《生物化学》课程教学资源（书籍文献）英文生化教材 Lippincott’s Illustrated Reviews Biochemistry, 5th 2010, Richard A. Harvey, PhD, Denise R. Ferrier, PhD

1.Amino Acids effect,is the result of the hydrophobicity of the nonpolar R-groups. rups thus hterr ot The Howe ment,such as a membrane,the nonpolar R-groups are found on the outside surface of the protein. pia env interactions in structure is discussed on p.19. mino acid Sickle cell anemia nbrane protein in the B subunit of hemoglobin (see p.36). Figure 1.4 2.Pi:rh amino acids in that proline' mary)amino group.It is frequently referred to as an imino acid dary amino The unique geometry of proline contributes to th 0026. COOH OOH B.Amino acids with uncharged polar side chains -C-H HjN- CH Proline Alanine pH(see Figure 1.3).Serine,threonine,and tyrosine each contain a polar hydroxyl group that can participate in hydrogen bond formatior Figure 1.5 (Figure 1.6 Comparison of the secondary of ine also participate in hydrogn bonds. COOH can become oxidized to form a dimer,cystine,which contains a 'HN-C-H bond (-S-S-).(See p.19 for Tyrosine Many extracellular proteins are stabilized by disulfide bonds.Albumin,a blood protein tha unctions as a transporter for a variety of 2.Side chains as sites of attachment for other compounds:The ure 1.6 polar hydr onine.and.rare oond between the group.In addition,the amide group of asparagine,as well a s the cermeorhreonine.canse ande cnains in glycoprote ins as ee p. 165

effect, is the result of the hydro phobicity of the nonpolar R-groups, which act much like droplets of oil that coalesce in an aqueous environment. The nonpolar R-groups thus fill up the interior of the folded protein and help give it its three-dimensional shape. However, for proteins that are located in a hydrophobic environ￾ment, such as a membrane, the nonpolar R-groups are found on the outside surface of the protein, interacting with the lipid envi￾ronment (see Figure 1.4). The importance of these hydrophobic interactions in stabilizing protein structure is discussed on p. 19. Sickle cell anemia, a sickling disease of red blood cells, results from the substitution of polar glutamate by nonpolar valine at the sixth position in the β subunit of hemoglobin (see p. 36). 2. Proline: Proline differs from other amino acids in that proline’s side chain and α-amino N form a rigid, five-membered ring struc￾ture (Figure 1.5). Proline, then, has a secondary (rather than a pri￾mary) amino group. It is frequently referred to as an imino acid. The unique geometry of proline contributes to the formation of the fibrous structure of collagen (see p. 45), and often interrupts the α-helices found in globular proteins (see p. 26). B. Amino acids with uncharged polar side chains These amino acids have zero net charge at neutral pH, although the side chains of cysteine and tyrosine can lose a proton at an alkaline pH (see Figure 1.3). Serine, threonine, and tyrosine each contain a polar hydroxyl group that can participate in hydrogen bond formation (Figure 1.6). The side chains of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also participate in hydrogen bonds. 1. Disulfide bond: The side chain of cysteine contains a sulf hydryl group (–SH), which is an important component of the active site of many enzymes. In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (–S–S–). (See p. 19 for a further discussion of disulfide bond formation.) Many extracellular proteins are stabilized by disulfide bonds. Albumin, a blood protein that functions as a transporter for a variety of molecules, is an example. 2. Side chains as sites of attachment for other compounds: The polar hydroxyl group of serine, threonine, and, rarely, tyrosine, can serve as a site of attachment for structures such as a phosphate group. In addition, the amide group of asparagine, as well as the hydroxyl group of serine or threonine, can serve as a site of attach￾ment for oligosaccharide chains in glycoproteins (see p. 165). Figure 1.6 Hydrogen bond between the phenolic hydroxyl group of tyrosine and another molecule containing a carbonyl group. C +H3N COOH CH2 Tyrosine Hydrogen bond O C O H H Carbonyl group 4 1. Amino Acids Figure 1.4 Location of nonpolar amino acids in soluble and membrane proteins. Cell membrane Polar amino acids ( ) cluster on the surface of soluble proteins. Cell Nonpolar amino acids ( ) cluster on the surface of membrane proteins. Nonpolar amino acids ( ) cluster in the interior of soluble proteins. Soluble protein Membrane protein Figure 1.5 Comparison of the secondary amino group found in proline with the primary amino group found in other amino acids, such as alanine. C +H3N COOH H CH3 Alanine COOH H Proline C CH2 +H2N H2C Primary amino group Secondary amino group CH2 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 4

Il.Structure of the Amino Acids C.Amino acids with acidic side chains The amino acids aspartic and glutamic acid are proton donors.At 1Unique first letter: ate or alutamate to e asize that these acids are negatively charged at physiologic pH(see Figure 1.3). : D.Amino acids with basic side chains 13.At h ionized and positively charged.In contrast,histidine is weakly basic idne is incorporated environment provided by the polypeptide chans of the protein.This hreonine is an important property of histidine that contributes to the role it plays in the functioning of proteins such as hemoglobin (see p.31). 3Similar sounding names: E.Abbreviations and symbols for commonly occurring amino acids ArgR (aRginine (e Each aminc acid name has =D and a one-letter mined by the following rules: vr Y (tYrosine" 4Letter close to initial letter: 2 Most co mino Asx B(near A) mon of these amino acids receives this letter as its symbol.For example,glycine is more common than glutamate,so G glycine Lys K( d amino acid 4.Letter close to initial letter:For the remaining amino acids a one letter symbol is assigned that is as close in the alphabet as possi Figure 1.7 ble to the initia terof the amino acid.for example,K-lysine Furthermore, assigne amacd or glutamine.and is assigned to an unidentified amino acid. F.Optical properties of amino acids The a-carbon of an amino acid is attached to four different chemica H has two hydog L-Alanine have an asyr metric center at the a-caon can designated D and L,that are mirror images of each other(Figure Figure1.8 omers. is a otics and in plant and bacterial cell walls.(See p.253 fora discus- 8aeatromsgdsane sion of D-amino acid metabolism.)

C. Amino acids with acidic side chains The amino acids aspartic and glutamic acid are proton donors. At physiologic pH, the side chains of these amino acids are fully ionized, containing a negatively charged carboxylate group (–COO– ). They are, therefore, called aspartate or glutamate to emphasize that these amino acids are negatively charged at physiologic pH (see Figure 1.3). D. Amino acids with basic side chains The side chains of the basic amino acids accept protons (see Figure 1.3). At physiologic pH the side chains of lysine and arginine are fully ionized and positively charged. In contrast, histidine is weakly basic, and the free amino acid is largely uncharged at physiologic pH. However, when histidine is incorporated into a protein, its side chain can be either positively charged or neutral, depending on the ionic environment provided by the polypeptide chains of the protein. This is an important property of histidine that contributes to the role it plays in the functioning of proteins such as hemoglobin (see p. 31). E. Abbreviations and symbols for commonly occurring amino acids Each amino acid name has an associated three-letter abbreviation and a one-letter symbol (Figure 1.7). The one-letter codes are deter￾mined by the following rules: 1. Unique first letter: If only one amino acid begins with a particular letter, then that letter is used as its symbol. For example, I = isoleucine. 2. Most commonly occurring amino acids have priority: If more than one amino acid begins with a particular letter, the most com￾mon of these amino acids receives this letter as its symbol. For example, glycine is more common than glutamate, so G = glycine. 3. Similar sounding names: Some one-letter symbols sound like the amino acid they represent. For example, F = phenylalanine, or W = tryptophan (“twyptophan” as Elmer Fudd would say). 4. Letter close to initial letter: For the remaining amino acids, a one￾letter symbol is assigned that is as close in the alphabet as possi￾ble to the initial letter of the amino acid, for example, K = lysine. Furthermore, B is assigned to Asx, signifying either aspartic acid or asparagine, Z is assigned to Glx, signifying either glutamic acid or glutamine, and X is assigned to an unidentified amino acid. F. Optical properties of amino acids The α-carbon of an amino acid is attached to four different chemical groups and is, therefore, a chiral or optically active carbon atom. Glycine is the exception because its α-carbon has two hydrogen substituents and, therefore, is optically inactive. Amino acids that have an asymmetric center at the α-carbon can exist in two forms, designated D and L, that are mirror images of each other (Figure 1.8). The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers. All amino acids found in proteins are of the L-configuration. However, D-amino acids are found in some antibi￾otics and in plant and bacterial cell walls. (See p. 253 for a discus￾sion of D-amino acid metabolism.) Figure 1.7 Abbreviations and symbols for the commonly occurring amino acids. Cysteine = Cys = C Histidine = His = H Isoleucine = Ile = I Methionine = Met = M Serine = Ser = S Valine = Val = V Alanine = Ala = A Glycine = Gly = G Leucine = Leu = L Proline = Pro = P Threonine = Thr = T Arginine = Arg = R (“aRginine”) Asparagine = Asn = N (contains N) Aspartate = Asp = D ("asparDic") Glutamate = Glu = E ("glutEmate") Glutamine = Gln = Q (“Q-tamine”) Phenylalanine = Phe = F (“Fenylalanine”) Tyrosine = Tyr = Y (“tYrosine”) Tryptophan = Trp = W (double ring in the molecule) Aspartate or = Asx = B (near A) asparagine Glutamate or = Glx = Z glutamine Lysine = Lys = K (near L) Undetermined = X amino acid Unique first letter: Most commonly occurring amino acids have priority: Similar sounding names: Letter close to initial letter: 1 2 3 4 Figure 1.8 D and L forms of alanine are mirror images. H3C HOOC D-Alanine H C NH3 + CH3 COOH L-Alanine H C + H3N II. Structure of the Amino Acids 5 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 5

6 1.Amino Acids IlI.ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS 8ead8on28eaoio08asansaaaeaea8te and basic amino acids contains an ionizable group in its side chain acids combine proton donors and bases as proton acceptors.Acids (or bases) described as'"weak"ionize to only a limited extent.The concentration of 8rotogsnaaueoussol ion is expressed as pH.wh ere pr tion and concen aonota8eakacaHanasc0ngaeba9e04 is described by the Henderson-Hasselbalch equation. OH H20 A.Derivation of the equation CH.COOM Consider the release of a proton by a weak acid represented by HA: acetfCcia.Ha t（acetate,A + proton salt form or conjugate base Buffer region 10 Ka =t] 05 06 o the pH both sides of the equation,multiplying both sides of the equation by Figure 1.9 h64easn688agapk-ogKoowa urve of acetic acid. pH=k+6网阁 B.Buffers A buffer is a solutio with solution,A Acan neutralize it,in the process being converted to HA.If a can neutra I, hut conjugate acid base pair can still serve as an effective buffer when the pH of a solution is within approximately +1 pH unit of the pKa.If the

III. ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α-amino groups. In addition, each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers. Recall that acids may be defined as proton donors and bases as proton acceptors. Acids (or bases) described as “weak” ionize to only a limited extent. The concentration of protons in aqueous solution is expressed as pH, where pH = log 1/[H+] or –log [H+]. The quantitative relationship between the pH of the solu￾tion and concentration of a weak acid (HA) and its con jugate base (A– ) is described by the Henderson-Hasselbalch equation. A. Derivation of the equation Consider the release of a proton by a weak acid represented by HA: HA →← H+ + A– weak proton salt form acid or conjugate base The “salt” or conjugate base, A– , is the ionized form of a weak acid. By definition, the dissociation constant of the acid, Ka, is [Note: The larger the Ka, the stronger the acid, because most of the HA has dissociated into H+ and A– . Conversely, the smaller the Ka, the less acid has dissociated and, therefore, the weaker the acid.] By solving for the [H+] in the above equation, taking the logarithm of both sides of the equation, multiplying both sides of the equation by –1, and substituting pH = –log [H+ ] and pKa = –log Ka, we obtain the Henderson-Hasselbalch equation: B. Buffers A buffer is a solution that resists change in pH following the addition of an acid or base. A buffer can be created by mixing a weak acid (HA) with its conjugate base (A– ). If an acid such as HCl is then added to such a solution, A– can neutralize it, in the process being converted to HA. If a base is added, HA can neutralize it, in the process being converted to A– . Maximum buffering capacity occurs at a pH equal to the pKa, but a conjugate acid/base pair can still serve as an effective buffer when the pH of a solution is within approximately ±1 pH unit of the pKa. If the 6 1. Amino Acids Figure 1.9 Titration curve of acetic acid. 03 4567 0 0.5 1.0 pH Equivalents OH– added Buffer region CH3COOH CH3COO– H20 FORM I (acetic acid, HA) FORM II (acetate, A– ) [I] = [II] pKa = 4.8 OH– H+ [I] > [II] [II] > [I] pH pKa log [A–] [HA] + Ka [A–] [HA] [H+] 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 6

Ill.Acidic and Basic Properties of Amino Acids OH H2O OH H2O THN-COOH HN-OO HN-COO CH. FORMI pK1=2.3 FORM II pK2=9.1 FORM Net charge =+1 Net charge=-1 BaCl8i0anenaidc.erhnalandbassotos iu aC)nd g a to5.8.with maximum buffering at pH 4.8.At pH values less than ues greater than the pKa the protonated base form ninant spe C.Titration of an amino acid 1.Dissociation of the carboxyl group:The titration curve of an amino acid can be analyzed in the same way as described for acetic acid. nsider alanine,for exa contains bo these an ups are protonated (shown in Figure 1.10).As the the solution is raised,the-COOH group of Form I can dissociate lar fo n of the molecule (see Figure 1.10).This form,also called a zwitterion,is h9g8exacomoianethtathasancwealtno创 2.Application of the Henderson-Hasselbalch equation:The dissoci- ation constant of the carboxyl group of an amino acid is called K1. use the e conta is a se d titra same way as described for acetic acid: K,=H四 7ofalhnpot see Fio rearranged and converted to its logarithmic form to yield:

amounts of HA and A– are equal, the pH is equal to the pKa. As shown in Figure 1.9, a solution containing acetic acid (HA = CH3 –COOH) and acetate (A– = CH3 –COO– ) with a pKa of 4.8 resists a change in pH from pH 3.8 to 5.8, with maximum buffering at pH 4.8. At pH values less than the pKa, the protonated acid form (CH3 – COOH) is the predominant species. At pH values greater than the pKa, the deprotonated base form (CH3 – COO– ) is the predominant species in solution. C. Titration of an amino acid 1. Dissociation of the carboxyl group: The titration curve of an amino acid can be analyzed in the same way as described for acetic acid. Consider alanine, for example, which contains both an α-carboxyl and an α-amino group. At a low (acidic) pH, both of these groups are proton ated (shown in Figure 1.10). As the pH of the solution is raised, the – COOH group of Form I can dissociate by donating a proton to the medium. The release of a proton results in the formation of the carboxylate group, – COO– . This structure is shown as Form II, which is the dipolar form of the molecule (see Figure 1.10). This form, also called a zwitterion, is the isoelectric form of alanine, that is, it has an overall (net) charge of zero. 2. Application of the Henderson-Hasselbalch equation: The dissoci￾ation constant of the carboxyl group of an amino acid is called K1, rather than Ka, because the molecule contains a second titratable group. The Henderson-Hasselbalch equation can be used to analyze the dissociation of the carboxyl group of alanine in the same way as described for acetic acid: where I is the fully protonated form of alanine, and II is the iso￾electric form of alanine (see Figure 1.10). This equation can be re arranged and converted to its logarithmic form to yield: III. Acidic and Basic Properties of Amino Acids 7 Figure 1.10 Ionic forms of alanine in acidic, neutral, and basic solutions. COOH FORM I Alanine in acid solution (pH less than 2) Net charge = +1 CH3 C +H3N H COO– FORM II Alanine in neutral solution (pH approximately 6) Net charge = 0 (isoelectric form) CH3 C +H3N H COO– FORM III Alanine in basic solution (pH greater than 10) Net charge = –1 CH3 H2N C H OH H20 – H+ OH H20 – H+ pK1 = 2.3 pK2 = 9.1 K1 [II] [I] [H+] 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 7

1.Amino Acids H=K:+log 3 Dissociation of the amin up:The second titratable。 a much weaker acid than the-COOH group and,therefore,has a much taionocontant 2.[Note:Its spKa is therefore HA-O (see Figure 1.10). CHa th FORM III .Ke e:s and ocatonofpol 1.10.Each titratable group has a pK that is numerically equal to the pH at which exactly one half of the protons have beer he n group (-NHa")is pK2. 15 pl=5.7 up,it isp ble to calculate the complete titration curve of a weak acid.Figure =2 change in pH that occ urs aur gthe addition copleeyaepro8naiedioeaaNouehetb8 egion -COOH/-COO-pa around nk buffer in the region around pK2. +HgN-C b.When pH= (2. CH CH nd ll of a FORMI FORM II the pH is equal to pK2(9.1),equal amounts of Forms ll and Ill are present in solution. Figure1.11 c.Isoelectric po DH The titration curve of alanine. as the dipolar Form l in which the aming and carboxl are ionized,but the net charge is zero.The isoelectric point ne pH at whicn an amino acid is el has only two dissociable hydrogens(one from the a-carboxyl and one from the to the pH at which the Forml(with a net charge of zero)pre dominates,and at which there are also equal amounts of Forms I(net charge of+1)and Il (net charge of-1)

3. Dissociation of the amino group: The second titratable group of alanine is the amino (– NH3 +) group shown in Figure 1.10. This is a much weaker acid than the – COOH group and, therefore, has a much smaller dissociation constant, K2. [Note: Its pKa is therefore larger.] Release of a proton from the protonated amino group of Form II results in the fully deprotonated form of alanine, Form III (see Figure 1.10). 4. pKs of alanine: The sequential dissociation of protons from the carboxyl and amino groups of alanine is summarized in Figure 1.10. Each titratable group has a pKa that is numer ically equal to the pH at which exactly one half of the protons have been removed from that group. The pKa for the most acidic group (–COOH) is pK1, whereas the pKa for the next most acidic group (– NH3 +) is pK2. 5. Titration curve of alanine: By applying the Hender son￾Hasselbalch equation to each dissociable acidic group, it is possi￾ble to calculate the complete titration curve of a weak acid. Figure 1.11 shows the change in pH that occurs during the addition of base to the fully protonated form of alanine (I) to produce the completely deprotonated form (III). Note the following: a. Buffer pairs: The – COOH/– COO– pair can serve as a buffer in the pH region around pK1, and the – NH3 +/– NH2 pair can buffer in the region around pK2. b. When pH = pK: When the pH is equal to pK1 (2.3), equal amounts of Forms I and II of alanine exist in solution. When the pH is equal to pK2 (9.1), equal amounts of Forms II and III are present in solution. c. Isoelectric point: At neutral pH, alanine exists predominantly as the dipolar Form II in which the amino and carboxyl groups are ionized, but the net charge is zero. The isoelectric point (pI) is the pH at which an amino acid is electrically neutral, that is, in which the sum of the positive charges equals the sum of the negative charges. For an amino acid, such as alanine, that has only two dissociable hydrogens (one from the α-carboxyl and one from the α-amino group), the pI is the average of pK1 and pK2 (pI = [2.3 + 9.1]/2 = 5.7, see Figure 1.11). The pI is thus midway between pK1 (2.3) and pK2 (9.1). pI corresponds to the pH at which the Form II (with a net charge of zero) pre￾dominates, and at which there are also equal amounts of Forms I (net charge of +1) and III (net charge of –1). 8 1. Amino Acids Figure 1.11 The titration curve of alanine. 0 2 4 6 8 10 0 1.0 2.0 pH Equivalents OH– added pK2 = 9.1 [II] = [III] 0.5 1.5 pK1 = 2.3 [I] = [II] pI = 5.7 Region of buffering Region of buffering 0 2 4 0 p [II] = [III] Region of buffering 6 8 10 pH pK2 = 9. = 2.3 p COOH FORM I CH3 C +H3N H COO– FORM III CH3 H2N C H COO– FORM II CH3 C +H3N H pH pK1 log [II] [I] + 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 8