Cell Chpt 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 kJ
ionic: 335 kJ | 12.6 kJ
hydrogen: 16.7 kJ | 4.2 kJ
van 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 expressed
using 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 noncovalent bonds that are formed, interactions of almost any affinity are possible—allowing rapid dissociation where appropriate.