Chapter 14: Introduction to Metabolism

Question 1

Purpose of this chapter?

Answer 1

In this chapter, we introduce the general features of metabolic reactions and the roles of ATP and other compounds as energy carriers. Because many metabolic reactions are also oxidation–reduction reactions, we review the thermodynamics of these processes. Finally, we examine some approaches to studying metabolic reactions.

to examine the reactions in which biological molecules are built and broken down. We must also consider how free energy is consumed in building cellular materials and carrying out cellular work and how free energy is generated from organic or other sources.

Question 2

What is metabolism?

Answer 2

Metabolism is the overall process through which living systems acquire and use free energy to carry out their various functions, is traditionally divided into two parts:

• Catabolism, how energy is gained from the break-down
• Anabolism, how energy is used for biosynthesis

Metabolism are the reactions by which biomolecules are built and broken down

Question 3

The principles that govern metabolism are the same in all organisms, a result of their common evolutionary origin and the constraints of the laws of thermodynamics. Many of the specific reactions of metabolism are common to all organisms, with variations due primarily to?

Answer 3

Differences in the sources of the free energy that supports them.

Question 4

catabolism carries an exer or endogenic reaction.
How about anabolism.
How does this tie together

Answer 4

In general, catabolic reactions carry out the exergonic oxidation of nutrient molecules. The free energy thereby released is used to drive such endergonic processes as anabolic reactions, the performance of mechanical work, and the active transport of molecules against concentration gradients.Exergonic and endergonic processes are often coupled through the intermediate synthesis of a “high-energy” compound such as ATP.
In an exergonic reaction, energy is released to the surroundings. The bonds being formed are stronger than the bonds being broken. In an endergonic reaction, energy is absorbed from the surroundings. The bonds being formed are weaker than the bonds being broken.

Question 5

What is Nutrition? How does it assist the body?

Answer 5

Nutrition, the intake and utilization of food, affects health, development, and performance. Food supplies the energy that powers life processes and provides the raw materials to build and repair body tissues.

Question 6

The nutritional requirements of an organism reflect?

Answer 6

its source of metabolic energy.

Question 7

What are the different sources of energy?

Answer 7

Autotrophs (Greek: autos, self + trophos, feeder), which can synthesize all their cellular constituents from simple molecules such as H2 O, CO2 , NH3 , and H2 S. There are two possible free energy sources for this process.
Chemolithotrophs (Greek: lithos, stone) obtain their energy through the oxidation of inorganic compounds such as NH3 , H2 S, or even Fe2+ :

Photoautotrophs do so via photosynthesis, a process in which light energy powers the transfer of electrons from inorganic donors to CO 2 to produce carbohydrates, (CH2O)n, which are later oxidized to release free energy.

Heterotrophs (Greek: hetero, other) obtain free energy through the oxidation of organic compounds (carbohydrates, lipids, and proteins) and hence ultimately depend on autotrophs for those substances.
Consume food made by autotroph

Question 8

Organisms can be further classified by the identity of?

Answer 8

the oxidizing agent for nutrient breakdown.

by their requirement for oxygen

Question 9

What are the oxidizing agents for nutrient breakdown? Which are animals?

Answer 9

Obligate aerobes (which include animals) must use O2, whereas anaerobes employ oxidizing agents such as sulfate or nitrate. Facultative anaerobes, such as E. coli, can grow in either the presence or the absence of O2 . Obligate anaerobes, in contrast, are poisoned by the presence of O2 .

Question 10

Classification of animal/mammalian nutrition?

Answer 10

Animals are obligate aerobic heterotrophs, whose nutrition depends on a balanced intake of the macronutrients proteins, carbohydrates, and lipids.These are broken down by the digestive system to their component amino acids, monosaccharides, fatty acids, and glycerol—the major nutrients involved in cellular metabolism—which are then transported by the circulatory system to the tissues.The metabolic utilization of the latter substances also requires the intake of O2 and water, as well as micronutrients composed of vitamins and minerals.

Question 11

Common vitamins, minerals, and trace elements

Answer 11

Vitamin A,D,E,K, B12,B7,C
Sodium, Magnesium, Calcium, Potassium
Iron, Copper, Zinc, Chromium

Question 12

What are vitamins?

Answer 12

Vitamins are organic molecules that an animal is unable to synthesize and must therefore obtain from its diet. Vitamins can be divided into two groups: water-soluble vitamins and fat-soluble vitamins.
Most Water-Soluble Vitamins Are Converted to Coenzyme

Question 13

What are metabolic pathways?

Answer 13

Metabolic pathways are series of connected enzymatic reactions that produce specific products. They are catalyzed by a distinct enzyme.

Question 14

What are the reactants, intermediates, and products in metabolic pathways called?

Answer 14

metabolites

Question 15

The types of enzymes and metabolites in a given cell vary with ?

Answer 15

the identity of the organism, the cell type, its nutritional status, and its developmental stage.

Question 16

Describe the degradative pathway. How is the free energy conserved? (Hint: What are the major free energy sources for biosynthetic reactions?)

Answer 16

In degradative pathways, the major nutrients, referred to as complex metabolites, are exergonically broken down into simpler products.

The free energy released in the degradative process is conserved by the synthesis of ATP from ADP + P i or by the reduction of a coenzyme such as NADP + to NADPH.

ATP and NADPH, generated through the degradation of complex metabolites.

Question 17

A striking characteristic of degradative metabolism is that ?

Answer 17

the pathways for the catabolism of a large number of diverse substances (carbohydrates, lipids, and proteins) converge on a few common intermediates, in many cases, a two-carbon acetyl unit linked to coenzyme A to form acetyl-coenzyme A (acetyl-CoA

Question 18

Overview of catabolism

Answer 18

Complex metabolites such as carbohydrates, proteins, and lipids are degraded first to their monomeric units, chiefly glucose, amino acids, fatty acids, and glycerol, and then to the common intermediate, acetyl-CoA. The acetyl group is oxidized to CO 2 via the citric acid cycle with concomitant reduction of NAD + and FAD to NADH and FADH2 . Reoxidation of NADH and FADH 2 by O 2 during electron transport and oxidative phosphorylation yields H2 O and ATP.

the breakdown of various foodstuffs to their monomeric units and then to acetyl-CoA. This is followed by the oxidation of the acetyl carbons to CO 2 by the citric acid cycle. When one substance is oxidized (loses electrons), another must be reduced (gain electrons. The citric acid cycle thus produces the reduced coenzymes NADH and FADH2, which then pass their electrons to O 2 to produce H2 O in the processes of electron transport and oxidative phosphorylation.

As metabolic fuels are oxidized to CO2 , electrons are transferred to molecular carriers that, in aerobic organisms, ultimately transfer the electrons to molecular oxygen. The process of electron transport results in a transmembrane proton concentration gradient that drives ATP synthesis (oxidative phosphorylation; Section 18-3). Even obligate anaerobes, which do not carry out oxidative phosphorylation, rely on the oxidation of substrates to drive ATP synthesis.

Question 19

4 major reactions in metabolic pathways?

Answer 19

1. oxidations and reductions (catalyzed by oxidoreductases),
2. group-transfer reactions (catalyzed by transferases and hydrolases), eliminations, isomerizations, a
3. rearrangements (catalyzed by isomerases and mutases)
4. reactions that make or break carbon–carbon bonds (catalyzed by hydrolases, lyases, and ligases).

Question 20

The more reduced a carbon atom is? this makes which biomolecule a more efficient food source?

Answer 20

the more free energy is released upon oxidation.
Fats are a more efficient food source than glucose because fats are more reduced

Question 21

The vast majority of interconversion steps of metabolites are catalyzed by?How

Answer 21

Enzymes, these Catalyze the Reactions of Metabolic Pathways.

the specificity of enzymes guarantees the efficiency of metabolic reactions by preventing the formation of useless or toxic by-products. Most importantly, enzymes provide a mechanism for coupling an endergonic chemical reaction (which would not occur on its own) with an energetically favorable reaction,

Question 22

Where do Metabolic Pathways Occur?

Answer 22

In specific cellular locations The compartmentation of the eukaryotic cytoplasm allows different metabolic pathways to operate in different locations

requires transport proteins to move metabolites in and out of specific compartments

Degradative and biosynthetic processes may occur in specialized compartments in the cell, or may involve several compartments.

Question 23

summarize the major function of each cellular compartment.

Question 24

what are used to move metabolites in and out of specific compartments

Answer 24

transport proteins

For example, a transport protein is required to move ATP, which is generated in the mitochondria, to the cytosol, where most of it is consumed

Question 25

in multicellular organisms, compartmentation occurs also on what higher levels?

Answer 25

tissues and organs

Question 26

An intriguing manifestation of specialization of tissues and subcellular compartments is the existence of _____, enzymes that catalyze the same reaction but are encoded by different genes and have different kinetic or regulatory properties.

Answer 26

isozymes

Different tissues often express different isozymes to match tissue function.

using different forms of the same enzyme to catalyze a given biochemical reaction. These different forms of the same enzyme are known as isozymes or isoenzymes. Isozymes arise from different genes, have different sequences of amino acids and a different structure yet catalyze the same reaction, have different properties and exhibit different enzymes kinetics and are usually controlled by different allosteric effectors.

Question 27

Thermodynamics Dictates ?

Answer 27

the Direction and Regulatory Capacity of Metabolic Pathways

Question 28

What are near-equilibrium reactions.
How are they controlled and reversed?

Answer 28

When the reactants are present at values close to their equilibrium values, [C]eq [D]eq /[A]eq [B] eq ≈ Keq , and ΔG ≈ 0. This is the case for many metabolic reactions,

Because their ΔG values are close to zero, they can be relatively easily reversed by changing the ratio of products to reactants.

Enzymes that catalyze near-equilibrium reactions tend to act quickly to restore equilibrium concentrations, and the net rates of such reactions are effectively controlled by the relative concentrations of substrates and products.

High catalytic activity of enzyme

Question 29

When the reactants are in excess of their equilibrium concentrations, the net reaction proceeds in what direction? Conversely, when products are in excess, the net reaction proceeds in what direction ?

Answer 29

When the reactants are in excess of their equilibrium concentrations, the net reaction proceeds in the forward direction until the excess reactants have been converted to products and equilibrium is attained.Conversely, when products are in excess, the net reaction proceeds in the reverse direction to convert products to reactants until the equilibrium concentration ratio is again achieved.

Question 30

Only a few other metabolic reactions function far from equilibrium; that is, they are irreversible. Known as?

Answer 30

Non equilibrium, when the max catalytic activity of the enzyme is low. Concentration of substrate/reactant is high and products is low.making ΔG ≪ 0 and saturated.This is because an enzyme catalyzing such a reaction has i cient catalytic activity (the rate of the reaction it catalyzes is too slow) to allow the reaction to come to equilibrium under physiological conditions.
Only changes in the activity of the enzyme—through allosteric interactions, for example—can significantly alter the rate.
These irreversible steps are used to regulate the metabolic pathway, by changing the activity of the enzyme.

Question 31

CONSEQUENCES OF IRREVERSIBLE STEPS

Answer 31

• Metabolic pathways are irreversible.
• Every metabolic pathway has a first “committed” step.
• Catabolic and anabolic pathways differ, because the “irreversible” reaction has to be circumvented when going in the opposite direction. This allows independent control of both pathways.

Question 32

what is a metabolic flux? must be controlled by what?

Answer 32

rate of flow) of metabolites through a metabolic pathway
The flux of material through a metabolic pathway varies with the activities of the enzymes that catalyze irreversible reactions.

Irreversible steps control metabolic flux

Question 33

equation for The flux of metabolites, J through each reaction step

How about for reactions that are from from equilibrium ?

Answer 33

the rate of the forward reaction, v f, less that of the reverse reaction, v r

In reactions that are far from equilibrium, v f≫ v r, the flux is essentially equal to the rate of the forward reaction (J ≈ vf ).

Question 34

flux is set by the rate-determining step of the pathway.Cells use several mechanisms to control flux through the rate-determining steps of metabolic pathways such as?

Answer 34

flux-controlling enzymes are regulated by allosteric mechanisms, covalent modification, substrate cycling, and changes in gene expression. induction or repression of enzyme production

• long-term control mechanism

Question 35

Use the words obligate, facultative, aerobic, anaerobic, autotroph, and heterotroph to describe the metabolism of a human, oak tree, E. coli, and Methanococcus jannaschii (an organism that lives in deepwater anoxic sediments).

Question 36

cell uses several forms of energy currency such as

Answer 36

the cell’s primary energy currency: ATP,compounds that contain thioester bonds, and reduced coenzymes such as NADH.

Question 37

Why is ATP a “high-energy” compound?

Answer 37

The free energy of the “high-energy” compound ATP is made available through cleavage of one or both of its phosphoanhydride bonds.

related to the large negative free energy change for hydrolysis of its phosphoanhydride bonds.

Question 38

What are phosphoryl group-transfer potentials

Answer 38

―the standard free energy of hydrolysis―is a means of comparing the tendency of organic molecules to transfer a phosphoryl group to an acceptor molecule.

they are a measure of the tendency of phosphorylated compounds to transfer their phosphoryl groups to water.

hydrolysis of several phosphorylated compounds o

Question 39

Cleavage of the phosphoanhydride bonds, i.e. transfer of a phosphoryl (or nucleotidyl) group, is highly endergonic or exergonic?

Answer 39

exergonic

Question 40

Why are the phosphoryl group-transfer reactions of ATP so exergonic? Several factors appear to be responsible for the “high-energy” character of phosphoanhydride bonds such as those in ATP:
Why are phosphoanhydride bonds “high-energy”?

Answer 40

1. The resonance stabilization of a phosphoanhydride bond is less than that of its hydrolysis products.
2. Of perhaps greater importance is the destabilizing effect of the electrostatic repulsions between the charged groups of a phosphoanhydride compared to those of its hydrolysis products. (Charge repulsions)
3. Another destabilizing influence, which is difficult to assess, is the smaller solvation energy of a phosphoanhydride compared to that of its hydrolysis products. (Stabilization by hydration)
4. Resonance stabilization of products larger than that of substrates.
5. Mutual repulsion of negatively charged groups larger in substrates than in products.
6. Smaller solvation energy of phosphoanhydride as compared to hydrolysis products.

Question 41

Furthermore, because ATP and its hydrolysis products are ions, ΔG also depends on?

Answer 41

pH, ionic strength, and Mg 2+complexation

Question 42

Why is ATP so stable, despite the large amount of free energy released by its hydrolysis?

Answer 42

In the absence of an appropriate enzyme, phosphoanhydride bonds are stable; that is, they hydrolyze quite slowly, despite the large amount of free energy released by these reactions. This is because these hydrolysis reactions have unusually high free energies of activation (ΔG‡ ; Section 11-2). Consequently, ATP hydrolysis is thermodynamically favored but kinetically disfavored

Question 43

Purpose of Coupled Reactions?

Answer 43

The hydrolysis of a “high-energy” compound, while releasing considerable free energy, is not in itself a useful reaction. However, the exergonic reactions of “high-energy” compounds can be coupled to endergonic processes to drive them to completion

Question 44

The thermodynamic explanation for the coupling of an exergonic and an endergonic process is based on ?

Answer 44

the additivity of free energy.

Question 45

How can you drive an endergonic reaction?

Answer 45

Couple it with an exergonic reaction.

Question 46

Describe Phosphoanhydride Hydrolysis and how it drives biochemical processes

Answer 46

The free energy of the phosphoanhydride bonds of “high-energy” compounds such as ATP can be used to drive reactions even when the phosphoryl groups are not transferred to another organic compound.

For example, ATP hydrolysis (i.e., phosphoryl group transfer directly to H2 O) provides the free energy for the operation of molecular chaperones (Section 6-5B), muscle contraction (Section 7-2B), and transmembrane active transport (Section 10-3).

Question 47

Inorganic Pyrophosphatase function?

Answer 47

Catalyzes Additional Phosphoanhydride Bond Cleavage by suppling additional “driving force”.

is an enzyme that catalyzes the conversion of one ion of pyrophosphate to two phosphate ions.[1] This is a highly exergonic reaction, and therefore can be coupled to unfavorable biochemical transformations in order to drive these transformations to completion.[2]

Question 48

Just as ATP drives endergonic reactions through the exergonic process of phosphoryl group transfer and phosphoanhydride hydrolysis, ATP itself can be regenerated by coupling its formation to a more highly exergonic metabolic process.

Answer 48

“High-energy” compounds other than ATP are essential for energy metabolism, in part because they help maintain a relatively constant level of cellular ATP.

Question 49

Explain how cellular ATP is replenished by phosphagens.

Answer 49

utilizes phosphocreatine and ADP to regenerate ATP in the cell when at rest (relies on concentration of substrate and products to determine if reaction should go forward or reverse)

Question 50

How is ATP regenerated?

Answer 50

• oxidative phosphorylation
• photophosphorylation
• substrate-level phosphorylation transfer of phosphoryl group from “high-energy” compound

Question 51

What is substrate-level phosphorylation.

Answer 51

ATP can therefore be formed from ADP by direct transfer of a phosphoryl group from a “high-energy” compound (e.g., phosphoenolpyruvate; Fig. 14-7b and Section 15-2J). Such a reaction is referred to as a substrate-level phosphorylation
the synthesis of ATP from ADP by phosphoryl group transfer from another compound.

Question 52

What is oxidative phosphorylation and photophosphorylation

Answer 52

Other mechanisms generate ATP indirectly, using the energy supplied by transmembrane proton concentration gradients. In oxidative metabolism this process is called oxidative phosphorylation
whereas in photosynthesis, it is termed photophosphorylation

As metabolic fuels are oxidized to CO2 , electrons are transferred to molecular carriers that, in aerobic organisms, ultimately transfer the electrons to molecular oxygen. The process of electron transport results in a transmembrane proton concentration gradient that drives ATP synthesis (oxidative phosphorylation; Section 18-3). Even obligate anaerobes, which do not carry out oxidative phosphorylation, rely on the oxidation of substrates to drive ATP synthesis.

Question 53

What Provides a “High-Energy” Reservoir for ATP Formation in muscle and nerve cells? How does it regenerate?

Answer 53

Phosphocreatine
Phosphocreatine is known as its quickest form of regeneration, by means of the enzyme creatine kinase

Question 54

Nucleoside Triphosphates Are Freely Interconverted. What regenerates/catalyzes the?

Answer 54

All these nucleoside triphosphates (NTPs) are synthesized from ATP
catalyzed by the nonspecific enzyme nucleoside diphosphate kinase
Nucleoside diphosphate kinase is resposible for regeneration of nucleoside triphosphates through the reversible reactions

Question 55

If a reaction leaves AMP, how can ATP be regenerated?

Answer 55

adenylate kinase

Question 56

What are Thioesters?

Answer 56

primitive “high-energy” compound
involved in substrate-level phosphorylation

The thioester bond appears in modern metabolic pathways as a reaction intermediate and in the form of acetyl-CoA he common product of carbohydrate, fatty acid, and amino acid catabolism.

Question 57

The common product of carbohydrate, lipid, and protein catabolism, is a “high-energy” thioester.

Answer 57

acetyl-CoA,

Question 58

oxidation–reduction reactions (also known as redox reactions) function?

Answer 58

supply living things with most of their free energy.

Question 59

Two of the most widely occurring electron carriers are?

Answer 59

nucleotide coenzymes:

nicotinamide adenine dinucleotide (NAD+ ) and
flavin adenine dinucleotide (FAD).

• The electron carriers NAD + and FAD accept electrons from reduced metabolites and transfer them to other compounds.

They accept high energy electrons and carry them ultimately to the electron transport chain where they are used to synthesize ATP molecules

Question 60

NAD + and FAD are not direct sources of energy, so what do they do?

Answer 60

When these electron carrier molecules accept the electrons, they are reduced into and form energy molecules NADH and FADH2 .

Question 61

The nicotinamide portion of NAD +(and its phosphorylated counterpart NADP+, is the site of?

Answer 61

reversible reduction, which formally occurs as the transfer of a hydride ion (H−; a proton with two electrons)
transfers two electrons

Question 62

The terminal electron acceptor in aerobic organisms?

Answer 62

O2

Question 63

The change in the electronic state of the ring system on reduction is reflected in what color changes in FAD and FADH2?

Answer 63

brilliant yellow (in FAD) to pale yellow (in FADH2).

Question 64

What are the metabolic roles of the coenzymes NAD + and FAD?

Answer 64

The metabolic functions of NAD +and FAD demand that they undergo reversible reduction so that they can accept electrons, pass them on to other electron carriers, and thereby be regenerated to participate in additional cycles of oxidation and reduction.

The coenzymes NAD + and FAD are reversibly reduced during the oxidation of metabolites.

Question 65

How do redox reactions occur? Loss of electrons is what? Gain of electrons is?

Answer 65

electrons are transferred from electron donor (reducing agent) to electron acceptor (oxidizing agent)

• loss of electrons = oxidation; gain of electrons = reduction

Question 66

The Nernst Equation Describes?

Answer 66

Oxidation–Reduction Reactions

Oxidation–reduction reactions resemble other types of group-transfer reactions except that the “groups” transferred are electrons, which are passed from an electron donor (reductant or reducing agent) to an electron acceptor (oxidant or oxidizing agent).

The Nernst equation describes the thermodynamics of oxidation–reduction reactions.

Question 67

Fe 3+ + e − ⇌ Fe2+

Cu + ⇌ Cu 2+ + e−

What are these, which is reduction, which is oxidation, and why?

Answer 67

Cu+ , the reductant, is oxidized to Cu 2+ while Fe3+ , the oxidant, is reduced to Fe2+ .

Redox reactions can be divided into two half-reactions, such as

Fe 3+ + e − ⇌ Fe2+

(reduction)

Cu + ⇌ Cu 2+ + e−

(oxidation)

Question 68

for electrons to be transferred, both half-reactions must?

Answer 68

occur simultaneously

Question 69

A half-reaction consists of an electron donor and its conjugate electron acceptor; in the oxidative half-reaction shown above, Cu + is the electron donor and Cu 2+ is its conjugate electron acceptor. Together these constitute what? Which is analogous to a conjugate acid–base pair (HA and A −

Answer 69

A redox couple or conjugate redox pair

Question 70

An important difference between redox pairs and acid-base pairs is?

Answer 70

is that the two half-reactions of a redox reaction, each consisting of a conjugate redox pair, can be physically separated to form an electrochemical cell

Question 71

What is an electrochemical cell? What is necessary to complete the electrical circuit?

Answer 71

In such a device, each half-reaction takes place in its separate half-cell, and electrons are passed between half-cells as an electric current in the wire connecting their two electrodes. A salt bridge is necessary to complete the electrical circuit by maintaining electroneutrality through the transfer of ions through the electrolyte-containing salt bridge.

The halfcell undergoing oxidation (here Cu + → Cu 2+ + e− ) passes the liberated electrons through the wire to the half-cell undergoing reduction (here e − + Fe 3+ → Fe2+)

Question 72

The free energy of redox reactions in aqueous medium can be determined by?

Answer 72

measuring the voltage difference between both half-cells. Look at doc for electrical work equation info
free energy change of a redox reaction can be determined by directly measuring its change in reduction potential with a voltmeter

Question 73

Equation for determining For electrical work?

Answer 73

DG = - n F*DE

n = moles of e - per moles of reactant
F = electrical charge of 1 mol e- 1 F (“Faraday”) = 96,485 C/mol
= 96,485 J/(V mol)

DE = electric potential difference

Question 74

Note that a positive Δℰ in results in a ?

Answer 74

negative ΔG

; in other words, a positive Δℰ indicates a spontaneous reaction, one that can do work.

Question 75

What is reduction potential

Answer 75

The reduction potential describes the tendency for an oxidized compound to gain electrons (become reduced); the change in reduction potential for a reaction describes the tendency for a given oxidized compound to accept electrons from a given reduced compound.

Question 76

What Can Be Determined by Measuring Reduction Potential Differences?

Answer 76

Spontaneity

free energy change of a redox reaction can be determined by directly measuring its change in reduction potential with a voltmeter. Such measurements make it possible to determine the order of spontaneous electron transfers among a set of electron carriers such as those of the electron-transport pathway that mediates oxidative phosphorylation in cells.

Question 77

equation for measurement of reduction potential?

Answer 77

For the overall redox reaction involving the two half-reactions, the difference in reduction potential, Δℰ°′, is defined as

Δℰ°′ = ℰ°′ (e − acceptor) − ℰ°′ (e − donor)

Question 78

Purpose of standard reduction potentials?

Answer 78

Standard Reduction Potentials Are Used to Compare Electron Affinities.

Question 79

The more positive the standard reduction potential…?

Answer 79

The higher the affinity for electrons, i.e. the higher the tendency to accept electrons and become reduced.

Question 80

Free energy and reduction potential are negatively related, meaning?

Answer 80

the greater the reduction potential, the more negative the free energy and the more favorable the reaction.