Biology - Chapter 8b and 9

1. size of the proton gradient 2. rate of ATP synthesis

When the protein gramicidin is integrated into a When the protein gramicidin is integrated into a membrane, an H+ channel forms and the membrane becomes very permeable to protons (H+ ions). If gramicidin is added to an actively respiring muscle cell, how would it affect the rates of electron transport, proton pumping, and ATP synthesis in oxidative phosphorylation? (Assume that gramicidin does not affect the production of NADH and FADH2 during the early stages of cellular respiration.) What decreases? (or goes to zero)

1. proton pumping rate 2. electron transport rate 3. rate of oxygen uptake

When the protein gramicidin is integrated into a When the protein gramicidin is integrated into a membrane, an H+ channel forms and the membrane becomes very permeable to protons (H+ ions). If gramicidin is added to an actively respiring muscle cell, how would it affect the rates of electron transport, proton pumping, and ATP synthesis in oxidative phosphorylation? (Assume that gramicidin does not affect the production of NADH and FADH2 during the early stages of cellular respiration.) What remains the same?

b and c (b) If it had one less O atom, it could be a subunit for replicating DNA. (c) Protein kinases use it to control the action of some enzymes.

Which answer is true of the molecule shown here?

High-energy collisions are less common than low-energy collisions.

Which fact is most important in explaining how enzymes speed reactions?

Glucose

Which molecule is metabolized in a cell to produce energy for performing work?

NADH and FADH2 donate their electrons to the chain.

Which of the following statements about the electron transport chain is true?

Oxygen holds electrons more tightly than hydrogen does, and the net charge is zero.

Which of the following statements is true of the bonds in a water molecule?

FADH2

Which of these is NOT a product of glycolysis?

acetyl CoA

Which of these is NOT a product of the citric acid cycle?

Fermentation

Which process is not part of the cellular respiration pathway that produces large amounts of ATP in a cell?

Electron transport and chemiosmosis

Which stage of glucose metabolism produces the most ATP?

They may not resemble the enzyme's substrates.

Which statement is characteristic of allosteric effectors?

a, b and c (a)Enzymes can be either proteins or RNA molecules. (b)When a cell makes an enzyme, it makes many copies. (c)Their substrate specificity involves matching of shapes.

Which statement is true of enzymes?

Glycolosis

Which step of the cellular respiration pathway can take place in the absence of oxygen?

Electronegativity

Which term describes the degree to which an element attracts electrons?

Anion and cation

Which terms describe two atoms when they form a bond in which electrons are completely transferred from one atom to the other?

b and c (b) Protein kinase (c) Allosteric effector

Which type of control agent exerts noncompetitive inhibition?

Substrate analog

Which type of control agent never speeds an enzyme's action?

The triphosphate chain of ATP has high free energy because it packs several negative charges into a small space. Reactions that "break ATP" are reactions that remove one or two phosphate groups from the chain. The shortened chain has fewer negative charges packed together and thus less free energy. Reactions always proceed in the direction that reduces free energy.

Why are reactions that break ATP spontaneous?

Triphosphate chains are unstable

Why is ATP a good source of energy for biological reactions?

The key is the enzyme's ability to use the abundant, low-energy collisions that abound at room temperature rather than waiting for rare high-energy collisions. To do this, enzymes often rely on a series of collisions to create a series of unique low-energy transition states. The graph below summarizes the energy relations.

Why is the enzyme's pathway very fast?

In the watery environment of the cell, the phosphate groups of the chain are partly ionized. The chain thus packs several negative charges into a small space. Remember that like charges repel each other: the charges in the chain would spring apart if they were not bound together. The phosphate chain thus is like a coiled spring, and like a coiled spring it stores energy.

Why is the triphosphate chain rich in energy?

NAD+

__________________is the compound that functions as the electron acceptor in glycolysis.

b and c (b) the free energy change for the reaction is positive. (c) equilibrium favors the reactants, not the products

A reaction is said to be unfavorable if ...

NAD+ Coenzyme A Pyruvate

Acetyl CoA formation: Net input

NADH Acetyl CoA CO2

Acetyl CoA formation: Net output

ADP ATP O2 Glucose

Acetyl CoA: Not input or output

pyruvate, ATP, and NADH

Among the products of glycolysis, which compounds contain energy that can be used by other biological reactions?

is an organic catalyst.

An enzyme _____.

No. Sometimes the substrates escape from the active site in their original form, as you see in the example below.

Are bound substrates always converted to products?

In some cases, both the enzyme and the substrate are distorted when they bind together. The distortion can weaken key bonds in the substrate, making it easier for a second collision to complete the reaction. This can replace a high-energy step (a collision between free substrates) with two low-energy steps that involve the enzyme.

Are changes in shape important in enzyme action?

is unchanged

As a result of its involvement in a reaction, an enzyme _____.

Strong covalent bonds join atoms in molecules. To make new bonds, colliding molecules must hit hard enough to create a high-energy transition state (an arrangement that is unstable enough to react). At body temperature, few collisions have that much energy, so most colliding molecules rebound without change. For more on this, see the lesson on Chemical Reactions in the Reactions and Equilibrium section.

Can you remind me why reactants are stable?

The enzyme called hexokinase shows induced fit clearly. Click on the glucose substrate or the enzyme and you'll see the enzyme's shape change. Induced fit may bring a reactive part of the enzyme near the substrate, leading to catalysis. That won't happen unless the bound molecule is the right substrate.

Can you show me induced fit?

Location: Inner mitochondrial membrane

Cellular locations of the four stages of cellular respiration : Oxidative phosphorylation

Location: Mitochondrial matrix

Cellular locations of the four stages of cellular respiration: Acetyl CoA formation

Location: Mitochondrial matrix

Cellular locations of the four stages of cellular respiration: Citric acid cycle (Krebs cycle)

Location: Cytosol

Cellular locations of the four stages of cellular respiration: Glycolysis

Acetyl CoA NAD+ ADP

Citric Acid Cycle: Net input

Coenzyme A NADH ATP CO2

Citric Acid Cycle: Net output

Glucose Pyruvate O2

Citric Acid Cycle: Not input or output

Sure did. Some enzymes are made of RNA, a polymer that more often stores hereditary information. This discovery surprised scientists and earned the discoverers a Nobel Prize. The most important catalytic RNA molecules are part of cellular structures called ribosomes, where they connect amino acids to make proteins. All life depends on the action of these catalytic RNAs.

Did you say some enzymes aren't made of proteins?

They often do. Check the example again: you'll see that the enzyme makes a covalent bond with one substrate. Later, it breaks the bond by reacting with another substrate. During these events, the enzyme donates H to one substrate and takes H from another substrate. Other enzymes differ, but chemical events like these are common.

Do enzymes react chemically with substrates?

Indeed it does. In some cases, the active site improves when a control agent such as an allosteric effector binds to the enzyme. The improved active site conducts more reactions per second. Click on the allosteric effector to see an example. Click the enzyme to reverse the effect.

Does a control agent ever speed up an enzyme?

...

During acetyl CoA formation and the citric acid cycle, all of the carbon atoms that enter cellular respiration in the glucose molecule are released in the form of CO2. Use this diagram to track the carbon-containing compounds that play a role in these two stages

Glucose utilization would increase a lot

During strenuous exercise, anaerobic conditions can result if the cardiovascular system cannot supply oxygen fast enough to meet the demands of muscle cells. Assume that a muscle cell's demand for ATP under anaerobic conditions remains the same as it was under aerobic conditions.

Each enzyme is highly specific in its action: it converts specific reactant molecules (the enzyme's substrates) into specific products. Enzyme specificity results from the enzyme having an active site that matches the substrates as a lock fits a key. On binding substrates, some active sites change shape for a better match, a process called induced fit. Click the stopcocks to add substrates.

Enzyme knowledge facts!!!

Lowering Ea

Enzymes speed reactions mainly by ...

decreasing Ea.

Enzymes work by _____.

The enzymes involved in ATP synthesis must be attached to a membrane to produce ATP The phosphate group added to ADP to make ATP comes from free inorganic phosphate ions

False statements

Hydrogen; polar

Gaseous hydrogen burns in the presence of oxygen to form water: 2H2 + O2 → 2H2 O + energy Which molecule is oxidized and what kind of bond is formed?

ADP NAD+ Glucose

Glycolysis: Net input

NADH ATP pyruvate

Glycolysis: Net output

CO2 Acetyl CoA Enzyme A O2

Glycolysis: Not input or output

b and c (b) It moves the reactive portion of the enzyme closer to the substrate. (c) The enzyme's active site changes shape to fit the correct substrate but not other molecules.

How can "induced fit" influence the specificity of an enzyme?

They use reactants that have more energy than ATP. The ultimate energy source is light, trapped by green chloroplasts in plant cells. The ATP made there is used to build sugars. Both plants and animals oxidize the sugars with the help of mitochondria, releasing energy to build ATP. To see these events, click on the mitochondrion and chloroplast.

How do cells rebuild ATP?

a and b (a) Chloroplasts use light energy to synthesize ATP. (b) Mitochondria synthesize ATP using energy that's released by oxidizing sugars and fats.

How do cells replace the energy-rich ATP that is destroyed in energy-coupled reactions?

The terminal phosphate of ATP is bound to the substrate.

How do cells use ATP to raise the energy level of reaction substrates?

Most effectors are bound by weak noncovalent interactions, so collisions can knock them away. An exception is covalently bound phosphate, which is removed by a chemical reaction. When effectors depart, forces within the enzyme restore its original shape. Attractions and repulsions between electrons and nuclei reshape the enzyme until they achieve a balance.

How do enzymes get back to normal after binding effectors?

An enzyme transfers an energy-rich part of the chain to the other molecule. In the example below, glucose receives ATP's third phosphate group. Phosphates have a lot of energy when they are linked in a chain, as in ATP. When phosphate is transferred to another molecule, some of the stored energy is transferred along with it.

How does ATP raise the energy level of other molecules?

Molecules in open solution usually hit at the wrong angle to react, and they wander apart after just a few collisions. By contrast, many enzymes hold substrates at the correct angle while they collide many times. These effects—correct orientation, longer contact—greatly increase the chance of reacting. For a mechanism involving substrate distortion, see How Enzymes Act.

How else do enzymes speed reactions?

Typical speeds range from 10 million times faster than the uncatalyzed reaction to trillions of times faster. An especially fast enzyme is urease, an enzyme that converts urea into carbon dioxide and ammonia. Soil microbes produce urease, which breaks down the urea that animals release in urine. Urease speeds the breakdown by a factor of 100 trillion.

How fast can enzymes work?

2

How many NADH are produced by glycolysis?

Some enzymes act on just one or two kinds of substrates. Others can work with a range of substrates. In all cases, though, the alternative substrates are members of just one or two classes of molecules. For instance, the enzyme sucrase is much more selective than the enzyme pepsin; but even pepsin only acts on proteins and water.

How selective are enzymes?

Both electron transport and ATP synthesis would stop

How would anaerobic conditions (when no O2 is present) affect the rate of electron transport and ATP production during oxidative phosphorylation? (Note that you should not consider the effect on ATP synthesis in glycolysis or the citric acid cycle.)

At some point the bond between the amino acid and the substrate must break

In an experiment with an enzyme, the 58th amino acid seems to form a covalent bond with a substrate molecule as part of the catalytic process. What would you say?

if one substrate is bound, the next binds more easily.

In cooperativity, ...

Pyruvate ... NADH

In fermentation _____ is reduced and _____ is oxidized.

proteins

In general, enzymes are what kinds of molecules?

2

In glycolysis there is a net gain of _____ ATP.

substrate-level phosphorylation

In glycolysis, ATP molecules are produced by _____.

glucose

In glycolysis, the carbon-containing compound that functions as the electron donor is _______________.

ATP

In glycolysis, what starts the process of glucose oxidation?

to function as the final electron acceptor in the electron transport chain

In mitochondrial electron transport, what is the direct role of O2?

Lactate and NAD+

In muscle cells, fermentation produces _____.

substrate-level phosphorylation

In the citric acid cycle, ATP molecules are produced by ___.

It is easier to remove electrons and produce CO2 from compounds with three or more carbon atoms than from a two-carbon compound such as acetyl CoA

In the oxidation of pyruvate to acetyl CoA, one carbon atom is released as CO2. However, the oxidation of the remaining two carbon atoms—in acetate—to CO2 requires a complex, eight-step pathway—the citric acid cycle. Consider four possible explanations for why the last two carbons in acetate are converted to CO2 in a complex cyclic pathway rather than through a simple, linear reaction.

...

In the sequential reactions of acetyl CoA formation and the citric acid cycle, pyruvate (the output from glycolysis) is completely oxidized, and the electrons produced from this oxidation are passed on to two types of electron acceptors.

Carbon dioxide

Into which molecule are all the carbon atoms in glucose ultimately incorporated during cellular respiration?

No, and multiple copies are needed for control. At any moment, some copies are bound to effectors; other copies are free. The effector concentration determines how many copies are active. This makes it possible to adjust the reaction rate over a wide range of values by adding or removing effectors. Use the slider to adjust the effector concentration.

Is there just one copy of the allosteric enzyme?

Fewer protons are pumped across the inner mitochondrial membrane when FADH2 is the electron donor than when NADH is the electron donor.

NADH and FADH2 are both electron carriers that donate their electrons to the electron transport chain. The electrons ultimately reduce O2 to water in the final step of electron transport. However, the amount of ATP made by electrons from an NADH molecule is greater than the amount made by electrons from an FADH2 molecule. Which statement best explains why more ATP is made per molecule of NADH than per molecule of FADH2?

pyruvate

Once the electron donor in glycolysis gives up its electrons, it is oxidized to a compound called ______________.

NADH ADP O2

Oxidative Phosphorylation: Net input

NAD+ ATP Water

Oxidative Phosphorylation: Net output

CO2 Glucose Coenzyme A Pyruvate Acetyl CoA

Oxidative Phosphorylation: Not input or output

ATP levels would fall at first, decreasing the inhibition of PFK and increasing the rate of ATP production

Suppose that a cell's demand for ATP suddenly exceeds its supply of ATP from cellular respiration. What correctly describes how this increased demand would lead to an increased rate of ATP production?

Cytosol

The first stages of cellular respiration occur in...

...

The four stages of cellular respiration do not function independently. Instead, they are coupled together because one or more outputs from one stage functions as an input to another stage. The coupling works in both directions, as indicated by the arrows in the diagram below. In this activity, you will identify the compounds that couple the stages of cellular respiration.

The unfavorable reaction is replaced by two favorable reactions.

The reaction A→B is unfavorable by itself, but through energy-coupling, cells can use ATP to convert A into B. How is this done?

NADH

The reduced form of the electron acceptor in glycolysis is__________.

Mitochondria

The second and third stages of cellular respiration occur in...

A bond must be broken between an organic molecule and phosphate before ATP can form. An enzyme is required in order for the reaction to occur One of the substrates is a molecule derived from the breakdown of glucose

True Statements

True

True or false? The potential energy in an ATP molecule is derived mainly from its three phosphate groups.

True

True or false? The reactions that generate the largest amounts of ATP during cellular respiration take place in the mitochondria.

In the absence of oxygen, electron transport stops. NADH is no longer converted to NAD+, which is needed for the first three stages of cellular respiration.

Under anaerobic conditions (a lack of oxygen), the conversion of pyruvate to acetyl CoA stops. What best describes the correct observation for this observation?

A control agent is a competitive inhibitor if it binds to the active site, where it competes with the substrate for binding. Its effect can be overcome by adding a great deal of substrate. An agent is noncompetitive if it binds at a location other than the active site, such as an allosteric site. No amount of substrate will overcome its effect.

What are competitive and noncompetitive inhibitors?

1. glycolysis 2. acetyl coenzyme A (acetyl CoA) formation 3. citric acid cycle (also known as the Krebs cycle) 4. oxidative phosphorylation (electron transport and chemiosmotic ATP synthesis)

What are the four stages of cellular respiration?

energy of activation

What does an enzyme reduce?

Glucose and oxygen

What does photosynthesis create and emit into the atmosphere?

acetyl CoA

What enters the citric acid cycle?

Before a reaction takes place, only weak noncovalent forces hold the enzyme and substrate together, as shown here. That makes it possible for the substrate to escape without reacting. But during the reaction, some enzymes go through a stage in which a covalent bond joins the enzyme and substrate. (If a covalent bond forms, a later step in the reaction breaks the bond.)

What holds the enzyme and substrate together?

Cooperativity occurs when an enzyme consists of several proteins with active sites. When no substrate is bound, the active sites are malformed, so it takes a hard collision to bind the first substrate. When one substrate molecule binds, a shape change improves the fit of other sites. This is a mechanism of allosteric control, in which substrates are allosteric effectors.

What is cooperativity?

Oxygen. (Processed through phosphorylation)

What is the final electron acceptor of cellular respiration?

Ionic.

What kind of bond is formed when lithium and fluorine combine to form lithium fluoride?

Carbon dioxide and water

What molecules are by-products of cellular respiration?

substrate

What name is given to the reactants in an enzymatically catalyzed reaction?

The mitochondrion

What organelle is the site of cellular respiration?

Photosynthesis

What process occurs in plant's chloroplast?

Glycolysis

What process occurs in the Cytosol?

Transfer of electrons to NADH and FADH2.

What process occurs in the citric acid cycle?

An enzyme is allosteric if specific kinds of small molecules (allosteric effectors) can change its activity by noncovalent binding to other parts of the enzyme (allosteric sites). The term allosteric means "other shape," and reflects the fact that effectors often have little resemblance to the enzyme's substrate.

What's an allosteric enzyme?

A reaction is unfavorable if it spontaneously runs in the direction of the reactants, not the products. That happens if the free energy of the products is higher than that of the reactants. For example, the reaction in the diagram is unfavorable when all substances are at 1 M concentration.

What's an unfavorable reaction?

None of these statements are false

What's false? (1) Enzymes may change shape when they bind substrates; (2) Enzymes provide no energy for the reaction, except collision energy; (3) Enzymes may release substrates.

reduced

When a compound accepts (gains) electrons, that compound becomes _______________. Such a compound is often referred to as an electron acceptor.

oxidized

When a compound donates (loses) electrons, that compound becomes ________________. Such a compound is often referred to as an electron donor.

an accumulation of effectors slows the pathway

When a pathway is subject to allosteric feedback inhibition, ...

There are many copies of the enzyme. X easily escapes from the allosteric site. When X detaches from an enzyme, the enzyme regains full activity.

When allosteric effector X binds to enzyme #1, the enzyme stops working. Nevertheless, the speed of the reaction can be altered by adjusting the concentration of X. How?