreceptor cells have ......... of protein in their membranes.
a greater diversity
essentially one type
The lipid bilayer can contain integral and peripheral membrane proteins. Match the protein type with its characteristics. ............ membrane proteins must have hydrophobic coils that pass through the core of the lipid bilayer.
Integral
Peripheral
Both types of
The lipid bilayer can contain integral and peripheral membrane proteins. Match the protein type with its characteristics. ............ membrane proteins can be covalently linked to a lipid inserted in the lipid bilayer.
Integral
Peripheral
Both types of
The lipid bilayer can contain integral and peripheral membrane proteins. Match the protein type with its characteristics. ............ membrane proteins can transduce an extracellular signal across the lipid bilayer
Integral
Peripheral
Both types of
The lipid bilayer can contain integral and peripheral membrane proteins. Match the protein type with its characteristics. ............ membrane proteins can serve functions on the intracellular and extracellular surfaces of the lipid bilayer.
Integral
Peripheral
Both types of
What are TWO important reasons water can diffuse across the lipid bilayer?
The concentration of water in biological systems is very high.
Water is polar and can hydrogen bond.
Water molecules are tiny.
Water is needed for reactions in the cytosol.
Water is bulky and hydrophobic.
How do sodium (Na+) ions and chloride (Cl- ) cross the plasma membrane?
The ions are so small that they can diffuse across.
The ions are charged and bind with water to diffuse across
The ions require integral membrane proteins to cross.
The ions require peripheral membrane proteins to cross.
The figure plots the % body fat of a sample of 5130 men. A patient of yours comes to office and is tested for body fat and is found to have 12% body fat. Does the patient have:
Too few lipid droplets?
Too many lipid droplets?
The right amount of lipid droplets?
Fill in the blank: Too few lipids can lead to ________.
lipodystrophy and cachexia
wasting disease
various forms of cancer
None of the above
What do adipocytes require to maintain a healthy lipid level?
An excess amount of adipose tissue
A shortage of adipose tissue
. Proper development, differentiation, and survival correct
None of the above
What is lipodystrophy?
Loss or failure to develop adequate amounts of adipose tissue for energy storage
. An increase in the amount of adipose tissue in the body
Destruction of white blood cells
None of the above
This image shows the process of triacylglycerol synthesis. Mutations in which of the enzymes shown are most often linked to lipodystrophy?
Mutations in GPAT
Mutations in PAP
Mutations in AGPAT
Mutations in MGAT
What two key proteins are important for pre-adipocyte differentiation?
AKT2 and nuclear receptor PPARγ
PKA and the insulin receptor
Lamin A and ZMPSTE24
None of the above
Where is fat stored in a healthy individual? (Select ALL that apply.)
Inside the gut lumen
In a thin layer under the skin (the subcutaneous fat)
Inside the liver and other internal organs
Around internal organs
Primarily in muscle fibers
Which of the following is correct regarding adipocytes?
Adipocytes contain multiple small lipid droplets
Adipocytes contain one very large lipid droplet
The adipocyte nucleus is in the center of the cell
Adipocytes contain large amounts of glycogen
How does the body handle excess fat?
The body can only sequester excess fat by increasing the size of existing adipocytes
The body can only sequester excess fat by growing additional adipocytes
The body can sequester excess fat by increasing both adipocyte size and cell number
Which of the following diseases are associated with ectopic fat deposition? (Select ALL that apply.)
Cachexia secondary to cancer
Lipodystrophy resulting from antiretroviral therapy
The metabolic syndrome resulting from a caloric imbalance
Neutral lipid storage disease, myopathy subtype
Which of the following statements is/are correct about cardiomyopathy and ichthyosis subtypes of neutral lipid storage disease? (Select ALL that apply.)
Both diseases are monogenic, meaning they result from the same ATGL mutation.
Each disease results from a unique genetic mutation
Ichthyosis results from an unknown ATGL-independent function of ABHD5 that affects the skin’s lipid matrix
Cardiomyopathy results only from impaired cell signaling due to reduced ATGL function
Ox phos agonists are currently being developed to treat ichthyosis
Where does the fat accumulated in obesity originate from?
It originates strictly from dietary intake of fat
It originates from excessive ATGL activity due to a monogenic mutation
It originates strictly from dietary intake of carbohydrates and proteins which are then converted to fat
. It originates from dietary intake of fat, carbohydrates, and proteins
Which TWO of the following are chemical characteristics of monosaccharides?
They contain multiple hydroxyl groups.
They contain an aldehyde or ketone group.
They contain a branching carbon backbone.
They contain a carbon-carbon double bond.
Every carbon in a monosaccharide is fully reduced
Which of the molecules below is a ketose sugar?
0%
0
0%
0
0%
0
0%
0
Which of the carbons in the molecule is a chiral center?
C1
C2
C3
C4
Which TWO of the following traits apply to the Fischer convention for naming stereoisomers?
Utilizes (+) and (-) designations
Utilizes (D) and (L) designations
Reflects stereochemistry at a multiple chiral centers
Requires drawing the compound, aldehyde at the top
Based on optical properties of the compound in solution
6 Based on its Fischer projection, how would you name the molecule shown below?
(+)-idose
(-)-idose
D-idose
L-idose
Glucose fails to re-colorize a Schiff reagent. What evidence does this Schiff reaction provide regarding the structure of glucose?
Glucose exists in the D-isoform
Glucose exists in the linear form.
Glucose does not have a reactive ketone group.
Glcuose does not have a reducing aldehyde group.
For glucose to cyclize, an alcohol group must attack a carbonyl group. Which carbon of linear glucose is bonded to the reactive alcohol?
C1
C2
C5
C6
For glucose to cyclize, an alcohol group must attack a carbonyl group. Which is the carbonyl carbon in glucose?
C1
C2
C5
C6
In the glucose molecules shown, which of the circled carbons will become the anomeric carbon in the cyclic structure?
A
B
D
C
During the cyclization reaction of sugar, what determines the alpha versus beta designation of the product?
Whether or not a new asymmetric carbon is formed
Whether the L or D isoform serves as the linear reactant
Whether the C5 hydroxyl attacks the front or back of the anomeric carbon
Whether the majority of the hydroxyl groups are above or below the plane of the ring
A sugar can include 'pyran-' or 'furan-' in its name. In this context, what aspect of sugar do these terms describe?
The orientation of the anomeric carbon
The number of carbon and oxygen atoms in the ring
The presence of carbon-carbon double bonds
The relative stability of the cyclic versus linear form
During the formation of a glycosidic linkage, the ..... of one cyclized monosaccharide reacts with the hydroxyl of a second monosaccharide.
hemiacetal
Carbonyl
Hydroxyl
During the formation of a glycosidic linkage, the hemiacetal of one cyclized monosaccharide reacts with the .......... of a second monosaccharide.
hemiacetal
Carbonyl
Hydroxyl
Which chemical group determines this is a 'reducing' disaccharide?
A
B
C
D
E
Which image represents the proper convention for carbon numbering in cyclic sugars?
0%
0
0%
0
0%
0
0%
0
What is the name for this glycosidic linkage?
1, 1 glycosidic linkage
1, 2 glycosidic linkage
1, 4 glycosidic linkage
1, 6 glycosidic linkage
Three disaccharides contain a 1, 4 glycosidic linkage. Which TWO molecules do NOT contain a 1, 4 glycosidic linkage?
0%
0
0%
0
0%
0
0%
0
0%
0
The enzyme glycogen synthase catalyzes which type of bond formation?
1, 1 glycosidic linkage
1, 2 glycosidic linkage
1, 4 glycosidic linkage
1, 6 glycosidic linkage
Which TWO of the listed molecules are the reactants of the enzyme glycogen synthase?
UDP-Glucose
Glucose 1-Phosphate
Reducing end of glycogen
Non-reducing end of glycogen
1, 4 glycosidic linkage
Which reactant of the glycogen branching enzyme has the hemiacetal group that will react to form a new glycosidic linkage?
UDP-Glucose
Glucose 1-Phosphate
Reducing end of a glycogen chain
Non-reducing end of a glycogen chain
Imagine a solution of 1.2% glucose in the presence of methylene blue. After shaking vigorously in an oxygen atmosphere, the solution rests for several minutes. The solution will be:
Blue
Clear
Imagine a solution of 1.2% glucose in the presence of methylene blue. After shaking vigorously in an oxygen atmosphere, the solution rests for several minutes. The solution will be clear. In addition, the methylene blue will be in a:
reduced state
oxidized state
Imagine a 1.2% solution of a disaccharide composed of two aldoses. Methylene blue is added to the solution. The aldoses are linked by an alpha 1,1 glycosidic linkage. After shaking vigorously in an oxygen atmosphere, the solution rests for several minutes. The solution will be:
Blue
Clear
Imagine a 1.2% solution of a disaccharide composed of two aldoses. Methylene blue is added to the solution. The aldoses are linked by an alpha 1,1 glycosidic linkage. After shaking vigorously in an oxygen atmosphere, the solution rests for several minutes. The solution will be blue. In addition, the methylene blue will be in a:
reduced state
oxidized state
The above molecule represents
Glucose
Glucose 6-phosphate
Fructose 6-phosphate
Fructose
The molecule is formed by the action of the first enzyme in glycolysis, called
Aldolase
Hexokinase
PFK-1
Enolase
You know that ATP is a major energy currency of cells. What are TWO energetic reasons that ATP is well-suited for this role?
The chemical structure of nucleotides makes reaction coupling particularly simple for ATP.
. ATP is readily synthesized from higher-energy molecules by substrate-level phosphorylation
ATP sequentially donates all three phosphates with an equal free energy of hydrolysis, thus it can store a large amount of energy in smaller "packets".
ATP phosphorylates many other molecules that have a lower free energy of hydrolysis
ATP phosphorylates many other molecules that have a higher free energy of hydrolysis.
What are TWO common features of reactions that are coupled together by cells?
Different enzymes catalyze them.
The same enzyme catalyzes them.
They share all of the same products and reactants.
They share some of the same products and reactants.
The difference of the standard free energies of the two reactions is exactly zero.
What does this reaction represent?
The final step in ethanol fermentation is the conversion of acetaldehyde to ethanol.
The second-to-last step in ethanol fermentation is the conversion of pyruvate to acetaldehyde.
The final step in lactate fermentation is the conversion of pyruvate to lactate.
The final step in glycolysis is the conversion of PEP to pyruvate.
Which of the following is why red blood cells cannot completely oxidize glucose to form carbon dioxide?
They are very small.
They lack mitochondria.
They contain a large amount of hemoglobin for oxygen transport.
They lack phosphofructokinase-1 (PFK-1), an essential glycolytic enzyme.
Which statement best describes the Cori cycle?
. It regenerates glucose from lactate generated anaerobically in red blood cells and muscle.
It generates fatty acids that red blood cells and muscle can consume.
It regenerates glucose from the products of aerobic respiration generated by red blood cells and muscle.
It generates 2,3 bisphosphoglycerate from 1,3 bisphosphoglycerate for a red blood cellspecific function.
Which molecule, produced by glycolysis in red blood cells, donates electrons to iron to maintain its reduced (Fe2+) state?Pyruvate
Lactate
NADH
ATP
Which molecule produced by glycolysis, or shunts of glycolysis, in red blood cells donates electrons to glutathione to neutralize reactive oxygen species (ROS)?
1,3 bisphosphoglycerate
2,3 bisphosphoglycerate
NADPH
ATP
What are TWO reasons NADH transfers electrons to iron (via cytochrome b5) in red blood cells?
To neutralize reactive oxygen species (ROS) using electrons transferred from iron
To regenerate NAD+ needed to drive glycolysis forward
To initiate the electron transport chain that is specific to red blood cells
To maintain hemoglobin-bound iron in its reduced (Fe2+) state
To maintain hemoglobin-bound iron in its oxidized (Fe3+) state
Which statement most accurately describes the difference between hemoglobin's T and R states?
In the R state, hemoglobin has a high affinity for oxygen, while in the T state, hemoglobin has a low affinity for oxygen.
In the T state, hemoglobin has a high affinity for oxygen, while in the R state, hemoglobin has a low affinity for oxygen.
In the R state, hemoglobin is bound to oxygen, while in the T state, hemoglobin is not bound to oxygen
. In the T state, hemoglobin is bound to oxygen, while in the R state, hemoglobin is not bound to oxygen.
Lactic acid .......... the affinity of hemoglobin for oxygen.
increases
does not affect
decreases
Carbon dioxide .......... the affinity of hemoglobin for oxygen.
increases
Does not affect
decreases
2,3 bisphosphoglycerate ..........the affinity of hemoglobin for oxygen
increases
does not affect
decreases
Which of the following is NOT a possible product of anaerobic fermentation in E. coli?
Water
Acetate
Ethanol
Succinate
Bacteria use linear fermentation pathways to regenerate a key molecule utilized in glycolysis.
Ethanol
Lactate
ATP
NAD+
What molecule is a common intermediate in some fermentation pathways in bacteria and aerobic respiration?
Ethanol
Lactate
Acetyl-CoA
Acetate
What is one common feature between aerobic and anaerobic respiration pathways such as denitrification and methanogenesis?
The final electron acceptor (oxygen) is shared between these pathways.
Glucose is universally the primary energy source for these pathways.
ATP synthesis is coupled to redox reactions with an ion gradient.
Both generate water as a reaction product.
Which definition best describes anaerobic respiration?
The final electron acceptor is nitrate or nitrite.
Carbon sources donate electrons to universal electron acceptors/donors such as NADH.
The final electron acceptor is either nitrate, nitrite, a metal, a sulfur compound, or carbon dioxide.
The final electron acceptor is not free oxygen.
What TWO factors are most likely to influence what types of bacteria dominate in a given soil environment?
The availability of nitrate in the environment
The standard reduction potential of the primary electron acceptor used by different resident bacteria
The availability of electron acceptors in the environment
The availability of fuel sources in the environment
The availability of ADP in the environment
Denitrifying bacteria form a proton gradient across their cell membrane to power the synthesis of ATP. What TWO factors (below) contribute to promoting the formation of the proton gradient?
Protons are pumped from the cytoplasm to the periplasm by the action of complexes I and III.
Protons are pumped from the periplasm to the cytoplasm by the action of complexes I and III.
Protons are consumed in the cytoplasm during the reduction steps of denitrification.
Protons are consumed in the periplasm during the reduction steps of denitrification.
Protons travel through ATP synthase down their concentration gradient.
Which statement best describes the human microbiome?
It is very homogeneous between different tissues but diverse. Most tissues are occupied by the same highly diverse collection of bacteria.
One different species of bacterium colonize each tissue.
There is high diversity between tissues and within tissues.
There is much greater diversity from person to person than tissue to tissue.
Which of the following is NOT a known function of the gut microbiome?
To protect against the invasion of pathogens by occupying a specific niche in the gut
To reinforce epithelial tight-junctions
To aid in the digestion of food
To promote immune and metabolic homeostasis
Bacteria utilize branched or linear fermentation pathways. Cells use the branched pathway to regenerate TWO molecules that are used to power the metabolic and catabolic reactions of the cell.
Formate
NADH
NAD+
Acetate
ATP
What is one common feature between aerobic and anaerobic respiration pathways?
The final electron acceptor (oxygen) is shared between these pathways.
Glucose is universally the primary energy source for these pathways.
ATP synthesis is coupled to redox reactions with an ion gradient.
Both generate water as a reaction product.
What TWO factors (below) most substantially contribute to the economic impacts of denitrifying bacteria?
Nitrate runs off of soil into bodies of water.
Nitrate is a major limiting nutrient for plants.
Denitrifying bacteria produce nitrogen gas.
Denitrifying bacteria remove nitrate from the soil.
Denitrifying bacteria remove nitric oxide from the soil.
Which two of the following are oxidized universal electron acceptors, taking electrons from the citric acid cycle and glycolysis?
FADH2
NADH
NAD+
FAD
Oxygen
Which of the following molecules is not a common fuel (electron) source to fuel heterotrophic cells?
Glucose
Water
Fatty acids
Amino acids
What are the TWO main fates of the carbons of acetyl-CoA produced from pyruvate by the pyruvate dehydrogenase complex?
Incorporation into sugars, such as glucose
Incorporation into fatty acids
Formation of amino acids by transamination
. Complete oxidation to form carbon dioxide
. Regeneration of pyruvate for biosynthetic pathways
Which TWO statements best describe the allosteric regulation of the PDH complex?
PDH is allosterically activated by its substrates.
PDH is allosterically inhibited by its substrates.
PDH is allosterically activated by its products.
PDH is allosterically inhibited by its products.
PDH is allosterically activated by ATP.
What is the primary function of the anaplerotic reactions?
. To donate electrons to NAD+ and FAD
To regenerate citric acid cycle intermediates
To generate ATP by substrate-level phosphorylation
To regenerate oxygen that is depleted by aerobic respiration
From the list below, select all of the major goals of the citric acid cycle: (Select ALL that apply.)
To produce carbon dioxide
To make GTP
To produce NADH
To make NAD+
To produce FADH2
To make precursors for the biosynthesis of fatty acids and amino acids
To consume oxygen
During the citric acid cycle, the acetyl group of the Acetyl CoA is fully oxidized and released as carbon dioxide. What are the three main sources of Acetyl CoA in the cell?
Pyruvate, citric acid, fatty acids
Fatty acids, amino acids, citric acid
Fatty acids, amino acids, pyruvate
Amino acids, glucose, NADH
Citric acid, glucose, pyruvate
It would be a beneficial metabolic gain if animals could possibly convert AcCoA into glucose. From the options below, select the two obstacles that prevent animals from making glucose from AcCoA.
There is no net degradation of fatty acids to provide enough AcetylCoA
In the cell, the conversion of AcCoA back to pyruvate is practically irreversible.
Animals generally do not have a pathway that can produce glucose from precursors; they can only oxidize and consume glucose
There is no net conversion of acetate to oxaloacetate. If there were, it would be possible to make glucose from AcCoA.
AcCoA can only be used in the cell to make citric acid in the citric acid cycle. Therefore it cannot be used for the biosynthesis of glucose.
The diagram below shows the integration of the AcCoA molecule into the citric acid cycle. Which TWO steps prevent vertebrates from extracting extra carbons and synthesizing glucose from AcCoA units?
Oxaloacetate to citrate
Citrate to isocitrate
Isocitrate to alpha-ketoglutarate
Alpha-ketoglutarate to succinyl-coA
. Succinyl-coA to succinate
Succinate to fumarate
Fumarate to malate
Malate to oxaloacetate
In the glyoxylate cycle, excess oxaloacetate is decarboxylated into phosphoenolpyruvate (PEP), which then can be converted into glucose via gluconeogenesis. Considering these two processes, how many turns of the glyoxylate cycle will be needed to make one glucose molecule?
One full turn
Two full turns
One and a half turns
Three turns
Six turns
Unlike eukaryotes that compartmentalize their glyoxylate cycle, prokaryotes, like bacteria, lack specialized organelles. The bacterial glyoxylate cycle and the citric acid cycle occur in the cytoplasm. How do bacteria regulate these two cycles when converting AcCoA into glucose?
Bacteria upregulate both the glyoxylate and the citric acid cycle enzymes to keep up with both cycles needed for cellular functions.
Bacteria upregulate the glyoxylate cycle enzymes and downregulate the citric acid cycle enzymes to divert AcCoA into the glyoxylate cycle.
Bacteria upregulate the citric acid cycle enzymes and downregulate the glyoxylate cycle because the citric acid cycle is always more important in the cell.
Bacteria downregulate the glyoxylate and the citric acid cycle enzymes to minimize consumption at all costs.
Microorganisms that can utilize the glyoxylate cycle only do so when required to shift their metabolism from the citric acid cycle to the glyoxylate cycle. What are the conditions that require this kind of change in these microorganisms? (Select ALL that apply.)
During the biosynthesis of the cellular building blocks
When the sugar resources are low
When all types of nutrients are abundant
. During the invasion of a host
Microorganisms that infect plant species can be stopped by using inhibitors of the glyoxylate cycle enzymes. While these inhibitors can stop the growth of pathogenic microorganisms, they do not kill the plants, even though the plant cells are also capable of using the glyoxylate cycle. What is the main reason for this?
Plant and bacterial glyoxylate cycles have no common enzymes. Therefore, bacterial inhibitors are ineffective against the plant glyoxylate cycle.
Glyoxysomes, membrane-enclosed and specialized organelles in plants, prevent bacterial inhibitors from accessing glyoxylate cycle enzymes.
Plants use the glyoxylate cycle during seed germination and cease it when fully grown. Therefore, plants will not be affected by inhibitors.
Plant cells would require higher concentrations of bacterial inhibitors to inhibit their glyoxylate cycle completely.
Itaconic acid is derived from the citric acid cycle of the host, and helps the infected host cells to fight against the pathogens by inhibiting the glyoxylate cycle. What are the possible ways that pathogens can resist the immune system and overcome the effects of itaconic acid to continue infection? (Select ALL that apply.)
By downregulating all of their glyoxylate cycle enzymes to prevent itaconic acid’s interaction
By upregulating isocitrate lyase enzyme to overcome the normal levels of itaconic acid
By degrading the itaconic acid
By upregulating the citric acid cycle enzymes
By upregulating the cis-aconitate enzyme only
Isocitrate lyase catalyzes the cleavage of isocitrate into two other molecules. What are these molecules?
glyoxylate and fumarate
succinate and acetyl CoA
malate and acetyl CoA
succinate and glyoxylate
acetyl CoA and glyoxylate
Mycobacterium tuberculosis invades the lungs and lives in lipid-rich, oxygen-poor environments. Inhibitors of isocitrate lyase are explored as drug treatments for tuberculosis. Among the reasons why isocitrate lyase (ICL) is a good drug target for tuberculosis infections in humans, which one is not true?
ICL is unique to microorganisms and plants and does not exist in humans.
ICL is an upstream target and the first committed branch point between the citric acid and the glyoxylate cycle in microorganisms.
The inhibition of ICL also inhibits the microorganism's citric acid cycle and helps further eradicate the pathogen.
The inhibition of ICL prevents the microorganism from converting acetyl units into glucose, thereby preventing their survival in the low nutrient environment.
The inhibition of ICL lowers the chance of persistent infections by pathogens.
Where is the electron transport chain localized in cells?
The cell membrane
The intermembrane space
The mitochondrial inner membrane
The mitochondrial outer membrane
3 Which TWO statements best describe the function of the universal electron carriers NAD+/NADH and FAD/FADH2 in human cells?
They donate electrons to power biosynthetic pathways such as fatty acid synthesis.
They accept electrons from intermediates of the citric acid cycle.
They donate electrons to intermediates of the citric acid cycle.
They accept electrons from the electron transport chain.
They donate electrons to the electron transport chain.
What is the primary function of the universal electron donor NADPH?
To donate electrons to the electron transport chain
To power the synthesis of ATP
To donate electrons to power anabolic reactions in the cytosol
To donate electrons to power the synthesis of proteins by the ribosome
A redox reaction has a positive ΔE. What does this say about the reaction?
The reaction is spontaneous.
The reaction is not spontaneous.
The reaction is spontaneous and proceeds very rapidly.
More information is needed to determine spontaneity or kinetics than provided.
Let's say you are studying an unusual electron transport chain in a new microbe. You have a list of the standard reduction potentials of the electron carriers. What method should you use to determine the order of the electron carriers in living cells? Consider that you want to order the electron transport chain from the first electron donor to the final electron acceptor.
Sort them according to their standard reduction potential (ΔE´0), lowest to highest.
. Sort them according to their physiological reduction potential (ΔE), lowest to highest.
Sort them according to their standard reduction potential (ΔE´0), highest to lowest.
Sort them according to their physiological reduction potential (ΔE), highest to lowest.
What are TWO approaches you might use to determine the order of electron transfer in an electron transport chain? Consider both theoretical and experimental approaches.
Rank the electron carriers in terms of their reduction potential (ΔE).
Rank the electron carriers regarding their standard reduction potential (ΔE´0).
Treat the cells with drugs to disrupt known steps in the electron transport chain and observe oxygen consumption.
Treat the cells with drugs to disrupt known steps in the electron transport chain and observe the production of ATP.
Treat the cells with drugs to disrupt known steps in the electron transport chain and observe the oxidation state of each electron acceptor/donor.
What type of chemical molecule is presented below?
Fully oxidized Coenzyme Q (also known as Q or ubiquinone)
Partially reduced Coenzyme Q (also known as QH or semiquinone)
. Fully reduced Coenzyme Q (also known as QH2 or ubiquinol)
An iron-sulfur center
What type of molecule is outlined below?
Fully oxidized Coenzyme Q (also known as Q or ubiquinone)
Fully reduced Coenzyme Q (also known as QH2 or ubiquinol)
A heme functional group, the redox component of the cytochromes
An iron-sulfur center, the redox component of many ETC proteins
Which of the below schematics most accurately depicts the flow of electrons through the electron transport chain?
0%
0
0%
0
0%
0
0%
0
Which of the following molecules is NOT an electron carrier participating in the electron transport chain?
FMNH2
Ubiquinol
Cytochrome c
NADPH
What is the final electron acceptor of the ETC in human cells?
O2
Ubiquinone
H2O
NAD+
How does electron transport help cells generate energy?
In each electron transfer step, heat is generated to power chemical reactions.
The ETC transmits electrons across the cell membrane, building up an electrical potential to drive ATP synthesis.
Protons are transmitted across the mitochondrial membrane by the ETC, building up a gradient which is used to drive ATP synthesis.
Electron transfer is directly coupled to ATP synthesis.
Which statement most accurately describes the function of the Q cycle?
To regenerate QH2 that is depleted by upstream steps in the ETC
To transfer a single electron to cytochrome c from the double electron carrier QH2
To build up a proton gradient to be used for ATP synthesis
To transfer a single electron from the double electron carrier QH2 to a semiquinone (QH)
Which statement most accurately describes the function of complexes I and II?
To transfer electrons from universal electron acceptors to cytochrome c
To transfer electrons from universal electron acceptors to coenzyme Q
To transfer electrons from coenzyme Q to cytochrome c
To transfer electrons from cytochrome c to oxygen
Which statement best describes how an electrochemical gradient is linked to the electron transport chain?
The exergonic transport of electrons is directly coupled to the endergonic transfer of protons from the intermembane space to the mitochondrial matrix.
The exergonic transport of electrons is directly coupled to the endergonic transfer of protons from the mitochondrial matrix to the intermembane space.
The exergonic transfer of protons from the mitochondrial membrane to the intermembrane space is directly coupled to the endergonic transport of electrons.
The exergonic transfer of protons from the intermembrane space to the mitochondrial matrix is directly coupled to the endergonic transport of electrons.
Which statement best describes how an electrochemical gradient is linked to ATP synthesis?
The exergonic movement of protons from the intermembane space to the mitochondrial matrix is coupled to the endergonic process of ATP synthesis.
The exergonic movement of protons from the mitochondrial matrix to the intermembane space is coupled to the endergonic process of ATP synthesis.
The exergonic process of ATP synthesis is coupled to the endergonic movement of protons from the intermembane space to the mitochondrial matrix.
. The exergonic process of ATP synthesis is coupled to the endergonic movement of protons from the mitochondrial matrix to the intermembrane space.
What is the function of the stator in the ATP synthase?
It forms the channel that protons pass through to power ATP synthesis.
It forms the asymmetric 'stalk' that changes the conformation of the ATP synthase
It rotates as protons pass through the a-chain and transfers rotation to the asymmetric 'stalk'.
It still holds one component of the ATP synthase so that it cannot rotate with respect to the 'stalk'.
What is the function of the c ring in the ATP synthase?
It forms the channel that protons pass through to power ATP synthesis.
It forms the asymmetric 'stalk' that changes the conformation of the ATP synthase.
It rotates as protons pass through the a-chain and transfers rotation to the asymmetric 'stalk'.
It still holds one component of the ATP synthase, so it cannot rotate relative to the ‚stalk.
What is the function of the structure formed by the γ- and εsubunits of the ATP synthase?
It forms the channel that protons pass through to power ATP synthesis.
It forms the asymmetric 'stalk' that changes the conformation of the ATP synthase.
It rotates as protons pass through the a-chain and transfers rotation to the asymmetric 'stalk'.
It still holds one component of the ATP synthase, so it cannot rotate relative to the 'stalk'.
What are TWO components of the F0 subunit of the ATP synthase?
c-ring
αβ ring
a chain
the stalk
the stator
How does ATP synthase promote the highly endergonic synthesis of ATP from ADP and inorganic phosphate?
By massively increasing the entropy component of the reaction to drive the reaction forward
By immediately removing ATP to drive the reaction forward following Le Chatelier's principle
. Via the transfer of a phosphate group from a higher energy molecule (IE substrate-level phosphorylation)
By stabilizing ATP in an ATP-ATP synthase complex with a free energy similar to the ADPATP synthase complex
The β-subunit of ATP synthase cycles between three different conformations. In which conformation is ATP synthesized?
The O conformation
The L conformation
The T conformation
The β-subunit of ATP synthase cycles between three different conformations. In which conformation is ATP released and exchanged for ADP and Pi?
The O conformation
The L conformation
The T conformation
Which TWO processes are NOT promoted by the proton motive force?
ATP synthesis
The transport of ATP out of the mitochondria
The exchange of ATP and ADP across the mitochondrial inner membrane
The symport of inorganic phosphate and hydrogen into the mitochondrial matrix
The transfer of protons into the intermembrane space by the electron transport chain
What two experimental results suggested that ATCase is subject to heterotropic allosteric regulation?
CTP inhibited ATCase activity.
Aspartate activated ATCase activity.
When dissociated into subunits, one of them had catalytic activity
When dissociated into subunits, one did not have catalytic activity and bound CTP.
One did not have catalytic activity and bound aspartate when dissociated into subunits.
Which of the following is an example of homotropic allosteric regulation?
A small molecule analog of a substrate binds an enzyme in its active site, which promotes a transition to the T state in other enzyme subunits.
The binding of a substrate to one subunit promotes the transition to the R state in other enzyme subunits.
A small molecule binds the enzyme at a site other than the active site, stabilizing the T state of the enzyme.
A small molecule binds the enzyme at a site other than the active site, stabilizing the R state of the enzyme.
Which of the following is an example of heterotropic allosteric activation?
A small molecule analog of a substrate binds an enzyme in its active site, this promotes a transition to the T state in other subunits of the enzyme.
The binding of a substrate to one subunit promotes the transition to the R state in other enzyme subunits.
A small molecule binds the enzyme at a site other than the active site, stabilizing the T state of the enzyme.
A small molecule binds the enzyme at a site other than the active site, stabilizing the R state of the enzyme.
From a regulatory standpoint, why does CTP inhibit ATCase?
CTP is the ultimate product of the metabolic pathway that begins with ATCase. When CTP is in sufficient quantity, it blocks its production at a very early step.
CTP is the first substrate of the metabolic pathway that begins with ATCase. High amounts of CTP inhibit the enzyme so that CTP can be shunted into other pathways.
CTP is an indicator of a high energy state in cells, so it inhibits an energy-generating pathway initiated by ATCase.
CTP is rapidly consumed when a cell is very metabolically active. By inhibiting ATCase, it negatively regulates the metabolic activity of cells.
What is the difference between an allosteric enzyme's T and R states?
Heterotropic allosteric regulators bind the T state; the R state is never bound.
Heterotropic allosteric regulators bind the R state; the T state is never bound.
The R state has a high affinity for the enzyme substrates; the T state does not.
The T state has a high affinity for the enzyme substrates; the R state does not.
How does the Monod-Wyman-Changeux (MWC) model relate substrate binding to the conformation of oligomeric cooperative enzymes?
The conformation of each monomer of the enzyme is independent. The binding of a substrate to a monomer favors the R state of that monomer, and the R state of one monomer favors the R state of other monomers in the protein.
The conformation of each monomer of the enzyme is connected. If one monomer switches to the R state, they all do. The binding of a substrate to a monomer favors the R state of that monomer (and thus the whole protein).
The conformation of each monomer of the enzyme is independent, but the conformation of a monomer depends on substrate binding. When unbound, the monomer is in the T state, and switches to the R state upon substrate binding. The R state of one monomer favors a switch to binding and the R state in other monomers.
The conformation of each monomer of the enzyme is connected. If one monomer switches to the R state, they all do. The binding of the substrate to a monomer does not affect the conformation of the protein.
Which of the following statements best describes how the KoshlandNemethy-Filmer (KNF) model relates substrate binding to the conformation of oligomeric cooperative enzymes?
The conformation of each monomer of the enzyme is independent. The binding of a substrate to a monomer favors the R state of that monomer, and the R state of one monomer favors the R state of other monomers in the protein.
The conformation of each monomer of the enzyme is connected. If one monomer switches to the R state, they all do. The binding of a substrate to a monomer favors the R state of that monomer (and thus the whole protein).
The conformation of each monomer of the enzyme is independent, but the conformation of a monomer depends on substrate binding. When unbound, the monomer is in the T state, and switches to the R state upon substrate binding. The R state of one monomer favors a switch to binding and the R state in other monomers.
The conformation of each monomer of the enzyme is connected. If one monomer switches to the R state, they all do. The binding of the substrate to a monomer does not affect the conformation of the protein.
What is homeostasis in the context of cellular metabolism?
All of the reactions in a cell are at a steady state.
All of the reactions in a cell are at an equilibrium state.
Cells alter metabolic fluxes in response to a perturbation to restore metabolic reactions to a steady state
Cells alter metabolic fluxes in response to a perturbation to restore metabolic reactions to an equilibrium state.
In the schematic below, the circles represent the reactants and products of successive reactions, labeled A through E. The abundance of the circles represents the abundance of each "molecule" in the pathway. Thermodynamically, each step in the pathway favors the products. Which TWO reactions are most likely to be enzyme-limited?
A
B
C
D
E
Imagine that there is a long-term drought. An organism undergoes a stable metabolic adaptation by changing the expression of many genes that relate to drought tolerance. What type of metabolic regulation is most likely at play here?
Allosteric regulation
Covalent modification of metabolic enzymes
Altered transcriptional regulation of metabolic enzymes
Imagine that you are exercising intensely. Your cells activate glycolysis to produce more energy. What type of regulation is most likely at play?
Allosteric regulation
Covalent modification of metabolic enzymes
Altered translational regulation of metabolic enzymes
Altered transcriptional regulation of metabolic enzymes
As a metabolic sensor, why is AMP particularly well suited as an allosteric regulator of PFK-1?
AMP is the best indicator of a low energy state in cells.
AMP is very abundant in cells, so it can impact PFK-1 activity very quickly.
. AMP is at low abundance in cells, so a small decrease in [ATP] leads to large changes in [AMP].
AMP has a very short half-life in cells, so changes in [AMP] only have a transient effect on the activity of PFK-1.
In the figure below, the black line represents the reaction velocity of purified PFK-1 in the presence of different amounts of its subtrate F6P. A sufficient quantity of ATP is present for the substrate-level phosphorylation that forms F1,6BP. The grey line represents the same reaction, with an unknown molecule added. Based on your knowledge of the regulation of PFK-1, what are TWO likely candidate molecules?
AMP
ADP
ATP
Citrate
F2,6 BP
What are TWO effects of Fructose 2,6 bisphosphate (F2,6 BP) on PFK-1 activity?
It is an allosteric inhibitor.
It is an allosteric activator.
It increases the sensitivity of PFK-1 to ATP.
It decreases the sensitivity of PFK-1 to ATP.
It has no effect on the sensitivity of PFK-1 to ATP.
Which of these glycolytic enzymes catalyzes a substrate-limited step of glycolysis?
PFK-1
Aldolase
Hexokinase
Pyruvate Kinase
Which molecule is an allosteric activator of pyruvate kinase?
F1,6 BP
F2,6 BP
Citrate
ATP
What are the main TWO fates of the glucose taken up by the liver when blood sugar levels are high?
Glucose is metabolized to produce more ATP via the citric acid cycle.
Glucose is shunted towards fatty acid synthesis.
Glucose is phosphorylated and stored in glucose granules.
Glucose is used to synthesize nucleic acids.
Glucose is used to synthesize glycogen.
{"name":"Biokjemi quizziiiii", "url":"https://www.quiz-maker.com/QWKVPXCFK","txt":"Of the elements below, two are much more abundant in the earth's crust than in living organisms. Mark the two elements., To how many different atoms does a carbon atom bond if it is in the following hybridization state : sp3, To how many different atoms does a carbon atom bond if it is in the following hybridization state : sp2","img":"https://www.quiz-maker.com/3012/CDN/88-4280284/spm.png?sz=1200-00940019150740505300"}
