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Amino Acids to Proteins
從氨基酸到蛋白質(zhì)
Life is most directly the work of proteins. Proteins allow organisms to grow and reproduce,the most fundamental properties of life. They provide shape and strength,and in many cases movement. They underlie cellular communication,but are also a key part of the boundaries that separate cells and organelles from their environment. In the cell,proteins are everywhere and do almost everything. In this chapter we examine the molecular composition of proteins,showing how the joining of small,simple molecules can produce large molecules with complicated shapes and extraordinary functions.
生命幾乎就是蛋白質(zhì)的杰作。蛋白質(zhì)讓生物得以生長(zhǎng)和繁殖,生長(zhǎng)和繁殖是生命最基本的特征。蛋白質(zhì)賦予了生物外形和力量,以及在許多情形中的運(yùn)動(dòng)功能。蛋白質(zhì)還是細(xì)胞通訊的基礎(chǔ),也是細(xì)胞膜的組成部分(正是細(xì)胞膜將細(xì)胞和細(xì)胞器與它們的環(huán)境分隔開)。在細(xì)胞中,蛋白質(zhì)無處不在,行使著幾乎所有功能。本章我們將學(xué)習(xí)蛋白質(zhì)的分子組成,了解簡(jiǎn)單小分子是如何連接在一起產(chǎn)生具有復(fù)雜形狀和超乎尋常功能的大分子的。
Protein Composition
蛋白質(zhì)的組成
Proteins are polymers of small molecules called amino acids(Figure 1.1).It is convenient to think of an amino acid as a carbon atom attached to four different chemical groups. Three of these are all always the same:an amino group,a carboxyl group,and a hydrogen atom. The fourth group is generally termed the side chain,or R group,and varies between different amino acids. There are 20 different amino acids commonly used to make proteins,and all 20 have different R groups. R groups have various sizes and chemical properties(Figures 1.2 and Figures 1.3).
蛋白質(zhì)是由稱為氨基酸的小分子組成的聚合物(圖1.1)。可以很方便地把氨基酸看成是由四個(gè)不同的化學(xué)基團(tuán)連接到一個(gè)碳原子上而形成的結(jié)構(gòu)。其中三個(gè)基團(tuán)總是相同,即氨基、羧基和氫原子。第四個(gè)基團(tuán)通常被稱為側(cè)鏈,或R基團(tuán),它隨氨基酸的不同而有變化。通常有20種不同的氨基酸被用來生產(chǎn)蛋白質(zhì),它們均具有不同的R基團(tuán)。R基團(tuán)大小不一,其化學(xué)性質(zhì)也不同(圖1.2和圖1.3)。
Amino acids are joined to each other by combining the amino end of one with the carboxyl end of another(Figure 1.4).Because all amino acids have these two ends,any amino acid can join to any other amino acid. The polymer that results from these combinations is linear,meaning that there are no branchpoints. Proteins can be composed of any combination of the twenty amino acids,in any number,attached in any order. In fact,this flexibility in composition is necessary to produce the wide variety of proteins that are used in nature.
氨基酸可以通過一個(gè)氨基酸上的氨基與另一個(gè)氨基酸上的羧基結(jié)合而互相連接起來(圖1.4)。由于所有氨基酸都具有這兩個(gè)基團(tuán),因此任何氨基酸都可以與任何其他氨基酸相連接。這種結(jié)合形成的聚合物是線性的,意味著它們沒有分支。蛋白質(zhì)可以由20種氨基酸以任何組合、任何數(shù)目和任何順序組成。事實(shí)上,這種在組成上的靈活性對(duì)于產(chǎn)生在自然界中用到的種類繁多的蛋白質(zhì)是必需的。
The bond that joins two amino acids in a protein is called a peptide bond. It is a kind of amide bond. The peptide bond is quite strong and rigid,and does not allow rotation. This is because the double-bond joining the carbon and oxygen is also distributed between the same carbon and the adjacent nitrogen. The redistribution of electron density gives a partial double-bond character to the carbon-nitrogen bond,which is the core component of the peptide bond. This partial double-bond character prevents the peptide bond from rotating easily.
在蛋白質(zhì)中連接兩個(gè)氨基酸之間的鍵叫做肽鍵。它是一種酰胺鍵。肽鍵很強(qiáng)并具有剛性,不允許旋轉(zhuǎn)。這是因?yàn)檫B接碳和氧的雙鍵也在同一個(gè)碳和鄰近的氮之間進(jìn)行分配。電子密度的重新分布使得碳-氮鍵具有部分雙鍵的特性,而碳-氮鍵是肽鍵的核心成分。這種部分雙鍵特性防止了肽鍵發(fā)生自由旋轉(zhuǎn)。
Although peptide bonds are rigid,amino acid chains are flexible because other bonds within each of the amino acids can rotate(Figure 1.5).As a result,although proteins are linear,they are not one-dimensional. The linear molecule bends,folds,and twists to form complicated three-dimensional structures. We explore protein structures in the next section.
雖然肽鍵具有剛性,但是氨基酸鏈還是容易彎曲的,因?yàn)槲挥诎被崂锩娴钠渌I都可以發(fā)生旋轉(zhuǎn)(圖1.5)。結(jié)果,雖然蛋白質(zhì)是線性的,但它們并不是一維的。線性的分子會(huì)發(fā)生彎曲、折疊和扭曲從而形成復(fù)雜的三維結(jié)構(gòu)。我們將在下一節(jié)中去探尋蛋白質(zhì)結(jié)構(gòu)方面的知識(shí)。
The ends of a protein have unique chemical properties. On one end,an amino group is left unreacted,unlike the other amino acids in the protein that have been polymerized. This end of the peptide is called the N-terminus(Figure1.5).On the other end,a carboxyl group remains unreacted. This end is called the C-terminus. Under cellular conditions,the N-terminus is usually positively charged,and the C-terminus is negatively charged. A protein’s termini provide a convenient way to indicate directionality. To indicate the position of an amino acid A in a protein relative to amino acid B,for example,we might say,“A is 5 amino acids away from B in the N-terminal direction.”
蛋白質(zhì)的末端具有獨(dú)特的化學(xué)性質(zhì)。在一個(gè)末端上保留了一個(gè)沒有發(fā)生反應(yīng)的氨基,它與其他已經(jīng)發(fā)生了聚合的氨基酸不同。這個(gè)末端叫做N-末端(圖1.5)。在另一個(gè)末端上有一個(gè)羧基保持著未發(fā)生反應(yīng)的狀態(tài)。這個(gè)末端叫做C-末端。在細(xì)胞中,通常N-末端帶有正電荷而C-末端帶有負(fù)電荷。蛋白質(zhì)的末端為說明蛋白質(zhì)的方向提供了方便。例如,要說明蛋白質(zhì)中氨基酸A相對(duì)于氨基酸B所處的位置,我們可以說:“A位于B的N-末端距離5個(gè)氨基酸之處。”
Note that in addition to the term protein,the term polypeptide can be used to refer to polymers in which amino acids are connected by peptide bonds. The distinction between these terms is not always clear. Polypeptide is a more general term that applies any time amino acids are polymerized by peptide bonds,even if the polymer is made synthetically and has no function.‘Protein’is more often used to describe one or more polypeptides that have a function in nature. The term peptide may also be used instead of‘polypeptide’or‘protein’,most frequently to refer to short polymers of amino acids.
請(qǐng)注意,除了蛋白質(zhì)這一術(shù)語(yǔ)外,多肽也可以用來指由肽鍵連接起來的聚合物。這兩個(gè)術(shù)語(yǔ)之間的區(qū)別并不是很清楚。多肽是更普遍的術(shù)語(yǔ),它適用于任何氨基酸經(jīng)由肽鍵得到的聚合物,即使此聚合物是人工合成并且是沒有功能的。“蛋白質(zhì)”更經(jīng)常地用來描述自然界中具有功能的一種或多種多肽。在描述氨基酸的短聚合物時(shí),術(shù)語(yǔ)肽也常常用來代替“多肽”或“蛋白質(zhì)”。