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第二章  核酸的结构与功能

1. DNA的变性与复性(denaturation and renaturation of DNA): 双链DNA(dsDNA)在变性因素(如过酸、过碱、加热、尿素等)影响下,解链成单链DNA(ssDNA)的过程称之为DNA变性。DNA变性后，生物活性丧失，但一级结构没有改变，所以在一定条件下仍可恢复双螺旋结构。热变性的DNA经缓慢冷却后，两条互补链可重新恢复天然的双螺旋构象，这一现象称为复性，也称退火。
DNA denaturation means that a DNA has lost its’ native conformation and double strand DNA is separated to single strand DNA by exposed to a destabilizing factor such as heat, acid, alkali,urea or amide. (when high temperature is used to denature DNA, the DNA is said to be melted).
DNA renaturation :Removing the denaturation factors or in proper condition the denatured DNA (ssDNA) restore native structure (dsDNA) and function. The process of  renaturation  of heat denatured DNA by slowly cooling is called annealing.
2．核酸分子杂交(hybridization of nucleic acids)：在DNA变性后的复性过程中，将不同来源的DNA单链分子或RNA分子放在同一溶液中，只要在DNA或RNA的单链分子之间存在着一定程度的碱基配对关系，就可以在不同的分子间形成杂化双链，这种现象称为核酸分子杂交。
Hybridization:
when heterogeneous DNA or RNA  are put together, they will become to heteroduplex via the base-pairing rules during renaturation if they are complementary in parts (not complete).  This is called molecular hybridization.

3．增色效应与减色效应(hyperchromic effect and hypochromic effect): DNA变性时，双螺旋松解，碱基暴露，OD260值增高称之为增色效应；除去变性因素后，单链DNA依碱基配对规律恢复双螺旋结构，OD260值减小称为减色效应。
Hyperchromic effect : The absorbance at 260 nm of a DNA solution increases when the double helix is melted into single strands at DNA denaturation.
Hypochromic effect: The absorbance at 260 nm of a DNA solution decreses when the single strands return into double helix at DNA renaturation.
4．Tm：DNA的变性从开始解链到完全解链，是在一个相当窄的温度范围内完成的。在这一范围内，紫外光吸收值达到最大值的50%时的温度称为DNA的解链温度。
Tm is melting temperature at which half (50%) of DNA molecules are denatured

第八章  核苷酸代谢

第十章  DNA的生物合成（复制）

1. 中心法则（the central dogma）：DNA的遗传信息转录为RNA，RNA通过翻译指导合成蛋白质。DNA还通过复制将遗传信息代代相传。1970年发现RNA能逆转录为DNA，是对中心法则的补充。
2. 基因和基因表达(gene and gene expression)：基因是为生物活性产物编码的DNA功能片段，这些产物主要是蛋白质或各种RNA。通过转录和翻译，将DNA分子上A，T，C，G四种符号所包含的序列信息，转变为蛋白质分子上20种氨基酸的序列信息的过程称为基因表达。
Gene : In molecular terms, it is a chromosomal DNA segment that codes for a single functional polypeptide chain or RNA molecule.
Gene expression :  Overall process by which gene products are made (most commonly production of a protein).
3. 半保留复制（semiconservative replication）：DNA生物合成时,母链DNA解开为两股单链,每股单链分别作为模板,以dNTP(dATP、dGTP、dCTP、dTTP)为原料,按照碱基配对(A－T、G－C)规律与模板上的碱基配对,经依赖DNA的DNA聚合酶(DNA-pol)催化,合成一条与模板互补的新链, 新形成的两个子代DNA 与亲代DNA碱基序列一致,子代DNA分子中一股单链是从亲代完整地接受过来, 另一股单链是新合成的,故称为半保留复制。  
Semiconservative replication :The two strands of DNA double helix are separated, each strand serves as a template for the synthesis of a new complementary strand, producing two daughter molecules. Each daughter molecule has one parental strand and one newly synthesized strand.
4. 端粒和端粒酶(telomere and telomerase)：端粒是位于真核细胞线性染色体末端的特殊结构,由一段串联重复的DNA短序列与端粒结合蛋白构成；端粒具有稳定染色体结构，防止末端降解和融合的功能，并维持DNA复制的完整性。端粒复制要靠具有逆转录酶性质的端粒酶来完成。端粒酶是一种由RNA和蛋白质构成的核糖核蛋白复合体，RNA分子含复制端粒DNA所需的核苷酸模板，蛋白质部分具有逆转录酶活性，同时具有核酸内切酶活性。可催化端粒DNA的合成，维持染色体的完整。
Telomere : Specialized structure at the end of a linear eukaryotic chromosome, which consists of tandem repeats of a short (Tn Gn)x-rich sequence on the 3’ ending strand and its complementary sequence on the 5' ending strand, allows replication of the extreme 5' ends of the DNA without loss of genetic information and maintains the stability of eukaryote chromosome. The 3’ end of the (Tn Gn)x- rich strand extends 12 - 16 nucleotides beyond the 5’ end of the complementary (Cn An)-rich strand. This region is bound by specific proteins that protect the ends of linear chromosomes from attack by exonucleases.
Telomerase : An RNA-containing reverse transcriptase that using the RNA as a template, adds nucleotides to the 3’ ending strand and thus prevents progressive shortening of eukaryotic linear DNA molecules during replication.  Containing: Human telomerase RNA, hTR ;Human telomerase associated protein 1, hTP1; Human telomerase reverse transcriptase, hTRT .
5.逆转录和逆转录酶(reverse transcription and reverse transcriptase)：指遗传信息从RNA流向DNA。即以RNA为模板,dNTP为原料,在逆转录酶催化下,合成与RNA互补的双链DNA的过程。逆转录酶 (依赖RNA的DNA聚合酶)为多功能酶, 具有三种酶活性：
1）RNA指导的DNA聚合酶：利用病毒RNA作模板合成一条互补DNA链；
2）RNase H：水解RNA-DNA杂化双链中的RNA链；
3）DNA指导的DNA聚合酶：以新合成的DNA链为模板合成另一条互补DNA链。
Reverse transcription: Synthesis of a double-strand DNA from an RNA template. Retrovirus---- A virus containing an RNA genome.
Reverse transcriptase: A DNA polymerase that uses RNA as its template.
It has RNA-dependent DNA polymerase;  RNAse H;  DNA-dependent DNA polymerase.  5'-3' direction.  Primer: a kind of tRNA within the host cell.  Substrate: dNTP.   Template: virus RNA .

第十一章  RNA的生物合成（转录）

1. 不对称转录(asymmetric transcription)：有两重含义,一是指双链DNA分子中只有一股单链作为转录模板(模板链)，另一股链不转录;二是模板链并非永远在同一单链上。
Asymmetric transcription: RNA is transcribed from only one of the DNA strands that serves as the template. The template strand of different genes is not always on the same strand of DNA.
2. 断裂基因(splite gene)：真核生物的结构基因是由若干个编码区和非编码区互相间隔但又连续镶嵌而成，这些基因称为断裂基因。
Split gene: eukaryotic structure gene consists of several coding regions and non-coding regions that are spaced and inlaid one other.  
3. 外显子和内含子(exon and intron)：在断裂基因及其初级转录产物上出现，并表达为RNA的核酸序列称为外显子。内含子是隔断基因线性表达而在剪接过程中被除去的核苷酸序列。
Exon: segments of eukaryotic gene (or of the primary transcript of that gene) that are saved as part of a functional, mature, mRNA, rRNA or tRNA molecular.
Intron: segments of eukaryotic gene (or of the primary transcript of that gene) that are removed by splicing during RNA processing and are not included in the mature, functional mRNA, rRNA, or tRNA.
4. 剪接体(splicesome)：由核内小型RNA（snRNA）和核内蛋白质组成的核糖核酸蛋白复合物，结合在hnRNA的内含子区域，并把内含子弯曲使两端互相靠近，有利于剪接过程的进行。
Spliceosome: a multicomponent complex containing proteins and snRNAs that are involved in mRNA splicing.

第十二章  蛋白质的生物合成（翻译）

1. 多聚核蛋白体(polyribosome)：是由一个mRNA分子与一定数目的单个核蛋白体结合而成的，呈串珠状排列。每个核蛋白体可以独立完成一条肽链的合成，所以多核蛋白体上可以同时进行多条肽链的合成，可以加速蛋白质合成速度，提高mRNA的利用率。
Polyribosome: several ribosomes are binding to one mRNA, each ribosome performs the synthesis of one peptide chain. Increasing the efficiency of protein synthesis.
2. 信号肽(signal peptide)：各种新生分泌蛋白的N端存在保守的氨基酸序列称信号肽，约13-36个氨基酸残基，可分为N端碱性区、疏水区和C端加工区三个区段。可将合成的蛋白质引导至细胞的适当靶部位，是决定蛋白质靶向输送特性的重要元件。
Signal peptide : A short amino-terminal sequence that directs a newly synthesized protein to a specific location(ER), which is subsequently cleaved away by signal peptidase. it consists of several basic amino acids, 10 to 15 hydrophobic amino acids and lytic site for signal peptidase.
3．开放阅读框架（open reading frame, ORF）：从mRNA 5¢端起始密码子AUG到3¢端终止密码子之间的核苷酸序列，各个三联体密码连续排列编码一条蛋白质多肽链，称为开放阅读框架。
Open reading frame (ORF): From the initiation coden AUG of mRNA 5’end to the stop coden UAA, UGA, UAG of 3’end and each codon specifies an amino acid, and the triplet codon sequence of it determines the amino acid sequence of a protein.

第十三章  基因表达调控

1．顺式作用元件（cis-acting element）
Cis-acting elements: It is the specific DNA sequences regulating gene    expression (control gene expression only on the same chromosome).It is the site binding RNA-pol and transcription factors.  
Promoter  Enhancer  Silencer
2．反式作用因子（trans-acting factor）
Trans-acting factors(transcription factors, TF): They are the protein factors that can interact with the cis-acting element of other gene, and control the transcription of other gene.
3．操纵子（operon）由2个以上编码序列与其上游的启动序列、操纵序列及其他调节序列共同构成的转录单位,称操纵子。
The operon consists of more than 2 coding sequences, promoter, operator  and other regulatory sequences clustered in the genome.
4．增强子（enhancer） 是真核生物基因上远离转录起始点（1～30kb）、增强启动子转录活性的正性调控元件.增强子与转录激活因子相互作用最终增强RNA聚合酶的活性，激活转录。它决定基因表达的时间和空间特异性, 其作用通常与其位置和方向无关, 增强子与启动子在结构上可重叠，功能上互相依赖。 由若干功能组件组成.

Enhancer : apart from transcription start site(1~30kb), determining the temporal and spatial specificity of gene expression, functions in different direction and distance on upstream or downstream, enhancing the activity of promoter, consisting of several functional elements→core sequence for specific TF binding, require promoter to exert its function.
5．管家基因（housekeeping gene）整个生命过程必不可少的一类基因，在几乎所有细胞和所有发育阶段都持续表达 ，其表达很少受环境因素的影响，表达水平一般较低 ，其表达只受启动子和RNA聚合酶相互作用的影响——组成性表达（constitutive gene expression）.
Housekeeping gene: It is the genes coding for proteins that are needed for basic life processes in all kinds of cells(such as enzymes for citric acid cycle). Expressing in almost all cells ,expressing in all life period,determined by the binding of promoter and RNA-pol ,seldom influenced by the environmental changes,housekeeping gene is constitutively expressed.
6.  启动子（promoter）由RNA聚合酶结合位点及周围的一组调控组件构成，一般处于基因的上游，包括至少一个转录起始点以及一个以上功能组件。决定转录起始准确性和频率。
Promoter : around RNA-pol binding site, about 7~20bp, consists of at least one initiation site and more than one functional elements, determining the initiation site and initiation frequency.

Chapter 14 Gene Recombination &Genetic Engineering

1. DNA recombination: A process in which DNA molecules are broken   and rejoined in new combination is named as DNA recombination, also called gene recombination.
2.DNA Cloning: To clone a piece of DNA, DNA is cut into fragments using restriction enzymes. The fragments are pasted into vectors that have been cut by restriction enzyme to form recombinant DNA. The recombinant DNA is needed to transfer and replicate DNA in a host cell. Finally we select those transformed cells that contain recombinant DNA. This serial process and related technique are called DNA cloning, also called gene cloning.
3. Genetic engineering:  All methods and related techniques to fulfill DNA cloning are called genetic engineering, also called recombinant DNA technology.    Usually we call DNA cloning as genetic engineering.
4. Target DNA: DNA you want to study.
Vectors: Plasmids, virus, bacteriophage
Scissors: restriction endonuclease
Glue: DNA ligase
Host cells: prokaryote or eukaryote
5. Restriction Endonuclease(RE): Restriction endonucleases are   enzymes that can recognize, bind to and hydrolyze specific nucleotide acid sequences in double-stranded DNA. They are isolated from bacteria.
6. Target DNA---- the DNA you are interested        “Foreign DNA”
Genomic DNA: A collection of DNA fragments representing all DNA in the     chromosomes of a cell or organism.
cDNA: made by reverse transcription, complementary to RNA(usually mRNA    or viral RNA).
7. Vector:  Vector is the DNA molecule that can carry the target DNA fragment into the host cell and replicate in the host cell.  e.g., plasmids, bacteriophage, virus.
Cloning vector--- carry target DNA and used for reproducing the DNA fragment.
Expression vector--- carry target DNA and used for gene expressing in the host cells.
8. Plasmids: Small circular dsDNA molecules, extra chromosomal loops of DNA. Can replicate autonomously in bacteria.  Contain genes for antibiotic resistance to allow selection by growth on media containing (or lacking) antibiotics. Contain several RE sites.
9. Genomic DNA library: The collection of bacteria clones that contain the entire DNA in the organism’s genome on vector of plasmids or    bacteriophage.
10. Genome: Total genetic materials (DNA) carried by an organism.
e.g. 3 x 109bp DNA of 46 chromosomes in human.
11. cDNA library:The collection of cloned cDNA molecules consisting of the fragments of all the mRNA produced by a type of cell.
12. cDNA:  cDNA comes from reverse transcription of RNA catalyzing by a reverse transcriptase that is a RNA-directed DNA polymerase.
13. α- complementation:  Some plasmid vectors(eg,pUC19)carry lacZ gene, whose product α fragment is the N-terminal of the β-galactosidase. Whereas, the mutant E.coli strain only synthesize the ω fragment, which is the C-terminal of the enzyme. Eitherα or ω fragment alone is nonfunctional. When the vector containing lacZ is introduced into mutant E.coli, both the α and ω fragments are present. So there is an interaction and a functionally intact β-galactosidase can form. This interaction is called α- complementation.

Chapter 15  The Reception and Transmission of Extracellular Information
1. Secondary messenger: small signaling molecules that are generated in the cell      in response to extracellular signals. They can activate many other downstream components. The most important second messengers are: Ca2+,   cAMP, cGMP, DAG, IP3, etc.
2. Third messenger : They send messages in nucleus, are usually DNA    binding proteins, can regulate gene transcription. Proteins encoded by immediate-early gene,c-fos, c-jun
3. G protein: GTP/GDP binding proteins membrane-associated protein consists of α, β, andγ subunits the α subunit of the G-protein binds GTP or GDP the βγsubunits binds to the α subunit when GDP is present. When the α subunit has GTP bound, the βγ-subunit leave, and the G-protein are active, then to activate adenylate cyclase (AC) and induce biological effect.

Chapter  20   Oncogenes and Tumor Suppressor Genes