2. Cell chemistry and bioenergetics

Question 1

What elements make up 96.5% of an organisms weight?

Answer 1

carbon (C), hydrogen (H), nitrogen (N), and oxygen (O)

Question 2

How are these atoms linked together?

Answer 2

The atoms of these ele- ments are linked together by covalent bonds to form molecules

Question 3

What is the benefit of covalent bonds?

Answer 3

Because covalent bonds are typically 100 times stronger than the thermal energies within a cell, they resist being pulled apart by thermal motions, and they are normally broken only during specific chemical reactions with other atoms and molecules.

Question 4

How can molecules be bound together?

Answer 4

Two different molecules can be held together by noncovalent bonds, which are much weaker

Question 5

Describe the bonds in a volume of water

Answer 5

In each water molecule (H2O) the two H atoms are linked to the O atom by covalent bonds. The two bonds are highly polar because the O is strongly attractive for electrons, whereas the H is only weakly attractive. Consequently, there is an unequal distribution of electrons in a water molecule, with a preponderance of positive charge on the two H atoms and of negative charge on the O. When a positively charged region of one water molecule (that is, one of its H atoms) approaches a negatively charged region (that is, the O) of a second water molecule, the electrical attraction between them can result in a hydrogen bond. These bonds are much weaker than covalent bonds and are easily broken by the random thermal motions that reflect the heat energy of the molecules. Thus, each bond lasts only a short time.

Question 6

What then is the relevance of these weak hydrogen bonds in a volume of water?

Answer 6

But the combined effect of many weak bonds can be profound. For example, each water molecule can form hydrogen bonds through its two H atoms to two other water molecules, producing a network in which hydrogen bonds are being continually broken and formed. It is only because of the hydrogen bonds that link water molecules together that water is a liquid at room temperature—with a high boiling point and high surface tension—rather than a gas.

Question 7

How are the characteristics of other molecules in the cell relevant to water? (2)

Answer 7

Molecules, such as alcohols, that contain polar bonds and that can form hydrogen bonds with water dissolve readily in water. Molecules carrying charges (ions) likewise interact favourably with water. Such molecules are termed hydrophilic, meaning that they are water-loving.Hydrophobic (water-hating) molecules, by contrast, are uncharged and form few or no hydrogen bonds, and so do not dissolve in water.

Question 8

What components of the cell are hydrophilic? Name 4

Answer 8

Many of the molecules in the aqueous environment of a cell necessarily fall into this category, including sugars, DNA, RNA, and most proteins.

Question 9

Give an important example of a hydrophobic molecule in the cell

Answer 9

Hydrocarbons are an important example. In these molecules all of the H atoms are covalently linked to C atoms by a largely nonpolar bond; thus they cannot form effective hydrogen bonds to other molecules. This makes the hydrocarbon as a whole hydrophobic—a property that is exploited in cells, whose membranes are constructed from molecules that have long hydrocarbon tails,

Question 10

Much of biology depends on the specific binding of different molecules caused by three types of noncovalent bonds. Name them

Answer 10

Electrostatic attractions (ionic bonds)Hydrogen bonds, and van der Waals attractions; and on a fourth factor that can push molecules together: the hydrophobic force.

Question 11

Comment on the strength of these non-covalent bonds

Answer 11

Each individual noncovalent attraction would be much too weak to be effective in the face of thermal motions, their energies can sum to create a strong force between two separate molecules

Question 12

Give an example of one of these bonds which demonstrates the sum of attractions

Answer 12

electrostatic forces aka ionic bonds- two molecules of complementary shap can have multiple sites of opposite charge which sum higher than sites which may have the same charge

Question 13

Name the Non-covalent bonds in order of strength

Answer 13

Covalent (for comparison): 377 kJ in vacuum ionic: 335 kJ in vacuum hydrogen: 16.7 kJ in vacuum van der waals attraction: 0.4 kJ in vacuum

Question 14

What effect does water have on non-covalent bonds?

Answer 14

by forming competing interactions with the involved molecules, water greatly reduces the strength of both electrostatic attractions and hydrogen bonds:Covalent: 377 kJ | 377 kJionic: 335 kJ | 12.6 kJhydrogen: 16.7 kJ | 4.2 kJvan der waals attraction: 0.4 kJ | 0.4 kJ

Question 15

Describe hydrogen bonds

Answer 15

This bond represents a special form of polar interaction in which an electropositive hydrogen atom is shared by two electronegative atoms. Its hydrogen can be viewed as a proton that has partially dissociated from a donor atom, allowing it to be shared by a second acceptor atom.

Question 16

Comment on the directionality of hydrogen and ionic bonds

Answer 16

Unlike a typical electrostatic interaction, this bond is highly directional—being strongest when a straight line can be drawn between all three of the involved atoms.

Question 17

Describe the fourth effect which brings molecules together

Answer 17

The fourth effect that often brings molecules together in water is not, strictly speaking, a bond at all. However, a very important hydrophobic force is caused by a pushing of nonpolar surfaces out of the hydrogen-bonded water network, where they would otherwise physically interfere with the highly favourable interactions between water molecules. Bringing any two nonpolar surfaces together reduces their contact with water; in this sense, the force is nonspecific.

Question 18

One of the simplest kinds of chemical reaction, and one that has profound significance in cells, takes place when a molecule containing a highly polar covalent bond between a hydrogen and another atom dissolves in water. Describe what happens

Answer 18

The hydrogen atom in such a molecule has given up its electron almost entirely to the companion atom, and so exists as an almost naked positively charged hydrogen nucleus—in other words, a proton (H+). When the polar molecule becomes surrounded by water molecules, the proton will be attracted to the partial negative charge on the O atom of an adjacent water molecule. This proton can easily dissociate from its original partner and associate instead with the oxygen atom of the water molecule, generating a hydronium ion (H3O+). The reverse reaction also takes place very readily, so in the aqueous solution protons are constantly flitting to and fro between one molecule and another.

Question 19

What are these substances with highly polar covalent bonds with hydrogen known as?

Answer 19

Substances that release protons when they dissolve in water, thus forming H3O+, are termed acids. The higher the concentration of H3O+, the more acidic the solution.

Question 20

Is H3O+ present in pure water?

Answer 20

H3O+ is present even in pure water, at a concentration of 10–7 M, as a result of the movement of protons from one water molecule to another

Question 21

By convention, what is the H3O+ concentration referred as? How is it quantified?

Answer 21

By convention, the H3O+ concentration is usually referred to as the H+ concentration, even though most protons in an aqueous solution are present as H3O+ .To avoid the use of unwieldy numbers, the concentration of H3O is expressedusing a logarithmic scale called the pH scale. Pure water has a pH of 7.0 and is said to be neutral—that is, neither acidic (pH <7) nor basic (pH >7).

Question 22

How are strong and weak acids defined?

Answer 22

Acids are characterized as being strong or weak, depending on how readily they give up their protons to water. Strong acids, such as hydrochloric acid (HCl), lose their protons quickly. Acetic acid, on the other hand, is a weak acid because it holds on to its proton more tightly when dissolved in water.

Question 23

What is the opposite of a base?

Answer 23

The opposite of an acid is a base. Any molecule capable of accepting a proton from a water molecule is called a base. Sodium hydroxide (NaOH) is basic (the term alkaline is also used) because it dissociates readily in aqueous solution to form Na+ ions and OH– ions. Because of this property, NaOH is called a strong base.

Question 24

What bases are more important in cells?

Answer 24

More important in living cells, however, are the weak bases—those that have a weak tendency to reversibly accept a proton from water. Many biologically important molecules contain an amino (NH2) group. This group is a weak base that can generate OH– by taking a proton from water: –NH2 + H2O → –NH3+ + OH–

Question 25

How are the presence of acids and bases regulated in a cell?

Answer 25

Because an OH– ion combines with a H3O+ ion to form two water molecules, an increase in the OH– concentration forces a decrease in the concentration of H3O+, and vice versa. A pure solution of water contains an equal concentration (10–7 M) of both ions, rendering it neutral. The interior of a cell is also kept close to neutrality by the presence of buffers: weak acids and bases that can release or take up protons near pH 7, keeping the environment of the cell relatively constant under a variety of conditions.

Question 26

If we disregard water and inorganic ions such as potassium, nearly all the molecules in a cell are based on carbon. What makes carbon so special?

Answer 26

Carbon is outstanding among all the elements in its ability to form large molecules; silicon is a poor second. Because carbon is small and has four electrons and four vacancies in its outermost shell, a carbon atom can form four covalent bonds with other atoms. Most important, one carbon atom can join to other carbon atoms through highly stable covalent C–C bonds to form chains and rings and hence generate large and complex molecules with no obvious upper limit to their size.

Question 27

What name is given to molecules formed by carbon?

Answer 27

The carbon compounds made by cells are called organic molecules. In contrast, all other molecules, including water, are said to be inorganic.

Question 28

What are common combinations of atoms that occur repeatedly in molecules made by cells called? Name 7 of them

Answer 28

Certain combinations of atoms, such as: the methyl (–CH3)hydroxyl (–OH)carboxyl (–COOH)carbonyl (–C=O)phosphate (–PO3^2–)sulfhydryl (–SH)and amino (–NH2) groups, occur repeatedly in the molecules made by cells. Each such chemical group has distinct chemical and physical properties that influence the behaviour of the molecule in which the group occurs.

Question 29

Describe the small organic compounds of the cell in regards to their weight, location and function

Answer 29

The small organic molecules of the cell are carbon-based compounds that have molecular weights in the range of 100–1000 and contain up to 30 or so carbon atoms. They are usually found free in solution and have many different fates. Some are used as monomer subunits to construct giant polymeric macromolecules. Many small molecules have more than one role in the cell—for example, acting both as a potential subunit for a macromolecule and as an energy source

Question 30

Name three of these giant polymeric subunits

Answer 30

proteins, nucleic acids, and large polysaccharides

Question 31

What else may be the function of these giant polymeric subunits?

Answer 31

Others act as energy sources and are broken down and transformed into other small molecules in a maze of intracellular metabolic pathways.

Question 32

Comment on the abundance of small organic molecules as opposed to macromolecules

Answer 32

Small organic molecules are much less abundant than the organic macromolecules, accounting for only about one-tenth of the total mass of organic matter in a cell. As a rough guess, there may be a thousand different kinds of these small molecules in a typical cell.

Question 33

All organic molecules are synthesized from and are broken down into the same set of simple compounds. As a consequence, the compounds in a cell are chemically related and most can be classified into a few distinct families. What are the four major families of small organic molecules?

Answer 33

the sugars, the fatty acids, the nucleotides, and the amino acids

Question 34

To what extent do these four families encompass all of the molecules in the cell?

Answer 34

Although many compounds present in cells do not fit into these categories, these four families of small organic molecules, together with the macromolecules made by linking them into long chains, account for a large fraction of the cell mass.

Question 35

How are macromolecules constructed from small organic molecules?

Answer 35

The macromolecules in cells are polymers that are constructed by covalently linking small organic molecules (called monomers) into long chains. They have remarkable properties that could not have been predicted from their simple constituents.

Question 36

What larger units do sugars form?

Answer 36

polysaccharides

Question 37

What larger units do fatty acids form?

Answer 37

fats, lipids, membranes

Question 38

What larger units do amino acids form?

Answer 38

Proteins

Question 39

What larger units do nucleotides form?

Answer 39

Nucleic acids

Question 40

Proteins are abundant and spectacularly versatile, performing thousands of distinct functions in cells. name and describe three of such functions

Answer 40

Many proteins serve as enzymes, the catalysts that facilitate the many covalent bond-making and bond-breaking reactions that the cell needs. Enzymes catalyse all of the reactions whereby cells extract energy from food molecules.Other proteins are used to build structural components, such as tubulin, a protein that self-assembles to make the cell’s long microtubules, or histones, proteins that compact the DNA in chromosomes.Yet other proteins act as molecular motors to produce force and movement, as for myosin in muscle.

Question 41

Although the chemical reactions for adding subunits to each polymer are different in detail for proteins, nucleic acids, and polysaccharides, they share important features. Describe how each polymer is constructed from monomers

Answer 41

Each polymer grows by the addition of a monomer onto the end of a growing chain in a condensation reaction, in which one molecule of water is lost with each subunit added. The stepwise polymerisation of monomers into a long chain is a simple way to manufacture a large, complex molecule, since the subunits are added by the same reaction performed over and over again by the same set of enzymes.

Question 42

Apart from some polysaccharides, what is significant about the monomers constructing most macromolecules?

Answer 42

Apart from some of the polysaccharides, most macromolecules are made from a limited set of monomers that are slightly different from one another—for example, the 20 different amino acids from which proteins are made.

Question 43

What feature of covalent bonds allow the polymer chain great flexibility?

Answer 43

Most of the covalent bonds in a macromolecule allow rotation of the atoms they join, giving the polymer chain great flexibility. In principle, this allows a macromolecule to adopt an almost unlimited number of shapes, or conformations, as random thermal energy causes the polymer chain to writhe and rotate.

Question 44

What constrains the shape of most biological macromolecules?

Answer 44

However, the shapes of most biological macromolecules are highly constrained because of the many weak noncovalent bonds that form between different parts of the same molecule. If these noncovalent bonds are formed in sufficient numbers, the polymer chain can strongly prefer one particular conformation, determined by the linear sequence of monomers in its chain

Question 45

In addition to influencing protein shape, how else do non-covalent bonds play a function with these proteins?

Answer 45

In addition to folding biological macromolecules into unique shapes, they can also add up to create a strong attraction between two different molecules. This form of molecular interaction provides for great specificity, inasmuch as the close multipoint contacts required for strong binding make it possible for a macromolecule to select out—through binding—just one of the many thousands of other types of molecules present inside a cell.

Moreover, because the strength of the binding depends on the number of non-covalent bonds that are formed, interactions of almost any affinity are possible—allowing rapid dissociation where appropriate.

Question 46

This type of binding (noncovalent; inter-molecule) underlie all forms of what protein function? What other roles can it play?

Answer 46

Binding of this type underlies all biological catalysis, making it possible for proteins to function as enzymes.

In addition, noncovalent interactions allow macromolecules to be used as building blocks for the formation of larger structures, thereby forming intricate machines with multiple moving parts that perform such complex tasks as DNA replication and protein synthesis.

Question 47

One property of living things above all makes them seem almost miraculously different from nonliving matter. What is this property?

Answer 47

They create and maintain order, in a universe that is tending always to greater disorder.

Question 48

What must cells do it order to create this order?

Answer 48

To create this order, the cells in a living organism must perform a never-ending stream of chemical reactions.

Question 49

Describe two broad ways in which these reactions are carried out

Answer 49

In some of these reactions, small organic molecules—amino acids, sugars, nucleotides, and lipids—are being taken apart or modified to supply the many other small molecules that the cell requires.

In other reactions, small molecules are being used to construct an enormously diverse range of proteins, nucleic acids, and other macromolecules that endow living systems with all of their most distinctive properties.

Question 50

Why is it unusual that many of these reactions take place inside a cell? How is this remedied?

Answer 50

The chemical reactions that a cell carries out would normally occur only at much higher temperatures than those existing inside cells. For this reason, each reaction requires a specific boost in chemical reactivity. This requirement is crucial, because it allows the cell to control its chemistry.

Question 51

How do these boosts in chemical reactivity come about?

Answer 51

The control is exerted through specialised biological catalysts. These are almost always proteins called enzymes, although RNA catalysts also exist, called ribozymes.

Question 52

What effect do enzymes have on these reactions?

Answer 52

Each enzyme accelerates, or catalyses, just one of the many possible kinds of reactions that a particular molecule might undergo. Enzyme-catalyzed reactions are connected in series, so that the product of one reaction becomes the starting material, or substrate, for the next

Question 53

What are the two opposing streams of chemical reactions in cells? What overall process do they encompass?

Answer 53

(1) the catabolic pathways break down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules that the cell needs as building blocks

(2) the anabolic, or biosynthetic, pathways use the small molecules and the energy harnessed by catabolism to drive the synthesis of the many other molecules that form the cell. Together these two sets of reactions constitute the metabolism of the cell

Question 54

What law of physics has profound implications for life?

Answer 54

The universal tendency of things to become disordered is a fundamental law of physics—the second law of thermodynamics—which states that in the universe, or in any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree of disorder always increases.

Question 55

What is used to describe or quantify this disorderedness?

Answer 55

The amount of disorder in a system can be quantified and expressed as the entropy of the system: the greater the disorder, the greater the entropy.

Question 56

Thus name two ways we could use to express the second law of thermodynamics

Answer 56

We can present the second law in terms of probability by stating that systems will change spontaneously toward those arrangements that have the greatest probability. e.g many more configurations result in 50-50 heads tails than 100-0 heads tails.

Another way to express the second law of thermodynamics is to say that systems will change spontaneously toward arrangements with greater entropy.

Question 57

Why is this second law so profound for life?

Answer 57

Living cells—by surviving, growing, and forming complex organisms—are generating order and thus might appear to defy the second law of thermodynamics. How is this possible? The answer is that a cell is not an isolated system: it takes in energy from its environment in the form of food, or as photons from the sun. It then uses this energy to generate order within itself.

Question 58

How is the second law of thermodynamics thus satisfied through cell activity?

Answer 58

In the course of the chemical reactions that generate order, the cell converts part of the energy it uses into heat. The heat is discharged into the cell’s environment and disorders the surroundings. As a result, the total entropy—that of the cell plus its surroundings—increases, as demanded by the second law of thermodynamics.

As the cell lives and grows, it creates internal order. But it constantly releases heat energy as it synthesizes molecules and assembles them into cell structures. Heat is energy in its most disordered form—the random jostling of molecules. When the cell releases heat it increases the intensity of molecular motions there (thermal motion)—thereby increasing the randomness, or disorder, of the sea. The second law of thermodynamics is satisfied because the increase in the amount of order inside the cell is always more than compensated for by an even greater decrease in order (increase in entropy) in the surrounding sea of matter

Question 59

How does this relationship between these chemical reactions and entropy bring up another law of thermodynamics?

Answer 59

Where does the heat that the cell releases come from? The first law of thermodynamics states that energy can be converted from one form to another, but that it cannot be created or destroyed. For example, an animal cell takes in foodstuffs and converts some of the energy present in the chemical bonds between the atoms of these food molecules (chemical-bond energy) into the random thermal motion of molecules (heat energy).

Question 60

Is this released heat therefore at a deficit of the organism then?

Answer 60

No, the heat-generating reactions inside the cell are directly linked to the processes that generate molecular order. It is the tight coupling of heat production to an increase in order that distinguishes the metabolism of a cell from the wasteful burning of fuel in a fire.

Question 61

All animal and plant cells are powered by energy stored in what?

Answer 61

All animal and plant cells are powered by energy stored in the chemical bonds of organic molecules, whether they are sugars that a plant has photosynthesized as food for itself or the mixture of large and small molecules that an animal has eaten.

Question 62

How is this energy extracted from food molecules?

Answer 62

In both plants and animals, energy is extracted from food molecules by a process of gradual oxidation, or controlled burning.

Question 63

What is meant by aerobic respiration?

Answer 63

The Earth’s atmosphere contains a great deal of oxygen, and in the presence of oxygen the most energetically stable form of carbon is CO2 and that of hydrogen is H2O.

A cell is therefore able to obtain energy from sugars or other organic molecules by allowing their carbon and hydrogen atoms to combine with oxygen to produce CO2 and H2O, respectively—a process called aerobic respiration.

Question 64

What are complimentary processes regarding aerobic respiration found in plants and animals?

Answer 64

Photosynthesis and respiration are complementary processes. This means that the transactions between plants and animals are not all one way. Plants, animals, and microorganisms have existed together on this planet for so long that many of them have become an essential part of the others’ environments. We therefore see that carbon utilisation forms a huge cycle that involves the biosphere (all of the living organisms on Earth) as a whole

Question 65

Describe the process of photosynthesis

Answer 65

photosynthesis converts the electromagnetic energy in sunlight into chemical-bond energy in sugars and other organic molecules. plants, algae, and cyanobacteria obtain the carbon atoms that they need for this purpose from atmospheric Co2 and the hydrogen from water, releasing o2 gas
as a by-product.

Question 66

How is this related to cellular respiration? Describe this process

Answer 66

The organic molecules produced by photosynthesis in turn serve as food for other organisms. many of these organisms carry out aerobic respiration,
a process that uses o2 to form Co2 from the same carbon atoms that had been taken up as Co2 and converted into sugars by photosynthesis. in the process, the organisms that respire obtain the chemical- bond energy that they need to survive.

Question 67

Did the first cells on earth likely carry out photosynthesis or respiration?

Answer 67

he first cells on the earth are
thought to have been capable of neither photosynthesis nor respiration. however, photosynthesis must have preceded respiration on the earth, since there is strong evidence that billions of years of photosynthesis were required before o2 had been released in sufficient quantity to create an atmosphere rich in this gas.

Question 68

How is the oxidisation of organic molecules more complex than that of a burning fire?

Answer 68

The cell does not oxidize organic molecules in one step, as occurs when organic material is burned in a fire. Through the use of enzyme catalysts, metabolism takes these molecules through a large number of reactions that only rarely involve the direct addition of oxygen

Question 69

What does the term oxidation refer to? What is its inverse?

Answer 69

Oxidation refers to more than the addition of oxygen atoms; the term applies more generally to any reaction in which electrons are transferred from one atom to another.

Oxidation in this sense refers to the removal of electrons, and reduction—the converse of oxidation—means the addition of electrons.

Question 70

Thus, what is the relationship between Cl => Cl- and Fe2+ => Fe3+ ?

Answer 70

Fe2+ is oxidised if it loses an electron to become Fe3+, and a chlorine atom is reduced if it gains an electron to become Cl–.

Question 71

Which of these processes are involved in the conversion of molecules to H2O and CO2?

Answer 71

When a sugar molecule is oxidised to CO2 and H2O, for example, the O2 molecules involved in forming H2O gain electrons and thus are said to have been reduced.

Question 72

Are oxidation and reduction relevant in the partial shifting of electrons in a covalent bond?

Answer 72

The terms “oxidation” and “reduction” apply even when there is only a partial shift of electrons between atoms linked by a covalent bond. The reduced atom has acquired a partial negative charge (δ–) as the positive charge on the atomic nucleus is now more than
equaled by the total charge of the electrons surrounding it, and conversely, X the oxidized atom has acquired a partial positive charge (δ+).

Question 73

Describe examples of this partial shifting of electrons. What is the name given to this type of bond?

Answer 73

When a carbon atom becomes covalently bonded to an atom with a strong affinity for electrons, such as oxygen, chlorine, or sulfur, for example, it gives up more than its equal share of electrons and forms a polar covalent bond.

Because the positive charge of the carbon nucleus is now somewhat greater than the negative charge of its electrons, the atom acquires a partial positive charge and is said to be oxidized. Conversely, a carbon atom in a C–H linkage has slightly more than its share of electrons, and so it is said to be reduced.

Question 74

What are meant by hydrogenation reactions?

Answer 74

When a molecule in a cell picks up an electron (e–), it often picks up a proton (H+) at the same time (protons being freely available in water). The net effect in this case is to add a hydrogen atom to the molecule.

Question 75

Are hydrogenation reactions oxidisation or reduction reactions?

Answer 75

Even though a proton plus an electron is involved (instead of just an electron), such hydrogenation reactions are reductions, and the reverse, dehydrogenation reactions are oxidations.

Question 76

Why is it especially easy to tell whether an organic molecule is being oxidised or reduced?

Answer 76

It is especially easy to tell whether an organic molecule is being oxidized or reduced: reduction is occurring if its number of C–H bonds increases, whereas oxidation is occurring if its number of C–H bonds decreases

Question 77

Describe the relationship between methane and carbon dioxide in terms of oxidisation and reduction

Answer 77

The single carbon atom of methane can be converted to that of carbon dioxide by the successive replacement of its covalently bonded hydrogen atoms with oxygen atoms. With each step, electrons are shifted away from the carbon, and the carbon atom becomes progressively more oxidised:

Methane
Methanol (one H becomes an OH group)
formaldehyde (lose 2 H atoms, C=O)
formic acid (One H becomes OH)
Carbon dioxide (O=C=O)

Each of these steps is energetically favourable under the conditions present inside a cell. Going backwards through these would be a series of reduction reactions.

Question 78

Consider the reaction
paper + O2 → smoke + ashes + heat + CO2 + H2O

How would you describe the activity of the atoms and molecules of the paper in terms of thermodynamics?

Answer 78

The atoms and molecules of the paper become dispersed and disordered. In the language of thermodynamics, there has been a loss of free energy; that is, of energy that can be harnessed to do work or drive chemical reactions.

Question 79

Describe the general principle of free energy

Answer 79

Chemical reactions proceed spontaneously only in the direction that leads to a loss of free energy. In other words, the spontaneous direction for any reaction is the direction that goes “downhill,” where a “downhill” reaction is one that is energetically favourable.

Question 80

Although the most energetically favourable form of carbon under ordinary conditions is CO2, and that of hydrogen is H2O, a living organism does not disappear in a puff of smoke, and the paper book in your hands does not burst into flames.

Why is this?

Answer 80

This is because the molecules both in the living organism and in the book are in a relatively stable state, and they cannot be changed to a state of lower energy without an input of energy: in other words, a molecule requires activation energy—a kick over an energy barrier—before it can undergo a chemical reaction that leaves it in a more stable state

Question 81

In the case of a burning book, the activation energy can be provided by the heat of a lighted match. What could happen in the case of a cell?

Answer 81

For the molecules in the watery solution inside a cell, the kick is delivered by an unusually energetic random collision with surrounding molecules—collisions that become more violent as the temperature is raised.

Question 82

How then, is the chemistry in a living cell tightly controlled?

Answer 82

The kick over energy barriers is greatly aided by a specialised class of proteins—the enzymes. Each enzyme binds tightly to one or more molecules, called substrates, and holds them in a way that greatly reduces the activation energy of a particular chemical reaction that the bound substrates can undergo.

Question 83

What can lower the activation energy of a reaction?

Answer 83

A substance that can lower the activation energy of a reaction is termed a catalyst; catalysts increase the rate of chemical reactions because they allow a much larger proportion of the random collisions with surrounding molecules to kick the substrates over the energy barrier.

Question 84

How effective are enzymes as catalysts?

Answer 84

Enzymes are among the most effective catalysts known: some are capable of speeding up reactions by factors of 10^14 or more. Enzymes thereby allow reactions that would not otherwise occur to proceed rapidly at normal temperatures.

Question 85

How frequent are uncatalysed chemical reactions in the cell?

Answer 85

for most biological reactions, this almost never happens without enzyme catalysis. even with enzyme catalysis, the substrate molecules must experience a particularly energetic collision to react. Raising the temperature will also increase the number of molecules with sufficient energy to overcome the activation energy needed for a reaction; but in marked contrast to enzyme catalysis, this effect is nonselective, speeding up all reactions

Question 86

What effect does an enzyme have on the equilibrium point of a reaction?

Answer 86

An enzyme cannot change the equilibrium point for a reaction. The reason is simple: when an enzyme (or any catalyst) lowers the activation energy for the reaction Y → X, of necessity it also lowers the activation energy for the reaction X → Y by exactly the same amount. The forward and backward reactions will therefore be accelerated by the same factor by an enzyme, and the equilibrium point for the reaction will be unchanged

Question 87

How then, do enzymes steer processes in the cell?

Answer 87

Despite the above limitation, enzymes steer all of the reactions in cells through specific reaction paths. This is because enzymes are both highly selective and very precise, usually catalyzing only one particular reaction. In other words, each enzyme selectively lowers the activation energy of only one of the several possible chemical reactions that its bound substrate molecules could undergo. In this way, sets of enzymes can direct each of the many different molecules in a cell along a particular reaction pathway.

Question 88

What, in terms of enzymes, does the success of a living organism attributable to?

Answer 88

The success of living organisms is attributable to a cell’s ability to make enzymes of many types, each with precisely specified properties.

Question 89

Describe these precisely specific properties

Answer 89

Each enzyme has a unique shape containing an active site, a pocket or groove in the enzyme into which only particular substrates will fit. Like all other catalysts, enzyme molecules themselves remain unchanged after participating in a reaction and therefore can function over and over again.

Question 90

How many reactions can a given enzyme catalyse over the space of a second?

Answer 90

An enzyme will often catalyse the reaction of thousands of substrate molecules every second. This means that it must be able to bind a new substrate molecule in a fraction of a millisecond.

Question 91

But both enzymes and their substrates are present in relatively small numbers in a cell. How do they find each other so fast?

Answer 91

Rapid binding is possible because the motions caused by heat energy are enormously fast at the molecular level.

Question 92

These molecular motions can be classified broadly into three kinds. Name them

Answer 92

(1) the movement of a molecule from one place to another (translational motion).

(2) the rapid back-and-forth movement of covalently linked atoms with respect to one another (vibrations).

(3) Rotations.

All of these motions help to bring the surfaces of interacting molecules together.

Question 93

How can the rates of molecular motions be best measured?

Answer 93

The rates of molecular motions can be measured by a variety of spectroscopic techniques.

Question 94

How can translational motion assist in speeding reactions?

Answer 94

Molecules are also in constant translational motion, which causes them to explore the space inside the cell very efficiently by wandering through it—a process called diffusion. In this way, every molecule in a cell collides with a huge number of other molecules each second.

Question 95

What is this movement of a molecule through the cell called/ described by?

Answer 95

As the molecules in a liquid collide and bounce off one another, an individual molecule moves first one way and then another, its path constituting a random walk

Question 96

How is the distance travelled by a molecule described by a random walk?

Answer 96

In such a walk, the average net distance that each molecule travels from its starting point is proportional to the square root of the time involved: that is, if it takes a molecule 1 second on average to travel 1 μm, it takes 4 seconds to travel 2 μm, 100 seconds to travel 10 μm, and so on.

Question 97

Comment on how the rate of collisions depends on the concentration of the substrate

Answer 97

Since enzymes move more slowly than substrates in cells, we can think of them as sitting still. The rate of encounter of each enzyme molecule with its substrate will depend on the concentration of the substrate molecule.

For example, some abundant substrates are present at a concentration of 0.5 mM. Since pure water is 55.5 M, there is only about one such substrate molecule in the cell for every 105 water molecules. Nevertheless, the active site on an enzyme molecule that binds this substrate will be bombarded by about 500,000 random collisions with the substrate molecule per second.

Question 98

Describe how, upon collision, the enzyme and the substrate interact

Answer 98

A random collision between the active site of an enzyme and the matching surface of its substrate molecule often leads immediately to the formation of an enzyme–substrate complex. A reaction in which a covalent bond is broken or formed can now occur extremely rapidly.

Question 99

How does the binding between molecules determine enzyme substrate dynamics?

Answer 99

Two molecules that are held together by noncovalent bonds can also dissociate. The multiple weak noncovalent bonds that they form with each other will persist until random thermal motion causes the two molecules to separate. In general, the stronger the binding of the enzyme and substrate, the slower their rate of dissociation.

In contrast, whenever two colliding molecules have poorly matching surfaces, they form few noncovalent bonds and the total energy of association will be negligible compared with that of thermal motion. In this case, the two molecules dissociate as rapidly as they come together, preventing incorrect and unwanted associations between mismatched molecules, such as between an enzyme and the wrong substrate.

Question 100

Although enzymes speed up reactions, they cannot by themselves force energetically unfavourable reactions to occur. In terms of a water analogy, enzymes by themselves cannot make water run uphill. Why is this an issue?

Answer 100

Cells, however, must do just that in order to grow and divide: they must build highly ordered and energy-rich molecules from small and simple ones.

Question 101

How can enzymes assist then, in producing energetically unfavourable reactions?

Answer 101

This is done through enzymes that directly couple energetically favourable reactions, which release energy and produce heat, to energetically unfavourable reactions, which produce biological order.

Question 102

What do cell biologists mean by the term “energetically favourable,” and how can this be quantified?

Answer 102

According to the second law of thermodynamics the uni- verse tends toward maximum disorder (largest entropy or greatest probability). Thus, a chemical reaction can proceed spontaneously only if it results in a net increase in the disorder of the universe. This disorder of the universe can be expressed most conveniently in terms of the free energy of a system.

Question 103

What is free energy, G an expression of then?

Answer 103

Free energy, G, is an expression of the energy available to do work—for example, the work of driving chemical reactions.

Question 104

When is the value of G of interest?

Answer 104

The value of G is of interest only when a system undergoes a change, denoted ∆G (delta G). The change in G is critical because ∆G is a direct measure of the amount of disorder created in the universe when a reaction takes place.

Question 105

Thus what is meant by energetically favoured reactions?

Answer 105

Energetically favorable reactions, by definition, are those that decrease free energy; in other words, they have a negative ∆G and disorder the universe

Question 106

Give an example of an energetically favourable reaction on the macroscopic scale

Answer 106

An example of an energetically favorable reaction on a macroscopic scale is the “reaction” by which a compressed spring relaxes to an expanded state, releasing its stored elastic energy as heat to its surroundings

Question 107

Give an example of an energetically favourable reaction on the microscopic scale

Answer 107

salt dissolving in water

Question 108

What then are energetically unfavourable reactions? How can they come about in the cell?

Answer 108

Conversely, energetically unfavourable reactions with a positive ∆G—such as the joining of two amino acids to form a peptide bond—by themselves create order in the universe. Therefore, these reactions can take place only if they are coupled to a second reaction with a negative ∆G so large that the ∆G of the overall process is negative

Question 109

As we have just described, a reaction Y ↔ X will go in the direction Y → X when the associated free-energy change, ∆G, is negative, just as a tensed spring left to itself will relax and lose its stored energy to its surroundings as heat. However in a chemical reaction what does is depend on aside from the energy stored in each individual molecule?

Answer 109

Also on the concentrations of the molecules in the reaction mixture. Remember that ∆G reflects the degree to which a reaction creates a more disordered—in other words, a more probable—state of the universe.

For a reversible reaction Y ↔ X, a large excess of Y over X will tend to drive the reaction in the direction Y → X. Therefore, as the ratio of Y to X increases, the ∆G becomes more negative for the transition Y → X (and more positive for the transition X → Y).

Question 110

The amount of concentration difference that is needed to compensate for a given decrease in chemical-bond energy (and accompanying heat release) is not intuitively obvious. How was this relationship determined?

Answer 110

In the late nineteenth century, the relationship was determined through a thermodynamic analysis that makes it possible to separate the concentration-dependent and the concentration-independent parts of the free-energy change

Question 111

Because ∆G depends on the concentrations of the molecules in the reaction mixture at any given time, it is not a particularly useful value for comparing the relative energies of different types of reactions. What is a better metric for this kind of analysis?

Answer 111

To place reactions on a comparable basis, we need to turn to the standard free-energy change of a reaction, ∆G°. The ∆G° is the change in free energy under a standard condition, defined as that where the concentrations of all the reactants are set to the same fixed value of 1 mole/liter. Defined in this way, ∆G° depends only on the intrinsic characters of the reacting molecules.