《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

24 2.Structure of Proteins Study Questions Choose the ONE correct answer. 2.1 A peptide bond: its compo A.has a partial double-bond character NH and B.is ionized at physiologic pH. D. gn conc configuration 2.2 Which one of the following statements is correct? =C.B-Bends ofte A.The a-helix can be composed of more than one provid polypeptide chain B.B-Sheets exist only in the antiparallel form. chain.Th C.B-Bends often contain proline. of tert ry st D.Domains are a type of secondary structure. osenw&hea06een%8cnierac ups f nds the- C=0 and 2.3 Which one of the following statements about protein structure is correct? A.Proteins consisting of one polypeptide can have B.The ary s tha beneoatoeachoternthepmaysequence C.The stability of quaterary structure in proteins is nal foldin mainly a result of covalent bonds among the subunits D.Tmedenataiecoiayea E.The information required for the correct folding of a noaen6meneasocaiethoughnoi8oaen uire 8oneonasaongaiepcpepae8emsequenceo heimer disease is asso protei con P-P entia. is as gAWhichone urs in A.It is associated with B-amyloidn abnormal protein inthebrai with an altered amino acid sequence. B.suts from accumulation of denatured proteins in the n an ie of Al Cre bnceabynegenei6s&encasenain dis F.It is caused by the infectious form of a host-cell

Study Questions Choose the ONE correct answer. 2.1 A peptide bond: A. has a partial double-bond character. B. is ionized at physiologic pH. C. is cleaved by agents that denature proteins, such as organic solvents and high concentrations of urea. D. is stable to heating in strong acids. E. occurs most commonly in the cis configuration. 2.2 Which one of the following statements is correct? A. The α-helix can be composed of more than one polypeptide chain. B. β-Sheets exist only in the antiparallel form. C. β-Bends often contain proline. D. Domains are a type of secondary structure. E. The α-helix is stabilized primarily by ionic interac￾tions between the side chains of amino acids. 2.3 Which one of the following statements about protein structure is correct? A. Proteins consisting of one polypeptide can have quaternary structure. B. The formation of a disulfide bond in a protein requires that the two participating cysteine residues be adjacent to each other in the primary sequence of the protein. C. The stability of quaternary structure in proteins is mainly a result of covalent bonds among the subunits. D. The denaturation of proteins always leads to irre￾versible loss of secondary and tertiary structure. E. The information required for the correct folding of a protein is contained in the specific sequence of amino acids along the polypeptide chain. 2.4 An 80-year-old man presented with impairment of higher intellectual function and alterations in mood and behavior. His family reported progressive disorientation and memory loss over the last 6 months. There is no family history of dementia. The patient was tentatively diagnosed with Alzheimer disease. Which one of the following best describes the disease? A. It is associated with β-amyloid —an abnormal protein with an altered amino acid sequence. B. It results from accumulation of denatured proteins that have random conformations. C. It is associated with the accumulation of amyloid precursor protein. D. It is associated with the deposition of neurotoxic amyloid peptide aggregates. E. It is an environmentally produced disease not influ￾enced by the genetics of the individual. F. It is caused by the infectious form of a host-cell protein. Correct answer = A. The peptide bond has a partial double-bond character. Unlike its compo￾nents—the α-amino and α-carboxyl groups—the –NH and –C=O of the peptide bond do not accept or give off protons. The peptide bond is not cleaved by organic solvents or urea, but is labile to strong acids. It is usually in the trans configuration. Correct answer = C. β-Bends often contain pro￾line, which provides a kink. The α-helix differs from the β-sheet in that it always involves the coiling of a single polypeptide chain. The β-sheet occurs in both parallel and antiparallel forms. Domains are elements of tertiary struc￾ture. The α-helix is stabilized primarily by hydro￾gen bonds between the –C =O and –NH– groups of peptide bonds. Correct answer = E. The correct folding of a pro￾tein is guided by specific interactions between the side chains of the amino acid residues of a polypeptide chain. The two cysteine residues that react to form the disulfide bond may be a great distance apart in the primary structure (or on sep￾arate polypeptides), but are brought into close proximity by the three-dimensional folding of the polypeptide chain. Denaturation may either be reversible or irreversible. Quaternary structure requires more than one polypeptide chain. These chains associate through noncovalent interactions. Correct answer = D. Alzheimer disease is asso￾ciated with long, fibrillar protein assemblies con￾sisting of β-pleated sheets found in the brain and elsewhere. The disease is associated with abnormal processing of a normal protein. The accumulated altered protein occurs in a β-pleated sheet configuration that is neurotoxic. The Aβ amyloid that is deposited in the brain in Alzheimer disease is derived by proteolytic cleavages from the larger amyloid precursor protein—a single transmembrane protein expressed on the cell surface in the brain and other tissues. Most cases of Alzheimer disease are sporadic, although at least 5–10% of cases are familial. Prion diseases, such as Creutzfeldt￾Jakob, are caused by the infectious form (PrPSc ) of a host-cell protein (PrPC). 24 2. Structure of Proteins 168397_P013-024.qxd7.0:02 Protein structure 5-20-04 2010.4.4 11:31 AM Page 24

Globular Proteins I.OVERVIEW The previous chapter descnbed the types of secondary and tertey e tions,widely diverse proteins can be constructed that are capable of various specialized functions.This chapter examines the relationship II.GLOBULAR HEMEPROTEINS .(See p.5 ictated by the ment created by the three-dimensional structure of the protein.For B s an electron car .76).In co enzyme that catalyzes the breakdown of hydrogen peroxide (see p.148).In hemoglobin and myoglobin.the two most abundant heme proteins in humans,the heme group serves to reversibly bind oxygen. 2 、-CH3 A.Structure of heme HgC- Heme is a complex of protoporphyrin IX and ferrous iron (Fe2) HC C-N ce C-NI N-C (Figure 3.1) Ihe iron is held in the cente e mole ee -CHa phyrin ring.In myoglobin and hemoglobin,one of these positions is H CH2 coordinated to the side chain of residue of the globin Figure 3.1 degradation of heme.) 65ee8r88tnh6aachromecy 25

I. OVERVIEW The previous chapter described the types of secondary and tertiary structures that are the bricks-and-mortar of protein architecture. By arranging these fundamental structural elements in different combina￾tions, widely diverse proteins can be constructed that are capable of various specialized functions. This chapter examines the relationship between structure and function for the clinically important globular hemeproteins. Fibrous structural proteins are discussed in Chapter 4. II. GLOBULAR HEMEPROTEINS Hemeproteins are a group of specialized proteins that contain heme as a tightly bound prosthetic group. (See p. 54 for a discussion of pros￾thetic groups.) The role of the heme group is dictated by the environ￾ment created by the three-dimensional structure of the protein. For example, the heme group of a cytochrome functions as an electron car￾rier that is alternately oxidized and reduced (see p. 76). In contrast, the heme group of the enzyme catalase is part of the active site of the enzyme that catalyzes the breakdown of hydrogen peroxide (see p. 148). In hemo globin and myoglobin, the two most abundant heme - proteins in humans, the heme group serves to reversibly bind oxygen. A. Structure of heme Heme is a complex of protoporphyrin IX and ferrous iron (Fe2+) (Figure 3.1). The iron is held in the center of the heme molecule by bonds to the four nitrogens of the porphyrin ring. The heme Fe2+ can form two additional bonds, one on each side of the planar por￾phyrin ring. In myo globin and hemoglobin, one of these positions is coordinated to the side chain of a histidine residue of the globin molecule, whereas the other position is available to bind oxygen (Figure 3.2). (See p. 278 for a discussion of the synthesis and degradation of heme.) 25 Globular Proteins 3 Figure 3.1 A. Hemeprotein (cytochrome c). B. Structure of heme. COO￾CH3 C H C H C C N C N N C N C C C C C C C C C HC C C H3C C CH3 C H CH2 CH3 C H H2C CH2 CH2 CH2 CH2 COO￾Fe C COO￾CH3 C H C N N C C C C C C C HC H3C C CH2 CH2 CH2 CH2 COO￾Fe Iron can form six bonds: four with porphyrin nitrogens, plus two additional bonds, one above and one below the planar porphyrin ring A B 168397_P025-042.qxd7.0:03 Hemoglobin 5-20-04 2010.4.4 1:04 PM Page 25

26 3.Globular Proteins A B Figure 3.2 A.Model of myoglobin showing helices A to H.B.Schematic diagram of the oxygen-binding site of myoglobin. B.Structure and function of myoglobin ilar to the individual subunit polypeptide chains of the hemo a-helix are term bythe pres o proline by B-bends and loops stabilized by hydrogen bonds and ionic bonds(see p.17). 2.Location of polar and nonpolar amino acid residues:The interior of the myoglobin molecule is composed almost entirely of nonpo- lar amino acids,。 ney are pa closely togeth er.forming a clustered residues (se ep.19)In contrast are located almost exclusively on the surface of the molecule. un The heme nalobin sits in which is lined withno nolar amino acids.Notable exceptions are two histidine residues (Figure 3e2el.ne.hepggTalhietideaF8lEgncsnaiecwoheronot vith the he inte to the ferrous iron.The protein,or globin,portion of myoglobin he rev dation)occurs only rarely

B. Structure and function of myoglobin Myoglobin, a hemeprotein present in heart and skeletal muscle, functions both as a reservoir for oxygen, and as an oxygen carrier that increases the rate of transport of oxygen within the muscle cell. Myoglobin consists of a single polypeptide chain that is structurally similar to the individual subunit polypeptide chains of the hemo - globin molecule. This homology makes myoglobin a useful model for interpreting some of the more complex properties of hemoglobin. 1. α-Helical content: Myoglobin is a compact molecule, with approxi￾mately 80% of its polypeptide chain folded into eight stretches of α-helix. These α-helical regions, labeled A to H in Figure 3.2A, are terminated either by the presence of proline, whose five-mem￾bered ring cannot be accommodated in an α-helix (see p. 16), or by β-bends and loops stabilized by hydrogen bonds and ionic bonds (see p. 17). 2. Location of polar and nonpolar amino acid residues: The interior of the myoglobin molecule is composed almost entirely of nonpo￾lar amino acids. They are packed closely together, forming a structure stabilized by hydrophobic interactions between these clustered residues (see p. 19). In contrast, charged amino acids are located almost exclusively on the surface of the molecule, where they can form hydrogen bonds, both with each other and with water. 3. Binding of the heme group: The heme group of myoglobin sits in a crevice in the molecule, which is lined with nonpolar amino acids. Notable exceptions are two histidine residues (Figure 3.2B). One, the proximal histidine (F8), binds directly to the iron of heme. The second, or distal histidine (E7), does not directly inter￾act with the heme group, but helps stabilize the binding of oxygen to the ferrous iron. The protein, or globin, portion of myoglobin thus creates a special microenvironment for the heme that permits the reversible binding of one oxygen molecule (oxygena￾tion). The simultaneous loss of electrons by the ferrous iron (oxi￾dation) occurs only rarely. 26 3. Globular Proteins Figure 3.2 A. Model of myoglobin showing helices A to H. B. Schematic diagram of the oxygen-binding site of myoglobin. A B Heme C B A E F G H D Oxygen molecule (O2) Heme F Helix E Helix Proximal histidine (F8) Distal histidine (E7) Fe 168397_P025-042.qxd7.0:03 Hemoglobin 5-20-04 2010.4.4 1:04 PM Page 26

Il.Globular Hemeproteins 3> A B egeaeoihenogonsowgtepopepiecebaeboneB.snpio时dawmngshowmnghehecae C.Structure and function of hemoglobin Hemoglobin is found exclusively in red blood cells(RBCs).where its main function is to transport()from the lngs to the capil Hemoglo 一食omono Each subunit has stretches of a-helical structure,and a heme-bind. npocket similar to that or myoglobin.However.the of O2 from the lungs to the cells of the body.Furthermore,the 9omhmbamgs8reemec0esepm23cbinareregulatedbyinierac Circulatory systems overcome this molecules such as hemoglobin are also required 8e9aa888ysotenaqueous 1.Quaternary structure of hemoglobin:The hemoglobin tetramer can be envisioned as being composed of two identical dimers. (and ()2.in v ers refe together.primarily by hydrophobic interactions(igure 3.).Note In this instance,hydrophobic amino acid residues are localized ecue,but also in a region on the -subunits and B-subunits in the

C. Structure and function of hemoglobin Hemoglobin is found exclusively in red blood cells (RBCs), where its main function is to transport oxygen (O2) from the lungs to the capil￾laries of the tissues. Hemoglobin A, the major hemoglobin in adults, is composed of four polypeptide chains—two α chains and two β chains—held together by noncovalent interactions (Figure 3.3). Each subunit has stretches of α-helical structure, and a heme-bind￾ing pocket similar to that described for myoglobin. However, the tetrameric hemoglobin molecule is structurally and functionally more complex than myoglobin. For example, hemoglobin can transport H+ and CO2 from the tissues to the lungs, and can carry four molecules of O2 from the lungs to the cells of the body. Furthermore, the oxygen-binding properties of hemoglobin are regulated by interac￾tion with allosteric effectors (see p. 29). Obtaining O2 from the atmosphere solely by dif￾fusion greatly limits the size of organisms. Circulatory systems overcome this, but transport molecules such as hemoglobin are also required because O2 is only slightly soluble in aqueous solutions such as blood. 1. Quaternary structure of hemoglobin: The hemoglobin tetramer can be envisioned as being composed of two identical dimers, (αβ)1 and (αβ)2, in which the numbers refer to dimers one and two. The two polypeptide chains within each dimer are held tightly together, primarily by hydrophobic interactions (Figure 3.4). [Note: In this instance, hydrophobic amino acid residues are localized not only in the interior of the molecule, but also in a region on the surface of each subunit. Interchain hydrophobic interactions form strong associations between α-subunits and β-subunits in the II. Globular Hemeproteins 27 Figure 3.3 A. Structure of hemoglobin showing the polypeptide backbone. B. Simplified drawing showing the helices. A B β2 α2 α1 β1 168397_P025-042.qxd7.0:03 Hemoglobin 5-20-04 2010.4.4 1:04 PM Page 27

28 3.Globular Proteins rm stable =7 aB dimer 2 oB dimer 2 02 "T,"or taut,structure of deoxyhemoglobin "R,"or relaxed,structure of oxyhemoglobin Figure 3.4 gran showing structural cha nge rom oxygenation and deoxygenation of hemoglobin dimers.]lonic and hydrogen bonds also occur between the mem s of the me st,the rs are ar e to mo bonds.The weaker interactions between these mobile dimers result in the two dimers occupying different relative positions in ompared w (se Figure plane of the he n is also linked to the mal histidine (F8).there is movement of the globin chains that alters the interface between the aB dimers.] a.T form:The deoxy form of hemoglobin is called the"T,"or taut (tense)form.In the torm,the two ap dimers interact through 00 a nt of the xygen-finity b.R form:The bindi oheotoygentohemoglobi caus s the rup relaxed form,in which the polypeptide chains have more freedom of mov emer (see Figur 3.4).The R form is the high- oxygen-aminity form D.Binding of oxygen to myoglobin and hemoglobin Myoglobin one because it cor —asyaeghecaseonmcheseooenbnigaesowpe s.The Figure 3.5)

dimers.] Ionic and hydrogen bonds also occur between the mem￾bers of the dimer. In contrast, the two dimers are able to move with respect to each other, being held together primarily by polar bonds. The weaker interactions between these mobile dimers result in the two dimers occupying different relative positions in deoxyhemoglobin as compared with oxyhemoglobin (see Figure 3.4). [Note: The binding of O2 to the heme iron pulls the iron into the plane of the heme. Because the iron is also linked to the proxi￾mal histidine (F8), there is movement of the globin chains that alters the interface between the αβ dimers.] a. T form: The deoxy form of hemoglobin is called the “T,” or taut (tense) form. In the T form, the two αβ dimers interact through a network of ionic bonds and hydrogen bonds that constrain the movement of the polypeptide chains. The T form is the low￾oxygen-affinity form of hemoglobin. b. R form: The binding of oxygen to hemoglobin causes the rup￾ture of some of the ionic bonds and hydrogen bonds between the αβ dimers. This leads to a structure called the “R,” or relaxed form, in which the polypeptide chains have more freedom of movement (see Figure 3.4). The R form is the high￾oxygen-affinity form of hemoglobin. D. Binding of oxygen to myoglobin and hemoglobin Myoglobin can bind only one molecule of oxygen, because it con￾tains only one heme group. In contrast, hemoglobin can bind four oxygen molecules —one at each of its four heme groups. The degree of saturation (Y) of these oxygen-binding sites on all myo￾globin or hemoglobin molecules can vary between zero (all sites are empty) and 100% (all sites are full, Figure 3.5). 28 3. Globular Proteins O2 O2 O2 Figure 3.4 Schematic diagram showing structural changes resulting from oxygenation and deoxygenation of hemoglobin. . Weak ionic and hydrogen bonds occur between αβ dimer pairs Some ionic and hydrogen bonds between αβ dimers are broken in the oxygenated state. "T," or taut, structure of deoxyhemoglobin "R," or relaxed, structure of oxyhemoglobin αβ αβ αβ dimer 1 αβ dimer 2 Strong interactions, primarily hydrophobic, between α and β chains form stable αβ dimers. 168397_P025-042.qxd7.0:03 Hemoglobin 5-20-04 2010.4.4 1:04 PM Page 28