EXAM 3 practice

In a metabolic pathway, a reaction that best serves as a committed step

has a large negative ∆G

The electrons released during oxidation reactions cannot be captured by

ADP

NAD+ can accept __ electrons and __ protons.

2, 1

DO organize ATP in ATPase enzyme pockets

Glutamate organizes a water to serve as the nucleophile

DO NOT organize ATP in ATPase enzyme pockets

The coordinated Mg2+ polarizes the gamma-phosphate, Arginine polarizes the nucleophilic water, Water binds the gamma-phosphate

The Thioester bond of Acetyl-CoA is favored for hydrolysis due to what?

The lack of resonance between the ketone oxygen and the sulfur atom

The benefit of measuring the initial rate of a reaction, V₀, is that early in the course of the conversion of substrate (S) to products

the rate of product formation is linear and the concentration of substrate will not have been lowered significantly

In a plot of 1/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will

move the intercept on the 1/[S] axis closer to zero

What are true statements about a plot of V0 versus [S] for an enzyme that follows Michaelis-Menten kinetics

Km is the [S] at which V₀ = ½ V_max, The y-axis is a rate term, with units of moles/unit time, At smaller values of [S], the initial velocity of the reaction, V₀, is also smaller, The shape of the curve is a rectangular hyperbola

True statements about enzymes

They need to be in their native conformation in order to be active, they increase the rate at which a reaction’s equilibrium is attained, they work by decreasing the amount of energy needed to carry out a biochemical reaction, they do not affect the position of a reaction’s equilibrium

Given five K_M values for the binding of substrates to a particular enzyme. Which has the strongest affinity?

the smallest value

Which of the following membranes would be the most fluid?

A bilayer made of lipids with saturated 18-carbon fatty acids.

A bilayer made of lipids with monounsaturated 16-carbon fatty acids.

A bilayer made of lipids with saturated 16-carbon fatty acids.

A bilayer made of lipids with monounsaturated 18-carbon fatty acids.

All of the above are equivalent in fluidity.

A bilayer made of lipids with monounsaturated 16-carbon fatty acids

general features of the lipid bilayer in biological membranes

The membrane lipids self-assemble in an aqueous environment to form the lipid bilayer, individual lipid molecules are free to diffuse laterally in one surface of the bilayer, the higher the proportion of unsaturated fatty acid chains in a membrane’s phosphoglycerides, the lower the transition temperature of the membrane

An antiporter and a symporter are examples of

Secondary active transporters

statements about the Na+-K+ ATPase

It only hydrolyzes ATP when both Na+ and K+ are present, its hydrolysis of ATP results in the pumping of 3 Na+ out of the cell and 2 K+ into the cell, it is a facilitator of transport that allows both K+ and Na+ ions to travel up a concentration gradient, it pumps Na+ ions up a concentration gradient

When muscle cells use glucose to generate ATP under anaerobic conditions, NAD+ must be regenerated by

converting pyruvate to lactate to sustain glycolysis

Substrate-level phosphorylation

ATP synthesis when the phosphate donor is a substrate with high-phosphoryl-transfer potential

What would be associated with LOW glycolysis rate?

Decreased levels of F1,6BP, Increased ATP levels, Phosphorylation of pyruvate kinase

What would be associated with HIGH glycolysis rate?

Increased AMP levels, High insulin levels

ATP is a co-substrate of the enzyme phosphofructokinase (PFK/PFK-1).  In most species ATP is also an inhibitor of PFK-1 at higher concentrations.  Which statement below would provide a suitable explanation for this discrepancy?

There are two sites on PFK-1 that bind ATP. One is the active site; the other is the regulatory site where inhibition occurs.

Given the following graph of the rate of PFK as a function of substrate concentration in the presence of two different effectors. Which of the following could be effector 1?

Fructose 2,6-bisphosphate

Pyruvate carboxylase consumes a(n) ___ to drive a carboxylation so that ___ could use the energy from decarboxylation to facilitate formation of phosphoenolpyruvate (PEP).

ATP, phosphoenolpyruvate carboxylkinase

Under anaerobic conditions, the net yield of one mole of glucose is

two moles of lactate and two moles of ATP

Pyruvate kinase is a tetrameric enzyme that can exist as a L (found mostly in liver) or M (found mostly in muscles) forms.  Which of the following statements comparing the L and M forms of pyruvate kinase is True

The L form is more likely to become phosphorylated in the presence of high level of glucagon

What is true about the transition state of an enzymatic reaction?

The state when the molecule being modified by the enzyme is neither the original substrate nor final product

Km

The concentration of substrate needed to reach ½ the Vmax

Carbohydrates are less-efficient fuel sources than fats because the carbon in carbohydrates is more

oxidized

Which of the following carries a hydride in catabolic pathways?

NADH

True statements about integral membrane lipids

Lipid bilayers are highly impermeable, Lipids in a bilayer rapidly diffuse laterally, They have a polar head group that interacts with water, Lipids can form bilayers that seal into vesicles, They have hydrophobic hydrocarbon tails that repel water, Lipids in a bilayer slowly exchange between leaflets

True statement about membrane transport

Solutes that cross a cell membrane by facilitated or passive diffusion will move down a concentration gradient

Kinases

enzymes that catalyze the transfer of a phosphoryl group from ATP to an acceptor

The product of aerobic glycolysis

pyruvate

One of the main roles of the liver is to act as a blood glucose buffer.  As such, glucose only enters the glycolic pathway in the liver when blood sugar levels exceed normal levels.  Entry of glucose from the blood supply into the liver is regulated by the GLUT2 receptors.  Which of the following mechanism is used by GLUT2 receptors to ensure that the liver only uses glucose in times of plenty?

Higher K_m than other Glut receptors

committed step

The first irreversible enzymatic reaction unique to a metabolic pathway

What is the role of Glycogenin?

Makes a primer for glycogen extension by glycogen synthase

Glucose 6-phosphatase

leads to the release of glucose from the liver to enter the blood stream

Branch points in glycogen

α-1,6 glycosidic bonds

Enzymatic steps apart of the oxidative phase of the PPP

6-phosphogluconolactonase, Pyruvate carboxylase, Phosphenolpyruvate carboxykinase, Pyruvate kinase.

The non-oxidative phase of PPP

creates ribose 5-phosphate for the production of DNA production

During Glucose 6-phosphate dehydrogenase activity, which reaction takes place?

Lactonase opens the glucose ring

The NADPH produced during the PPP is the reducing power for the synthesis of

Fatty acids

McCardle syndrome is due to a skeletal muscle deficiency of glycogen phosphorylase. What would be observed in such a patient with this syndrome?

Skeletal muscle has high level of glycogen with normal structure

Glycogen phosphorylase releases glucose units from glycogen in what state?

As glucose 1-phosphate

What glycogen storage diseases affects only organs composed of lysosome rich cells?

Pompe disease

Cytosolic Ca2+ plays an important role during glycogen synthesis. What leads to increase in cytosolic Ca2+?

Phospholipase-C is activated, which cleaves PI(4,5)P2 to release IP3. IP3 binds to a specific receptor on the endoplasmic reticulum, which triggers the release of Ca2+ into the cytoplasm

Why does the liver need glucagon and epinephrin in activation of glycogen breakdown?

Epinephrin is needed to bind alpha-adrenergic receptors to activate the phosphoinositide pathway to release Ca2+ from the endoplasmic reticulum

In the phosphopentose isomerase reaction of the pentose phosphate pathway Ribulose 5-phosphate is converted to Ribose 5-phosphate. What happens to the carbonyl?

The carbonyl is moved from the carbon-2 position of Ribulose to carbon-1 of Ribose 5-P

Cells can use different pathways to meet certain needs. Which combination of pathways are used when more NADPH is needed than ribose 5-phosphate?

The oxidative and non-oxidative parts of the PPP in addition to gluconeogenesis

NADPH is required for the killing of microorganisms that are phagocytosed by white blood cells such as macrophages and neutrophils. What is true regarding this?

The NADPH-dependent respiratory burst leads to the eventual formation of HOCl and hydroxyl radicals that cause cellular damage to the microorganism, During an NADPH-dependent respiratory burst myeloperoxidase is used to convert H2O2 to HOCL, NADPH oxidase converts O2 to superoxide as part of the respiratory burst, NADPH is used by iNOS to generate NO as part of the respiratory burst

In a hypothetical enzyme-catalyzed reaction, an active site serine attacks the substrate and becomes temporarily covalently bonded to the substrate. In a later step, that bond is broken and the substrate-free enzyme is regenerated. Which catalytic strategy does this describe?

Covalent catalysis

Why is the Lineweaver-Burk plot useful for determining Vmax?

The hyperbola approaches Vmax only at very high [S], but in the Lineweaver-Burk plot the line can be extended to its Y-intercept, 1/Vmax.

The figure below compares an enzyme catalyzed reaction with and without an inhibitor. What would you expect to observe if a large excess of substrate were added to the inhibited reaction?

The reaction velocity would level off at a lower speed than the Vmax of the uninhibited reaction.

What statement about catabolism and anabolism is true?

Catabolism oxidizes fuels and produces ATP and NADH, which anabolism uses to build macromolecules.

The figure below shows the active site of an ATPase with ATP bound. Which role is correctly described?

The positively charged arginine finger stabilizes negative charge that develops on the γ-phosphate in the transition state.

Phosphorylating glucose with inorganic phosphate is thermodynamically unfavorable, yet hexokinase readily forms glucose 6-phosphate using ATP. What makes the hexokinase reaction favorable?

There are two processes which are coupled through a shared phosphoryl group transferred directly from ATP, so their individual ΔG values add to a negative value.

Phospholipase A2 removes the fatty acid at position 2 of phosphatidylcholine, producing lysophospholipid. If PLA2 acts on one leaflet of a flat membrane, what changes in lipid shape and curvature preference is expected in that leaflet?

Cylindrical lipid becomes an inverted cone, which favors positive curvature.

If you administer a drug to a patient that inhibits cAMP phosphodiesterase, which outcome do you expect?

Prolong the response to the hormonal signal.

In a FRAP (Fluorescence Recovery after Photobleaching) experiment, what would you expect to observe if the labeled lipid molecules were chemically cross linked so that they could not move within its leaflet?

Slower or no recovery

The two graphs below compare PFK-1 behavior at different fructose 2,6 bisphosphate (F2,6BP) concentrations. A mutant PFK-1 cannot respond to f2,6BP but still binds ATP and fructose 6-phosphate. Which of the following is the most likely expected behavior of the mutant PFK-1?

It would resemble the 0 µM F-2,6-BP curves; lower activity at low fructose 6-phosphate and stronger inhibition as ATP rises

Why must the products of steps 6–10 be counted twice for each glucose that enters glycolysis?

Aldolase (Step 4) splits fructose 1,6-bisphosphate into two triose phosphates, both of which eventually enter Step 6 as glyceraldehyde 3 phosphate, so two molecules go through the payoff phase.

The figure below shows how various dietary sugars enter glycolysis. Which statement about fructose is supported by the figure?

In liver, fructose becomes triose phosphates, whereas in adipose tissue it is primarily converted to fructose 6-phosphate.

In anaerobic glycolysis, lactate dehydrogenase converts pyruvate to lactate. What is the main purpose of this reaction?

To regenerate NAD+ from NADH so that glycolysis can continue.

Glycogen phosphorylase uses inorganic phosphate (phosphorolysis) rather than water (hydrolysis) to cleave glycosidic bonds. What advantage does this feature provide to the muscle cell?

The glucose 1-phosphate released becomes glucose 6-phosphate without consuming ATP.

The graph below shows the sources of glucose for the brain after a meal followed by extended fasting. Which of the following statements is correct?

Liver glycogen runs out, so more glucose must be made from non carbohydrate precursors