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MICROBIOLOGY · REFERENCE DESK

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This collection combines attributed Wikipedia excerpts and original SciAtlas bilingual definitions under CC BY-SA 4.0. Excerpts were extracted and shortened; machine-assisted Chinese translations are labeled. Original entries provide further reading. Language versions may differ in emphasis and do not replace standards. Concepts can appear in several disciplines; consult standards and original literature for rigorous use.

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Microbiology

Borg (microbiology)

博格(微生物学)

Borgs 是在生活在缺氧环境(如深泥)的甲烷氧化古菌(特别是 Methanoperedens spp.)中发现的大型(高达约 1 Mbp)染色体外线性 DNA 元件。它们在从湿地、含水层和河床环境以及加利福尼亚州和科罗拉多州废弃的汞矿中分离出来的生物体中被发现。 2022 年,Basem Al-Shayeb 和 Jill Banfield 首次描述了博格怪。博格怪的本质仍不清楚;它们被认为是“巨型线性质粒”或巨型病毒。至少已鉴定出 19 种不同的类型,所有这些类型都同时存在于 Methanoperedens 中,并且具有许多相同的基因。 Methanoperedens 的主染色体仅比其宿主的博格人大三倍左右。据推测,Borgs 可能会增强 Methanoperedens 厌氧氧化甲烷和生产蛋白质的能力。

Borgs are large (up to ~1 Mbp) extrachromosomal linear DNA elements found in methanotrophic archaea (specifically Methanoperedens spp.) that live in oxygen-starved environments such as deep mud. They have been found in organisms isolated from wetland, aquifer, and riverbed environments, as well as a deserted mercury mine, in California and Colorado. They were first described by Basem Al-Shayeb and Jill Banfield in 2022. The nature of Borgs remains unclear; they are thought to be "giant linear plasmids" or giant viruses. At least 19 different types have been identified, all of which co-occur within Methanoperedens, which shares many of their genes. Methanoperedens' main chromosome is only about three times larger than the Borgs it hosts. It is speculated that Borgs may augment Methanoperedens' capacity for anaerobic oxidation of methane and protein production.

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Microbiology

Branches of microbiology

微生物学的分支

微生物学的分支可分为纯科学和应用科学。微生物学也可以根据分类学进行分类,如细菌学、真菌学、原生动物学和藻类学。微生物学的特定分支之间以及与其他学科之间存在相当大的重叠,并且这些分支的某些方面可以超出微生物学的传统范围。一般来说,微生物学领域可以分为更基础的分支(纯微生物学)和应用微生物学(生物技术)。在更基础的领域,生物体作为学科本身在更深(理论)层面上进行研究。应用微生物学是指将微生物应用于某些过程(例如酿造或发酵)的领域。

The branches of microbiology can be classified into pure and applied sciences. Microbiology can be also classified based on taxonomy, in the cases of bacteriology, mycology, protozoology, and phycology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines, and certain aspects of these branches can extend beyond the traditional scope of microbiology In general the field of microbiology can be divided in the more fundamental branch (pure microbiology) and the applied microbiology (biotechnology). In the more fundamental field the organisms are studied as the subject itself on a deeper (theoretical) level. Applied microbiology refers to the fields where the micro-organisms are applied in certain processes such as brewing or fermentation.

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Microbiology

Breed method

养殖方法

繁殖法是一种用于计数牛奶中微生物的实验室技术。它是由美国生物学家塞缪尔·凯特·普雷斯科特和罗伯特·斯坦利·布里德于 1910 年提出的。它是一种体细胞计数方法,可了解活微生物和死微生物的数量。当该方法仅描述活生物体时称为“活菌计数”。微生物定量的方法有很多,包括显微镜方法、库尔特计数器、质谱法(用于估计细胞质量)以及形成和生长细菌菌落的细胞培养方法。

Breed method is a laboratory technique used for counting microorganisms in milk. It was introduced in 1910 by American biologists Samuel Cate Prescott and Robert Stanley Breed. It is a method for somatic cell count, to know the number of living and dead microorganisms. When the method only recounts living organisms is called "viable count". There are many methods for the quantification of microorganisms, including microscopy methods, Coulter counter, Mass Spectrometry (for estimating cell mass), and Cell Culture methods which form and grow colonies of bacteria.

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Microbiology

Cellular microbiology

细胞微生物学

细胞微生物学是一门连接微生物学和细胞生物学的学科,在分子水平上研究微生物与宿主细胞之间的相互作用。细胞微生物学试图利用病原微生物作为细胞生物学研究的工具,并利用细胞生物学的方法来了解微生物的致病性。几十年来,微生物的毒素和毒力因子一直被用来影响真核细胞的过程并对其进行研究。人们越来越发现,在细胞上应用纯化的毒素并不总能提供完整的信息,了解毒素在致病性中的作用、毒素促进微生物的方式、毒素的产生方式以及毒素与其宿主细胞对应物的共同进化至关重要。

Cellular microbiology is a discipline that bridges microbiology and cell biology to investigate interactions between microorganisms and host cells at the molecular level. Cellular microbiology attempts to use pathogenic microorganisms as tools for cell-biology research, and to employ cell-biology methods to understand the pathogenicity of microorganisms. Toxins and virulence factors from microbes have been used for decades to influence processes in eukaryotic cells and to study them. It has increasingly appeared that applying a purified toxin on a cell does not always provide the complete picture, and that understanding the role of the toxin in pathogenicity, the way the toxin promotes the microbe, the way the toxin is produced and the co-evolution of the toxin and its host-cell counterparts, is crucial.

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Microbiology

Changestat

变化统计

Changestat 是一种连续培养方法,用于在单次实验中获取各种环境条件下微生物代谢的定量数据。每个changestat始终以连续培养实验(恒化器、恒浊器)开始,但在达到稳定状态后,应用环境参数的平滑且缓慢的变化。两种最常见的 Changestat 技术是 Accelerostat (A-stat) 和稀释率统计 (D-stat)。在 A-stat 的情况下,变化的环境参数是稀释率 (D, h),它会导致特定生长率 (μ, h) 的增加。当正确选择稀释加速度 (a) 时,则 D = μ,如恒化器中那样。已经用大肠杆菌和乳酸乳球菌研究了选择正确稀释加速的问题,得出推荐范围为 0.01-0.005 小时。

Changestat is a continuous cultivation method that is used for acquiring quantitative data of a microorganism's metabolism at various environmental conditions within a single experiment. Every changestat always starts as a continuous cultivation experiment (chemostat, turbidostat), but after reaching steady state, smooth and slow change of an environmental parameter is applied. Two most common changestat techniques are accelerostat (A-stat) and dilution rate stat (D-stat). In case of A-stat the changing environmental parameter is dilution rate (D, h) that causes the increase of specific growth rate (μ, h). When the acceleration of dilution (a) is chosen correctly then D = μ as in chemostat. The problem of choosing the correct acceleration of dilution has been studied with Escherichia coli and Lactococcus lactis resulting recommended range of 0.01-0.005 h.

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Microbiology

Chrompodellid

色足科

Chrompodellids 是属于 Alveolata 超群的单细胞原生生物门。它由两个不同的多系鞭毛类群组成:colpodellids(吞噬性捕食者)和 chromerids(作为珊瑚共生体的光合藻类)。这些类群是独立发现和描述的,但分子系统发育分析表明,它们混合在一个与顶复门关系最近的进化枝中,它们被统称为色足类。由于其研究历史,它们被分别称为 Chromerida 或 Colpodellida (ICZN)/Colpodellales (ICN)。 Chrompodellids 是单细胞原生生物门,包含两个功能不同的类群:光合作用的“chromerids”和捕食性吞噬的“colpodellids”。

Chrompodellids are a phylum of single-celled protists belonging to the Alveolata supergroup. It comprises two different polyphyletic groups of flagellates: the colpodellids, phagotrophic predators, and the chromerids, photosynthetic algae that live as symbionts of corals. These groups were independently discovered and described, but molecular phylogenetic analyses demonstrated that they are intermingled in a clade that is the closest relative to Apicomplexa, and they became collectively known as chrompodellids. Due to the history of their research, they are variously known as Chromerida or Colpodellida (ICZN)/Colpodellales (ICN). Chrompodellids are a phylum of unicellular protists containing two functionally different groups: the photosynthetic "chromerids" and the predatory phagotrophic "colpodellids".

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Microbiology

Enzyme

酶

酶(英语:enzyme,/ˈɛnzaɪm/),又称酵素,是一类大分子生物催化剂。酶能加快化学反应的速度(即具有催化作用)。由酶催化的反应中,反应物称为底物,生成的物质称为产物。几乎所有细胞内的代谢过程都离不开酶。酶能大大加快这些过程中各化学反应进行的速率,使代谢产生的物质和能量能满足生物体的需求。细胞中酶的类型对可在该细胞中发生的代谢途径的类型起决定作用。对酶进行研究的学科称为酶学(enzymology)。 目前已知酶可以催化超过5000种生化反应。大部分酶是蛋白质,有少部分酶是具有催化活性的核糖核酸(RNA)分子,这些酶被称为核酶。酶的特异性是由其独特的三级结构决定的。 和所有的催化剂一样,酶通过降低反应激活能来加快化学反应速率。一些酶可以将底物转化为产物的速率提高数百万倍。一个比较极端的例子是乳清苷-5'-磷酸脱羧酶。该酶可以使在无催化剂条件下需要进行数百万年的化学反应在几毫秒内完成。从化学原理上讲,酶和其它所有催化剂一样,反应不会使其物质量发生变化。酶亦不能改变化学平衡,这一点和其它催化剂也是一样的。酶和其它催化剂的不同之处在于,它们的专一性要强得多。一些分子可以影响酶的活性。如酶抑制剂能降低酶的活性,酶激活剂能提高酶的活性。许多药物及毒物是酶的抑制剂。当超出或小于适宜的温度和pH值后,酶的活性会显著下降。 酶在工业和人们的日常生活中的应用也非常广泛。例如,药厂用特定的合成酶来合成抗生素;洗衣粉中添加酶能加速附着在衣物上的蛋白质、淀粉或脂肪渍的分解;嫩肉粉中加入木瓜蛋白酶能将蛋白质分解为稍小的分子,使肉的口感更嫩滑。

An enzyme is a biological macromolecule, usually a protein, that acts as a biological catalyst, accelerating chemical reactions without being consumed in the process. The molecules on which enzymes act are called substrates, which are converted into products. Nearly all metabolic processes within a cell depend on enzyme catalysis to occur at biologically relevant rates. A metabolic pathway is typically composed of a series of enzyme-catalyzed steps. The study of enzymes is known as enzymology, and a related field focuses on pseudoenzymes—proteins that have lost catalytic activity but may retain regulatory or scaffolding functions, often indicated by alterations in their amino acid sequences or unusual 'pseudocatalytic' behavior. Enzymes are known to catalyze over 5,000 types of biochemical reactions. Other biological catalysts include catalytic RNA molecules, or ribozymes, which are sometimes classified as enzymes despite being composed of RNA rather than protein.

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Microbiology

Catalysis

催化

催化(catalysis)或催化作用,是利用催化剂参与,改变化学反应速率而不影响化学平衡的作用。广泛发生于无机物反应、有机物反应、生物体内反应。 许多化学工业要利用催化作用来获得需要的反应速率。催化也是一种化工单元过程,催化剂本身在反应中不会被消耗,但催化剂会改变反应速率,一催化剂亦可能参与复数的催化反应。正催化剂可加速反应;负催化剂或抑制剂则会与反应物反应进而降低化学反应。可提高催化剂活性的物质称为促进剂;降低催化剂活性者则称为催化毒。 相较于未催化的反应,同温度的催化反应拥有较低的活化能。催化剂可以借由结合反应物达到极化的效果,如酸催化剂之于羰基化合物的合成;催化剂也可产生非自然的反应中间物,如以四氧化锇催化烯烃的双羟基化中产生的锇酸盐酯;催化剂亦可造成反应物的裂解,如制氢时产生的单原子氢。 很多物质都可以做催化剂,在无机物反应中,通常利用酸、碱、金属或金属化合物作为催化剂,在有机物反应中多用有性的蛋白质分子——酶作为催化剂,生物体内许多化学反应都依赖酶来进行的。 催化反应可以发生在均相催化和多相催化中,也可以发生在复相催化中:

Catalysis (, kə-TAL-iss-iss) is the increase in rate of a chemical reaction due to an added substance known as a catalyst ( KAT-əl-ist). Catalysts are not consumed by the reaction and remain unchanged after the reaction. If the reaction is rapid and the catalyst is recycled quickly, a very small amount of catalyst often suffices; mixing, surface area, and temperature are important factors in reaction rate. Catalysts generally react with one or more reactants to form intermediates that subsequently give the final reaction product, in the process of regenerating the catalyst. The rate increase occurs because the catalyst allows the reaction to occur by an alternative mechanism which may be much faster than the noncatalyzed mechanism. However the noncatalyzed mechanism does remain possible, so that the total rate (catalyzed plus noncatalyzed) can only increase in the presence of the catalyst and never decrease.

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Microbiology

Metabolism

新陈代谢

新陈代谢(/məˈtæbəlɪzəm/,源自希腊语 μεταβολή (metabolē)“变化”)是指生物体内发生的一组维持生命的化学反应。新陈代谢的三个主要功能是将食物中的能量转化为细胞过程可用的形式;将食物转化为大分子(生物聚合物)的组成部分,例如蛋白质、脂质、核酸和一些碳水化合物;以及代谢废物的排泄。这些酶催化反应使生物体能够生长、繁殖、维持其结构并对环境做出反应。新陈代谢这个词也可以指生物体中发生的所有化学反应,包括消化以及物质进入不同细胞和不同细胞之间的运输。从更广泛的意义上讲,细胞内发生的一组反应称为中间(或中间)代谢。

Metabolism (/məˈtæbəlɪzəm/, from Greek μεταβολή (metabolē) 'change') refers to the set of life-sustaining chemical reactions that occur within living organisms. The three main functions of metabolism are the conversion of energy in food into a usable form for cellular processes; the conversion of food to building blocks of macromolecules (biopolymers) such as proteins, lipids, nucleic acids, and some carbohydrates; and the excretion of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow, reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, including digestion and the transportation of substances into and between different cells. In a broader sense, the set of reactions occurring within the cells is called intermediary (or intermediate) metabolism.

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Microbiology

Metabolite

代謝產物

在生物化学中,代谢物是新陈代谢的中间产物或最终产物。该术语通常用于小分子。代谢物具有多种功能,包括燃料、结构、信号传导、对酶的刺激和抑制作用、自身的催化活性(通常作为酶的辅因子)、防御以及与其他生物体的相互作用(例如色素、气味剂和信息素)。初级代谢物直接参与正常的“生长”、发育和繁殖。乙烯是工业微生物大规模生产的初级代谢物的例子。次级代谢产物不直接参与这些过程,但通常具有重要的生态功能。例子包括抗生素和颜料,例如树脂和萜烯等。

In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones). A primary metabolite is directly involved in normal "growth", development, and reproduction. Ethylene exemplifies a primary metabolite produced large-scale by industrial microbiology. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include antibiotics and pigments such as resins and terpenes etc.

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Microbiology

Active metabolite

活性代謝產物

活性代谢物或药理活性代谢物是外源物质(例如药物或环境化学品)的生物活性代谢物。活性代谢物可能产生治疗作用,也可能产生有害作用。

An active metabolite, or pharmacologically active metabolite, is a biologically active metabolite of a xenobiotic substance, such as a drug or environmental chemical. Active metabolites may produce therapeutic effects, as well as harmful effects.

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Microbiology

Enzyme inhibitor

酶抑制剂

酶抑制剂是一种与酶结合并阻断其活性的分子。酶是加速生命必需的化学反应的蛋白质,其中底物分子转化为产物。酶通过将底物与其活性位点结合来促进特定的化学反应,活性位点是酶上的一个特殊区域,可加速反应中最困难的步骤。酶抑制剂通过与酶的活性位点结合(从而防止底物本身结合)或通过与酶上的另一个位点结合来阻止(“抑制”)该过程,从而阻止酶对反应的催化。酶抑制剂可以可逆或不可逆地结合。不可逆抑制剂与酶形成化学键,从而抑制酶直至化学键断裂。

An enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which substrate molecules are converted into products. An enzyme facilitates a specific chemical reaction by binding the substrate to its active site, a specialized area on the enzyme that accelerates the most difficult step of the reaction. An enzyme inhibitor stops ("inhibits") this process, either by binding to the enzyme's active site (thus preventing the substrate itself from binding) or by binding to another site on the enzyme such that the enzyme's catalysis of the reaction is blocked. Enzyme inhibitors may bind reversibly or irreversibly. Irreversible inhibitors form a chemical bond with the enzyme such that the enzyme is inhibited until the chemical bond is broken.

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Microbiology

Enzyme inducer

酵素誘導物

酶诱导剂是一类通过与酶结合并激活它,或通过增加酶编码基因的表达来增加酶的代谢活性的药物。酶诱导剂的例子之一是细胞色素 P450 酶,它将有助于药物在生物体内更快地代谢。酶诱导剂在制药领域对于了解药物相互作用非常重要。研究表明某些药物会增加诱导剂的活性,例如抗生素。它与酶抑制剂相反。有一些特定类型的酶诱导剂可以产生细胞保护途径,在预防和治疗癌症和其他疾病(包括心血管疾病和神经退行性疾病)中发挥作用。酶诱导剂可以是天然存在的或合成的。

An enzyme inducer is a type of drug that increases the metabolic activity of an enzyme, either by binding to the enzyme and activating it, or by increasing the expression of the gene coding for the enzyme. One of the examples of enzyme inducers can be Cytochrome P450 enzymes, which will help to metabolize the drugs faster in the organism. Enzyme inducers are important in the pharmaceutical field to learn drug interactions. Studies show that certain drugs will increase the activity of the inducer, examples could be antibiotics. It is the opposite of an enzyme repressor. There are specific types of enzyme inducers that create cytoprotective pathways that play a role in prevention and treatment of cancer and other diseases including cardiovascular disease and neurodegenerative diseases. Enzyme inducers can be either naturally occurring or synthetically made.

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Microbiology

Non-competitive inhibition

非竞争性抑制

非竞争性抑制是酶抑制的一种类型,其中抑制剂降低酶的活性并与酶结合得同样好,无论它是否已经结合底物。这与竞争性抑制不同,竞争性抑制在抑制剂存在的情况下酶底物的结合亲和力会降低。无论底物是否已经结合,抑制剂都可以与酶结合,但如果它在一种状态或另一种状态下与酶结合具有更高的亲和力,则称为混合抑制剂。

Non-competitive inhibition is a type of enzyme inhibition where the inhibitor reduces the activity of the enzyme and binds equally well to the enzyme regardless of whether it has already bound the substrate. This is unlike competitive inhibition, where binding affinity for the substrate in the enzyme is decreased in the presence of an inhibitor. The inhibitor may bind to the enzyme regardless of whether the substrate has already been bound, but if it has a higher affinity for binding the enzyme in one state or the other, it is called a mixed inhibitor.

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Microbiology

Michaelis–Menten kinetics

米-门二氏动力学

米-门二氏动力学(英语:Michaelis-Menten kinetics),又称米氏动力学,以德国生物化学家莱昂诺尔·米夏埃利斯和加拿大医师莫德·门滕的名字命名,是酶动力学中一个极为重要的方程,可以描述多种非变异构酶动力学现象,其表示式为: V 0 = V m a x [ S ] K M + [ S ] {\displaystyle V_{0}=V_{max}{\frac {[S]}{K_{M}+[S]}}}

In biochemistry, Michaelis–Menten kinetics, named after Leonor Michaelis and Maud Menten, is the simplest case of enzyme kinetics, applied to enzyme-catalysed reactions involving the transformation of one substrate into one product. In 1913, Michaelis and Menten expanded on Victor Henri's fundamental equation of enzyme kinetics, which was established in 1902. It takes the form of a differential equation describing the reaction rate v {\displaystyle v} (rate of formation of product P, with concentration p {\displaystyle p} ) as a function of a {\displaystyle a} , the concentration of the substrate A (using the symbols recommended by the IUBMB).

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Microbiology

Hill equation (biochemistry)

希尔方程 (生物化学)

在生物化学中,若已经有配体分子结合在一个高分子上,那么新的配体分子与这个高分子的结合作用就常常会被增强(亦被称作协同结合)。以阿奇博尔德·希尔命名的希尔系数(Hill coefficient)提供了量化这种效应的方法。 希尔方程(英语:Hill equation)描述了高分子被配体饱和的分数,是一个关于配体浓度的函数;被用于确定受体结合到酶或受体上的合同性程度。此方程首次于1910年由阿奇博尔德·希尔阐释出来以表述为何血红蛋白的氧气结合曲线会呈现S型。 当系数为1时,表明结合作用是完全独立的,而不取决于已经有多少配体已经结合上去。大于一的数表示正协同,而小于一的数表示负协同。希尔系数最初被设计出来是用于解释氧气协同地结合到血红蛋白上的过程(此系统的希尔系数为2.8~3)。

In biochemistry and pharmacology, the Hill equation refers to two closely related equations that reflect the binding of ligands to macromolecules, as a function of the ligand concentration. A ligand is "a substance that forms a complex with a biomolecule to serve a biological purpose", and a macromolecule is a very large molecule, such as a protein, with a complex structure of components. Protein-ligand binding typically changes the structure of the target protein, thereby changing its function in a cell. The distinction between the two Hill equations is whether they measure occupancy or response. The Hill equation reflects the occupancy of macromolecules: the fraction that is saturated or bound by the ligand. This equation is formally equivalent to the Langmuir isotherm. Conversely, the Hill equation proper reflects the cellular or tissue response to the ligand: the physiological output of the system, such as muscle contraction. The Hill equation was originally formulated by Archibald Hill in 1910 to describe the sigmoidal O2 binding curve of hemoglobin.

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Microbiology

Dissociation constant

解离常数

在化学、生物化学及药理学中,解离常数(英语:dissociation constant, K d {\displaystyle K_{d}} )是一种特定类型的平衡常数,用于衡量一较大物体与另一较小组分分开(解离)的倾向,也可以描述配合物解体成组分分子或盐分裂为其组分离子。解离常数是缔合常数的倒数。对于一些特定的盐,解离常数亦可被称为电离常数。

In chemistry, biochemistry, and pharmacology, a dissociation constant (KD) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules, or when a salt splits up into its component ions. The dissociation constant is the inverse of the association constant. In the special case of salts, the dissociation constant can also be called an ionization constant.

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Microbiology

Affinity chromatography

亲和色谱法

亲和色谱法(英语:Affinity chromatography,又称为亲和层析)是一种利用固定相的结合特性来分离分子的色谱方法。亲和色谱在凝胶过滤色谱柱上连接与待分离的物质有一定结合能力的分子,并且它们的结合是可逆的,在改变流动相条件时二者还能相互分离。亲和色谱可以用来从混合物中纯化或浓缩某一分子,也可以用来去除或减少混合物中某一分子的含量。

Affinity chromatography is a method of separating a biomolecule from a mixture, based on a highly specific macromolecular binding interaction between the biomolecule and another substance. The specific type of binding interaction depends on the biomolecule of interest; antigen and antibody, enzyme and substrate, receptor and ligand, or protein and nucleic acid binding interactions are frequently exploited for isolation of various biomolecules. Affinity chromatography is useful for its high selectivity and resolution of separation, compared to other chromatographic methods.

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Microbiology

Western blot

西方墨點法

Western印迹法(英语:Western blot)或称“蛋白质转渍法”、“免疫印迹法”(immunoblot)或“西式吸印杂交”,是在分子生物学、生物化学和免疫遗传学中常用的一种实验方法,也是HIV检测的方法之一。 利用特定抗体能够专一结合其抗原蛋白质的原理来对样品进行着色,通过分析着色的位置和着色深度获得特定蛋白质在所分析的细胞或组织中的表达情况的信息,来分析检测特定蛋白质的生物学检测技术。 发明者一般认为是美国斯坦福大学的乔治·斯塔克(George Stark)。在尼尔·伯奈特(Neal Burnette)于1981年所著的《分析生物化学》(Analytical Biochemistry)中首次被称为“Western印迹法”。

The Western blot (sometimes called the protein immunoblot), or Western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract, and to visualize, distinguish, and quantify the different proteins in a complicated protein combination. Western blot technique uses three elements to achieve its task of separating a specific protein from a complex: separation by size, transfer of protein to a solid support, and marking target protein using a primary and secondary antibody to visualize. A synthetic or animal-derived antibody (known as the primary antibody) is created that recognizes and binds to a specific target protein. The electrophoresis membrane is washed in a solution containing the primary antibody, before excess antibody is washed off. A secondary antibody is added which recognizes and binds to the primary antibody.

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Microbiology

Edman degradation

埃德曼降解法

Edman 降解由 Pehr Edman 开发,是一种对肽中氨基酸进行测序的方法。在此方法中,氨基末端残基被标记并从肽上裂解,而不破坏其他氨基酸残基之间的肽键。

Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.

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Microbiology

Protein folding

蛋白质折叠

蛋白质折叠(英语:Protein folding)是蛋白质获得其功能性结构和构象的物理过程。通过这一物理过程,蛋白质从无规则卷曲折叠成特定的功能性三维结构。在从mRNA序列翻译成线性的氨基酸链时,蛋白质都是以去折叠多肽或无规则卷曲的形式存在。 蛋白质的基本单位为氨基酸,而蛋白质的一级结构指的就是其氨基酸序列。蛋白质会由所含氨基酸残基的亲水性、疏水性、带正电、带负电等特性通过残基间的相互作用而折叠成一立体的三级结构。 根据克里斯琴·B·安芬森(1972年的诺贝尔化学奖得主)的研究,蛋白质可由加热或置于某些化学环境而变性,三级结构解体;而当环境回复到原本的状态时,蛋白质可于不到一秒的时间折叠至原先的立体结构,不论试验几次,蛋白质都仅此一种立体结构,于是安芬森提出一个结论:蛋白质分子的一级结构决定其立体结构(安芬森法则)。 安芬森的研究结果非常重要,因为蛋白质的功能取决于其立体结构,而目前根据已知某基因序列可翻译获得对应蛋白质的氨基酸序列,即蛋白质的一级结构;如果从蛋白质的一级结构就能知道立体结构,那么即可直接从基因推测其编码蛋白质所对应的生物学功能。虽然蛋白质可在短时间中从一级结构折叠至立体结构,研究者却无法在短时间中从氨基酸序列计算出蛋白质结构,甚至无法得到准确的三维结构。因此,研究蛋白质折叠的过程,可以说是破译折叠密码的过程。 目前蛋白质的再折叠依然遵从先使用胍或脲变性,然后逐渐降低胍或者脲的浓度,也就是逐渐降低对蛋白质天然“回缩”能力的干扰。使其自然回到天然的最低能量状态。只是这个过程无法很好的控制肽链与肽链之间和肽链内部形成错误折叠的干扰。

Protein folding is the physical process by which a protein, after synthesis by a ribosome as a linear chain of amino acids, changes from an unstable random coil into a more ordered three-dimensional structure. This structure permits the protein to become biologically functional or active. The folding of many proteins begins even during the translation of the polypeptide chain. The amino acids interact with each other to produce a well-defined three-dimensional structure, known as the protein's native state. This structure is determined by the amino-acid sequence or primary structure. The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded, indicating that protein dynamics are important.

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Microbiology

Structural motif

结构模体

在链状生物分子(例如蛋白质或核酸)中,结构基序是常见的三维结构,出现在各种不同的、进化上不相关的分子中。结构基序不必与序列基序相关联;它可以由不同蛋白质或RNA中不同且完全不相关的序列来表示。

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have to be associated with a sequence motif; it can be represented by different and completely unrelated sequences in different proteins or RNA.

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Microbiology

Protein engineering

蛋白質工程

蛋白质工程是通过设计和生产非天然多肽(通常通过改变自然界中发现的氨基酸序列)来开发有用或有价值的蛋白质的过程。这是一门年轻的学科,在理解蛋白质折叠和识别蛋白质设计原理方面进行了大量研究。它已被用来改善许多工业催化酶的功能。这也是一个产品和服务市场,预计到 2017 年价值将达到 1680 亿美元。蛋白质工程有两种一般策略:合理的蛋白质设计和定向进化。这些方法并不相互排斥;研究人员通常会同时应用两者。未来,对蛋白质结构和功能的更详细了解以及高通量筛选的进步可能会极大地扩展蛋白质工程的能力。

Protein engineering is the process of developing useful or valuable proteins through the design and production of unnatural polypeptides, often by altering amino acid sequences found in nature. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles. It has been used to improve the function of many enzymes for industrial catalysis. It is also a product and services market, with an estimated value of $168 billion by 2017. There are two general strategies for protein engineering: rational protein design and directed evolution. These methods are not mutually exclusive; researchers will often apply both. In the future, more detailed knowledge of protein structure and function, and advances in high-throughput screening, may greatly expand the abilities of protein engineering.

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Microbiology

Protein primary structure

蛋白質一級結構

蛋白质一级结构(protein primary structure)是肽或蛋白质中氨基酸的线性序列,即氨基酸序列(amino acid sequence)。按照惯例,蛋白质的一级结构被报道从氨基末端(N)端到羧基末端(C)端。蛋白质生物合成最通常由细胞中的核糖体进行。肽也可以在实验室中合成。蛋白质一级结构可以直接进行蛋白质测序,或从DNA序列推断。 在生物化学里,生物分子的一级结构是其分子组成和分子间化学键结的精确模样。对于一典型的无分支、无交叉的生物聚合物(如DNA、RNA或典型的细胞内蛋白质等分子),其第一结构等同于描述其单体单位的序列,即如DNA序列和肽序列。“一级结构”这一名词在Linderstrom-Lang于1951年的Lane Medical Lectures上首次被提到。一级结构和一级序列有一点相似,即使在二级或三级结构中并没有平行的概念。

Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences.

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Microbiology

Oligonucleotide

寡核苷酸

寡核苷酸(oligonucleotides)又称寡核糖核苷酸,是短 DNA 或 RNA低聚物,在基因检测、研究和法医学方面有广泛的应用。寡核苷酸通常在实验室里通过固相化学合成法制备,并可以按照用户的需求合成指测序列的小片段核酸,对基因合成、聚合酶链式反应(PCR)、DNA测序、分子克隆至关重要。在自然界中,寡核苷酸通常以小RNA分子的形式出现 ,在基因表达的调控中发挥作用(如microRNA);或者是较大核酸分子分解后的降解中间体。 寡核苷酸的特点是由构成整个分子的核苷酸残基序列决定的。寡核苷酸的长度通常用"-mer"(来自希腊语meros,代表"部分"的意思)来表示。例如,具有6个核苷酸(nucleotide, nt)的寡核苷酸,被称为六聚体,而一个25 nt的寡核苷酸通常被称为 "25-mer"。寡核苷酸很容易以序列互补的方式与各自的互补寡核苷酸、DNA或RNA结合形成双链体,或较少的更高级别的混合体。这一基本特性是使用寡核苷酸作为探针来检测DNA或RNA特测序列的基础。使用寡核苷酸的应用包括DNA微阵列,Southern印迹,等位基因特异性寡核苷酸分析, 荧光原位杂交(FISH),PCR和人工基因的合成。 寡核苷酸由2'-脱氧核糖核苷酸组成,可以在骨架上或脱氧核糖的2号位进行修饰,以达到不同的药理效果。这些修饰使寡核苷酸具有新的特性,使其成为反义的关键因素。

Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small fragments of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules. Oligonucleotides are characterized by the sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by "-mer" (from Greek meros, "part"). For example, an oligonucleotide of six nucleotides (nt) is a hexamer, while one of 25 nt would usually be called a "25-mer".

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Microbiology

Genetic code

遗传密码

遗传密码(Genetic code)又称遗传编码,是遗传信息的传递规则,将DNA或mRNA序列以三个核苷酸为一组的“密码子(codon)”翻译为蛋白质的氨基酸序列,以用于蛋白质合成。几乎所有的生物都使用同样的遗传密码,称为“标准遗传密码”;即使是非细胞结构的病毒,它们也是使用标准遗传密码。有些具感染性的致病因子,使用一些稍微不同的遗传密码,如朊毒体以蛋白质为遗传密码。密码子简并性是遗传密码的突出特征。

Genetic code is a set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The codons specify which amino acid will be added next during protein biosynthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often called the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in mitochondria) exist.

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Microbiology

Methylation

甲基化

甲基化(英语:methylation)指向底物引入甲基的过程,一般是以甲基取代氢原子。 在生物系统内,甲基化是经酶催化的,这种甲基化涉及重金属修饰、基因表达的调控、蛋白质功能的调节以及核糖核酸(RNA)加工。重金属修饰可以在生物系统外发生。组织样本的化学甲基化也是组织染色的方法之一。

Methylation, in the chemical sciences, is the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and biology. In biological systems, methylation is catalyzed by enzymes; such methylation can be involved in modification of heavy metals, regulation of gene expression, regulation of protein function, and RNA processing. In vitro methylation of tissue samples is also a way to reduce some histological staining artifacts. The reverse of methylation is demethylation.

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Microbiology

CRISPR

成簇规律间隔短回文重复序列(CRISPR)

CRISPR(IPA:/ˈkrɪspər/;DJ:/ˈkrispə/;KK:/ˈkrɪspɚ/)是由日本科学家于1987年在大肠杆菌的基因组中发现到特别规律的DNA序列。即某一小段DNA会一直重复,重复片段之间又有相等长的间隔,此序列就是“Clustered Regularly Interspaced Short Palindromic Repeats,简称: CRISPR”亦可称“CRISPR-associated proteins,简称: Cap”;中文各别译为“规律间隔成簇短回文重复序列”和“规律间隔成簇短回文重复序列及其相关蛋白基因”。 CRISPR是存在于细菌、古菌中的一种基因,该类基因组中含有曾经攻击过该细菌的病毒之基因片段。细菌透过这些基因片段来侦测并抵抗相同病毒的攻击,并摧毁其DNA。这类基因组是细菌免疫系统的关键组成部分。透过这些基因组,人类可以准确且有效地编辑生物体内的部分基因,也就是CRISPR/Cas9基因编辑技术。

CRISPR (; acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic CRISPR is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral (i.e. anti-phage) defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea. Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and open up specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within living organisms.

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Microbiology

Guide RNA

引导核糖核酸

向导RNA(guide RNA,gRNA),也称为单链向导RNA(single guide RNA,sgRNA)。是作用于动质体(kinetoplastid)体内一种称为RNA编辑(RNA editing)的后转录修饰过程中。也是一种小型非编码RNA。可与pre-mRNA配对,并在其中插入一些尿嘧啶(U),产生具有作用的mRNA。

Guide RNA (gRNA) or single guide RNA (sgRNA) is a short sequence of RNA that guides a CRISPR-associated protein to its nucleic acid sequence target by Watson-Crick base pairing. In bacteria and archaea, gRNAs are a part of the CRISPR-Cas system that serves as an adaptive immune defense that protects the organism from viruses. Here the short gRNAs serve as detectors of foreign DNA and direct the Cas-enzymes that degrades the foreign nucleic acid.

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Microbiology

Ribosome-binding site

核糖体结合位点

核糖体结合位点(英语:Ribosome-binding site),简称RBS,是位于信使核糖核酸(mRNA)起始密码子上游,在翻译起始时可结合核糖体的序列。

A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes. Ribosome recruitment in eukaryotes is generally mediated by the 5' cap present on eukaryotic mRNAs.

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