分子生物學(xué)第1章

1、1 / 45Chapter 1 Amino Acids to Proteins從氨基酸到蛋白質(zhì)從氨基酸到蛋白質(zhì)2 / 45Chapter 1 Amino Acids to Proteins1.1 Protein Composition1.2 Protein Conformations1.3 Protein Structure and Function: A Few Examples1.4 The Dynamics of Proteins1.5 Experiments1.1 蛋白質(zhì)的組成蛋白質(zhì)的組成1.2 蛋白質(zhì)的構(gòu)象蛋白質(zhì)的構(gòu)象1.3 蛋白質(zhì)的結(jié)構(gòu)與蛋白質(zhì)的結(jié)構(gòu)與 功能：幾個例子功能：幾個例子

2、1.4 蛋白質(zhì)動力學(xué)蛋白質(zhì)動力學(xué)1.5 實驗研究實驗研究3 / 45Chapter 1 Amino Acids to ProteinsLife is most directly the work of proteins. Proteins allow organisms to grow and reproduce. They provide shape, strength and movement. In the cell, proteins are everywhere and do almost everything. 生命幾乎就是蛋白質(zhì)生命幾乎就是蛋白質(zhì)的杰作。蛋白質(zhì)讓生的杰作。蛋白質(zhì)讓

3、生物可以生長和繁殖。物可以生長和繁殖。它們?yōu)樯锾峁┝送馑鼈優(yōu)樯锾峁┝送庑魏土α?，以及運動形和力量，以及運動功能。功能。在細(xì)胞中，蛋白質(zhì)無在細(xì)胞中，蛋白質(zhì)無處不在，行使著幾乎處不在，行使著幾乎任何功能。任何功能。4 / 45 紅細(xì)胞含有大量攜氧的血紅蛋白紅細(xì)胞含有大量攜氧的血紅蛋白螢火蟲的熒光素酶消耗螢火蟲的熒光素酶消耗ATP催化底物發(fā)光催化底物發(fā)光犀牛是唯一的一種具有完全由角蛋白犀牛是唯一的一種具有完全由角蛋白組成角的動物。組成角的動物。5 / 451.1 Protein CompositionProteins are composed of small molecules called

4、amino acids. Carbon atom attachs to four different chemical groups. hydrogen atomR groupDifferent amino acids have different R groups.6 / 45The twenty amino acids and abbreviationThey can be divided into four groups according to the property of their R groups.96237 / 45Structures of hydrophobic amin

5、o acids脂脂 肪族和芳香族支鏈肪族和芳香族支鏈維持蛋白質(zhì)三維結(jié)構(gòu)中起著重要作用（蛋白質(zhì)的疏水核心）維持蛋白質(zhì)三維結(jié)構(gòu)中起著重要作用（蛋白質(zhì)的疏水核心）8 / 45Structures of the hydrophilic amino acids這類氨基酸的側(cè)鏈這類氨基酸的側(cè)鏈都能與水形成氫鍵都能與水形成氫鍵，因此易溶于水。，因此易溶于水。 R基團有基團有極性極性但一般不解離。但一般不解離。9 / 45Structures of acidic and basic amino acidsNegative chargePositive charge胍基胍基咪唑基咪唑基 acidic R gro

6、upsbasic R groupsAsp and Glu carry negative charges,Lys, Arg and His carry positive charges at physiological pH value (7.27.6).10 / 4520種氨基酸三字符必需記?。悍N氨基酸三字符必需記住： 丙丙 精精 天天 酰氨酰氨 半半 谷谷 酰氨酰氨 甘甘 組組 異亮異亮 亮亮 賴賴 甲硫甲硫 苯丙苯丙 脯脯 絲絲 蘇蘇 色色 酪酪 纈纈11 / 45The formation of a peptide bondThe carboxyl group of one amino

7、acid can react with the amino group of another amino acid to form a peptide bond(amide bond-酰胺鍵酰胺鍵). Proteins can be composed of any combination of twenty amino acids, in any number and in any order. Any amino acid can join to any other amino acid.12 / 45uPartial double bond / 部分雙鍵部分雙鍵 Double-bond j

8、oining the carbon and oxygen is also distributed between the same carbon and the adjacent nitrogen. This means that the peptide bond exists as an intermediate between a single bond and double bond.Redistribution of electron density gives a partialdouble bond character to carbon-nitrogen bond. Charac

9、ter of peptide bond：13 / 45由于由于C=O雙鍵中的雙鍵中的電子云電子云與與N原子原子的的未共用電子對未共用電子對發(fā)生發(fā)生“電電子共振子共振”，共振產(chǎn)生的結(jié)果：，共振產(chǎn)生的結(jié)果：限制繞肽鍵自由旋轉(zhuǎn)而產(chǎn)生鍵限制繞肽鍵自由旋轉(zhuǎn)而產(chǎn)生鍵的平均化的平均化。(2)、一般的、一般的C-N單鍵單鍵 肽鍵肽鍵 C-N 一般的一般的C=N雙鍵雙鍵 （鍵長（鍵長1.49 ) （鍵長（鍵長1.32） （鍵長（鍵長1.27) 因此具有因此具有部分雙鍵的性質(zhì)部分雙鍵的性質(zhì)，不能沿不能沿C-N自由旋轉(zhuǎn)自由旋轉(zhuǎn)14 / 45uRigid and flexible bonds Peptide bond

10、 has partial double-bond character. it cannot rotate easily, so it is rigid . But other bonds can rotate freely.So the amino acid chains are flexible. Actually, protein molecules bend, fold, and twist to form complicated three-dimensional structures. 15 / 45肽鍵平面肽鍵平面:由于肽鍵具有部分雙鍵的性質(zhì)，使參與由于肽鍵具有部分雙鍵的性質(zhì)，使參

11、與肽鍵構(gòu)成的肽鍵構(gòu)成的六個原子被束縛在同一平面上六個原子被束縛在同一平面上，這一平，這一平面稱為肽平面面稱為肽平面(peptide plane) 但由于但由于 -碳原子碳原子與其他原子之間均形成與其他原子之間均形成單鍵單鍵，因，因此此兩相鄰的平面結(jié)構(gòu)可以作相對旋轉(zhuǎn)兩相鄰的平面結(jié)構(gòu)可以作相對旋轉(zhuǎn)。其旋轉(zhuǎn)角其旋轉(zhuǎn)角分別為分別為和和，可描述多肽鏈的所有可能構(gòu)象。，可描述多肽鏈的所有可能構(gòu)象。16 / 45N-terminus and C-terminus The ends of a protein chain are different. On one end, there is an amino

12、group. This end is called the N-terminus. On the other end, there is a carboxyl group. And it is called the C-terminus. disabled amino acidic group17 / 451.2 Protein Conformations 1.2.1 Describing Protein Structure1.2.2 Chemical and Physical Basis for Protein FoldingThe flexibility of certain bonds

13、in a polypeptide allows the chain to fold into complicated three-dimensional structures. Different conformations of proteins give them specialized functions18 / 451.2.1 Describing Protein Structure To simplify discussion of protein conformations, four levels of protein structure have been defined.Pr

14、imary structure: sequence of amino acids Secondary structures： helix and sheet are the two major forms Tertiary structure：more complicated conformation of the whole polypeptide. It is composed of various secondary structures. Quaternary structure： shape of a protein that has multiple subunits. Each

15、subunit has its own tertiary structure. 19 / 45(1)(1)蛋白質(zhì)的二級蛋白質(zhì)的二級(Secondary structure)結(jié)構(gòu)結(jié)構(gòu) 指肽鏈指肽鏈主鏈的主鏈的折疊和盤繞方式。它折疊和盤繞方式。它只涉及肽只涉及肽鏈主鏈的構(gòu)象及鏈內(nèi)或鏈間形成的氫鍵鏈主鏈的構(gòu)象及鏈內(nèi)或鏈間形成的氫鍵。 （1 1）-helix( (螺旋螺旋) ) （2 2）-sheet( (折迭折迭) ) （3 3） -turn( (轉(zhuǎn)角轉(zhuǎn)角/ /U U形轉(zhuǎn)折形轉(zhuǎn)折/ /回折回折) ) （4 4）random coil( (無規(guī)卷曲無規(guī)卷曲) )20 / 45（1）Secondary

16、structure： helix helix is a helical twisting of the polypeptide . H of an amino group interacts with a carbonyl oxygen four amino acids away. In an helix, the R groups of the amino acids stick out from the helix. Hydrogen bond21 / 45 從從N-末端出發(fā)，每個氨基酸殘基的末端出發(fā)，每個氨基酸殘基的 N-H 與前面隔三與前面隔三個氨基酸殘基的個氨基酸殘基的C=O 形成氫

17、鍵，形成氫鍵，這樣構(gòu)成的由一個這樣構(gòu)成的由一個氫鍵閉合的環(huán)，包含氫鍵閉合的環(huán)，包含-?個原子個原子肽鏈上所有的肽鍵都能參與氫鍵的形成肽鏈上所有的肽鍵都能參與氫鍵的形成，以維持螺旋以維持螺旋結(jié)構(gòu)的穩(wěn)定結(jié)構(gòu)的穩(wěn)定. . 22 / 45(2) sheet Hydrogen bondThe binding occurs between polypeptide stretchesthat lie approximately parallel to each other.Hydrogen bonds are formed between the hydrogen atoms and oxygen on s

18、eparate stretches of the polypeptide chain.- -折疊是由折疊是由兩條或多條幾乎完全伸展的肽鏈平行排列兩條或多條幾乎完全伸展的肽鏈平行排列，通過通過鏈間的氫鍵鏈間的氫鍵交聯(lián)而形成的扇面狀片層構(gòu)象交聯(lián)而形成的扇面狀片層構(gòu)象23 / 45- -碳原子碳原子總是處于折疊的角上，氨基酸的總是處于折疊的角上，氨基酸的R基基團團交替分布在片層的兩側(cè)。交替分布在片層的兩側(cè)。 側(cè)鏈側(cè)鏈( (C -C鍵鍵) )幾幾乎垂直于折疊片平面。乎垂直于折疊片平面。24 / 45Parallel and antiparallel sheetsParallel sheet: stre

19、tches have same directions. Anti-parallel :different directions. N-terminus of the top stretch is on the left, but that of the middle stretch is on the right. And that of the bottom one is on the left again. 25 / 45 永久性卷發(fā)（燙發(fā)）原理：永久性卷發(fā)（燙發(fā)）原理： -角蛋白角蛋白在濕熱條件下伸展為在濕熱條件下伸展為 -構(gòu)象構(gòu)象，當(dāng)涂上氧化當(dāng)涂上氧化劑使劑使很多的很多的二硫鍵交聯(lián)二硫

20、鍵交聯(lián)，因此當(dāng)外力解除后，肽鏈又，因此當(dāng)外力解除后，肽鏈又恢復(fù)原狀恢復(fù)原狀。26 / 45（3 3）蛋白質(zhì)的蛋白質(zhì)的 - -轉(zhuǎn)角轉(zhuǎn)角( ( -turn) )蛋白質(zhì)分子的多肽鏈上常出現(xiàn)蛋白質(zhì)分子的多肽鏈上常出現(xiàn)180180的回折，的回折，這種陡然改變方向的肽段即這種陡然改變方向的肽段即-轉(zhuǎn)角。轉(zhuǎn)角。27 / 45特征：特征： 主鏈骨架本身以大約主鏈骨架本身以大約180180回折回折; ; 在回折部分，涉及在回折部分，涉及四個四個氨基酸殘基氨基酸殘基; ; 彎曲處彎曲處第一個第一個AAAA殘基的殘基的 C=OC=O 與與第四個第四個AAAA殘基的殘基的 N-HN-H之間形成氫鍵，使之間形成氫鍵，使

21、- -轉(zhuǎn)角成為比較穩(wěn)定的結(jié)構(gòu)。轉(zhuǎn)角成為比較穩(wěn)定的結(jié)構(gòu)。 28 / 45(3)Tertiary structure / 三級結(jié)構(gòu)三級結(jié)構(gòu)helix sheetTurn It is three-dimensional structure of whole polypeptide It is mostly composed of various secondary structures.helical ribbonsflat arrowsturns that connect the helices and sheets. 29 / 45(4)Quaternary structure One subu

22、nit 由由兩個或兩個兩個或兩個以上的具有獨立以上的具有獨立三級結(jié)構(gòu)三級結(jié)構(gòu)的的亞基（亞基（subunit）按照一定按照一定排布方式排布方式，通過，通過非共價鍵非共價鍵締合而形成的具有一定締合而形成的具有一定空間結(jié)構(gòu)的蛋白質(zhì)分子稱為四級結(jié)構(gòu)?？臻g結(jié)構(gòu)的蛋白質(zhì)分子稱為四級結(jié)構(gòu)。Each subunit has own tertiary structure.multiple subunits30 / 4531 / 45Please note here, if a protein has only one polypeptide chain, the highest level it can hav

23、e is structure.Only when a protein has more than one polypeptide chain, can it have quaternary structure.tertiary肌紅蛋白肌紅蛋白32 / 45lets examine what physical interactions happen in the process of protein folding. 1.2.2 Chemical and Physical Basis for Protein Folding1) Covalent bonding2) Hydrogen bondin

24、g3) Ionic bonding4) Van der Waals forces5) Hydrophobic interaction33 / 451) Covalent bond / 共價鍵共價鍵Shared electronsHHH+1H+1+1+1Covalent bondThe strongest bond that joins atoms. A pair of electrons is shared between two atoms. Two electrons from two hydrogen atoms are shared between these two atoms. A

25、 single covalent bond is formed.34 / 45Covalent bond / 共價鍵共價鍵Covalent bondThe peptide bonds are covalent bonds. The bonds within amino acids are also covalent bonds. 35 / 45Covalent bonddisulfide bondCovalent bonds can form between amino acids that are not adjacent in polypeptide.Each cysteine has a

26、 sulfhydryl group (SH). Two sulfhydryl groups can react to form a disulfide bond(二硫鍵二硫鍵).It hold distant parts of the protein together very tightly. 36 / 452) Hydrogen bond / 氫鍵氫鍵Hydrogen bondHydrogen bond is result of interactions betweenpartial negative charges and partial positive charges. Oxygen

27、 atom brings partial negative charge. Hydrogen atoms bring partial positive charge.Interaction between oxygen and hydrogen atoms forms the hydrogen bond.37 / 45氫鍵（氫鍵（hydrogen bond）的形成常見于連接在一的形成常見于連接在一電負(fù)性電負(fù)性很強的原子上的很強的原子上的氫原子氫原子，與另一電負(fù)性很強，與另一電負(fù)性很強的的原子之間，原子之間，如如 C=O H-N。Hydrogen bond / 氫鍵氫鍵38 / 45Hydrog

28、en bond helices and sheets are formed with hydrogen bonds. Hydrogen bond can also form between individual amino acids when partial positive hydrogen atoms are near the partial negative O atoms.39 / 45Na+11Cl+173) Ionic bond / 離子鍵離子鍵The ionic bond of sodium chloride, NaCl Ions are atoms that have gai

29、ned or lost one or more electrons and have full positive or negative charges. Ions with opposite charges attract each other and pulled to each other, forming the ionic bond.40 / 45GluLysnegative charge positive chargeIn proteins, most ionic bonds form between the amino acids with acidic R group and

30、Basic R group.41 / 454) Van der Waals forces / 范德華力范德華力Atom 1Atom 2van der Waals force These areas with slightly different charge concentrations can attract to each other. The attraction between such differently charged areas is called van der Waals force.It occurs because cloud of electrons are shi

31、fted, causing atom itself have positive charge in one area, and negative charge in another area.42 / 45Van der Waals forces vs. Ionic bondAtom 1Atom 2Van der Waals forcesThe atom itself has negative and positive parts.The interaction is transient.Ionic bondThe whole atom is either negative or positi

32、ve parts.The interaction is stable.Atom 1Atom 243 / 45Van der Waals forces vs. hydrogen bondAtom 1Atom 2Van der Waals forcesThe atom itself has negative and positive partsThe interaction is transientHydrogen bond.The whole atom is either partially negative orpositiveThe interaction is stableAtom 1At

33、om 2+44 / 455) Hydrophobic interaction非極性物質(zhì)非極性物質(zhì)在在含水的極性環(huán)境含水的極性環(huán)境中存在時，會產(chǎn)生中存在時，會產(chǎn)生一種一種相互聚集的力相互聚集的力，這種力稱為疏水鍵或疏水作用，這種力稱為疏水鍵或疏水作用力（力（hydrophobic interaction）Hydrophobic interaction is the tendency for non-polar molecules to gather near each other, away from water molecules.? But what causes this movement

34、? 45 / 45Nonpolar molecules are forced togetherWater molecules get contacts with each other.when non-polar molecules mix with water, they force the water molecules into relatively ordered structures that surround the non-polar molecules. However, according to the second law of thermodynamics, system

35、s always tend toward increasing disorder. Thus, the two kinds of molecules to simply avoid each other. The apparent result is that the non-polar molecules are attracted to each other. 46 / 45For proteins that exist in water, the effect of this hydrophobic interaction is that non-polar amino acids ar

36、e forced into the center of the protein, away from the watery environment of the cell. 47 / 451.3 Protein Structure and Function Protein chains can fold into complex structures. Proteins can have very different structures and very different functions.碳酸酐酶碳酸酐酶The reaction allows CO2 to dissolve in bl

37、ood. It can cause this reaction to occur 10,000,000 times faster than normal .active sitestructure and shapesubstrate moleculescarbonic acid48 / 45Actin / 肌動蛋白肌動蛋白 Filaments line inside of cells and are often used to provide support, Actin is a small and simple protein. It can join with other actin

38、to form long and thin actin filament. somewhat like poles holding up a tent. Actin filaments in a cell as seen by flourescence microscopy49 / 45Kinesin / 驅(qū)動蛋白驅(qū)動蛋白Kinesin is used to carry cellular components, like organelles, from one end of a cell to another. The cargo is bound to central head regio

39、n, while the two legs attach to microtubules. As a result, the protein walks along the microtubule toward its destination. microtubuleHead regionThe structure of kinesin includes a pair of legs.50 / 451.4 The Dynamics of ProteinsProteins are dynamic. This means that their structures are not frozen a

40、s fixed shapes. Their structures and even functions can change under different conditions.Actincarbonic anhydrase51 / 45Induced-fit vs. lock-and-key modelsWhen some enzymes catalyze reactions, their active site changes structure in order to fit well with substrate molecules. This catalysis mechanism is called an induced-fit model(誘導(dǎo)契合機理誘導(dǎo)契合機理). In some cases catalysis occurs without a change in structure at the active site; this is called a lock-and-key mechanism（鎖鑰機理）（鎖鑰機理）. Substract reaction causes change of