Essential Cell Biology 5th edition
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.
- Page 33 and 34: ContentsxxxiGENETICS AS AN EXPERIME
- Page 35 and 36: CHAPTER ONE1Cells: The FundamentalU
- Page 37 and 38: Unity and Diversity of Cells3mechan
- Page 39 and 40: Unity and Diversity of Cells5nucleo
- Page 41 and 42: Cells Under the Microscope7The Inve
- Page 43 and 44: Cells Under the Microscope9cytoplas
- Page 45 and 46: The Prokaryotic Cell110.2 mm(200 µ
- Page 47 and 48: The Prokaryotic Cell13SUPER-RESOLUT
- Page 49 and 50: The Prokaryotic Cell15(A)HSV10 µmF
- Page 51 and 52: The Eukaryotic Cell17nucleusnuclear
- Page 53 and 54: The Eukaryotic Cell19chloroplastsch
- Page 55 and 56: The Eukaryotic Cell21lysosomenuclea
- Page 57 and 58: The Eukaryotic Cell23duplicatedchro
- Page 59 and 60: PANEL 1-2 CELL ARCHITECTURE 25ANIMA
- Page 61 and 62: Model Organisms27(C)(D)(A) (B) (E)
- Page 63 and 64: Model Organisms29Figure 1-34 Drosop
- Page 65 and 66: Model Organisms31INTRODUCE FRAGMENT
- Page 67 and 68: Model Organisms33(A) (B) (C)50 µm
- Page 69 and 70: Model Organisms35TABLE 1-2 SOME MOD
- Page 71 and 72: Questions37• Free-living, single-
- Page 73 and 74: CHAPTER TWO2Chemical Components of
- Page 75 and 76: Chemical Bonds41number of protons.
- Page 77 and 78: Chemical Bonds43+atoms+SHARING OFEL
- Page 79 and 80: Chemical Bonds45Four electrons can
- Page 81 and 82: Chemical Bonds47Because of the favo
- Page 83: Chemical Bonds49Some Polar Molecule
- Page 87 and 88: Small Molecules in Cells53optical i
- Page 89 and 90: Small Molecules in Cells55can be re
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- Page 93 and 94: Macromolecules in Cells59Figure 2-3
- Page 95 and 96: Macromolecules in Cells61ultracentr
- Page 97 and 98: Macromolecules in Cells63BBAAthe su
- Page 99 and 100: Questions65KEY TERMSacid electrosta
- Page 101 and 102: 67C-O COMPOUNDSMany biological comp
- Page 103 and 104: 69WATER AS A SOLVENTMany substances
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- Page 107 and 108: 73α AND β LINKSThe hydroxyl group
- Page 109 and 110: 75LIPID AGGREGATESFatty acids have
- Page 111 and 112: 77ACIDIC SIDE CHAINSNONPOLAR SIDE C
- Page 113 and 114: 79NOMENCLATUREThe names can be conf
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- Page 123 and 124: Free Energy and Catalysis89thermody
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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