Essential Cell Biology 5th edition

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50 CHAPTER 2 Chemical Components of CellsFigure 2–16 In aqueous solutions, theconcentration of hydroxyl (OH – ) ionsincreases as the concentration of H 3 O +(or H + ) ions decreases. The product ofthe two values, [OH – ] x [H + ], is always 10 –14(moles/liter) 2 . At neutral pH, [OH – ] = [H + ],and both ions are present at 10 –7 M. Alsoshown are examples of common solutionsalong with their approximate pH values.ACIDIC[H + ]moles/literpH1 010 –1 110 –2 210 –3 310 –4 4[OH – ]moles/liter10 –1410 –1310 –1210 –1110 –10some solutions and theirpH valuesbattery acid (0.5)stomach acid (1.5)lemon juice (2.3), cola (2.5)orange juice (3.5)beer (4.5)10 –5 510 –9black coffee (5.0), acid rain (5.6)10 –6 610 –8urine (6.0), milk (6.5)NEUTRAL10 –7 710 –7pure water (7.0)10 –8 810 –6sea water (8.0)10 –9 910 –5hand soap (9.5)10 –10 1010 –4milk of magnesia (10.5)BASIC10 –11 1110 –3household ammonia (11.9)10 –12 1210 –2non-phosphate detergent (12.0)10 –13 1310 –1bleach (12.5)10 –14 141caustic soda (13.5)QUESTION 2–5A. Are there H 3 O + ions present inpure water at neutral pH (i.e., at pH= 7.0)? If so, how are they formed?B. If they exist, what is the ratioof H 3 O + ions to H 2 O molecules atneutral pH? (Hint: the molecularweight of water is 18, and 1 liter ofwater weighs 1 kg.)Molecules that accept protons when dissolved in water are called bases.Just as the defining property of an acid is that it raises the concentrationof H 3 O + ions by donating a proton to a water molecule, so the definingECB5 n2.100-2.16property of a base is that it raises the concentration of hydroxyl (OH – )ions by removing a proton from a water molecule. Sodium hydroxide(NaOH) is basic (the term alkaline is also used). NaOH is considered astrong base because it readily dissociates in aqueous solution to formNa + ions and OH – ions. Weak bases—which have a weak tendency toaccept a proton from water—however, are more important in cells. Manybiologically important weak bases contain an amino (NH 2 ) group, whichcan generate OH – by taking a proton from water: –NH 2 + H 2 O → –NH+ 3 +OH – (see Panel 2–2, pp. 68–69).Because an OH – ion combines with a proton to form a water molecule,an increase in the OH – concentration forces a decrease in the H + concentration,and vice versa (Figure 2–16). A pure solution of water containsan equal concentration (10 –7 M) of both ions, rendering it neutral (pH 7).The interior of a cell is kept close to neutral by the presence of buffers:mixtures of weak acids and bases that will adjust proton concentrationsaround pH 7 by releasing protons (acids) or taking them up (bases) wheneverthe pH changes. This give-and-take keeps the pH of the cell relativelyconstant under a variety of conditions.SMALL MOLECULES IN CELLSHaving looked at the ways atoms combine to form small molecules andhow these molecules behave in an aqueous environment, we now examinethe main classes of small molecules found in cells and their biologicalroles. Amazingly, we will see that a few basic categories of molecules,formed from just a handful of different elements, give rise to all theextraordinary richness of form and behavior displayed by living things.A Cell Is Formed from Carbon CompoundsIf we disregard water, nearly all the molecules in a cell are based on carbon.Carbon is outstanding among all the elements in its ability to formlarge molecules. Because a carbon atom is small and has four electronsand four vacancies in its outer shell, it readily forms four covalent bonds

Small Molecules in Cells51with other atoms (see Figure 2–9). Most importantly, one carbon atomcan link to other carbon atoms through highly stable covalent C–C bonds,producing rings and chains that can form the backbone of complex moleculeswith no obvious upper limit to their size. These carbon-containingcompounds are called organic molecules. By contrast, all other molecules,including water, are said to be inorganic.In addition to containing carbon, the organic molecules produced by cellsfrequently contain specific combinations of atoms, such as the methyl(–CH 3 ), hydroxyl (–OH), carboxyl (–COOH), carbonyl (–C=O), phosphoryl(–PO 3 2– ), and amino (–NH 2 ) groups. Each of these chemical groups hasdistinct chemical and physical properties that influence the behavior ofthe molecule in which the group occurs, including whether the moleculetends to gain or lose protons when dissolved in water and with whichother molecules it will interact. Knowing these groups and their chemicalproperties greatly simplifies understanding the chemistry of life. The mostcommon chemical groups and some of their properties are summarizedin Panel 2–1 (pp. 66–67).Cells Contain Four Major Families of Small OrganicMoleculesThe small organic molecules of the cell are carbon compounds withmolecular weights in the range 100–1000 that contain up to 30 or socarbon atoms. They are usually found free in solution in the cytosol andhave many different roles. Some are used as monomer subunits to constructthe cell’s polymeric macromolecules—its proteins, nucleic acids,and large polysaccharides. Others serve as energy sources, being brokendown and transformed into other small molecules in a maze ofintracellular metabolic pathways. Many have more than one role in thecell—acting, for example, as both a potential subunit for a macromoleculeand as an energy source. The small organic molecules are muchless abundant than the organic macromolecules, accounting for onlyabout one-tenth of the total mass of organic matter in a cell. But smallorganic molecules adopt a huge variety of chemical forms. Nearly 4000different kinds of small organic molecules have been detected in thewell-studied bacterium Escherichia coli.All organic molecules are synthesized from—and are broken downinto—the same set of simple compounds. Both their synthesis and theirbreakdown occur through sequences of simple chemical changes thatare limited in variety and follow step-by-step rules. As a consequence,the compounds in a cell are chemically related, and most can be classifiedinto a small number of distinct families. Broadly speaking, cellscontain four major families of small organic molecules: the sugars, thefatty acids, the amino acids, and the nucleotides (Figure 2–17). Althoughmany compounds present in cells do not fit into these categories, thesefour families of small organic molecules—together with the macromoleculesmade by linking them into long chains—account for a large fractionof a cell’s mass (Table 2–2).small organic building blocksof the cellSUGARSFATTY ACIDSAMINO ACIDSNUCLEOTIDESlarger organic moleculesof the cellPOLYSACCHARIDES, GLYCOGEN,AND STARCH (IN PLANTS)FATS AND MEMBRANE LIPIDSPROTEINSNUCLEIC ACIDSFigure 2–17 Sugars, fatty acids, aminoacids, and nucleotides are the four mainfamilies of small organic moleculesin cells. They form the monomericbuilding blocks, or subunits, for largerorganic molecules, including most of themacromolecules and other molecularassemblies of the cell. Some, like the sugarsand the fatty acids, are also energy sources.

50 CHAPTER 2 Chemical Components of Cells

Figure 2–16 In aqueous solutions, the

concentration of hydroxyl (OH – ) ions

increases as the concentration of H 3 O +

(or H + ) ions decreases. The product of

the two values, [OH – ] x [H + ], is always 10 –14

(moles/liter) 2 . At neutral pH, [OH – ] = [H + ],

and both ions are present at 10 –7 M. Also

shown are examples of common solutions

along with their approximate pH values.

ACIDIC

[H + ]

moles/liter

pH

1 0

10 –1 1

10 –2 2

10 –3 3

10 –4 4

[OH – ]

moles/liter

10 –14

10 –13

10 –12

10 –11

10 –10

some solutions and their

pH values

battery acid (0.5)

stomach acid (1.5)

lemon juice (2.3), cola (2.5)

orange juice (3.5)

beer (4.5)

10 –5 5

10 –9

black coffee (5.0), acid rain (5.6)

10 –6 6

10 –8

urine (6.0), milk (6.5)

NEUTRAL

10 –7 7

10 –7

pure water (7.0)

10 –8 8

10 –6

sea water (8.0)

10 –9 9

10 –5

hand soap (9.5)

10 –10 10

10 –4

milk of magnesia (10.5)

BASIC

10 –11 11

10 –3

household ammonia (11.9)

10 –12 12

10 –2

non-phosphate detergent (12.0)

10 –13 13

10 –1

bleach (12.5)

10 –14 14

1

caustic soda (13.5)

QUESTION 2–5

A. Are there H 3 O + ions present in

pure water at neutral pH (i.e., at pH

= 7.0)? If so, how are they formed?

B. If they exist, what is the ratio

of H 3 O + ions to H 2 O molecules at

neutral pH? (Hint: the molecular

weight of water is 18, and 1 liter of

water weighs 1 kg.)

Molecules that accept protons when dissolved in water are called bases.

Just as the defining property of an acid is that it raises the concentration

of H 3 O + ions by donating a proton to a water molecule, so the defining

ECB5 n2.100-2.16

property of a base is that it raises the concentration of hydroxyl (OH – )

ions by removing a proton from a water molecule. Sodium hydroxide

(NaOH) is basic (the term alkaline is also used). NaOH is considered a

strong base because it readily dissociates in aqueous solution to form

Na + ions and OH – ions. Weak bases—which have a weak tendency to

accept a proton from water—however, are more important in cells. Many

biologically important weak bases contain an amino (NH 2 ) group, which

can generate OH – by taking a proton from water: –NH 2 + H 2 O → –NH

+ 3 +

OH – (see Panel 2–2, pp. 68–69).

Because an OH – ion combines with a proton to form a water molecule,

an increase in the OH – concentration forces a decrease in the H + concentration,

and vice versa (Figure 2–16). A pure solution of water contains

an equal concentration (10 –7 M) of both ions, rendering it neutral (pH 7).

The interior of a cell is kept close to neutral by the presence of buffers:

mixtures of weak acids and bases that will adjust proton concentrations

around pH 7 by releasing protons (acids) or taking them up (bases) whenever

the pH changes. This give-and-take keeps the pH of the cell relatively

constant under a variety of conditions.

SMALL MOLECULES IN CELLS

Having looked at the ways atoms combine to form small molecules and

how these molecules behave in an aqueous environment, we now examine

the main classes of small molecules found in cells and their biological

roles. Amazingly, we will see that a few basic categories of molecules,

formed from just a handful of different elements, give rise to all the

extraordinary richness of form and behavior displayed by living things.

A Cell Is Formed from Carbon Compounds

If we disregard water, nearly all the molecules in a cell are based on carbon.

Carbon is outstanding among all the elements in its ability to form

large molecules. Because a carbon atom is small and has four electrons

and four vacancies in its outer shell, it readily forms four covalent bonds

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