H. Lodish - Molecular Cell Biology (5ed, Freeman, 2003) (796244), страница 17
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With rare exceptions, onlythe L forms of amino acids are found in proteins. We discussthe properties of the covalent peptide bond that links aminoacids into long chains in Chapter 3.To understand the structures and functions of proteins,you must be familiar with some of the distinctive propertiesof the amino acids, which are determined by their sidechains. The side chains of different amino acids vary in size,shape, charge, hydrophobicity, and reactivity.
Amino acidscan be classified into several broad categories based primarily on their solubility in water, which is influenced by thepolarity of their side chains (Figure 2-13). Amino acids withpolar side chains are hydrophilic and tend to be on the surfaces of proteins; by interacting with water, they make proteins soluble in aqueous solutions and can form noncovalentinteractions with other water-soluble molecules. In contrast,amino acids with nonpolar side chains are hydrophobic; theyavoid water and often aggregate to help form the waterinsoluble cores of many proteins.
The polarity of amino acidside chains thus is responsible for shaping the final threedimensional structure of proteins.A subset of the hydrophilic amino acids are charged (ionized) at the pH (≈7) typical of physiological conditions (seeSection 2.3). Arginine and lysine are positively charged; aspartic acid and glutamic acid are negatively charged (theircharged forms are called aspartate and glutamate). Thesefour amino acids are the prime contributors to the overallcharge of a protein. A fifth amino acid, histidine, has an im-idazole side chain, which can shift from being positivelycharged to uncharged with small changes in the acidity ofits environment:CH2CNHHCCHHNCCCCH2HNHpH 5.8HNpH 7.8The activities of many proteins are modulated by shifts inenvironmental acidity through protonation of histidine sidechains.
Asparagine and glutamine are uncharged but havepolar side chains containing amide groups with extensivehydrogen-bonding capacities. Similarly, serine and threonineare uncharged but have polar hydroxyl groups, which alsoparticipate in hydrogen bonds with other polar molecules.The side chains of hydrophobic amino acids are insolubleor only slightly soluble in water.
The noncyclic side chainsof alanine, valine, leucine, isoleucine, and methionine consistentirely of hydrocarbons, except for the one sulfur atom inmethionine, and all are nonpolar. Phenylalanine, tyrosine,and tryptophan have large bulky aromatic side chains.In later chapters, we will see in detail how hydrophobicresidues line the surface of proteins that are embedded withinbiomembranes.Lastly, cysteine, glycine, and proline exhibit special rolesin proteins because of the unique properties of their sidechains.
The side chain of cysteine contains a reactivesulfhydryl group (OSH), which can oxidize to form a covalent disulfide bond (OSOSO) to a second cysteine:HNHCCH2COHNHCOCCH2SH HSSSNHCH2CHCONHCHCOCH2Regions within a protein chain or in separate chainssometimes are cross-linked through disulfide bonds. Disulfidebonds are commonly found in extracellular proteins, wherethey help stabilize the folded structure.
The smallest aminoacid, glycine, has a single hydrogen atom as its R group. Itssmall size allows it to fit into tight spaces. Unlike the othercommon amino acids, the side chain of proline bends aroundto form a ring by covalently bonding to the nitrogen atom(amino group) attached to the C. As a result, proline is veryrigid and creates a fixed kink in a protein chain, limiting howa protein can fold in the region of proline residues.2.2 • Chemical Building Blocks of Cells▲▲ FIGURE 2-12 Common structure of amino acids. The COO−carbon atom (C) of each amino acid is bonded to four chemicalgroups. The side chain, or R group, is unique to each type ofamino acid (see Figure 2-13).
Because the C in all amino acids,except glycine, is asymmetric, these molecules have two mirrorimage forms, designated L and D. Although the chemicalproperties of such optical isomers are identical, their biologicalactivities are distinct. Only L amino acids are found in proteins.COO−NH3+CαH39NH3+CαHRD isomerRL isomerHYDROPHOBIC AMINO ACIDSCOOH N3CCOOH N3HCCH3COOHH N3CHHCCH3CHH3CCOOCH3H N3CH2H3CCH3CCOOH N3HCCH2CH2CHCH2CH3HCOOH N3CCOOH N3HCCH2Valine(Val or V)Isoleucine(Ile or I)Methionine(Met or M)Acidic amino acidsH N3CCOOH N3HCH N3COOH N3HCCH2CH2CNHCH2CH2CHNHNH2CCH N3Histidine(His or H)CHCOOH3NCHHCOHCH2OHCH3Serine(Ser or S)Threonine(Thr or T)COOHH N3CH2Arginine(Arg or R)Tryptophan(Trp or W)COOCOOH N3COOH 2NCHCOOH3NSPECIAL AMINO ACIDSCOOH3NCCH2HCOOH N3CHH2CSHCysteine(Cys or C)HCOOHCH NCH22Glycine(Gly or G)CH2Proline(Pro or P)CHCH2CH2CCH2OCH 2NGlutamate(Glu or E)CHNHPolar amino acids with uncharged R groupsCH2NH2Lysine(Lys or K)HAspartate(Asp or D)CHNHCH2Tyrosine(Tyr or Y)COOCH2NH3Phenylalanine(Phe or F)CH2CH2CHOHCH2HCH2CCCOOBasic amino acidsCOO3NSLeucine(Leu or L)HYDROPHILIC AMINO ACIDSHHCH2CH3Alanine(Ala or A)COOAsparagine(Asn or N)OGlutamine(Gln or Q)▲ FIGURE 2-13 The 20 common amino acids used tobuild proteins.
The side chain (R group; red) determines thecharacteristic properties of each amino acid and is the basisfor grouping amino acids into three main categories: hydrophobic,hydrophilic, and special. Shown are the ionized forms that exist atthe pH (≈7) of the cytosol. In parentheses are the three-letter andone-letter abbreviations for each amino acid.40CHAPTER 2 • Chemical FoundationsSome amino acids are more abundant in proteins thanother amino acids. Cysteine, tryptophan, and methionine arerare amino acids; together they constitute approximately 5percent of the amino acids in a protein. Four amino acids—leucine, serine, lysine, and glutamic acid—are the most abundant amino acids, totaling 32 percent of all the amino acidresidues in a typical protein.
However, the amino acid composition of proteins can vary widely from these values.PURINESNH2CN1HC 2NH26HC 235C4CNN78 CH9N54HOOPhosphateHH23OHRibose1HHH32OH1HOCH24OHHOH5POHOCH2OOOHRiboseAdenosine 5-monophosphate(AMP)4HN178 CHC29CNH2N63N5C478 CH9CNNHHAdenine (A)Guanine (G)O(b)CN13CN5CPYRIMIDINESTwo types of chemically similar nucleic acids, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are the principalinformation-carrying molecules of the cell.
The monomersfrom which DNA and RNA are built, called nucleotides, allhave a common structure: a phosphate group linked by aphosphoester bond to a pentose (a five-carbon sugar molecule)that in turn is linked to a nitrogen- and carbon-containing ringstructure commonly referred to as a “base” (Figure 2-14a).
InRNA, the pentose is ribose; in DNA, it is deoxyribose (Figure2-14b). The bases adenine, guanine, and cytosine are foundin both DNA and RNA; thymine is found only in DNA, anduracil is found only in RNA.Adenine and guanine are purines, which contain a pair offused rings; cytosine, thymine, and uracil are pyrimidines,which contain a single ring (Figure 2-15). The bases are oftenabbreviated A, G, C, T, and U, respectively; these same singleletter abbreviations are also commonly used to denote theentire nucleotides in nucleic acid polymers.
In nucleotides,Adenine6NFive Different Nucleotides AreUsed to Build Nucleic Acids(a)O5OHOCH24HOHHHOHCHN3CO2412H2-Deoxyribose▲ FIGURE 2-14 Common structure of nucleotides.(a) Adenosine 5'-monophosphate (AMP), a nucleotide presentin RNA. By convention, the carbon atoms of the pentose sugarin nucleotides are numbered with primes. In natural nucleotides,the 1' carbon is joined by a linkage to the base (in this caseadenine); both the base (blue) and the phosphate on the 5'hydroxyl (red) extend above the plane of the furanose ring.(b) Ribose and deoxyribose, the pentoses in RNA and DNA,respectively.NH2C6CHN4HN35CHC2C5C61NOCH3N3CCHOHHUracil (U)2415CH6CHNHThymine (T)Cytosine (C)▲ FIGURE 2-15 Chemical structures of the principal basesin nucleic acids.
In nucleic acids and nucleotides, nitrogen 9 ofpurines and nitrogen 1 of pyrimidines (red) are bonded to the1 carbon of ribose or deoxyribose. U is only in RNA, and T isonly in DNA. Both RNA and DNA contain A, G, and C.the 1 carbon atom of the sugar (ribose or deoxyribose) isattached to the nitrogen at position 9 of a purine (N9) or atposition 1 of a pyrimidine (N1). The acidic character of nucleotides is due to the phosphate group, which under normalintracellular conditions releases a hydrogen ion (H), leaving the phosphate negatively charged (see Figure 2-14a).Most nucleic acids in cells are associated with proteins,which form ionic interactions with the negatively chargedphosphates.Cells and extracellular fluids in organisms contain smallconcentrations of nucleosides, combinations of a base and asugar without a phosphate.
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