Biological Pathways 生物途径（通路）

Biological Pathways 生物途径

A biological pathway is a series of interactions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move. Some of the most common biological pathways are involved in metabolism, the regulation of gene expression, and the transmission of signals. Pathways play a key role in advanced studies of genomics.

Most common types of biological pathways:

Metabolic pathway
Genetic pathway
Signal transduction pathway

生物途径是细胞分子之间的一系列相互作用，使得产生某种特定产物或使得某些细胞发生变化。这种途径可以引发新分子的组合，例如脂肪或蛋白质。途径还可以打开和关闭基因，或刺激细胞移动。一些最常见的生物学途径比如说，代谢，基因表达的调控和信号的传递。途径在基因组学的高级研究中起着关键作用。

最常见的生物途径：

代谢途径
遗传途径
信号传导途径

Metabolic Pathway 代谢途径

In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes.[1]:26 In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell.[2] These enzymes often require dietary minerals, vitamins, and other cofactors to function.

Different metabolic pathways function based on the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. For instance, the electron transport chain, and oxidative phosphorylation all take place in the mitochondrial membrane. In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell.

There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with the utilization of energy (anabolic pathway) or break down of complex molecules by releasing energy in the process (catabolic pathway). The two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the energy required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the amphibolic pathway, which can be either catabolic or anabolic based on the need for or the availability of energy.

Pathways are required for the maintenance of homeostasis within an organism and the flux of metabolites through a pathway is regulated depending on the needs of the cell and the availability of the substrate. The end product of a pathway may be used immediately, initiate another metabolic pathway, or be stored for later use. The metabolism of a cell consists of an elaborate network of interconnected pathways that enable the synthesis and breakdown of molecules (anabolism and catabolism).

在生物化学中，代谢途径是细胞内发生的一系列关联的化学反应。酶促反应的反应物，产物和中间产物统称为代谢产物，它们是通过酶催化所调整的一系列化学反应。在大多数代谢途径中，一种酶的产物充当下一反应的底物。但是，有些副产品被认为是废物，需要从细胞里清除。这些酶通常需要膳食中的矿物质，维生素和其他辅助因子才能发挥作用。

不同的代谢途径根据真核细胞中的位置以及该途径在细胞给隔层中的重要性而起作用。例如，电子传输链和氧化磷酸化都发生在线粒体膜上。相反，糖酵解，磷酸戊糖途径和脂肪酸生物合成都发生在细胞的细胞质中。

代谢途径有两种，其特征是利用能量合成分子的能力（合成代谢途径）或通过在分解复杂分子中释放能量的能力（代谢途径）。两种途径相辅相成，一种途径释放的能量被另一种途径消耗掉。分解代谢途径的降解过程提供了进行合成代谢途径生物合成所需的能量。除两个不同的代谢途径外，还有两性代谢途径，根据能量的需要或可获得性，它可以是分解代谢的或合成代谢的。

维持生物体内动态平衡所需的途径是通过代谢途径的代谢量而调节的，这取决于细胞的需求和底物的可用性。途径的终产物可以立即使用，启动另一个代谢途径，或储存起来以备后用。细胞的新陈代谢由相互连接的途径组成的精细网络组成，这些途径使分子的合成和分解（代谢和分解代谢）成为可能。

Gene Ontology 基因本体

基因本体(GO)

基因本体论（GO）从三个方面描述了我们对生物学领域的了解：

细胞组分（cellular component）：细胞的每个部分和细胞外环境。
分子功能（molecular function）：可以描述为分子水平的活性（activity），如催化（catalytic）或结合（binding）活性。
生物过程（biological process）：生物学过程指由一个或多个分子功能有序组合而产生的系列事件。较大的过程或通过多种分子活动完成的“生物程序”。更加广泛的生物学过程术语的例子是DNA修复或信号转导。更具体的术语的例子是葡萄糖跨膜转运的嘧啶核苷生物合成过程。

这三个ontology下面又可以独立出不同的亚层次，层层向下构成一个ontologies的树型分支结构。可以说， GO是生物学的统一化工具

Phenotype and genotype 表现型和基因型（遗传型）

The genotype of an organism is defined as the sum of all its genes. The phenotype of an organism is the observable physical or biochemical characteristics of an organism, determined by both genetic make-up and environmental influences.

基因型又称遗传型，它反映生物体的遗传构成，即从双亲获得的全部基因的总和。表现型是指生物体所有性状的总和。但整个生物体的表现型是无法具体表示的。基因型、表现与环境之间的关系，可用如下公式来表示:表现型=基因型+环境。

Gene Knockout and Gene Knockdown

The RNA interference pathway is often exploited in experimental biology to study the function of genes in cell culture and in vivo in model organisms. Double-stranded RNA is synthesized with a sequence complementary to a gene of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway. Using this mechanism, researchers can cause a drastic decrease in the expression of a targeted gene. Studying the effects of this decrease can show the physiological role of the gene product. Since RNAi may not totally abolish expression of the gene, this technique is sometimes referred as a "knockdown", to distinguish it from "knockout" procedures in which expression of a gene is entirely eliminated.
Gene knockdown refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification (a change in the DNA of one of the organism's chromosomes) or by treatment with a reagent such as a short DNA or RNAoligonucleotide with a sequence complementary to either an mRNA transcript or a gene. If genetic modification of DNA is done, the result is a "knockdown organism". If the change in gene expression is caused by an oligonucleotide binding to an mRNA or temporarily binding to a gene, this results in a temporary change in gene expression without modification of the chromosomal DNA and is referred to as a "transient knockdown".
A gene knockout (abbreviation: KO) is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism). Also known as knockout organisms or simply knockouts, they are used in learning about a gene that has been sequenced, but which has an unknown or incompletely known function. Researchers draw inferences from the difference between the knockout organism and normal individuals.

基因剔除(Gene Knockout)：是指一种遗传工程技术，可改变生物的遗传基因，令特定的基因功能丧失作用，从而使部分功能被屏障，并可进一步对生物体造成影响此技术是由马里奥·卡佩奇、马丁·埃文斯与奥利弗·史密斯所开发，最初是以基因剔除小鼠（knockout mouse，昵称：KO mouse）完成实验，三人并因此获得2007诺贝尔医学奖。

基因敲减(Gene Knockdown)：泛指降低目的基因的表达，干扰基因的表达，还没有到达Knockout的地步。

文献中knockdown一词的正确理解是什么

Epigenetics literally means "above" or "on top of" genetics. It refers to external modifications to DNA that turn genes "on" or "off." These modifications do not change the DNA sequence, but instead, they affect how cells "read" genes.

Screen

筛选；gene screen：基因筛选；