生命出现之时:40亿年前的海洋化学

Encyclopedie environnement - origine vie océan - origin life oceans

  大约40亿年前,大部分地球被一片巨大的海洋覆盖。这片海洋含有大量有机小分子,它们在生命出现之前就存在了,所以也被称为“前生命质体”。它们究竟是什么?是原位合成还是来自太空?它们如何结合形成长的聚合物?这些聚合物有些是遗传信息的载体,另一些则负责复制所有基本分子并将它们连接成聚合物。一切都不可预知。这些聚合物并不稳定,化学键也很难产生。但是我们仍想一探究竟。这一切得益于化学的极度精妙,它把这些问题交给能量和时间来解决。本文试图给出一些可以帮助我们理解生命起源过程的证据。

1. 很久以前,在一个不那么远的星系

  大约46亿年前,在一个叫做银河系的螺旋星系的偏心位置,形成了一个巨大的物质圆盘。构成这个圆盘的大多数气体、颗粒和块体聚集并融合,形成了一颗恒星——太阳。少量保留下来的残留物质形成了行星和小的天体、矮行星和小行星。我们的地球,确切地说是原地球,就是在那个时候形成的。五千万年后(与天文时间的尺度相比这点时间不算多),这个原始地球被一个非常巨大的天体——忒伊亚(Theia)——一个火星大小的小行星撞击。月球和我们现今的地球就诞生于这次巨大的撞击中[1]

  在这次撞击前,地球大气层很可能含有大量氢——这是原始太阳盘的主要成分。但是这次撞击威力如此巨大,轻元素被排出,产生了一个富含二氧化碳(CO2)、氮气(N2)和水蒸气(H2O)的全新大气圈。此时地球仍然很热但是冷却得相当快。水蒸气持续凝结,倾盆大雨持续不断地从天而降,地表形成了第一个独特的浩瀚的海洋。

  在这片海洋之下,地幔的上部冷却凝固形成了初始的地壳。原始的构造板块逐渐形成。我们已经可以看到一些可能从海洋中浮现出来的原始大陆、分散的岛屿,以及很可能比现今火山活跃得多的火山。我们的星球仍然充满能量!年轻的太阳形态更小,能量更弱,而地球充盈的能量恰恰弥补了这一缺陷。如果没有地球释放的能量,如果没有大气中高比例二氧化碳造成的显著的温室效应,很可能所有的水都变成了冰。在这片冰层里会诞生什么样的生命?毫无疑问,什么也没有…

  就在月球诞生后,在原始地球穿过忒伊亚(Theia)轨道之时,地球遭受了许多小行星的撞击,这些小行星可能给地球带来了大量额外的水,也许还包括有机分子。地球的强势恢复标志着这些灾难性的撞击最终于38亿年前画上了句点(也许只是“几乎”结束了:我们仍然无法避免灾难性的撞击。恐龙的灭亡证明了这一点!)。

  在这场“大撞击”结束之前,生命可能就已经出现了,但这方面的证据仍然很贫乏。即使生命出现了,它们能从这些反复出现的灾难中幸存下来吗?(参阅一位天文学爱好者兼地质学家眼中的生命起源)。

2. 如此多水!如此多水!

  接下来,让我们把自己置于距今接近40亿年前的冥古宙末期。当时,地球上形成了巨大的海洋、极度活跃的火山和大陆的雏形。月球正逐渐远离地球,但它远远没有抵达现今的轨道:而是位于现今距离的三分之一处。因此,当时潮汐的力量是巨大的,是如今的二十多倍,风也很大。即使它正在降温,当时海洋的温度也可能比今天更高

  我们很难知道海洋当时的 pH 值(pH值,即氢势,是溶液酸度(pH 值低于7)或碱度(pH 值高于7)的指标。 pH值等于7称为中性溶液)虽然海洋目前是略微碱性(约8.1),但由于人类二氧化碳的排放,海洋会逐渐酸化。在水中, CO2 会形成一种酸——碳酸。现今大气中的二氧化碳比生命诞生之初少得多,所以当时的海洋也许是酸性极强的,这对潜在的化学反应产生了影响。原始海洋当然也含有离子。像现今的海水一样,钠(Na+)和氯(Cl)占主导地位,海水已经咸了!还有钙、镁、溴化物,甚至还有比今天多得多的碘化物。

  起初,人们认为原始大气因含有大量的氢、甲烷和氨而具有很强的还原性。但如果有含氢的话,忒伊亚(Theia)的冲击会导致这种轻气体被排出到太空中。然而大气不是氧化性的,因为那时的大气不含或含有少量分子氧(O2)。我们可以通过测定最古老的含三价铁的矿床的年龄来确定地球上氧气大量出现的时间。事实上,当铁暴露在含氧的水中时,就会生锈。也就是说,它被氧化成三价铁(Fe3+),三价铁不溶于水。然而,在没有氧气的情况下,铁会形成可溶的亚铁离子(Fe2+)。

  因此,我们现今的海洋和原始海洋间有一个主要的区别:原始海洋含有可溶的亚铁离子

3. 大量的小分子

环境百科全书-海洋化学-生命起源以前物质合成
图1. 生命起源以前物质合成的示例。
“糖”代表的是一种含有5个碳原子的戊糖,这只是众多例子之一。类似地,这也可能是除甘氨酸、丝氨酸和半胱氨酸的其他氨基酸的合成机制。(图 1 formose reaction 甲醛聚糖反应;formaldehyde 甲醛;hydroxyacetaldehyde 羟基乙醛;some steps 一系列中间反应阶段;“sugars”糖;glycine  甘氨酸;Strecker reaction  斯特雷克氨基酸合成反应;serine  丝氨酸;cystein 半胱氨酸;amino acids 氨基酸)

  原始海洋中也含有有机分子。含有两个碳原子的分子很容易由二氧化碳或甲烷(CH4)形成。二氧化碳可以还原为甲醛(H2CO,图 1),甲醛通过“甲醛聚糖反应”首先生成羟乙醛(一种双碳分子),然后形成更长的分子:糖。一个厨师会说,有了这些糖和氯化钠,原始海洋是又甜又咸的!

  除了糖之外,构建一个活细胞至少还需要两类分子:蛋白质和核酸。这些分子都含有氮。在生命起源之前的海洋中,这些氮的来源是什么?很可能是氨(NH3) 和氢氰酸(HCN)。当这两种化合物与甲醛反应时,它们会生成最简单的氨基酸: 甘氨酸。这种分子是通过一个叫做斯特雷克氨基酸合成的基本反应产生的,这个反应是以德国化学家阿道夫·斯特雷克(Adolph Strecker)的名字命名的,他于19世纪中叶发现这种反应过程。这种醛类的合成反应可以得到各种氨基酸,例如由羟基乙醛合成丝氨酸(图 1)。

  这些氨基酸是蛋白质聚合物的基本成分。正如我们刚才所看到的,它们很容易合成:因此它们很可能存在于原始海洋中。

  那么携带遗传信息的核酸前体DNA呢?它们的合成稍微复杂一点。不太明显的是,它们同时存在。但是它们在生命起源之前的合成是可能的。核糖可以通过前面提到的甲醛聚糖反应得到,核酸碱基可以从氰化氢中得到,此外最近研究人员发现了直接获取核糖碱基复合物的途径。

  然而,DNA 和 RNA 链的合成引出了关于磷的来源问题。磷广泛存在于这些携带遗传信息的聚合物中。在我们氧化的世界中,这种元素通常以磷酸盐的形式存在,特别是不溶于水的磷酸钙。那么非氧化性的在原始海洋中是否存在磷酸盐(可溶)?否则,可溶性磷的来源是什么?这是一个尚未解决的问题[2]

  另一个重要元素是,目前存在于两种维持生命的氨基酸——蛋氨酸和半胱氨酸中。它从活火山、喷气孔、许多热液泉中大量释放,通常以硫化氢(H2S)的形式释放。因此,可以合理地假设原始海洋含有硫化氢,那么也必然含有小的含硫分子,如半胱氨酸。

  如果我们肯定(有些人会说:几乎肯定)没有来自星系空间的外星人踏上过我们的星球,那么这里提到的一些分子则有可能是由数以百万计的撞击地球的小行星带来的,特别是在大撞击时期。例如,罗塞塔探测器(Rosetta)对小行星67P/Chourioumov-Guérassimenko(被称为“Chouri”)的探测访问表明,它包含水、氨、甲醛、氢氰酸、硫化氢……但也包含更复杂的有机分子,包括甘氨酸。这种小氨基酸是通过地球上一次可能发生的合成反应生成的,上文已述(参阅 如何研究彗星的有机分子?)。

  那么第一个甘氨酸:是地球本源的还是外星来源的其他氨基酸呢? DNA 的碱基呢?没人知道。但可以肯定的是,当大规模撞击停止时,当这种可能的外星来源枯竭时,当所有这些来自外星的小分子都用完了,必然只能依靠地球本源合成。正如我们所看到的,它们是完全可能的。外星假说,哪怕无法反驳,对解释地球上生命的诞生并不重要。

环境百科全书-海洋化学-化学反应
图2. 距今40亿年前,地壳刚刚形成,大部分被含有可溶性亚铁离子的浩瀚海洋覆盖。
小行星带来了水和小的有机分子。其他分子是在海洋中形成的。氢氰酸 HCN 的存在一方面允许 RNA 碱基的合成,另一方面允许氨基酸的合成,氨基酸聚合时产生第一个肽。(图 2  Asteroid 小行星;Atmosphere 大气圈;vapour 蒸气;Ocean 海洋;Crust 地壳;Magma 岩浆;bases 碱基;sugar 糖;Glycine 甘氨酸;Cysteine  半胱氨酸;Serine  丝氨酸;peptides  多肽)

  图2总结了所有这些化学反应。

  现在的问题是这些分子的浓度如何?这是一个非常重要的问题:在给定反应中,起始化合物浓度越稀,反应越慢。当然,距离生命诞生,时间还够。但许多小分子聚合产物在水中并不非常稳定。我们必须做足准备,且足够快,使它们在重新分解为小分子之前继续生长,形成越来越长、越来越复杂的分子。这就引出了两个问题:地球上有多少水?水里有多少质量的有机分子?

  多少水?最贴合实际的假设是不比今天多也不比今天少,粗略地说,大约13.6 亿立方千米,四舍五入大约1021升(十万亿亿升)——甚至省略的部分都是一个巨大的数字!

  在这片海洋中,究竟存在多少将形成生命的有机分子,想弄清楚这一点是非常复杂的。目前的陆地生物圈含有2000千兆吨(20000亿吨 = 2*1018克)有机碳。在真正“有机”的生命出现前,这种形式的小分子不太可能有更多了。

  让我们简单做一个计算:200 亿亿克除以100000亿亿升,即每升水含有两毫克有机碳。这个浓度很低,但不是全然荒谬。这很可能还高估了哈达亚海洋中的有机分子浓度,实际浓度可能更低。由于原始海洋不断的被巨大潮汐搅动,化学反应相当迅速,此时的浓度分布怎可能大致均匀?

  在1871年,达尔文(Darwin)写信给他的朋友约瑟夫·胡克(Joseph Hooker)时,就已经表明了这个问题:“但是,如果我们可以想象(哦,这属于大胆想象了)在一个温暖的小池塘里,存在着各种各样的氨和磷盐、光、热、电等,蛋白质化合物以化学方式形成,为之后经历的更复杂的变化做好了准备。”

  这就是温暖的小池塘的起源,它的确让许多探究生命起源的研究者为之着迷。达尔文假设他的小池塘是足够浓缩的,化学过程就可以一直进行,直到合成一个足够长的氨基酸链,即“蛋白复合物”。

  在新兴的大陆上可能有一些小的水域,但其中的有机分子浓度是否比在全球海洋中更高?也许分子集中在最初的海滩上,或者在一些裂缝里?火山周围有更多的有机化合物吗?或者在海底热泉喷口(热气从喷口喷出)附近?我们难道不应该设想一些特别有效的反应,即使在浓度非常稀的条件下也能产生聚合物(例如蛋白质)吗?

4. 成功的关键:能量和催化

  对于一个化学反应,以下两点是必需的:

  • 首先是可能发生的,这是一个热力学问题。
  • 其次是足够快的,这是一个动力学问题。

  然而这只是推理:40亿年前,没有什么事情是确定的。

环境百科全书-海洋化学-氨基酸合成二肽
图3. 两个氨基酸合成一个二肽的过程。
箭头长度的差异意味着平衡向两个氨基酸转移。尤其是水的形成,抑制了二肽的合成。(图3  2 monomers 两个单体;2 amino acids 两个氨基酸;dimer 二聚体;dipeptide 二肽)

  从热力学的观点来看,重要的是起始分子和形成分子的相对稳定性。构建聚合物是一个循序渐进的过程。首先,两个单体产生一个二聚体,二聚体延伸成三聚体,以此类推,直到形成很长的链。因此,一开始,两个单体形成一个二聚体,一个水分子被消除。无论是肽(图 3)还是核酸,二聚体的稳定性都远低于单体。换句话说,二聚体裂解反应(水解)是有利的。因此,平衡向单体转移。尤其是水解会消耗一个水分子,这在水中会得到助力;而肽键缩合会在二聚体之外形成一个水分子,在水中这个过程会受到抑制。正是由于水分子形成会导致聚合反应受抑制,一些作者在考虑生命起源的最初情景时会寻找含水尽可能少的环境,特别是原始大陆的海岸,在那里可以找到相对干燥的地方。

  在动力学方面也好不到哪里去。要使两个分子一起反应,它们必须处于激活状态,也就是说需要给它们一定的能量。需要提供的能量越高,两个单体相遇(称为“冲击”)越不容易发生反应,即反应越慢。然而,形成蛋白质或核酸二聚体雏形所需的能量是巨大的。

  浪费时间?不,因为尽管如此,很明显地是生命已经出现了。要做到这一点,至少需要:

  • 一种能量丰富的分子。通过将自己裂解成两个碎片,释放出它所包含的大部分能量。如果这与二聚体(例如二肽)的形成同时发生,那么这两种能量将相互补偿,整个过程将受到热力学的促进;
  • 一种催化剂,也是一种化学物质:一种分子或者固体表面,(参阅 早期细胞的起源:工程师的观点)能够促进两个单体形成二聚体。有效碰撞(真正形成二聚体的分子之间的碰撞)的数量将大大增加,在原始海洋中,反应将达到合理的速率。
环境百科全书-海洋化学-ATP在多肽生物合成的作用
图4. ATP(三磷酸腺苷)在多肽生物合成中的作用。
前两个反应是由一种蛋白质-氨基酰基 tRNA 聚合酶催化的。第三个发生在核糖体内两个tRNA 分子的末端,核糖体本身由大量的 RNA 链组成。这最后一步是由 RNA 催化的,这是研究人员提出存在一个以 RNA 为主的原始世界(RNA 世界)的有力论据。(图 4 ATP 三磷酸腺苷(ATP);an anhydride  酸酐;an ester  酯;an amide  酰胺;the peptide being synthesized正在合成的多肽)

  在生物体中广泛使用的高能分子是 ATP(图 4),一种三磷酸腺苷。磷酸键断裂释放出的能量足以平衡要合成的二聚体的不稳定性。在肽合成过程中,甚至允许先形成比二聚体本身更不稳定的中间体,再形成二聚体。首先形成混合磷酸羧酸酐,然后形成酯,最后形成酰胺(肽)。总的来说,这包括三个步骤,每一个步骤本身都很慢,因此需要催化剂参与。所以,原始海洋中早期多肽的形成可能需要一段时间。

  因此,要解释生命的出现,首先需要确定至少一种分子能量来源(考虑到在原始海洋中 ATP 存在的可能性极小,因为它蕴含的能量过于庞大),另一方面也需要确定最初的催化剂(目前在活细胞中使用的那些氨酰基 tRNA 合成酶以及其他酶,对于前生物质体来说是过于复杂的)。

  问题已经提出,其他一切都只是假设。今天最普遍接受的假说是“RNA世界[3](参阅 最初细胞的起源:工程师的观点):它认为生命起源的早期,最先出现的重要聚合物是 RNA,它既是遗传信息的载体,也是催化剂。事实上,目前活细胞中的一些 RNA 的确具有催化性质(尽管绝大多数生物催化剂是蛋白质)。关于能量来源:如果不利用三磷酸腺苷(ATP)中的能量,就不可能形成 RNA。然而,三磷酸腺苷(ATP)不太可能存在于原始海洋中,这是该假说的问题之一。但它具有协调遗传信息和催化作用的优点。

  另一方面,蛋白质不携带遗传信息,但它们是比 RNA 好得多的催化剂。这种遗传信息的匮乏是否能排除蛋白质是生命历史早期中真正重要的聚合物的可能性?也许不能……目前研究发现,一些肽能够直接在蛋白质上合成,并不需要核酸的帮助。这些肽被称为“非核糖体的”,因为它们不是在核糖体(RNA 复合物)中合成的。然而,它们也不是“随机”产生的,作者们认为存在一种特殊密码,它与传统遗传密码(通过 RNA 将 DNA 翻译成蛋白质)并不相同。这种“非核糖体的”密码将蛋白质转化为肽(可以说肽转化为肽)。它是一个复杂的密码,基于10个氨基酸的集合(在编码蛋白质中):它能够精确地选择氨基酸,并将其引入到要合成的肽中。因此,没有什么能够阻止我们发挥想象,也许“前遗传学(pre-genetic)”信息,即使是粗略的信息,最初也可能是由氨基酸链携带的。

环境百科全书-海洋化学-催化三联体的作用原理
图5. 催化三联体的作用原理,这里是半胱氨酸-组氨酸-天冬氨酸三联体。
锯齿链代表肽链。这一反应形成了硫酯,它是一种高能分子,将用于后续的反应,如水解。   酰胺的形成是另一种可能的后续反应。(图 5 cysteine 半胱氨酸;histidine 组氨酸;aspartate 天冬氨酸;thioester 硫酯;acid 酸;amide 酰胺;peptide 肽)

  尽管催化蛋白是复杂的分子,但它们的活动通常基于相当简单的原理。例如在水解酶和转移酶中发现的催化三联体。它需要三种氨基酸:一种醇或硫醇、一种碱基和一种酸。在图5中,参与反应的是一种硫醇和半胱氨酸。由于蛋白质链下游的组氨酸(碱基),导致半胱氨酸失去了质子而携带负电荷,这使它能够与 C=O双键的正碳发生反应。天冬氨酸的存在可以激活组氨酸。在这种情况下,反应产物是硫酯,这是继三磷酸腺苷之后的另一种高能分子。随后硫酯可能发生其他反应,例如与水反应生成酸(含有三联体的蛋白质是一种水解酶),或与另一个有机分子反应(三联体是转移酶的活性位点)。

  当然,在我们目前的蛋白质中,这些三联体是由连接它们的氨基酸链精确定位的。正因为如此,每一个三联体蛋白质都是特异化的,只对同样明确定义的分子进行一种特定类型的反应。但是,在40亿年前原始海洋中,有三联体存在吗?毫无疑问,它们当时的特异程度低得多,在某种程度上“擅长一切”。擅长一切有何不可?图6展示了一个极度简化的三联体的例子。分子的立体化学(或称“手性”)是非常明确的:这是一个极其重要的问题,一个完整的生命起源模型必须解释这个问题[4]

环境百科全书-海洋化学-脂肪酸链
图6. 左图:一种极端简化三联体;右图:三种脂肪酸。
左图分子(假设的)是环状的。它含有3种氨基酸(半胱氨酸、组氨酸和天冬氨酸)。没有迹象表明这种催化剂具有催化活性。右图是长的有机链,含有 CH2 重复单元,末端带有一个羧酸基团。(图 6 cysteine 半胱氨酸; aspartate 天冬氨酸;histidine 组氨酸;caprylic acid 羊脂酸;lauric acid 月桂酸;palmitic acid 棕榈酸)

  最后,如果没有分隔结构、细胞或类似的东西,如膜或壁,我们很难想象生命将如何存在。早期的膜可能是由缠绕的或有序的肽粘合在一起形成的。它们也可能含有长的疏水性有机链,即脂肪酸链(图 6)。由于蛋白质和硫醇化学,目前合成这些脂肪酸是有可能的。

  人们所描绘的生命诞生之时的世界可以说更多是一个多肽的世界,而不是核酸的世界。硫通过半胱氨酸和硫酯会发挥非常核心的作用,把它与一个可能的世界密切联系,这个世界甚至更原始、更“矿物”,即铁-硫世界[5] [6]。这引发了人们对亚铁离子特殊作用的思考,亚铁是可溶的,因此是可用的,能够为所有这些肽提供电子和能量。

 


参考资料及说明

[1] https://en.wikipedia.org/wiki/Moon. 关于月球的起源,在这篇文章中我们将找到阐释这种巨大影响的替代假说。

[2] Goldford J.E., Hartman H., Smith T.F. & Segré D. (2017) Remnants of an ancient metabolism without phosphates. Cell 168, 1-9. http://dx.doi.org/10.1016/j.cell.2017.02.001

[3] https://en.wikipedia.org/wiki/RNA_world

[4] https://en.wikipedia.org/wiki/Chirality_(chemistry)

[5] https://en.wikipedia.org/wiki/Iron-sulfur protein

[6] Valley Y., Shalayel I. et al. (2017) At the very beginning of life on Earth: The thiol-rich peptide (TRP) world hypothesis. Int. J. Dev. Biol. 61: 471-478. http://doi.org/10.1387/ijdb.170028yv


环境百科全书由环境和能源百科全书协会出版 (www.a3e.fr),该协会与格勒诺布尔阿尔卑斯大学和格勒诺布尔INP有合同关系,并由法国科学院赞助。

引用这篇文章: VALLÉE Yannick (2024年3月12日), 生命出现之时:40亿年前的海洋化学, 环境百科全书,咨询于 2024年12月9日 [在线ISSN 2555-0950]网址: https://www.encyclopedie-environnement.org/zh/vivant-zh/once-upon-a-time-life-chemistry-in-earths-ocean-4-billion-years-ago/.

环境百科全书中的文章是根据知识共享BY-NC-SA许可条款提供的,该许可授权复制的条件是:引用来源,不作商业使用,共享相同的初始条件,并且在每次重复使用或分发时复制知识共享BY-NC-SA许可声明。

Once upon a time when life appeared: chemistry in the earth’s ocean 4 billion years ago

Encyclopedie environnement - origine vie océan - origin life oceans

Some 4 billion years ago, the Earth was largely covered by a huge ocean. This ocean contained a large number of small organic molecules, which are called “prebiotics” because they were there before life appeared. What were they? Were they synthesized on site or did they come from space? How did they bind to form long polymers, some of them carrying genetic information, others working to reproduce all the basic molecules and then aggregate them into polymers? Nothing was certain in advance! The polymers were not stable, the bonds were difficult to create. Yet here we are. It is therefore good that a chemistry of extreme subtlety found the energy and time necessary to set itself up. This article gives some hints to try to understand what may have happened.

1. A long time ago, in a galaxy not so far away

About 4.6 billion years ago, in an off-centre location in the spiral galaxy we call the Milky Way, a vast disc of matter was formed. Most of the gases, grains, blocks that made up this disc have concentrated and fused, to form a star, the Sun. The little amount of residual matter that remained formed planets and smaller objects, dwarf planets and asteroids. Our Earth, in fact a proto-Earth, was formed at that time. Fifty million years later (not much compared to the scale of astronomical time) this proto-Earth was struck by a very massive object, Theia, a planetoidSmall celestial body with some characteristics of a planet. The term refers to structures as varied as asteroids, dwarf planets, protoplanets, etc. the size of Mars. From this gigantic shock came the Moon and our present Earth [1].

Before this shock, it is likely that the Earth’s atmosphere contained a lot of hydrogen, the major component of the proto-solar disk. But the shock was huge. The light elements were expelled. A new atmosphere resulted, rich in carbon dioxide (CO2), nitrogen (N2) and water vapour (H2O). The Earth was still very hot. However, it cools down quite quickly. The water vapour condensed and fell in an incessant torrential rain to form a first, unique and immense ocean.

Under this ocean, the upper part of the Earth’s mantle solidified, forming a first crust. The first tectonic plates gradually took place. Perhaps emerging from the ocean, we could already see some proto-continents, scattered islands, probably volcanoes much more active than our current volcanoes. Our planet was still full of energy! This compensated the weakness of the young Sun, which was smaller and less powerful than today. Without the energy released by the planet, without the significant greenhouse effect resulting from the high proportion of CO2 in the atmosphere, it is quite possible that all the water has become ice. What kind of life could have been born in this ice? No doubt, none…

Just as the proto-Earth crossed Theia’s path, after the birth of the Moon, the Earth was struck by many asteroids that probably brought it a good amount of extra water, perhaps also organic molecules. After an intense rebound from these cataclysmic bombardments, they ended 3.8 billion years ago (well, almost ended: we are still not immune to a catastrophic shock. Dinosaurs would not say the opposite!).

It is not impossible that life appeared before the end of this “great late bombardmentPeriod in the history of the solar system extending approximately 4.1 to 3.9 billion years ago, during which there was a significant increase in meteoric or cometary impacts on the telluric planets.“, but the evidence in this regard remains tenuous. And even if it had started, would it have survived these repeated disasters? (see The origin of life as seen by a geologist who loves astronomy).

2. So much water! So much water!

So let us place ourselves, a little less than 4 billion years ago, at the end of a geological era called the Hadean. At that time, the Earth had a gigantic ocean, hyperactive volcanoes, embryos of continents. The Moon was moving away from it, but it was far from reaching its current orbit: it was still three times closer. As a result, the force of the tides was gigantic, more than twenty times greater than it is today. The winds were impressive. Even if it was cooling down, the ocean temperature was probably warmer than it is today.

It is difficult to know its pHAbreviation for Hydrogen Potential, a measure of the activity of the hydrogen ion (or proton) in a solution. The pH is an indicator of the acidity (pH below 7) or alkalinity (pH above 7) of a solution. A solution of pH 7 is called neutral: it is currently slightly basic (around 8.1) but is progressively acidified because of human CO2 emissions. In water, CO2 forms an acid: carbonic acid. There is much less CO2 in the atmosphere today than when life was born. Perhaps the ocean was therefore rather acidic at the time, which had an impact on the chemistry that could occur there. Of course, it contained ions. As today sodium (Na+) and chlorides (Cl) dominated. The ocean was already salty! There was also calcium, magnesium, bromides, and even much more iodides than today.

At first it was thought that the primitive atmosphere was very reductive, that it contained a lot of hydrogen, methane, ammonia. But we saw it, if there had been hydrogen, the shock with Theia caused the expulsion of this light gas into space. However, the atmosphere was not oxidizing. It contained very little or no molecular oxygen (O2). We can date the appearance of a significant amount of O2 on Earth by determining the age of the oldest deposits containing ferric iron. Indeed, when iron is exposed to water containing oxygen, it rusts. That is to say, it is oxidized to ferric iron (Fe3+). Ferric iron is not soluble in water. Without oxygen, however, iron forms ferrous ions (Fe2+) which are soluble.

There is therefore a major difference between our present ocean and the primitive ocean: the latter contained dissolved ferrous iron, not ours.

3. A fullness of small molecules

Figure 1. Examples of prebiotic syntheses. The “sugar” represented, a pentose, with 5 carbon atoms, is only one example among many. Similarly, it is possible to consider the synthesis of other amino acids than glycine, serine and cysteine.

This ocean also contained organic molecules. From CO2 or methane (CH4), molecules with two carbon atoms are easily formed. CO2 can be reduced to formaldehyde (H2CO, Figure 1) which by a reaction called “formose reactionWord formed by the contraction of the terms formaldehyde and aldose. This reaction, discovered by the Russian chemist Alexander Boutlerov in 1861, consists in polymerizing formaldehyde to form sugars including pentoses (sugars with five carbon atoms). This reaction is important in the abiotic formation processes of living molecules.” first gives  hydroxyacetaldehydeMolecule of chemical structure C2H4O2. It is the simplest molecule that has both a hydroxyl group (OH) and an aldehyde group (CHO). (a molecule with two carbons) and then longer molecules that are sugars. A cook would say that with these sugars in addition to sodium chloride, the Hadaean ocean was sweet and sour!

In addition to sugars, at least two types of molecules are needed to build a living cell: proteins and nucleic acids. These molecules all contain nitrogen. What could be the sources of this nitrogen in the prebiotic ocean? Probably ammonia (NH3), and hydrocyanic acid (HCN). When these two compounds react with formaldehyde they give the simplest amino acid, glycine. This molecule is synthesized through an essential reaction called Strecker synthesis, named after Adolph Strecker, a Germanic chemist, who discovered it in the mid-19th century. This synthesis, from other aldehydes, can give various amino acids, for example serine from hydroxyacetaldehyde (Figure 1).

These amino acids are the basic components of the polymers that are proteins. As we have just seen, they could be synthesized quite easily: they were therefore most likely present in the early ocean.

What about nucleic acid precursors, DNAA abbreviation for deoxyribonucleic acid. DNA is a macromolecule composed of nucleotide monomers formed of a nitrogenous base (adenine, cytosine, guanine or thymine) linked to deoxyribose, itself linked to a phosphate group. It is a nucleic acid, like ribonucleic acid (RNA). Present in all cells and in many viruses, DNA contains genetic information, called genome, that enables the development, functioning and reproduction of living beings. The DNA molecules of living cells are formed by two antiparallel strands wrapped around each other to form a double helix.RNA is a macromolecule consisting of a sequence of ribonucleotides (adenine, cytosine, guanine, guanine, uracil) linked together by nucleotide bonds and performing many functions within the cell. It is a nucleic acid, like DNA., which carries genetic information? Their synthesis is a little more complex. It is less obvious that all of them were present. But it is possible to write prebiotic syntheses for each of them. The riboseRibose is a ose (sugar) made up of a chain of five carbon elements and an aldehyde function. It is a component of RNA used in genetic transcription. It is related to deoxyribose, which is a component of DNA. It is also present in many molecules important in metabolic processes (in particular ATP or adenosine triphosphate). can thus be obtained by the formose reaction already mentioned, nucleic bases from hydrogen cyanide, and direct access paths to ribose-base complexes have recently been published by researchers.

The synthesis of DNA and RNA chains nevertheless raises the question of the source of phosphorus. It is indeed abundantly present in these polymers that carry genetic information. In our world oxidantIn chemistry, a chemical element is oxidizing when it gives one or more electrons during an oxidation-reduction reaction (see also oxidation-reduction and reductant in the glossary). world, this element is generally found in the form of phosphate, especially calcium phosphate, insoluble in water. Were there phosphates (soluble) in the primitive non-oxidizing ocean? If not, what was the source of soluble phosphorus? This is an open question [2].

Another important element is the sulphur present today in two life-sustaining amino acids, methionine and cysteine. It is released in significant amounts from active volcanoes, fumaroles, many hydrothermal springs, often in the form of hydrogen sulfide (H2S). It is therefore reasonable to assume that the primitive ocean contained hydrogen sulphide, and consequently small sulphur molecules, such as the amino acid cysteine.

If we are certain (some would say: almost certain) that no little green man from intergalactic space has ever set foot on our planet, it is not impossible that some of the molecules mentioned here have landed on Earth, brought by the millions of asteroids that struck it, especially during the Great Late Bombardment. Thus, the magnificent visit of the Rosetta probe to the asteroid 67P/Chourioumov-Guérassimenko, known as “Chouri”, showed that it contained water, ammonia, formaldehyde, hydrocyanic acid, hydrogen sulphide… but also more complex organic molecules including glycine, this small amino acid of which we have described above a possible synthesis on Earth (Read How to study the organic molecules of comets?).

So the first glycine: “terrestrial” or “extraterrestrial”? What about the other amino acids? What about the bases of DNA? No one knows it. But what is certain is that when the massive bombardments stopped, when this possible alien source dried up, when all these alien molecules were used, terrestrial syntheses had to take over. As we have seen, they are quite possible. The extraterrestrial hypothesis, if it cannot be refuted, is not essential to describe the birth of life on Earth.

Figure 2. 4 billion years ago, a first Earth crust was formed, largely covered by a vast salty ocean containing soluble ferrous iron. Asteroids brought water and small organic molecules. Other molecules were formed in the ocean. The presence of hydrocyanic acid HCN then allowed on the one hand the synthesis of RNA bases, on the other hand that of amino acids which, upon polymeriziation, gave first peptides.

Figure 2 summarizes all this chemistry.

There remains the problem of the concentration of these molecules. This is a very important question: the more diluted the starting compounds of a given reaction are, the slower the reaction is. Certainly life had time ahead of it. However many products resulting from the condensation of small molecules are not very stable in water. We must be able to do enough, fast enough, so that they continue to grow, to form longer and longer molecules, more and more complex, before separating again into small starting components. This raises two questions: How much water was there on Earth? And this water, what mass of organic molecules did it contain?

How much water? The most realistic hypothesis is to consider that there were, roughly speaking, no more or less than today, i.e. about 1.36 billion km3, i.e. by rounding off a thousand billion billion litres, which is not insignificant!

Knowing how many organic molecules there were on the way to life is much more complicated. The current terrestrial biosphere contains 2,000 gigatonnes (2,000 billion tonnes = 2 billion billion grams) of organic carbon. It is very unlikely that there were more, in the form of small molecules, at a time when precisely “organic” life had not yet appeared.

Let’s do the math: 2 billion billion billion grams divided by 1,000 billion billion litres, that’s 2 milligrams of organic carbon per litre of water. It is a low concentration, but it is not totally ridiculous. It is probable that this leads to an overestimated idea of the concentration of organic molecules in the Hadaean ocean. The actual concentration was probably even lower. So? How can we envisage fairly rapid reactions in this ocean, continuously stirred by gigantic tides, and therefore roughly homogeneous?

Darwin himself had already expressed the problem when he wrote to his friend Joseph Hooker in 1871:” “But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, light, heat, electricity etcetera present, that a protein compound was chemically formed, ready to undergo still more complex changes [..] ” »

This is the origin of this small warm little pond, which has truly made so many researchers in search of the origins of life fantasize. Darwin assumed that his small pond is concentrated enough for the chemistry to progress to the synthesis of a long enough chain of amino acids, the “protein compound”.

There may have been small bodies of water on the emerging continents, but were the organic molecules more concentrated there than in the global ocean? Maybe molecules concentrated on the first beaches, or in a few cracks? Were there more organic compounds around the volcanoes? Or at the bottom of the ocean, near hydrothermal vents from which hot gas escapes? Shouldn’t we instead imagine particularly effective reactions that make it possible to build polymers (proteins, for example) even under very diluted conditions?

4. The keys to success: energy and catalysis

For a chemical reaction to occur, it is necessary:

  • that it is possible, it is a matter of thermodynamics,
  • that it is fast enough, it is a matter of kinetics. in chemistry, kinetics describes the evolution of chemical systems over time, i.e. the passage from an initial state to an end state. The laws of chemical kinetics make it possible to determine the specific velocity of a chemical reaction..

However, a priori, 4 billion years ago, nothing was as it should have been!

Figure 3. Synthesis of a dipeptide from two amino acids. The difference in the length of the arrows means that the balance is shifted towards the two amino acids. The formation of water, in particular, inhibits the synthesis of dipeptide.

From a thermodynamic point of view, what matters is the relative stability of the starting molecules and the formed molecules. Building a polymer is a step-by-step process. First, two monomersBasic constituents of complex molecules (proteins, complex sugars, nucleic acids, etc.). The successive sequence of these molecules (identical or different), gives rise to a polymer structure. Thus amino acids form proteins, oses form complex sugars, nucleotides form nucleic acids. give a dimer, which will be elongated into a trimer and so on, up to very long chains. At first, therefore, two monomers form a dimer and a molecule of water is eliminated. In both peptides (Figure 3) and nucleic acids, dimers are much less stable than monomers. In other words, it is the dimer cut-off reaction (a hydrolysis) that is favoured. The balance is therefore shifted towards the monomers. This especially as this hydrolysis consumes a molecule of water, which in water is favourable, while condensation forms a molecule of water next to the dimer, which is unfavourable. It is this problem of unfavourable formation of a water molecule that leads some authors to seek for the least aqueous environments possible to place their origin of life scenario, the coasts of the first continents in particular, where relatively dry places could undoubtedly be found.

It’s no better on the kinetic side. For two molecules to react together, they must be activated, i.e. they must be supplied with a certain amount of energy. The higher the energy to be supplied, the greater is the probability that two monomers will meet (referred to as “shocks”) without reacting. In other words, the slower is the reaction. However, the energy required to form an embryonic dimer of protein or nucleic acid is high.

Waste of time? No, since despite all this, it is quite certain that life has appeared. To do this, you need at least:

  • an energy-rich molecule. By cutting itself into two fragments, this molecule will release a large part of the energy it contains. If this happens simultaneously to the formation of a dimer (e.g. a dipeptide), then the two energies will compensate each other and the overall process will be promoted by thermodynamics;
  • a catalyst, i.e. a chemical species, a molecule, but also sometimes the surface of a solid, (see Origin of the first cells: the engineer’s point of view) capable of helping the formation of a dimer from two monomers. The number of effective shocks (those that really form the dimer) will then be much higher, and the reaction will reach a reasonable rate in the prebiotic ocean.
Figure 4. The role of ATP (adenosine triphosphate) in the biological synthesis of peptides The first two reactions are catalysed by a protein, an aminoacyl RNAt synthetase. The third one takes place on the end of two tRNA molecules within the ribosome, which itself is massively composed of RNA chains. That this last stage is catalysed by RNA is a strong argument for the researchers who propose the existence of a primitive world where RNA’s (the RNA world) predominated.

The energy-rich molecule used today in living organisms is ATP (Figure 4), a triphosphate. The breaking of a phosphate bond releases enough energy to counterbalance the instability of the dimers to be synthesized. In peptide synthesis, this will even allow to reach the dimer via intermediates even less stable than the dimer itself. First a mixed phosphoric carboxylic anhydride is formed, then an ester and finally an amide (the peptide). In total, this involves three steps, each of which is inherently slow. Catalysts are therefore involved. Thus, it probably took time for the very first peptides to form in the primitive ocean.

Explaining the appearance of life therefore requires identifying at least one molecular source of energy (knowing that it is highly unlikely that ATP existed in the early ocean, it is too rich in energy), and on the other hand initial catalysts (being understood that those used today in living cells, aminoacyl tRNA synthetasesFamily of enzymes that catalyse the esterification of amino acids on the 3′ end of transfer RNA (tRNA). Preserved in all living organisms, these enzymes help to translate the genetic message into proteins. The amino acids thus added to the end of the tRNAs are then incorporated by the ribosome into the polypeptide chain (protein) being synthesized. There is an aminoacyl tRNA synthetase for each of the 20 amino acids present in proteins. Each of these enzymes recognizes an amino acid and one or more iso-acceptor tRNAs. Their function is essential to the accuracy of the translation of the genetic code, as they ensure that the amino acid thus esterified at the end of the tRNA corresponds to the correct anticodon. and others, are much too complex to be prebiotic).

The problem being posed, everything else is only a hypothesis. The most commonly accepted today is that of the “RNA world” [3] (see Origin of the first cells: the engineer’s point of view). It assumes that the first significant polymers were RNA’s, both repositories of first genetic information and catalystsElement (organic or mineral) that accelerates or slows down a chemical reaction. Used in very small quantities and specific to a given reaction, the catalyst does not appear in the reaction equation; it does not influence the direction of evolution of the transformation, nor the composition of the system in the final state. An enzyme is a biological catalyst.. In fact, some RNA’s in current living cells have catalytic properties (although the vast majority of biological catalysts are proteins). With regard to the energy source: it is impossible to form RNA’s without using the energy contained in triphosphates. However, it is unlikely that triphosphates could have existed in the early ocean. This is one of the difficulties of the hypothesis. But it has the advantage of reconciling genetic information and catalysis.

On the other hand, proteins do not carry genetic information, but they are much better catalysts than RNA. Does this lack of genetic information preclude the idea that proteins could have been the first really important polymers in the history of life? Maybe not… Today indeed, some peptides are manufactured directly on proteins, without the help of nucleic acids. These peptides are called “non-ribosomal” because they are not manufactured in ribosomesA complex composed of RNA and ribosomal proteins, associated with a membrane (at the granular endoplasmic reticulum) or free in the cytoplasm. The function of the ribosome is to translate the genetic code into proteins, through messenger RNAs (mRNAs). The enzymatic activity of the ribosome being carried by rRNAs, the ribosome is a ribozyme. Common to all cells (prokaryotes and eukaryotes), the structure and composition of the ribosome varies according to the organisms. In prokaryotes, the ribosome is said to be 70S (S corresponding to the Sverdberg sedimentation unit) and consists of subunits 50S and 30S. The ribosome of eukaryotes is called 80S, formed by the two subunits 60S and 40S., RNA complexes. However, they are not made “at random” and authors have proposed the existence of a code different from the traditional genetic code (which translates DNA into proteins via RNA). This “non-ribosomal” code translates proteins into peptides (one could say peptides into peptides). It is a complex code, based on sets of ten amino acids (in the coding protein): it allows to precisely choose the amino acid to be introduced into the peptide to be synthesized. There is therefore nothing to prevent us from imagining that “pre-genetic” information, even sketchy information, could have been originally carried by amino acid chains.

Figure 5. Principle of action of a catalytic triad, here a cysteine – histidine – aspartic acid triad. The zigzag links represent peptide chains. A thioester is formed. It is a high-energy molecule that will be used for subsequent reactions such as hydrolysis. The formation of an amide is another possible follow-up.

Although catalytic proteins are complex molecules, their activity is generally based on fairly simple principles. This is the case for catalytic triads found in hydrolases and transferases. Three amino acids are required: an alcohol or z thiol, a base and an acid. In Figure 5, it is a thiol, cysteine, that acts. Thanks to histidine (the base) located further down the protein chain, this cysteine loses its proton. It then carries a negative charge, which allows it to react with the positive carbon of the C=O double bond. Aspartic acid is there to activate histidine. The reaction product is, in this case, a thioester, another example, after triphosphates, of a high-energy molecule. This thioester may then undergo other reactions, for example with water to make an acid (the protein that contains the triad is then a hydrolase), or with another organic molecule (the triad is the active site of a transferase).

Of course, in our current proteins, these triads are positioned very precisely by the amino acid chains that bind them. Thanks to this, each triad protein is specialized and only performs one type of reaction on molecules that are also well defined. But, 4 billion years ago, in the primitive ocean, could there be triads? They would undoubtedly have been much less specific, to a certain extent “good at everything”. Why not? Figure 6 shows such an example of a very simplified triad. The stereochemistry of the molecule, or “chirality”, is specified: it is a very essential question, which a complete model of the origin of life must explain [4].

Figure 6. On the left: extreme simplification of a triad. The molecule (hypothetical) is cyclic. It contains the 3 amino acids (cysteine, histidine and aspartic acid). There is no indication that this one would have catalytic activity. On the right: three examples of fatty acids. These are long organic chains, where the CH2 unit repeats itself, terminated by an acid function.

Finally, we cannot imagine life without the existence of partitioned structures, cells or something similar to them, so membranes or walls. The first membranes may have been formed from entangled or more ordered peptides glued together. They may also have contained long hydrophobic organic chains, those of fatty acids (Figure 6). It is possible to synthesize these fatty acids today thanks to proteins and thiolester chemistry.

The world in which life has appeared that is then delineated would be a world of peptides much more than a world of nucleic acids. Sulphur, through cysteine and thioesters, would have played a very central role, linking it to a possible world that is even more primitive, more “mineral”, the iron-sulphur world [5], [6]. This leads us to reflect on the specific role that ferrous iron, which is soluble, therefore available, could have played in providing electrons, and therefore energy, in relation to all these peptides.

 


References and notes

[1] https://en.wikipedia.org/wiki/Moon. About the birth of the moon, we will find in this article alternative hypotheses to the giant impact.

[2] Goldford J.E., Hartman H., Smith T.F. & Segré D. (2017) Remnants of an ancient metabolism without phosphates. Cell 168, 1-9. http://dx.doi.org/10.1016/j.cell.2017.02.001

[3] https://en.wikipedia.org/wiki/RNA_world

[4] https://en.wikipedia.org/wiki/Chirality_(chemistry)

[5] https://en.wikipedia.org/wiki/Iron-sulfur protein

[6] Valley Y., Shalayel I. et al. (2017) At the very beginning of life on Earth: The thiol-rich peptide (TRP) world hypothesis. Int. J. Dev. Biol. 61: 471-478. http://doi.org/10.1387/ijdb.170028yv


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引用这篇文章: VALLÉE Yannick (2019年4月2日), Once upon a time when life appeared: chemistry in the earth’s ocean 4 billion years ago, 环境百科全书,咨询于 2024年12月9日 [在线ISSN 2555-0950]网址: https://www.encyclopedie-environnement.org/en/life/once-upon-a-time-life-chemistry-in-earths-ocean-4-billion-years-ago/.

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