📚 Amino Acids, Proteins and DNA | 氨基酸、蛋白质与DNA
Amino acids are the monomers from which proteins are built. Proteins regulate virtually every biochemical process in living cells, while DNA stores the genetic information that codes for these proteins. In this article, we explore the fundamental chemistry of amino acids, the condensation polymerisation that forms peptides and proteins, the hierarchy of protein structure, the architecture of DNA and RNA, and the role of cisplatin as an anti-cancer drug.
氨基酸是构成蛋白质的单体。蛋白质调控着活细胞中几乎所有的生化过程，而DNA储存着编码这些蛋白质的遗传信息。在本文中，我们探讨氨基酸的基本化学、形成肽和蛋白质的缩合聚合反应、蛋白质结构的层次、DNA和RNA的架构，以及顺铂作为抗癌药物的作用。
1. Amino Acids: Structure and Properties | 氨基酸：结构与性质
An α-amino acid contains an amino group (-NH₂) and a carboxylic acid group (-COOH) both attached to the same carbon atom, known as the α-carbon. The general formula for an α-amino acid is:
α-氨基酸同时含有一个氨基（-NH₂）和一个羧基（-COOH），二者均连接在同一个碳原子（称为α-碳）上。α-氨基酸的通式为：
H₂N-CH(R)-COOH
The R group (side chain) differs for each of the 20 naturally occurring amino acids. In glycine, R is simply a hydrogen atom; in alanine, R is a methyl group (-CH₃); in cysteine, R contains a thiol group (-CH₂SH). The varied chemical nature of the R groups (non-polar, polar, acidic or basic) is what gives different proteins their distinctive properties and functions.
R基团（侧链）在20种天然氨基酸中各不相同。在甘氨酸中，R仅为氢原子；在丙氨酸中，R为甲基（-CH₃）；在半胱氨酸中，R含有巯基（-CH₂SH）。R基团不同的化学性质（非极性、极性、酸性或碱性）赋予了不同蛋白质独特的性质和功能。
The presence of both an acidic group (-COOH) and a basic group (-NH₂) in the same molecule makes amino acids amphoteric: they can react as acids with bases and as bases with acids. This dual character is central to understanding their behaviour in aqueous solution.
同一分子中同时存在酸性基团（-COOH）和碱性基团（-NH₂），使氨基酸具有两性：它们能与碱反应表现为酸，也能与酸反应表现为碱。这种双重特性是理解其水溶液行为的关键。
2. Zwitterions and Isoelectric Point | 两性离子与等电点
In the solid state and in neutral aqueous solution, an amino acid does not exist as the uncharged H₂N-CH(R)-COOH molecule. Instead, a proton is transferred from the carboxyl group to the amino group, forming a doubly charged ion called a zwitterion:
在固态和中性水溶液中，氨基酸并不以不带电的H₂N-CH(R)-COOH分子形式存在。相反，一个质子从羧基转移到氨基，形成称为两性离子的双电荷离子：
H₂N-CH(R)-COOH ⇌ ⁺H₃N-CH(R)-COO⁻
The zwitterion carries both a positive charge (-NH₃⁺) and a negative charge (-COO⁻), yet the overall molecule is electrically neutral. This explains why amino acids have relatively high melting points and are highly soluble in water, since the zwitterionic form involves strong ionic interactions between molecules.
两性离子同时携带一个正电荷（-NH₃⁺）和一个负电荷（-COO⁻），但整个分子呈电中性。这解释了为什么氨基酸具有相对较高的熔点且易溶于水，因为两性离子形式在分子间产生强烈的离子相互作用。
In acidic solution, the -COO⁻ group is protonated, giving the cation ⁺H₃N-CH(R)-COOH. In alkaline solution, the -NH₃⁺ group is deprotonated, giving the anion H₂N-CH(R)-COO⁻. The pH at which the amino acid exists predominantly as the neutral zwitterion is called the isoelectric point.
在酸性溶液中，-COO⁻基团被质子化，生成阳离子⁺H₃N-CH(R)-COOH。在碱性溶液中，-NH₃⁺基团被去质子化，生成阴离子H₂N-CH(R)-COO⁻。氨基酸主要以中性两性离子形式存在时的pH称为等电点。
3. Optical Isomerism in Amino Acids | 氨基酸的光学异构
With the exception of glycine (R = H), all amino acids are chiral. The α-carbon is bonded to four different groups: -NH₂, -COOH, -H and -R. This makes the α-carbon a chiral (stereogenic) centre, and therefore amino acids exist as two enantiomers:
除甘氨酸（R = H）外，所有氨基酸都是手性的。α-碳与四个不同的基团键合：-NH₂、-COOH、-H和-R。这使得α-碳成为手性（立体）中心，因此氨基酸以两种对映体形式存在：
H₂N-C*(R)(H)-COOH (two mirror-image forms)
The two enantiomers are non-superimposable mirror images and have identical chemical reactivity in achiral environments, but they rotate plane-polarised light in opposite directions: one is designated L (levorotatory, rotating left) and the other D (dextrorotatory, rotating right). Naturally occurring proteins are composed exclusively of L-amino acids. This stereochemical specificity is essential because enzymes, being chiral themselves, can distinguish between the two enantiomers.
两种对映体是不可重叠的镜像，在非手性环境中具有相同的化学反应活性，但它们使平面偏振光向相反方向旋转：一种标记为L（左旋），另一种标记为D（右旋）。天然蛋白质仅由L型氨基酸组成。这种立体化学特异性至关重要，因为酶本身是手性的，能够区分两种对映体。
4. Peptide Bond Formation and Polypeptides | 肽键的形成与多肽
Amino acids undergo condensation polymerisation to form peptides and proteins. In a condensation reaction, two amino acids join together with the elimination of a water molecule. The carboxyl group of one amino acid reacts with the amino group of another:
氨基酸通过缩合聚合反应形成肽和蛋白质。在缩合反应中，两个氨基酸连接在一起，同时脱去一分子水。一个氨基酸的羧基与另一个氨基酸的氨基反应：
H₂N-CH(R)-COOH + H₂N-CH(R’)-COOH → H₂N-CH(R)-CO-NH-CH(R’)-COOH + H₂O
The new bond formed between the carbon atom of one amino acid and the nitrogen atom of the next is called a peptide bond (an amide linkage, -CO-NH-). A dipeptide is formed from two amino acids, a tripeptide from three, and a polypeptide from many. Proteins are naturally occurring polypeptides that contain one or more polypeptide chains.
一个氨基酸的碳原子与下一个氨基酸的氮原子之间形成的新键称为肽键（酰胺键，-CO-NH-）。两个氨基酸形成二肽，三个氨基酸形成三肽，多个氨基酸形成多肽。蛋白质是含有一条或多条多肽链的天然多肽。
The peptide bond is planar and rigid due to partial double-bond character between the carbon and nitrogen atoms. This restricts rotation and is fundamental to the way proteins fold into defined three-dimensional structures.
由于碳原子与氮原子之间存在部分双键特征，肽键是平面且刚性的。这限制了旋转，是蛋白质折叠成确定三维结构的基础。
5. Hydrolysis of Proteins | 蛋白质的水解
The hydrolysis of a protein is the reverse of condensation polymerisation: peptide bonds are broken by the addition of water, regenerating the individual amino acids. This can be achieved in two main ways.
蛋白质的水解是缩合聚合的逆反应：肽键通过水的加入而断裂，重新生成单个氨基酸。这可以通过两种主要方式实现。
Acid hydrolysis: Refluxing the protein with concentrated hydrochloric acid for approximately 24 hours breaks all peptide bonds, yielding a mixture of amino acids. The resulting amino acid mixture can then be separated and identified using chromatography (e.g. thin-layer or paper chromatography), and the sequence of amino acids in the original protein can be deduced by careful analysis.
酸水解：将蛋白质与浓盐酸回流约24小时，可断裂所有肽键，得到氨基酸混合物。所得氨基酸混合物可通过色谱法（如薄层色谱或纸色谱）分离和鉴定，并通过仔细分析推断原蛋白质中的氨基酸序列。
Enzymatic hydrolysis: Protease enzymes catalyse the hydrolysis of peptide bonds under mild conditions (body temperature, neutral pH). Digestive enzymes such as pepsin in the stomach and trypsin in the small intestine break down dietary proteins into absorbable amino acids. Enzymatic hydrolysis is highly specific: each protease cleaves the peptide bond only at particular positions in the chain, determined by the amino acid sequence.
酶水解：蛋白酶在温和条件（体温、中性pH）下催化肽键水解。胃中的胃蛋白酶和小肠中的胰蛋白酶等消化酶将膳食蛋白质分解为可吸收的氨基酸。酶水解具有高度特异性：每种蛋白酶仅在链中特定位置切断肽键，具体位置由氨基酸序列决定。
6. Protein Structure: Primary and Secondary | 蛋白质结构：一级与二级
The structure of a protein is described at four levels, each building on the one before.
蛋白质的结构从四个层次描述，每一层都建立在前一层之上。
Primary structure is the precise sequence of amino acids in the polypeptide chain, held together by covalent peptide bonds. The primary structure is determined directly by the sequence of bases in the DNA gene that codes for the protein. Even a single amino acid substitution can have dramatic consequences: in sickle-cell anaemia, one glutamic acid residue is replaced by valine in the β-globin chain of haemoglobin, altering the protein’s shape and function.
一级结构是多肽链中氨基酸的精确序列，由共价肽键连接。一级结构直接由编码该蛋白质的DNA基因中的碱基序列决定。即使是单个氨基酸的替换也会产生严重后果：在镰刀型贫血症中，血红蛋白β-珠蛋白链中的一个谷氨酸残基被缬氨酸替换，改变了蛋白质的形状和功能。
Secondary structure refers to the regular, repeating arrangement of the polypeptide chain in space, stabilised by hydrogen bonds between the -N-H group of one peptide bond and the -C=O group of another. The two most common secondary structures are:
二级结构指多肽链在空间中规则的、重复的排列方式，由一条肽键的-N-H基团与另一条肽键的-C=O基团之间的氢键稳定。最常见的两种二级结构是：
- α-Helix: The chain coils into a right-handed spiral. Each -N-H group forms a hydrogen bond with the -C=O group of the fourth amino acid along the chain, giving approximately 3.6 residues per turn. The R groups project outward from the helix.
- α-螺旋：链卷曲成右手螺旋。每个-N-H基团与沿链相隔第四个氨基酸的-C=O基团形成氢键，每圈约3.6个残基。R基团从螺旋向外伸出。
- β-Pleated sheet: The chain is almost fully extended, and neighbouring chains (or neighbouring sections of the same chain) lie side by side. Hydrogen bonds form between the -N-H and -C=O groups of adjacent strands, creating a pleated, sheet-like structure. Silk fibroin is rich in β-pleated sheets.
- β-折叠片：链几乎完全伸展，相邻链（或同一链的相邻区段）并排排列。相邻链的-N-H和-C=O基团之间形成氢键，产生褶皱的片状结构。蚕丝蛋白富含β-折叠片。
7. Protein Structure: Tertiary and Quaternary | 蛋白质结构：三级与四级
Tertiary structure is the overall three-dimensional shape of a single polypeptide chain. It is determined by interactions between the R groups of amino acids that are often far apart in the primary sequence but become close together in the folded structure. These interactions include:
三级结构是单条多肽链的整体三维形状。它由一级序列中相距较远但在折叠结构中彼此靠近的氨基酸R基团之间的相互作用决定。这些相互作用包括：
- Ionic bonds between oppositely charged side chains, e.g. between -NH₃⁺ of a lysine residue and -COO⁻ of an aspartate residue.
- 离子键：带相反电荷的侧链之间，例如赖氨酸残基的-NH₃⁺与天冬氨酸残基的-COO⁻之间。
- Hydrogen bonds between polar or charged side chains and between side chains and water molecules.
- 氢键：极性或带电侧链之间，以及侧链与水分子之间。
- Disulfide bridges (-S-S-) formed by the oxidation of two cysteine residues: two -SH groups react to form a covalent -S-S- linkage. These strong covalent bonds lock parts of the chain together and are particularly important in extracellular proteins such as insulin and antibodies.
- 二硫键（-S-S-）：由两个半胱氨酸残基氧化形成：两个-SH基团反应生成共价-S-S-键。这些强共价键将链的某些部分锁定在一起，在胰岛素和抗体等细胞外蛋白质中尤为重要。
- Hydrophobic interactions between non-polar R groups, which cluster together in the interior of the protein, away from water.
- 疏水相互作用
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