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Biochemistry

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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Biochemistry

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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Biochemistry

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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Biochemistry

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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Biochemistry

Gene expression

基因表現

基因表达(英语:gene expression)又称基因表现,是用基因中的信息来合成基因产物的过程。产物通常是蛋白质,但对于非蛋白质编码基因,如tRNA和小核RNA(snRNA),产物则是RNA。所有已知生物都通过基因表达来生成生命所需的高分子物质。 基因表达的过程可概分为:DNA转录、RNA剪接、RNA转译、蛋白质转译后修饰,这四大步骤。基因表达调控控制细胞的结构与功能,同时也是细胞分化、形态发生及生物体的多功能性和适应性的基础。不同的时间、不同的环境,以及不同部位的细胞,或是基因在细胞中的含量差异,皆可能使基因产生不同的表现。基因调节也可以作为进化变化的底物,因为基因表达的时间,位置和数量的控制可以对基因在细胞或多细胞生物体中的功能(作用)具有深远的影响。 在遗传学中,基因表达是基因型产生表现型(即可观察的性状)的最基本的层次。

Gene expression is the process by which the information contained within a gene is used to produce a functional gene product, such as a protein or a functional RNA molecule. This process involves multiple steps, including the transcription of the gene's sequence into RNA. For protein-coding genes, this RNA is further translated into a chain of amino acids that folds into a protein, while for non-coding genes, the resulting RNA itself serves a functional role in the cell. Gene expression enables cells to utilize the genetic information in genes to carry out a wide range of biological functions. While expression levels can be regulated in response to cellular needs and environmental changes, some genes are expressed continuously with little variation.

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Biochemistry

Enzyme Commission number

酶学委员会编号

酶学委员会编号或酶编号(英语:Enzyme Commission number),简称EC编号或EC号(EC number),是一种基于酶催化化学反应而制定数字分类方案。作为酶命名法 / 酶学委员会命名法(enzyme nomenclature)系统,同时会为各种酶给予一个建议的名称,且每个EC编号都与相应酶催化反应的推荐名称相关联。 EC编号并非针对不同种类的酶,而是针对酶催化的反应。如果不同的酶(例如来自不同生物体的酶)催化相同的反应,则它们会获得相同的EC编号。此外,通过趋同进化,完全不同的蛋白质折叠可以催化相同的反应(这些有时被称为非同源同功能酶)因此会被分配相同的EC编号。相比之下,联合蛋白数据库标识符通过氨基酸序列唯一地指定蛋白质。

The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. As a system of enzyme nomenclature, every EC number is associated with a recommended name for the corresponding enzyme-catalyzed reaction. EC numbers do not specify enzymes but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. Furthermore, through convergent evolution, completely different protein folds can catalyze an identical reaction (these are sometimes called non-homologous isofunctional enzymes) and therefore would be assigned the same EC number. By contrast, UniProt identifiers uniquely specify a protein by its amino acid sequence.

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Biochemistry

FASTA format

FASTA格式

在生物信息学中,FASTA格式是一种用于记录核酸序列或肽序列的文本格式,其中的核酸或氨基酸均以单个字母编码呈现。该格式同时还允许在序列之前定义名称和编写注释。这一格式最初由FASTA软件包定义,但现今已是生物信息学领域的一项标准。 FASTA简明的格式降低了序列操纵和分析的难度,令序列可被文本处理工具和诸如Python、Ruby和Perl等脚本语言处理。

In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format allows for sequence names and comments to precede the sequences. It originated from the FASTA software package and has since become a near-universal standard in bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages.

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Biochemistry

Flow cytometry

流式细胞术

流式细胞术 (FC) 是一种用于检测和测量细胞或颗粒群的物理和化学特性的技术。在此过程中,含有细胞或颗粒的样品悬浮在液体中并注入流式细胞仪仪器中。样品被聚焦,理想情况下一次让一个细胞流过激光束,其中散射的光是细胞及其成分的特征。细胞通常用荧光标记进行标记,因此光被吸收,然后以一定波长带发射。可以快速检查数以万计的细胞,并由计算机处理收集的数据。流式细胞术常用于基础研究、临床实践和临床试验。流式细胞仪的用途包括:

Flow cytometry (FC) is a technique used to detect and measure the physical and chemical characteristics of a population of cells or particles. In this process, a sample containing cells or particles is suspended in a fluid and injected into the flow cytometer instrument. The sample is focused to ideally flow one cell at a time through a laser beam, where the light scattered is characteristic to the cells and their components. Cells are often labeled with fluorescent markers so light is absorbed and then emitted in a band of wavelengths. Tens of thousands of cells can be quickly examined and the data gathered are processed by a computer. Flow cytometry is routinely used in basic research, clinical practice, and clinical trials. Uses for flow cytometry include:

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Biochemistry

Fluorescence anisotropy

荧光各向异性

荧光各向异性或荧光偏振是荧光团发射的光沿不同偏振轴具有不相等强度的现象。该领域的早期先驱包括 Aleksander Jablonski、Gregorio Weber 和 Andreas Albrecht。 Lakowicz 的书中介绍了荧光偏振的原理以及该方法的一些应用。

Fluorescence anisotropy or fluorescence polarization is the phenomenon where the light emitted by a fluorophore has unequal intensities along different axes of polarization. Early pioneers in the field include Aleksander Jablonski, Gregorio Weber, and Andreas Albrecht. The principles of fluorescence polarization and some applications of the method are presented in Lakowicz's book.

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Biochemistry

Proteomics

蛋白质组学

蛋白质组学是对蛋白质的大规模研究。蛋白质组是由生物体或系统产生或修饰的整套蛋白质。蛋白质组学是一个跨学科领域,涵盖从蛋白质组成、结构和活性的整体水平对蛋白质组的探索。虽然蛋白质组的规模和复杂性非常巨大,但最近的技术进步大大扩展了蛋白质组分析的灵敏度和范围。蛋白质组学通常指蛋白质和蛋白质组的大规模实验分析,但通常特指蛋白质纯化和质谱分析。事实上,无论是在由数百万个细胞组成的大样本中,还是在单个细胞中,质谱分析都是分析蛋白质组的最强大的方法。

Proteomics is the large-scale study of proteins. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics is an interdisciplinary field that covers the exploration of proteomes from the overall level of protein composition, structure, and activity. While the scale and complexity of the proteome is formidable, recent technological progress has substantially expanded the sensitivity and scope of proteome analysis. Proteomics generally denotes the large-scale experimental analysis of proteins and proteomes, but often refers specifically to protein purification and mass spectrometry. Indeed, mass spectrometry is the most powerful method for analysis of proteomes, both in large samples composed of millions of cells, and in single cells.

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Biochemistry

Structural biology

结构生物学

结构生物学涉及生物材料在各个组织层面的结构分析。在 19 世纪和 20 世纪初,结构研究很大程度上局限于肉眼或通过放大镜和光学显微镜可见的结构。 20 世纪,人们开发了多种实验技术来检查生物分子的 3D 结构。最突出的技术是 X 射线晶体学、核磁共振和电子显微镜。 X 射线的发现及其在蛋白质晶体中的应用改变了结构生物学,使研究人员能够确定生物分子的原子细节三维结构。同样,核磁共振波谱可以获取有关蛋白质结构和动力学的信息。

Structural biology is concerned with the structural analysis of biological material at every level of organization. During the 19th and early 20th centuries, structural studies were largely limited to structures visible to the naked eye or through magnifying glasses and light microscopes. In the 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography, nuclear magnetic resonance, and electron microscopy. The discovery of X-rays and their application to protein crystals transformed structural biology by allowing researchers to determine the three-dimensional structures of biological molecules in atomic detail. Likewise, NMR spectroscopy allowed information about protein structure and dynamics to be obtained.

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Biochemistry

Cell biology

细胞生物学

细胞生物学,细胞生物学或细胞学,是研究细胞的结构、功能和行为的生物学分支。所有生物体都是由细胞组成的。细胞是生命的基本单位,负责有机体的生存和功能。细胞生物学涵盖原核细胞和真核细胞,子主题包括细胞代谢、细胞通讯、细胞周期、生物化学和细胞组成的研究。细胞研究是利用显微镜技术、细胞培养和细胞分级进行的。这些用于研究细胞如何发挥作用,最终深入了解更大的生物体。了解细胞的组成部分以及细胞如何工作是所有生物科学的基础,对于癌症和其他疾病等生物医学领域的研究也至关重要。

Cell biology, cellular biology, or cytology, is the branch of biology that studies the structure, function, and behavior of the cells. All organisms are made of cells. A cell is the basic unit of life that is responsible for the living and functioning of an organism. Cell biology encompasses both prokaryotic and eukaryotic cells, with subtopics including the study of cell metabolism, cell communication, cell cycle, biochemistry, and cell composition. The study of cells is performed using microscopy techniques, cell culture, and cell fractionation. These are used for research into how cells function, which ultimately gives insight into larger organisms. Knowing the components of cells and how cells work is fundamental to all biological sciences and is essential for research in biomedical fields such as cancer, and other diseases.

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Biochemistry

GC-content

GC含量

GC含量(GC-content,guanine-cytosine content)是分子生物学和遗传学的术语,指研究对象(例如放线菌)的全基因组(DNA 或 RNA 分子)或其片段中,含氮碱基鸟嘌呤(G)或胞嘧啶(C)任何一个所占的百分比。一种生物的基因组或特定DNA、RNA片段有特定的GC含量。 在DNA链中G和C是以三个氢键相连,而T和A则是两个氢键相连的。氢键的多少体现连接的能量,氢键多的不容易被打断。 在双链DNA中,腺嘌呤与胸腺嘧啶(A/T)之比,以及鸟嘌呤与胞嘧啶(G/C)之比都是1。但是,(A+T)/(G+C)之比则随DNA的种类不同而异。GC含量愈高,DNA的密度也愈高,同时热及碱不易使之变性,因此利用这一特性便可进行DNA的分离或测定。 测定GC含量的方法有:Tm法,HPLC法

In molecular biology and genetics, GC-content (or G+C content or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of an implied four total bases, also including adenine and thymine in DNA and adenine and uracil in RNA. GC-content may be given for a certain fragment of DNA or RNA or for an entire genome. When it refers to a fragment, it may denote the GC-content of an individual gene or section of a gene (domain), a group of genes or gene clusters, a non-coding region, or a synthetic oligonucleotide such as a primer.

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Biochemistry

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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Biochemistry

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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Biochemistry

Reaction rate constant

速率常数

在化学动力学中,反应速率常数,又称速率常数 k或 λ是化学反应速率的量化表示方式。 对于反应物A和反应物B反应成生成物C的化学反应,反应速率可表示成此式: d [ C ] d t = k ( T ) [ A ] m [ B ] n {\displaystyle {\frac {d[C]}{dt}}=k(T)[A]^{m}[B]^{n}} k(T)是反应速率常数,会随温度改变。假设反应发生在固定容积内,[A]和[B]代表两种反应物的莫耳浓度。 指数m和n称为反应级数,取决于反应机理,可由实验测定。将m和n相加,可得到反应的总级数。

In chemical kinetics, a reaction rate constant or reaction rate coefficient (⁠ k {\displaystyle k} ⁠) is a proportionality constant which quantifies the rate and direction of a chemical reaction by relating it with the concentration of reactants.

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Biochemistry

Arrhenius equation

阿伦尼乌斯方程

阿瑞尼斯方程(英语:Arrhenius equation)是化学反应的速率常数与温度之间的关系式,适用于基元反应和非基元反应,甚至某些非均相反应。其不定积分形式为: k = A e − E a / R T {\displaystyle \ k=Ae^{{-E_{a}}/{RT}}} 或 ln ⁡ k = − E a R T + ln ⁡ A {\displaystyle \ \ln k=-{\frac {E_{a}}{RT}}+\ln A} 其中: k {\displaystyle \ k} 为反应的速率常数; A {\displaystyle \ A} 称为指前因子/阿伦尼乌斯常数,单位与 k…

In physical chemistry, the Arrhenius equation is a formula for the temperature dependence of reaction rates. In 1889 while working with Wilhelm Ostwald at Leipzig University, Svante Arrhenius proposed the equation on the basis of the work of Dutch chemist Jacobus Henricus van 't Hoff, who had noted in 1884 that the Van 't Hoff equation for the temperature dependence of equilibrium constants suggests such a formula for the rates of both forward and reverse reactions. This equation has a vast and important application in determining the rate of chemical reactions and for calculation of energy of activation. Arrhenius provided a physical justification and interpretation for the formula. Currently, it is best seen as an empirical relationship. It can be used to model the temperature variation of diffusion coefficients, population of crystal vacancies, creep rates, and many other thermally induced processes and reactions. The Eyring equation, developed in 1935, also expresses the relationship between rate and energy.

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Biochemistry

Peptide-mass fingerprint

肽质量指纹图谱

在生物信息学中,肽质量指纹或肽质量图是来自正在分析的消化蛋白质的肽混合物的质谱。质谱充当指纹,因为它是一种可以用于识别蛋白质的模式。 1993 年开发的形成肽质量指纹的方法包括分离蛋白质,将其分解成单个肽,并通过某种形式的质谱测定肽的质量。一旦形成,肽质量指纹可用于在数据库中搜索相关蛋白质甚至基因组序列,使其成为注释蛋白质编码基因的强大工具。质量指纹分析的一大优势是它的执行速度比肽测序快得多,但结果同样有用。

In bio-informatics, a peptide-mass fingerprint or peptide-mass map is a mass spectrum of a mixture of peptides that comes from a digested protein being analyzed. The mass spectrum serves as a fingerprint in the sense that it is a pattern that can serve to identify the protein. The method for forming a peptide-mass fingerprint, developed in 1993, consists of isolating a protein, breaking it down into individual peptides, and determining the masses of the peptides through some form of mass spectrometry. Once formed, a peptide-mass fingerprint can be used to search in databases for related protein or even genomic sequences, making it a powerful tool for annotation of protein-coding genes. One major advantage to mass fingerprinting is that it is significantly faster to carry out than peptide sequencing, yet the results are equally useful.

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Biochemistry

Flux balance analysis

通量平衡分析

在生物化学和系统生物学中,通量平衡分析 (FBA) 是一种利用代谢网络的基因组规模重建来模拟细胞或整个单细胞生物(例如大肠杆菌或酵母)代谢的数学方法。基因组规模重建描述了生物体基于其整个基因组的所有已知或假设的生化反应。这些重建通过关注代谢物之间的相互转化来模拟代谢,识别哪些代谢物参与细胞或生物体中发生的各种反应,并确定编码催化这些反应的酶(如果有)的基因。

In biochemistry and systems biology, flux balance analysis (FBA) is a mathematical method for simulating the metabolism of cells or entire unicellular organisms, such as E. coli or yeast, using genome-scale reconstructions of metabolic networks. Genome-scale reconstructions describe all known or hypothesized biochemical reactions in an organism based on its entire genome. These reconstructions model metabolism by focusing on the interconversions between metabolites, identifying which metabolites are involved in the various reactions taking place in a cell or organism, and determining the genes that encode the enzymes which catalyze these reactions (if any).

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Biochemistry

Fluxomics

通量组学

通量组学描述了寻求确定生物实体内代谢反应速率的各种方法。虽然代谢组学可以提供生物样品中代谢物的即时信息,但代谢是一个动态过程。通量组学的意义在于代谢通量决定细胞表型。它的另一个优点是基于代谢组,其成分比基因组或蛋白质组少。 Fluxomics属于随着高通量技术的出现而发展起来的系统生物学领域。系统生物学认识到生物系统的复杂性,并具有解释和预测这种复杂行为的更广泛目标。

Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. While metabolomics can provide instantaneous information on the metabolites in a biological sample, metabolism is a dynamic process. The significance of fluxomics is that metabolic fluxes determine the cellular phenotype. It has the added advantage of being based on the metabolome which has fewer components than the genome or proteome. Fluxomics falls within the field of systems biology which developed with the appearance of high throughput technologies. Systems biology recognizes the complexity of biological systems and has the broader goal of explaining and predicting this complex behavior.

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Biochemistry

Gene set enrichment analysis

基因集富集分析

基因集富集分析 (GSEA)(也称为功能富集分析或通路富集分析)是一种识别在大量基因或蛋白质中过度代表的基因或蛋白质类别的方法,这些基因或蛋白质类别可能与不同的表型(例如不同的生物体生长模式或疾病)相关。该方法使用统计方法来识别显着富集或缺失的基因组。转录组学技术和蛋白质组学结果通常会识别数千个基因,用于分析。研究人员进行高通量实验来产生基因组(例如,在不同条件下差异表达的基因),通常希望检索该基因组的功能图谱,以便更好地了解潜在的生物过程。

Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g. different organism growth patterns or diseases). The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes, which are used for the analysis. Researchers performing high-throughput experiments that yield sets of genes (for example, genes that are differentially expressed under different conditions) often want to retrieve a functional profile of that gene set, in order to better understand the underlying biological processes.

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Biochemistry

Gene co-expression network

基因共表达网络

基因共表达网络是一种无向图,每个节点代表基因,如果二者存在明显的共表达关系,就用一个边连接两个节点。 对不同的样本或者不同的实验条件建立基因表达谱后,可以通过查看不同样本间产生相似表达模式的基因对建立基因共表达网络。原因是,两个共表达基因在不同的样本中应以相同模式变化。共同表达的基因是由同一转录控制程序控制、功能相关、同一通路或蛋白结构的组成部分,所以基因共表达网络具有生物学意义。 基因共表达网络不指定共表达关系的方向和类型。然而在基因调控网络中,边是有方向的,代表着反应、变换、互作、激活或者抑制的生化过程。而基因共表达网络并不尝试判定因果关系,边只代表基因之间的相关或者依赖关系。有类似功能或参与统一生物功能的基因会产生很多相互作用,在基因共表达网络中会体现为模块或连接丰富的子图。 基因共表达网络一般是用高通量基因表达谱技术(如微阵列和RNA测序)生成的数据集建立的。

A gene co-expression network (GCN) is an undirected graph, where each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a significant co-expression relationship between them. Having gene expression profiles of a number of genes for several samples or experimental conditions, a gene co-expression network can be constructed by looking for pairs of genes which show a similar expression pattern across samples, since the transcript levels of two co-expressed genes rise and fall together across samples. Gene co-expression networks are of biological interest since co-expressed genes are controlled by the same transcriptional regulatory program, functionally related, or members of the same pathway or protein complex. The direction and type of co-expression relationships are not determined in gene co-expression networks; whereas in a gene regulatory network (GRN) a directed edge connects two genes, representing a biochemical process such as a reaction, transformation, interaction, activation or inhibition.

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