上海交大_生物化学__CHAPTER2

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1、Proteins play crucial roles in virtually all biological processesenzymatic catalysts酶促反应的催化剂 enzymes exhibit enormous catalytic power; several thousand enzymes characterized鉴定 and many of them crystallized结晶; nearly all known enzymes are proteins, so they are central in determining the pattern of ch

2、emical transformation in biological systemstransport and storage储存和转运(小分子和离子) specific proteins are transporters 运载蛋白of many small molecules and ions; e.g. hemoglobin, myoglobin, transferrin运铁蛋白, ferritin铁蛋白 coordinated motion协调运动 proteins are the major component of musclemechanical support机械支撑 high

3、 tensile strength 抗张强度of skin and bone is due to the presence of collagen胶原, a fibrous纤维状 proteinimmune protection免疫保护 Antibodies抗体 are highly specific proteins that recognize and combine with: viruses, bacteria, and cells from other organisms generation and transmission of nerve impulses神经刺激的产生和传递

4、the response of nerve cells to specific stimuli is mediated by receptor proteins, e.g. Rhodopsin视紫红质 control of growth and differentiation生长和分化的调控 controlled sequential expression of genetic information is essential for the orderly growth and differentiation, e.g. repressor protein阻遏蛋白, growth facto

5、r protein, insulin. Proteins serve in all cells as sensors传感器 that control the flow of energy and matter. Several key properties enable proteins to participate in such a wide range of functions 1.Proteins are linear polymers built of monomer units called amino acids. Proteins are the embodiment of t

6、he transition from the one-dimensional world of sequences to the three-dimensional world of molecules capable of diverse activities. 体现了一维序列向(能执行多种生物学功能的)三维空间结构的过渡 2.Protein contain a wide range of functional groups. Alcohols, thiols巯基, thioethers硫酯, carboxylic acids, carboxamides羧酰胺, and a variety

7、of basic groups. 3.proteins can interact with one another and with other biological macromolecules to form complex assemblies. Macromolecular machines: accurate replication of DNA, the transmission of signals within cells, and many other essential processes. 4.Some proteins are quite rigid, whereas

8、others display limited flexibility. Rigid ones: as structural elements in the cytoskeleton or in connective tissue. Parts with limited flexibility: as hinges铰链区, springs弹性区, and levers杠杆. proteins are built from a repertoire of 20 AA as the basic structural units of protein, an -AA consists of an am

9、ino group氨基, a carboxyl group羧基, a hydrogen atom, and a distinctive R group all of the 4 groups bonded to an-carbon atom. so named because it is adjacent to the carboxyl (acidic) group an R group is referred to as a side chain側链 AA in solution at neutral pH are predominantly dipolar ions偶极离子 (or zwi

10、tterions兼性离子) in the dipolar form of AA, the amino group is protonated (-NH3+)质子化 and the carboxyl group is dissociated (-COO)解离 the ionization state of AA varies with pH only L AA are constituents of proteins twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, and

11、 chemical reactivity are commonly found in proteins the remarkable range of functions mediated by proteins results from the diversity and versatility of these 20 kinds of building blocks the simplest one: Gly (glycine)甘 R group: H it is unique in being optically inactive 唯一(不具有不对称碳原子从而)不具光 学活性的AA Al

12、a (alanine)丙 comes next R group: CH3 (methyl group甲基) Larger hydrocarbon side chain (3 and 4 C atoms): Val (valine)缬, Leu (leucine)亮, and Ile (isoleucine)异亮. These side chains are hydrophobic疏水. The 3-D structure of water soluble proteins is stabilized by the coming together of hydrophobic side chai

13、ns to avoid contact with water 上述AA(的側链是疏水的因而)属非极性AA(Gly除外, 脂肪族中性AA),水溶性蛋白因这些疏水侧链聚集在一起(避免与水接触)而使其三维结构保持稳定 Pro (proline)晡 differ from others in that its side chain is bonded to both the nitrogen and the -carbon atom其侧链(除同-碳原子外)还同(氨基)氮原子成键(形成吡咯环), 因此,它只是-亚AA(而不是真正意义上的-AA) Three AA with aromatic side:

14、Phe (phenylalanine)苯丙, Tyr (tyrosine)酪 with a reactive hydroxyl group, Trp (tryptophan)色具吲哚环. Phe and Trp are highly hydrophobic Cys (cysteine)半胱 and Met (methionine)甲硫(蛋) contain sulfur atom in their side chain. Both these sulfur-containing side chains are hydrophobic疏水. The sulfydryl group巯基 of Cy

15、s is highly reactive. Cys plays a special role in shaping some proteins by forming disulfide links二硫键 Ser (serine) 丝 and Thr (threonine)苏 contain aliphatic脂族的 hydroxyl groups羟基 which make them much more hydrophilic 亲水的and reactive. Thr and Ile contain two centers of asymmetry苏和异亮含两个不对称中心 (all other

16、AA, in the basic set of 20, except for Gly, contain a single asymmetric center) Lys (lysine)赖 and Arg (arginine)精 with very polar side chains, which render them highly hydrophilic. They are positively charged at neutral pH. His (histidine)组 can be uncharged or positively charged. His is often found

17、in the active sites of enzymes, where its imidazole咪唑 ring can readily switch between these states to catalyze the making and breaking of bonds. His经常参与酶的活性中心的构成,它是唯一 一个R基(咪唑基)的pKa值在7附近的AA. Asp (aspartate)天冬 and Glu (glutamate)谷 with acidic side chains. Gln (glutamine)谷氨酰胺 and Asn (asparagine)天冬酰胺 a

18、re the uncharged derivatives of Glu and Asp. Seven AA (Arg, Lys, His, Asp, Glu, Cys and Tyr) have readily ionizable side chains易离子化的側链按R基化学结构分类: 1.脂肪族AA (1)中性AA: Gly, Ala, Val, Leu, Ile 5个(2)含羟基或硫的 AA: Ser, Thr, Cys, Met 4个(3)酸性AA及其酰胺: Asp, Glu, Asn, Gln 4个(4)碱性AA: Lys, Arg 2个; 共15个 2.芳香族AA Phe , Ty

19、r, Trp 3个 3.杂环族AA His, Pro 2个按R基极性性质分类:1.非极性R基AA: Ala, Val, Leu, Ile, Phe, Trp, Pro, Met 8个 2.不带电荷的极性R基AA: Ser, Thr, Tyr, Asn, Gln, Cys, Gly 7个 3.带正电荷的R基AA: Lys, Arg,His 3个 4.带负电荷的R基AA: Asp, Glu 2个 AA are linked by peptide bonds肽键 to form polypeptide chains In proteins, the-carboxyl group of one AA

20、is joined to the-amino group of another AA by a peptide bond (or amide bond酰胺键) many AA joined by peptide bonds form a polypeptide chain An AA unit in a polypeptide is called a residue残基 Amino-terminal residue with the-amino group, carboxyl-terminal residue with the-carboxyl group Main chain (or bac

21、k bone)(regularly repeating part) and side chain (variable part) Some proteins contain disulfide bonds. The resulting disulfide is called cystine.胱氨酸 Intracellular胞内 proteins lack disulfide bonds, whereas extracellular胞外 proteins often contain several.从而胞内蛋白还原程度高 nonsulfur cross-links derived from L

22、ys side chains may also be present in some proteins (e.g. collagen). proteins have unique AA sequences that are specified by genes The determination of the AA sequence of insulin (1953) is a landmark in biochemistr y because it showed for the first time that a protein has a precisely defined AA sequ

23、ence. The AA sequences of proteins are genetically determined the sequence of nucleotides in DNA, the molecule of heredity, specifies a complementary互补 sequence of nucleotides in RNA, which in turn specifies the AA sequence of a protein DNA中脱氧核苷酸序列 RNA中核苷酸序列多肽链(蛋白)中AA序列 each of the 20 AA is encoded

24、by one or more specific sequences of three nucleotides proteins in all organisms are synthesized from their constituent AA by a common mechanism AA sequences are impor tant because of the knowledge on them are very helpful and essential in elucidating its mechanism of action (e.g. the catalytic mech

25、anism of an enzyme)阐明蛋白功能(酶催化机制) analyses of relations between AA sequences and 3-D structures of proteins are uncovering the rules that govern the folding of polypeptide chains 揭示多肽链折叠的规则, AA序列还是DNA中遗传信息和(执行其生物学功能的)蛋白三维结构之间的联系 genetic message in DNA AA sequence 3-D structure that performs a protein

26、s biological function the sequence determination is part of molecular pathology. Alterations in AA sequence can produce abnormal function and disease e.g. sickle-cell anemia AA序列的改变导致疾病:镰状细胞贫血病, cystic fibrosis囊性纤维化 the sequence of a protein reveals much about its evolutionary history进化史 protein mod

27、ification and cleavage修饰 confer new capabilities many of the set of 20 AA can be modified after synthesis of a polypeptide chain to enhance its capabilities N-terminal of many proteins are acetylated 乙酰化, which makes them more resistant to degradation 许多蛋白的N端被乙酰化,从而具有较强的抗(被蛋白酶)降解能力 In newly synthesi

28、zed collagen胶原, many proline residues become hydroxylated to form hydroxyproline 羟晡氨酸(stabilize the fiber) Vc deficiency insufficient hydroxylation of collagen scur vy 坏血病 VK deficiency insufficient-carboxyglutamate 羧基谷氨酸 in prothrombin凝血素 hemorrhage出血 Antibodies抗体 acquire carbohydrate糖units on spec

29、ific Asn residues (make a protein more hydrophilic亲水)细胞分泌的抗体需加入糖使得更亲水 a protein can be made more hydrophobic by the addition of a FA脂肪酸 to an -amino group or a Cys sulfhydr yl group巯基 蛋白加入脂肪酸后则更疏水 many hormones (e.g. epinephrine肾上腺素) alter the activities of enzymes by stimulating the phosphorylation

30、磷酸化 of the hydroxyl AA (Ser and Thr) phosphoserine and phosphothreonine are the most ubiquitous modified AA in proteins growth factor (e.g. insulin)act by triggering the phosphorylation 触发磷酸化of the hydroxyl group of Tyr residues. The phosphate groups on these three modified AA can readily be removed

31、, enabling them to act as reversible switches in regulating cellular processes Some oncogenes致癌基因 act by stimulating excessive phosphorylation of Tyr residues on proteins(调控细胞分化的蛋白) many proteins are cleaved and trimmed剪切 after synthesis digestive enzymes: inactive precursors前体 stored safely in panc

32、reas胰腺 released into intestine activated by peptide bond cleavage in blood clotting, soluble fibrinogen血纤蛋白原 is converted into insoluble fibrin血纤蛋白by peptide bond cleavage many polypeptide hormones (e.g. adrenocorti-cotropic hormone促肾上腺皮质激素) arise from the splitting裂解 of a single large precursor pro

33、tein, a molecular cornucopia丰饶之角(分子宝库) proteins of poliovirus脊髓灰质炎病毒 are produced by cleavage of a giant polyprotein precursor巨多蛋白前体 several key proteins of HIV-1 arise by specific cleavage of a long precursor modification and cleavage as essential features of protein formation and function. These f

34、inishing touches account for much of the versatility, precision, and elegance of protein action and regulation (蛋白合成后的)修饰和切割使得其功能和调控(方式)具有极其多样性并且精确无误 the peptide unit is rigid and planar刚性和同一平面的 A striking characteristic of proteins is that they have well-defined 3-D structures stretched-out or rand

35、omly arranged polypeptide is devoid of biological activity散乱、随机排列的蛋白不具生物学活性 function arises from conformation构象, which is 3-D arrangement of atoms in a structure AA sequences are important because they specify the conformation of proteins氨基酸序列规定了蛋白构象 polypeptide chains can fold into regular structur

36、es such as thehelix The helix is a rodlike structure. The tightly coiled卷曲 polypeptide main chain forms the inner part of the rod, and the side chains extend outward in a helical array it is stabilized by hydrogen bonds between the NH and CO groups of the main chain. Thus, all the main-chain CO and

37、NH groups are hydrogen bonded. 3.6 AA per turn of helix(3.61.5 ), so AA spaced 3 or 4 apart in the linear sequence are spatially quite close to one another in an helix. In contrast, AA 2 apart are situated on opposite sides of the helix and are unlikely to make contact. Thehelix found in proteins is

38、 right-handed (clockwise)右手螺旋,顺时针 Thehelix content of proteins ranges widely (0100%) Chymotrypsin胰凝乳蛋白酶 is virtually devoid of it, about 75% of myoglobin肌红蛋白 and hemoglobin ishelical single-strandedhelices are usually short (less than 45 埃) However, two or morehelices can entwine缠绕 to form very stab

39、le structures (more than 1000 埃 ), calledhelical coiled coils卷曲螺旋, e.g. in myosin肌球蛋白 and tropomyosin原肌球蛋白 (in muscle), fibrin血纤维蛋白 (in blood clots), keratin角蛋白 (in hair), filaments纤丝 (in cytoskeleton of cells) The elucidation of the structure of thehelix is a landmark in molecular biology because i

40、t demonstrated that the conformation of a polypeptide chain can be predicted if the properties of its components are rigorously and precisely known pleated sheets折叠片 are stabilized by hydrogen bonding between strands A polypeptide chain in apleated sheet, called a strand, is almost fully extended完全伸

41、展.(axial distance between adjacent AA: 3.5 in pleated sheet, 1.5 inhelix) Another difference is that it is stabilized by hydrogen bonds between NH and CO groups in different polypeptide strands(chain)不同多肽股(链)之间的氢键 polypeptide chains can reverse direction by making hairpin turns most proteins have co

42、mpact, globular shapes owing to reversals in the direction of their polypeptide chains. Many of these are accomplished by a common structural element called theturn 转角 the essence of this hairpin turn is that the CO group of residue n of a polypeptide is hydrogen-bonded to the NH group of residue n+

43、3 a polypeptide chain can abruptly reverse its direction turn often connect antiparallelstrands, hence their name also known as reverse turns or hairpin bends发夹转角 the triple-stranded collagen胶原 helix is stabili-zed by proline and hydroxyproline羟晡氨酸 a special type of helix is present in collagen, the

44、 most abundant protein of mammals. It is the main fibrous component of skin, bone, tendon腱, car tilage软骨, and teeth.胶原原纤维的基本结构单位是原胶原分子(MW 285 x 103),由三股缠绕的多肽链(每股约1000个残基)组成. it contains three helical polypeptide chains, each nearly 1000 residues long nearly every third residue is Gly (33%) Pro (13%)

45、 is also present to a much greater extent Collagen contains 4-hydroxyproline (Hyp, 9%) Gly-x-y (x 经常是Pro, y 经常是Hyp) The sequence Gly-Pro-Hyp recurs frequently collagen is a rod-shaped molecule. The helical motif of its three chains is entirely different from that of thehelix hydrogen bonds within a

46、strand are absent无链内氢键(因非常伸展) each of the three collagen helices is stabilized by steric repulsion空间排斥 of the pyrrolidone rings吡咯环 of the Pro and Hyp residues this helical form is much more open than the tightly coiled helix the three strands wind around each other to form a superhelical cable the t

47、hree strands are hydrogen bonded to each other, the H donors are the NH of Gly, while the acceptors are the CO of “x” residues on the other chains. The hydroxyl groups of Hyp residues also participate in hydrogen bonding the only residue that can fit in an interior position is Gly三股螺旋中的每条链的第三个残基面向或位

48、于拥挤的中心轴处,唯一能适合此位置的残基是甘氨酸 proteins are rich in hydrogen-bonding potentiality潜能 all reversible molecular interactions (the forces that determine the 3-D architecture of proteins) in biological systems are mediated by (分子间如此,分子内部也是这样) electrostatic bonds静电键 hydrogen bonds van der Waals bonds side chain

49、s of 11 of the 20 fundamental AA also can par ticipate in hydrogen bonding The side chains of Trp and Arg can serve as hydrogen bond donors only Like the peptide unit itself, the side chains of Asn, Gln, Ser, and Thr can serve as hydrogen bond donors and acceptors The hydrogen-bonding capabilities o

50、f Lys (and terminal amino group), Asp and Glu (and terminal carboxyl group), Tyr, and His vary with pH. The hydrogen-bonding modes of these ionizable residues are pH-dependent water-soluble proteins fold into compact structures with nonpolar cores Myoglobin肌红蛋白 myoglobin is an extremely compact mole

51、cule, which is built primarily of helix(eight).(single polypeptide chain, with heme血红素 prothetic group) about 70% of the main chain is folded intohelices much of the rest of the chain forms turns between helices 4 of the turns contain Pro, which tends to disrupt helices because of steric hindrance位阻

52、 by its rigid five-membered ring the folding of the main chain of myoglobin is complex and devoid of symmetr y不具对称性 The striking fact is that the interior consists almost entirely of nonpolar residues (e.g. Leu, Val, Met, Phe) The only polar residues inside are two His, which play critical roles in

53、the binding of heme oxygen Its outside consists of both polar and nonpolar residues The space-filling model also shows that there is very little empty space inside the polypeptide chain therefore folds spontaneously so that its hydrophobic side chains are buried and its polar, charged chains are on

54、the surface ribonuclease A核糖核酸酶A this pancreatic enzyme胰酶 exemplifies a rather different mode of protein folding this single polypeptide chain of 124 residues is folded mainly intostrands it also contains a tightly packed, highly nonpolar interior it is further stabilized by four disulfide bond inte

55、gral membrane proteins整合性膜蛋白(膜内在蛋白) they are designed differently from proteins that are soluble in aqueous solution the permeability barrier渗透性屏障 of membranes is formed by lipids, which are highly hydrophobic thus, the part of a membrane protein that spans this region must have a hydrophobic exteri

56、or the transmembrane portion of a membrane protein usually consists of bundles束 of helices with nonpolar side chains facing out 膜蛋白的跨膜部分通常由-螺旋(束)组成(非极性侧链朝外) there are four basic levels of structure in protein architecture primary structure is the AA sequence secondary structure refers to the spatial

57、 arrangement of AA residues that are near one another in the linear sequence some of these steric relationships are of a regular kind, giving rise to a periodic structure thehelix andstrand are elements of secondary structure tertiary structure refers to the spatial arrangement of AA residues that a

58、re far apar t in the linear sequence, and to the pattern of disulfide bonds the dividing line between secondary and tertiary structure is a matter of taste quaternar y structure refers to the spatial arrangement of subunits and the nature of their contacts only proteins containing more than one poly

59、peptide chain exhibit this level of structural organization hemoglobin consists of twoand twochains the subunit interfaces in this tetramer四聚体 participate in transmitting information between distant binding sites for O2, CO2, and H+ viruses make the most of a limited amount of genetic information by

60、 forming coats that use the same kind of subunit repetitively in a symmetric array(如:二十面体60-聚对称球状体) Two other levels of organization: supersecondary structure refers to clusters簇 of secondar y structure. e.g. unit Domain结构域: some polypeptide chains fold into two or more compact regions that may be j

61、oined by a flexible segment of polypeptide chain, rather like pearls on a string 结构域:多肽链在二级结构或超二级结构的基础上形成三级结构的局部折叠区,它是相对独立的紧密球状实体. 对较小的球状蛋白质分子或亚基,结构域即三级结构(这些蛋白质分子或亚基是“单结构域”的);对较大的球状蛋白质分子或亚基,其三级结构往往由两个或多个结构域缔合而成(它们是“多结构域”的) these compact globular units are called domains range in size from about 100

62、to 400 AA residues e.g. a 25-kd L chain of an antibody is folded into two domains these domains resemble each other which suggests that they arose by duplication of a primordial原始 gene an important principle: protein domains are often encoded by distinct parts of genes called exons一个外显子编码一个结构域 the A

63、A sequence of a protein specifies its 3-D structure Ribonuclease核糖核酸酶 is a single polypeptide chain consisting of 124 AA residues its 4 disulfide bonds can be cleaved reversibly by reducing them with -mercaptoethanol -巯基乙醇 ribonuclease can be reduced by-mercaptoethanol in urea尿素(8M) or guanidine hyd

64、rochloride(6M)胍基盐酸 into a random-coil 无规卷曲conformation the product was fully reduced, randomly coiled polypeptide chain devoid of enzymatic activity, or denatured the denatured enzyme (freed of urea and-mercaptoethanol by dialysis透析) slowly regained the enzymatic activity (-SH oxidized by air) nearl

65、y all the original enzymatic activity (physical and chemical properties of the refolded enzyme) was regained information needed to specify the complex 3-D structure of ribonuclease is contained in its AA sequence: sequence specifies conformation it had only 1% of the enzymatic activity of the native

66、 protein(if it was reoxidized in 8M urea which was then removed) the reason is that wrong disulfide pairings were formed when reduced ribonuclease was reoxidized while it was still in 8M urea (then dialyzed to remove) the reduced molecule was reoxidized the “scrambled” ribonuclease spontaneously converted into fully active, native one when trace amount of -mercaptoethanol were added to an aqueous solution of the protein this process was driven entirely by the decrease in free energy as the scram