生化生物化学第2

1、Chapter 2:Protein Composition and Structure崔莉cuiliBiochemistrySixth EditionBerg Tymoczko StryerIntroductionProtein: 生物功能的主要载体，于身体各个组织Ø Macromolecules(数千数十万）Ø Versatile （组成-结构-功能）Ø Structure and Function（激素、酶）Maintain bloodsugarat appropriate levelsStructure and Crystals of human insul

2、in. IOUTLINES结构单元、聚合方式以及聚合后的形成的结构形态1. Proteins Are Built from a Repertoire of 20 Amino Acids2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains3. Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and

3、 Turns and LoopsOUTLINES4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores5. Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional StructureOUTLINES结构单元、聚合

4、方式以及聚合后的形成的结构形态1. Proteins Are Built from a Repertoire of 20 Amino Acids2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains3. Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops1.Pr

5、oteins Are Built from a Repertoire of 20 Amino AcidsDNA的结构单元：核苷酸 4 种Versatile（组成-结构-功能）蛋白质的结构单元：氨基酸 20 种1.Proteins Are Built from a Repertoire of 20 Amino Acids蛋白质的结构单元SconfigurationFigure 2.4 The L and D isomers of amino acids. L and D isomers are mirror images of each other. Only L aminoacids are

6、found in proteins1.Proteins Are Built from aRepertoire of 20 Amino AcidsDistinctive R goroup: sides, shape, charge, hydrogenbonding capacity, hydrophobic character.兼性离子Ionization state as a function of pH.1.Proteins Are Built from a Repertoire of 20 Amino AcidsDistinctive R goroup:Ø 按侧链性质划分：

7、16;按侧链结构划分：Aliphatic（15）Aromatic（3）Heterocyclic（2）I）Non-polar （8）Aliphatic（5）Aromatic（2）Heterocyclic（1）II）Polar（12）活性基团Uncharged（1+1+2+3） Acidic （2）Basic （3）1.Proteins Are Built from aRepertoire of 20 Amino Acids（1）非极性氨基酸：R基为脂肪侧链（5）：丙氨酸缬氨酸亮氨酸异亮氨酸甲硫氨酸1.Proteins Are Built from aRepertoire of 20 Amino

8、Acids（1）非极性氨基酸：R基为脂肪侧链（5）：名称你结构与功能特点异亮氨酸、亮氨酸、缬氨酸均含有较大的疏水侧链，其刚性结构特征及疏水相互作用都对蛋白折 叠有重要的影响力，常作为水溶性蛋白的内部支撑结构甲硫氨酸是多肽链生物的起始氨基酸；参与体内含硫化合物代谢及甲基化 反应丙氨酸转氨酶中的氨基供体1.Proteins Are Built from a Repertoire of 20 Amino Acids（1）非极性氨基酸：R基为杂环脂肪侧链（1）：脯氨酸名称结构与功能特点N原子在杂环中移动的脯氨酸度受到限制，常位于多肽链的转角处1.Proteins Are Built from a Re

9、pertoire of 20 Amino Acids（1）非极性氨基酸：R基为芳香侧链（2）：苯丙氨酸色氨酸名称结构与功能特点苯丙氨酸、色氨酸侧链结构大且极性较弱或无极性，常位于水溶性蛋白的内部1.Proteins Are Built from a Repertoire of 20 Amino Acids（2）极性氨基酸：不带电荷（7,中性氨基酸）：天冬酰胺谷胺酰胺甘氨酸1 (-H)半胱氨酸+1 (-SH)酪氨酸丝氨酸+3 (-OH)苏氨酸+ 2 (-CONH2)1.Proteins Are Built from a Repertoire of 20 Amino Acids（2）极性氨基酸：不

10、带电荷（7,中性氨基酸）：名称结构与功能特点半胱氨酸氧化状态下，多肽链中不相邻的两个半胱氨酸通过二硫键相连，增强蛋白质结构的性；巯基易与重金属离子结合酪氨酸侧链结构大且极性较弱，常位于水溶性蛋白的内部甘氨酸是唯一不不对称结构的氨基酸，有较大的旋转度，赋予多肽链更多的柔性；是最小的氨基酸，能够于空间致密的蛋白质中，如胶原丝氨酸、苏氨酸侧链短，所含羟基常作为酶反应中的供氢体；亲水性强，位于水溶性蛋白表面天冬酰胺、谷氨酰胺极性酰胺键一般不具有反应性，作为氢键的受体和供体，在碱性和温度下不，会发生脱酰胺反应，形成酸性侧链1.Proteins Are Built from a Repertoire of

11、 20 Amino Acids（2）极性氨基酸：带正电荷（3，碱性氨基酸）：赖氨酸精氨酸组氨酸1.Proteins Are Built from aRepertoire of 20 Amino Acids（2）极性氨基酸：带正电荷（3，碱性氨基酸）：名称结构与功能特点组氨酸咪唑基团容易发生质子化，进而影响其所在的蛋白质构象，因此是许 多蛋白质功能的调节机制赖氨酸、精氨酸有带正电荷的柔性侧链，常作为蛋白的亲水表面，且易于结合带有负 电荷的其他，如DNA1.Proteins Are Built from a Repertoire of 20 Amino Acids（2）极性氨基酸：带负电荷（2，酸

12、性氨基酸）：天冬氨酸谷氨酸名称结构与功能特点天冬氨酸、谷氨酸携带强负电荷，常位于水溶性蛋白的表面；可结合带正电荷的或金属离子1.Proteins Are Built from a Repertoire of 20 Amino Acids蛋白质中的氨基酸依据极性的分类总结类 别主要氨基酸非极性脂肪族氨基酸丙氨酸、缬氨酸、亮氨酸、异亮氨酸、甲硫氨酸芳香族氨基酸苯丙氨酸杂环氨基酸脯氨酸、色氨酸极性不带电荷的氨基酸（中性氨基酸）甘氨酸、丝氨酸、半胱氨酸、苏氨酸、天冬酰胺、谷氨酰胺、酪氨酸带负电荷的氨基酸（酸性氨基酸）天冬氨酸、谷氨酸带正电荷的氨基酸（碱性氨基酸）赖氨酸、精氨酸、组氨酸1.Protein

13、s Are Built from a Repertoire of 20 Amino AcidsOUTLINES结构单元、聚合方式以及聚合后的形成的结构形态1. Proteins Are Built from a Repertoire of 20 Amino Acids2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains3. Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Su

14、ch As the Alpha Helix, the Beta Sheet, and Turns and Loops2. Primary Structure: Amino AcidsAre Linked by Peptide Bonds蛋白质的一级结构：N末端氨基酸 肽键肽链二硫键（共价键）C末端 牛胰岛素2. Primary Structure: Amino Acids Are Linked by Peptide BondsPeptide-bond formation：肽链的骨架肽键：缩合脱水肽链：2. Primary Structure: Amino Acids Are Linked by

15、 Peptide BondsAmino acid sequences have direction.Amino acid sequences have direction. This illustration of the penta- peptide Try-Gly-Gly-Phe-Leu (YGGFL) shows the sequence from N- terminus to C-terminus.量：128；氨基酸残基平均量：110氨基酸平均2. Primary Structure: Amino Acids Are Linked by Peptide BondsTrans and c

16、is peptide bonds.反式结构为优势结构Figure 2.25Trans and cis peptide bonds. The trans form isstrongly favored because of steric clashes that occur in the cis form.2. Primary Structure: Amino Acids Are Linked by Peptide BondsTrans and cis X-Pro bonds.因为碰撞的情况相似，所以两种结构的能量水平相似Figure 2.26 Trans and cis X-Pro bonds

17、. The energies of these forms are similar to one another because steric clashes occur in both forms.2. Primary Structure: Amino Acids Are Linked by Peptide BondsTypical bond lengths within a peptide unit.反式结构的参数Figure 2.24 Typical bond lengths within a peptide unit. Thepeptide unit isshown in the tr

18、ans configuration.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds:肽氮原子上的孤对电子与羰基具有共轭作用组成肽键的原子处于同一平面2. Primary Structure: Amino Acids Are Linked by Peptide BondsPlannar peptide bonds肽键具有部分双键性质，不能旋转。多肽链柔软但构象受限肽Figure 2.23Peptide bonds are planar.In a pair of linked aminoacids, six atoms (

19、Ca, C, O, N, H, and Ca ) lie in a plane. Side chainsare shown as green balls.2. Primary Structure: Amino Acids Are Linked by Peptide BondsCa键的旋转：两个单键旋转,两个平面之间形成的角度称肽相邻肽为扭角(Torsion angle)或二面角(dihedral angle)。 Ca-C ：y ;Ca-N ：f2. Primary Structure: Amino Acids Are Linked by Peptide BondsRotation about

20、bonds in a polypeptide.Figure 2.27 Rotation about bonds in a polypeptide. The structure of each amino acid in a polypeptide can be adjusted by rotation about two single bonds. Phi (f) is the angle of rotation about the bond between the nitrogen and the a-carbon atoms, whereas psi (y) is the angle of

21、 rotation about the bond between the a-carbon and the carbonyl carbon atoms.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds(Left) A view down the bond between the nitrogen and the a-C atoms, showing how f is measured. (Right) A view down the bond between the a-C and the carbonyl carbon

22、 atoms, showing how y is measured.2. Primary Structure: Amino Acids Are Linked by Peptide BondsFigure 2.28 A Ramachandran diagram showing the values of f and y. Not all f and y values are possible without collisions between atoms. The most favorable regions are shown in dark green; borderline region

23、s are shown in light green. The structure on the right is disfavored because of steric clashes.2. Primary Structure: Amino Acids Are Linked by Peptide BondsComponents of a polypeptide chain：R基之间的相互作用能量的构象2. Primary Structure: Amino Acids Are Linked by Peptide BondsThe formation of a disulfide bond：二

24、硫键氧化脱氢Figure 2.21Cross-links. The formation of a disulfide bondfrom two cysteine residues is an oxidation reaction.2. Primary Structure: Amino Acids Are Linked by Peptide BondsProteins Have Unique Amino Acid Sequences Specified by GenesFigure 2.22 Amino add sequence of bovine insulin.2. Primary Stru

25、cture: Amino Acids Are Linked by Peptide Bonds作用力 + 旋转 - 高级结构Question and DiscussionOUTLINES结构单元、聚合方式以及聚合后的形成的结构形态1. Proteins Are Built from a Repertoire of 20 Amino Acids2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains3. Secondary Structure: Polypeptide Chain

26、s Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and LoopsOUTLINES4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores5. Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures6. The Amino Acid

27、Sequence of a Protein Determines Its Three-Dimensional Structure3. Secondary Structure: a Helix, b Sheet, Turns and Loops一级结构 +蛋白的作用力 - 平衡 - 高级结构3. Secondary Structure: a Helix, b Sheet, Turns and Loops蛋白结构可视化数据库： PDB ID： 2C81 3. Secondary Structure: a Helix, b Sheet, Turns and Loops维持三维结构的作用力：3. Se

28、condary Structure: a Helix, b Sheet, Turns and Loops主链肽基之间形成最大数目的内氢键，同时保氢键：持大多数能成氢键的侧链处于蛋白质与水相互作用。表面，将Ø蛋白质二级结构的主要作用力3. Secondary Structure: a Helix, b Sheet, Turns and Loops链间氢键链内氢键蛋白质结构：-螺旋和-片层，有规则的重复结构3. Secondary Structure: a Helix, b Sheet, Turns and Loops-螺旋 (- helix)：肽平面同一轴旋转，螺旋一周，沿轴上升的距离

29、即螺距为0.54nm,含3.6个氨基酸残基；两个氨基酸之间的距离为0.15nm;肽链内形成氢键，氢键的取向几乎与轴平行，第一个氨基酸残基的酰胺基团的-C=O基与第四个氨基酸残基酰胺基团的-NH2基形成氢键。3. Secondary Structure: a Helix, b Sheet, Turns and Loops右手a-螺旋3. Secondary Structure: a Helix, b Sheet, Turns and LoopsFigure 2.31 Ramachandran diagram for helices. Both right-and left-handedhelic

30、es lie in regions of allowed conformations in the Ramachandrandiagram. However, essentially all a helices in proteins are right-handed.y ：-47°f ：-57 °3. Secondary Structure: a Helix, b Sheet, Turns and Loops球-棒模型绸带结构圆柱结构3. Secondary Structure: a Helix, b Sheet, Turns and LoopsFigure 2.29 S

31、tructure of the a helix. A ribbon depiction with the a-carbon atoms and side chains (green) shown.3. Secondary Structure: a Helix, b Sheet, Turns and LoopsFigure 2.29 Structure of the a helix. A side view of a ball-and- stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups

32、.3. Secondary Structure: a Helix, b Sheet, Turns and Loops（C）从末端向螺旋骨架内部观测的结构图，其中侧链（绿色）向螺旋外凸出。（D）图C的空间填充模型，表明螺旋内部核堆积紧密。3. Secondary Structure: a Helix, b Sheet, Turns and Loops富含-螺旋的蛋白质：铁储存蛋白由24个蛋白，是生物用于储存铁离子的主要蛋白。铁储存蛋白Figure 2.33 A largely a-helical protein.Ferritin, an iron-storage protein, is buil

33、t from a bundle of a helices.3. Secondary Structure: a Helix, b Sheet, Turns and Loops-片层（ - sheet）：b-折叠是由两条或多条几乎完全伸展的肽链平行排列，通过链间的氢键交联而形成；肽链的主链呈锯齿桩折叠构象；a-碳原子总是处于折叠的角上，氨基酸的R基团处于折叠的棱角上并与棱角垂直；3. Secondary Structure: a Helix, b Sheet, Turns and Loopsb-折叠有两种类型：平行式：即所有肽链的N-端都在同一边反平行式：即相邻两条肽链的方向相反绸带结构3. Se

34、condary Structure: a Helix, b Sheet, Turns and Loops相邻的b -链排列方向相反。一条链某一氨基酸残基的C=O和NH2基团与配对链单个相邻氨基酸的NH和C=O基团分别形成氢键An anti parallel b sheet. Adjacent b strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacentstrand, stabil

35、izing the structure3. Secondary Structure: a Helix, b Sheet, Turns and Loops相邻b -链方向相同。一条链某一氨基酸残基的C=O和NH2基团分别与配对链一个氨基酸的NH2和该氨基酸下游第二位氨基酸残基的C=O基团形成氢键A parallel b sheet. Adjacent b strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on

36、the adjacent strand.3. Secondary Structure: a Helix, b Sheet, Turns and Loops平行式：反平行式：Figure 2.34 Ramachandran diagram for b strands. The red area shows the sterically allowed conformations of extended, b- strand-like structuresy ：+135°f ：-139°y ：+113°f ：-119°3. Secondary Structu

37、re: a Helix, b Sheet, Turns and LoopsFigure 2.38 Structure of a mixed B sheet.3. Secondary Structure: a Helix, b Sheet, Turns and Loops球-棒结构模型片层结构Figure 2.39 A twisted b sheet. (A) A ball and-stick m.(B) Aschematic m. (C) The schematic view rotated by 90 degrees toillustrate the twist more clearly.3

38、. Secondary Structure: a Helix, b Sheet, Turns and Loops富含-片层的蛋白质：在长链脂肪骏的摄取、转运及代谢调节中发挥着重要作用脂肪酸结合蛋白Figure 2.40 A protein rich in b sheets. The structure of afatty acid-binding protein.3. Secondary Structure: a Helix, b Sheet, Turns and Loops蛋白质结构：-转角和无规卷曲，非重复性结构改变多肽链的3. Secondary Structure: a Helix,

39、b Sheet, Turns and Loops-转角（ - turn）：由四个氨基酸残基组成，Gly、Pro残基较多弯曲处的第一个氨基酸残基的 -C=O 和第四个残基的 N-H 之间形成氢键，形成一个的环状结构。蛋白质倒转肽链方向3. Secondary Structure: a Helix, b Sheet, Turns and Loops无规卷曲（ random coil）：又称卷曲，是没有一定规律的松散肽链结构柔性强，酶功能部位经常处于这种构象区域3. Secondary Structure: a Helix, b Sheet, Turns and Loops抗体蛋白表面有环状结构的区

40、域Figure 2.42 Loops on a protein surface.A part of an anti-body molecule has surface loops (shown in red) that mediateinteractions with other molecules.4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores蛋白质的三级结构(Tertiary Structure)是指在结构基础上，肽链的不同区段的侧链基团相互作用在空

41、间进一步盘绕、折叠形成的三维结构。主链和侧链构象在内的特征维系这种特定结构的要有氢键、疏水键、离子键和范等。尤其是疏水键，在蛋白质三级结构中起着重要作用。可溶性蛋白折叠成结构紧密的疏水核4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores在侧链疏水键作用下不规则折叠4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores模体(mo

42、tif，超结构)：数个至数十个AA组成的具有自身相对构象和功能的小区域，模体可结构域，也可。结构的组合结构形式有3种：，超细胞色素C的结构细胞核抗原的结构纤溶酶原的结构4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores结构域(domain) ：在结构或超结构的基础上，多肽链可形成在三级结构层次上的局部折叠区，称为结构域。从30氨基酸残基到400氨基酸残基不等。免疫细胞表面蛋白CD4的胞外部分Figure 2.52Protein domains. The ce

43、ll-surface protein CD4consists of four similar domains.4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores肌红蛋白的三维结构Three-dimensional structure of myoglobin. (A) A ribbon diagram showsthat the protein consists largely of a-helices. (B) A space-filling min th

44、esame orientation shows how tightly packed the folded protein is. Notice that the heme group is nestled into a crevice in the compact protein with only an edge exposed. One helix is blue to allow comparison of the two structuraldepictions.4. Tertiary Structure: Water-Soluble Proteins Fold into Compa

45、ct Structures with Nonpolar Cores血红蛋白的氨基酸分布Distribution of amino acids in myoglobin. (A) A space-filling mofmyoglobin with hydrophobic amino acids shown in yellow, charged amino acids in blue, and others in white. Notice that the surface has many charged amino acids, as well as some hydrophobic amin

46、o acids. (B) In this cross-sectional view notice that mostly hydrophobic amino acids are found on the inside of the structure, whereas the charged amino acids are foundon the protein surface.4. Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores外膜蛋白“内外翻转”肽链中所有

47、原子在三维空间的排布位置，间作用力的综合结果"Inside out" amino acid distribution in porin. The outside of porin (which contacts hydrophobic groups in membranes) is covered largely with hydrophobic residues, whereas the center includes a water-filled channel lined with charged and polar amino acids.5. Quaternary

48、 Structure: Multisubunit蛋白质的四级结构(Quaternary Structure)是指由多条各自具有完整三级结构的肽链通过非共价键连接起来的结构形式；肽链通常称为或亚Subunit各间的结合要是氢键和离子键5. Quaternary Structure: MultisubunitQuaternary structure：多蛋白内多肽链之间的相互作用l-噬菌体的cro蛋白是DNA结合蛋白，两个相同的二聚体Figure 2.53 The Cro protein of bacteriophage l is a dimer of identical subunits.5. Q

49、uaternary Structure: Multisubunit人血红蛋白a2b2四聚体（红色）是完全相同的，两个ba2b2四聚体中两个a色）也完全相同。（黄The a2b2 tetramer of human hemoglobin.6. The Amino Acid Sequence Determines Its Three-Dimensional Structure蛋白质折叠是一种高度协调的过程，氨基酸序列决定三维结构6. The Amino Acid Sequence Determines Its Three-Dimensional Structure1） 蛋白质的构象是其正常生理功能

50、的基础常见的蛋白质变性剂：尿素盐酸胍-巯基乙醇破坏二硫键和非共价作用：破坏蛋白质的折叠The disulfide bonds can be cleaved reversibly by b-mercaptoethanolAgents for disrupting noncovalent bonds: Urea and Guanidinium chloride 6. The Amino Acid Sequence Determines Its Three-Dimensional Structure-巯基乙醇将二硫键还原为游离半胱氨酸Figure 2.57 Role of b-mercaptoeth

51、anol in reducing disulfide bonds. Note that, as the disulfides are reduced, the b-mercap- toethanol is oxidized and forms dimers.6. The Amino Acid Sequence Determines Its Three-Dimensional Structure蛋白质变性：当一个蛋白质处于螺旋松散没有正常生物活性状态时，我们称这个蛋白质已经变性（denatured)。核糖核酸酶Figure 2.58 Reduction and denaturation of r

52、ibonuclease.6. The Amino Acid Sequence Determines Its Three-Dimensional Structure折叠状态转化成非折叠状态。增加变性剂浓度，大多数蛋白质从折叠状态变成非折叠状态的转变过程很急。Figure 2.63 Transition from folded to unfolded state. Most proteins show a sharp transition from the folded to the unfolded form on treatment with increasing concentrations

53、 of denaturants.6. The Amino Acid Sequence Determines Its Three-Dimensional Structure蛋白质折叠不是随机搜寻，而是逐步折叠正确的Figure 2.66 Proposed folding pathway of chymotrypsin inhibitor. Local regions with sufficient structural preference tend to adopt their favored structures initially (1). These structures come to

54、gether to form a nucleus with a nativelike, but still mobile, structure (4). This structure then fully condenses to form the native, more rigid structure (5).6. The Amino Acid Sequence Determines Its Three-Dimensional Structure蛋白质复性：采用透析的除去-巯基乙醇和尿素，核糖核酸酶的活性又慢慢恢复。蛋白质变性后不一定能够复性Re-establishing correct di