II.Acidic and Basic Properties of Amino Acids Separation of plasma proteins by charge typically ABICARBONATE AS A BUFFER ●pH=pK+ogH8 the positive electrode at a rate determined by ·& ty pattern are suggestiv ● in respiratory acidos QereLhaegropHbothanachediotheacaton additional pochains. entially charo C02+H20=H2C03=H+HC03 or a base are defined as amphoteric,and are referred to as ampholytes (amphoteric electrolytes) BDRUG ABSORPTION D.Other applications of the Henderson-Hasselbalch equation ●pH=pk+log8gh me p dc now ●&,a ple,in the bicarbonate buffer system the Henderson-Hasselbalch 9Cotioneihoshtsnhebcatonaeonconcentalion The eque asic drugs.For example.most drugs are either weak acids or weak bases(Figure 1.12B).Acidic drugs(HA)release a proton(H*),caus- OMAC ing a charged anion(A)to form HA2 H*+A- Weak bases (BH')can also release a H'.However.the protonated form of basic drugs is usually charged,and the loss of a proton pro- duces the uncharged base (B) BH2 B+H d ncha meate through membranes and A-cannot.For a weak base.such as morphine.the uncharged orm.B. ates through the cell he effec ve c BLOO mined by the relative concentrations of the charged and uncharged forms.The ratio between the two forms is determined by the pH at the site of nd by the stre gth of the wea acid or 1.12 The ure nde -Hasselbalch drug is found on either side of a membrane that separates two com- s in ot HCO trations H,for example,the stomach (pH 1.0-1.5) 4. or B.the ionic forms of drugs
Separation of plasma proteins by charge typically is done at a pH above the pI of the major proteins, thus, the charge on the proteins is negative. In an electric field, the proteins will move toward the positive electrode at a rate determined by their net negative charge. Variations in the mobility pattern are suggestive of certain diseases. 6. Net charge of amino acids at neutral pH: At physiologic pH, amino acids have a negatively charged group (– COO–) and a positively charged group (– NH3 +), both attached to the α-carbon. [Note: Glutamate, aspartate, histidine, arginine, and lysine have additional potentially charged groups in their side chains.] Substances, such as amino acids, that can act either as an acid or a base are defined as amphoteric, and are referred to as ampholytes (amphoteric electrolytes). D. Other applications of the Henderson-Hasselbalch equation The Henderson-Hasselbalch equation can be used to calculate how the pH of a physiologic solution responds to changes in the concentration of a weak acid and/or its corresponding “salt” form. For example, in the bicarbonate buffer system, the Henderson-Hasselbalch equation predicts how shifts in the bicarbonate ion concentration, [HCO3 – ], and CO2 influence pH (Figure 1.12A). The equation is also useful for calculating the abundance of ionic forms of acidic and basic drugs. For example, most drugs are either weak acids or weak bases (Figure 1.12B). Acidic drugs (HA) release a proton (H+), causing a charged anion (A– ) to form. HA H+ + A– Weak bases (BH+) can also release a H+. However, the protonated form of basic drugs is usually charged, and the loss of a proton produces the uncharged base (B). BH+ B + H+ A drug passes through membranes more readily if it is uncharged. Thus, for a weak acid such as aspirin, the uncharged HA can permeate through membranes and A– cannot. For a weak base, such as morphine, the uncharged form, B, penetrates through the cell membrane and BH+ does not. Therefore, the effective concentration of the permeable form of each drug at its absorption site is determined by the relative concentrations of the charged and uncharged forms. The ratio between the two forms is determined by the pH at the site of absorption, and by the strength of the weak acid or base, which is represented by the pKa of the ionizable group. The Henderson-Hasselbalch equation is useful in determining how much drug is found on either side of a membrane that separates two compartments that differ in pH, for example, the stomach (pH 1.0–1.5) and blood plasma (pH 7.4). →← →← Figure 1.12 The Henderson-Hasselbalch equation is used to predict: A, changes in pH as the concentrations of HCO3 – or CO2 are altered; or B, the ionic forms of drugs. H2CO3 HCO3 - H+ CO2 + H2O + BICARBONATE AS A BUFFER An increase in HCO3 – causes the pH to rise. Pulmonary obstruction causes an increase in carbon dioxide and causes the pH to fall, resulting in respiratory acidosis. pH = pK + log [HCO3 – ] [CO2] DRUG ABSORPTION At the pH of the stomach (1.5), a drug like aspirin (weak acid, pK = 3.5) will be largely protonated (COOH) and, thus, uncharged. Uncharged drugs generally cross membranes more rapidly than charged molecules. pH = pK + log [Drug-H] [Drug– ] A B A HA - Lipid membrane LUMEN OF STOMACH STOMACH LUNG ALVEOLI BLOOD H+ H+ H+ A HA - H+ III. Acidic and Basic Properties of Amino Acids 9 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 9
10 1.Amino Acids ALinked concept boxes IV.CONCEPT MAPS Amino acids can d todrstandng of theseconadv Release H des the student with ng is a g series of biochemical concept maps to graphically illustrate relationships ninamopss-linked ideas presented in a chapter,and to show how the informatio archic fashion,with the most inclusive,most general concepts at the top is produced by- so the student t can readily find the best ways ntegrate new information into knowledge they already possess. ads to→ A.How is a concept map constructed? 1.Concept boxes and links:Educators define concepts as"per ceived regularities in events or objects."In our biochemical maps, is consumed by- concepts include abs energy),pro cepts are prioritized with the central idea positioned at the top of Concepts cross-linkec rawnohscates the to other boo in the bet Lippincott Series cept boxes to show which are related.The label on the line lationship between two concepts.tes me crea should be read (Figure 1.14). 2.Cross-links:Unlike linear flow ch relationships between ideas represented in different parts of the or en the map othe links can thus identify concepts that are central to more than one discipline,empowering students to be effective in clinical situa 2 the United States M dical petween facts.in contrast to within inear text. V.CHAPTER SUMMARY oup is dissociated.forming the nega tonated(-NHa').Each amino acid also contains one of 20 distinctive
IV. CONCEPT MAPS Students sometimes view biochemistry as a blur of facts or equations to be memorized, rather than a body of concepts to be understood. Details provided to enrich understanding of these concepts inadvertently turn into distractions. What seems to be missing is a road map—a guide that provides the student with an intuitive understanding of how various topics fit together to make sense. The authors have, therefore, created a series of biochemical concept maps to graphically illustrate relationships between ideas presented in a chapter, and to show how the information can be grouped or organized. A concept map is, thus, a tool for visualizing the connections between concepts. Material is represented in a hierarchic fashion, with the most inclusive, most general concepts at the top of the map, and the more specific, less general concepts arranged beneath. The concept maps ideally function as templates or guides for organizing information, so the student can readily find the best ways to integrate new information into knowledge they already possess. A. How is a concept map constructed? 1. Concept boxes and links: Educators define concepts as “perceived regularities in events or objects.” In our biochemical maps, concepts include abstractions (for example, free energy), processes (for example, oxidative phosphorylation), and compounds (for example, glucose 6-phosphate). These broadly defined concepts are prioritized with the central idea positioned at the top of the page. The concepts that follow from this central idea are then drawn in boxes (Figure 1.13A). The size of the type indicates the relative importance of each idea. Lines are drawn between concept boxes to show which are related. The label on the line defines the relationship between two concepts, so that it reads as a valid statement, that is, the connection creates meaning. The lines with arrowheads indicate in which direction the connection should be read (Figure 1.14). 2. Cross-links: Unlike linear flow charts or outlines, concept maps may contain cross-links that allow the reader to visualize complex relationships between ideas represented in different parts of the map (Figure 1.13B), or between the map and other chapters in this book or companion books in the series (Figure 1.13C). Crosslinks can thus identify concepts that are central to more than one discipline, empowering students to be effective in clinical situations, and on the United States Medical Licensure Exam ination (USMLE) or other examinations, that bridge disciplinary boundaries. Students learn to visually perceive nonlinear relationships between facts, in contrast to cross-referencing within linear text. V. CHAPTER SUMMARY Each amino acid has an α-carboxyl group and a primary α-amino group (except for proline, which has a secondary amino group). At physiologic pH, the α-carboxyl group is dissociated, forming the negatively charged carboxylate ion (– COO– ), and the α-amino group is protonated (– NH3 +). Each amino acid also contains one of 20 distinctive 10 1. Amino Acids Figure 1.13 Symbols used in concept maps. Amino acids (fully protonated) Release H+ can A B Linked concept boxes Microbiology Lippincott's Illustrated Reviews Protein turnover Degradation of body protein Synthesis of body protein is produced by is consumed by Amino acid pool Amino acid pool leads to Concepts cross-linked within a map C Concepts cross-linked to other chapters and to other books in the Lippincott Series . . . how the protein folds into its native conformation . . . how altered protein folding leads to prion disease, such as CreutzfeldtJakob disease Simultaneous synthesis and degradation Structure of Proteins 2 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 10
V.Chapter Summary Amino acids are composed of when protonated can a-Carboxyl group a-Amino group Side chains Release H' (-COOH) -NH2) (20 different ones) pn9aoeg0pR2 grouped as Weak acids Henderso polar Buffering capacity ent e inte pH=pKa when [HA]=[A] 82 roteins,mos hus,the how the the role that the cid play
V. Chapter Summary 11 Figure 1.14 Key concept map for amino acids. Deprotonated (COO– ) at physiologic pH On the outside of proteins that function in an aqueous environment and in the interior of membrane-associated proteins In the interior of proteins that function in an aqueous environment and on the surface of proteins (such as membrane proteins) that interact with lipids Weak acids Release H+ pH = pKa when [HA] = [A–] Buffering occurs ±1 pH unit of pKa Buffering capacity Maximal buffer when pH = pKa Protonated (NH3 + ) at physiologic pH described by grouped as and act as is is In proteins, most α-COO– and α-NH3 + of amino acids are combined through peptide bonds. Therefore, these groups are not available for chemical reaction. Thus, the chemical nature of the side chain determines the role that the amino acid plays in a protein, particularly . . . Nonpolar side chains Alanine Glycine Isoleucine Leucine Methionine Phenylalanine Proline Tryptophan Valine Uncharged polar side chains Asparagine Cysteine Glutamine Serine Threonine Tyrosine Henderson-Hasselbalch equation: [A–] [HA] Amino acids Side chain dissociates to –COO– at physiologic pH Side chain is protonated and generally has a positive charge at physiologic pH characterized by characterized by found found found found predicts predicts predicts predicts Acidic side chains Aspartic acid Glutamic acid Basic side chains Arginine Histidine Lysine α-Carboxyl group (–COOH) α-Amino group (–NH2) Side chains (20 different ones) are composed of when protonated can . . . how the protein folds into its native conformation. Structure of Proteins 2 pH = pKa + log 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 11
12 1.Amino Acids side chains attached to the caon atom.The chemical nature of this side chain determines the function of uncharged polar,acidic.or basic.All free amino acids.plus charged amino acids in peptide chains.can serve as buffers.The quantitative relationship between the pH of a solution and the concentration of a weak acid (HA)and its conjugate base (A)is described by the Henderson-Hasselbalch equation.Buffering occurs within +1pH unit of the p -carbon of each amin acid (excep our a oups a e,a chira eins synthesized by the human body Study Questions Choose the ONE correct answer. 1.1 The letters A through E designate certain regions on is correct? Correct answer =C.C represents the isoelectri ay between p 05 tmaemgmbier,8 where ine is 24 B.Point Brepresents a region of minimal buffering. C.Point C represents the region where the net charge D.Pg2Nnes ents the pK of glycine's carboxyl Epoelorgce 1.2 Which one of the following statements conceming the pepti A Th amino group roup)
Correct answer = C. C represents the isoelectric point or pI, and as such is midway between pK1 and pK2 for this monoamino monocarboxylic acid. Glycine is fully protonated at Point A. Point B represents a region of maximum buffering, as does Point D. Point E represents the region where glycine is fully deprotonated. Correct answer = D. The two cysteine residues can, under oxidizing conditions, form a disulfide bond. Glutamine’s 3-letter abbreviation is Gln. Proline (Pro) contains a secondary amino group. Only one (Arg) of the seven would have a positively charged side chain at pH 7. Correct answer = negative electrode. When the pH is less than the pI, the charge on glycine is positive because the α-amino group is fully protonated. (Recall that glycine has H as its R group). 12 1. Amino Acids side chains attached to the α-carbon atom. The chemical nature of this side chain determines the function of an amino acid in a protein, and provides the basis for classification of the amino acids as nonpolar, uncharged polar, acidic, or basic. All free amino acids, plus charged amino acids in peptide chains, can serve as buffers. The quantitative relationship between the pH of a solution and the concentration of a weak acid (HA) and its con jugate base (A–) is described by the Henderson-Hasselbalch equation. Buffering occurs within ±1pH unit of the pKa, and is maximal when pH = pKa, at which [A– ] = [HA]. The α-carbon of each amino acid (except glycine) is attached to four different chemical groups and is, therefore, a chiral or optically active carbon atom. Only the L-form of amino acids is found in proteins synthesized by the human body. Study Questions Choose the ONE correct answer. 1.1 The letters A through E designate certain regions on the titration curve for glycine (shown below). Which one of the following statements concerning this curve is correct? A. Point A represents the region where glycine is deprotonated. B. Point B represents a region of minimal buffering. C. Point C represents the region where the net charge on glycine is zero. D. Point D represents the pK of glycine’s carboxyl group. E. Point E represents the pI for glycine. 1.2 Which one of the following statements concerning the peptide shown below is correct? Gly-Cys-Glu-Ser-Asp-Arg-Cys A. The peptide contains glutamine. B. The peptide contains a side chain with a secondary amino group. C. The peptide contains a majority of amino acids with side chains that would be positively charged at pH 7. D. The peptide is able to form an internal disulfide bond. 1.3 Given that the pI for glycine is 6.1, to which electrode, positive or negative, will glycine move in an electric field at pH 2? Explain. 0 2 4 6 8 10 0 1.0 2.0 pH Equivalents OH– added 0.5 1.5 A B C D E 168397_P001-012.qxd7.0:02 Protein structure 5-20-04 2010.4.4 9:45 AM Page 12
Structure of Proteins I.OVERVIEW CHa The 20 amino acids commonly found in proteins are joined together by ree di analyzed by considering the molecule in terms of four organizational levels,namely,primary.secondary,tertiary,and quaternary(Figure 2.1). se hierarchies of opnoiens.aug9estnghatherearegenraleseegarainghneaway in which proteins achieve their native,functional form.These repeated structural IIL.PRIMARY STRUCTURE OF PROTEINS ry structure tant because many genetic diseases result in prote amino acid sequen s which nghabnol d loss o and the mutated proteins are known.this information may be used to diagnose or study the disease. A.Peptide bond and the o-amino group of another.For example,valine and alanine can form the dipep ond(Figure 2.2) Yegal3nmethroughtheormationofapepitde (see p.20).Prolonged exposure tostron o acid or base at elevated Figure 2.1 temperatures is required to hydrolyze these bonds nonenzymically. Four hierarchies of protein structure
Structure of Proteins 2 I. OVERVIEW The 20 amino acids commonly found in proteins are joined together by peptide bonds. The linear sequence of the linked amino acids contains the information necessary to generate a protein molecule with a unique three-dimensional shape. The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels, namely, primary, secondary, tertiary, and quaternary (Figure 2.1). An examination of these hierarchies of increasing complexity has revealed that certain structural elements are repeated in a wide variety of proteins, suggesting that there are general “rules” regarding the ways in which proteins achieve their native, functional form. These repeated structural elements range from simple combinations of α-helices and β–sheets forming small motifs, to the complex folding of polypeptide domains of multifunctional proteins (see p. 18). II. PRIMARY STRUCTURE OF PROTEINS The sequence of amino acids in a protein is called the primary structure of the protein. Understanding the primary structure of proteins is important because many genetic diseases result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. If the primary structures of the normal and the mutated proteins are known, this information may be used to diagnose or study the disease. A. Peptide bond In proteins, amino acids are joined covalently by peptide bonds, which are amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another. For example, valine and alanine can form the dipeptide valylalanine through the formation of a peptide bond (Figure 2.2). Peptide bonds are not broken by conditions that denature proteins, such as heating or high concentrations of urea (see p. 20). Prolonged exposure to a strong acid or base at elevated temperatures is required to hydrolyze these bonds non enzymically. Figure 2.1 Four hierarchies of protein structure. N C C H H N C C H O CH3 H N H C O C O N C C N H H O C C C N H O C C O O H N C C N H N H R R C C R C R Quaternary 4 structure Tertiary 3 structure 2 Secondary structure Primary 1 structure H 13 168397_P013-024.qxd7.0:02 Protein structure 5-20-04 2010.4.4 11:31 AM Page 13