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Section 3: Molecular Biology

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  1. Section 3: Molecular Biology Bilingual teaching as a reform Is a stretch of dynamic biochemistry Focus on the biosynthesis of 3 macromolecules: DNA: replication RNA: transcription Protein: translation

  2. Chapter 29 An Overview of Genetic Information Life is produced by the metabolism of macromolecules Which are macromolecules? The function of life is executed by proteins, which encoded by nucleic acid The second genetic codon The second genetic codon……

  3. 生物进化的C值矛盾 (C value paradox of nucleotide) 最大C值 (Maximum C value) The total amount of DNA in the genome of haploid is a characteristic of each living species known as its Maximum C value(单倍体基因组总DNA 的含量) 最小C值 (Minimum c value) The total amount of DNA for encoding the genes information is termed its Minimum c value (编码基因信息的总DNA含量)

  4. 显花植物 鸟类 哺乳类 爬行类 两栖类 硬骨鱼类 软骨鱼类 赖皮类 甲壳类 昆虫类 软体动物 蠕虫类 霉菌 藻类 真菌 G+细菌 G-细菌 枝原体 C value paradox of nucleotide A Is not linearly correlative with evolution extent B The standard deviation varies in the same genus C C value is far from c value. (Euk. 人体 c = C/10) ( Prok. Φx174 c >C )

  5. Eukaryote DNA chromosomes (2C) (2N) 两栖鲵 168.0 pg(10-12g) 24 肺鱼 100 38 蝾螈 85.3 24 警蛙 28.2 24 牛 6.4 60 人 6.4 46 绵羊 5.7 54 果蝇 0.2 8 贝母 196.7 24 豌豆 28 12 玉米 11 20 Prokaryote DNA (C) Salmonella 0.0143 pg E.coli 0.0040 T2 0.00022 λ 0.0000055 ΦΧ174 0.000005 Repeat sequence

  6. DNA的复杂度:单倍体细胞基因组中非重复序列的碱基对数DNA的复杂度:单倍体细胞基因组中非重复序列的碱基对数 单一序列长度愈小(重复度愈大) kinetic complexity(K.C.)愈小 Cot(1/2)值小(复性愈快) poly(A ) K.C. = 1 Cot(1/2) = 2 × 10-6 T4 DNA K.C. = 1.7 × 106 Cot(1/2) = 0.3 E.coli DNA K.C. = 4.2×106 bp Cot(1/2) = 9

  7. DNA as a major genetic material Experiment 1:

  8. Experiment 2: Marked protein by 35S Marked DNA by 32P

  9. 35S can not enter the new cells. However, 32P was found in the new cells.

  10. Experiment 3: German Fraenkel Extract the RNA and protein of the virus individually. Put them into the surface of the healthy leaves. RNA caused the disease. While protein can not. Conclusion: Genetic material is RNA not protein.

  11. Gregory Johann Mendel (1822-1884)

  12. But where is the “genetic factor”? 7 traits phenotype

  13. Founder of modern genetics: Thomas Hunt Morgan Tied genetic factor (gene) with chromosomes. Sexual linkage by drosophila is regarded as the third discover in genetics because it brings together a specific gene and chromosomes. If 2 genes are near in the same chromosome, maybe linked heredity. If far, maybe exchanged-heredity. Opportunity for exchange can be viewed as the distance of 2 genes

  14. Essence of the genes One gene, one enzyme One peptide, one gene Trait——protein——gene:Forward Biology Gene——protein——trait: Reverse Biology

  15. Mostly in chromosome Semi-autonomous organelle or plasmid Nucleus Cytoplast Heredity DNA

  16. Category of genetic materials In most cases DNA works as genetic material RNA works in some viruses Protein?

  17. Functional diversity of RNA Transferring and processing genetic information Focused on protein synthesis Messenger RNA Transfer RNA Ribosome RNA

  18. RNA processing genetic information Cut Trimming Adding General process Modification Isomerization Splicing Editing Recoding sequence Recoding Alternative transcript

  19. Recoding 1.Correcting tRNA and the second system of genetic codon 赭石突变(UAA) 琥珀突变(UAG) 乳白突变(UGA) nonsense mutations 2.Sometimes tRNA will transfer an amino acid in nonsense mutations.

  20. RNA interfering干涉(干扰,RNAi) The small double-strand RNA can inhibit gene expression. C. Elegans or petunias (牵牛花)? More effective than Antisense RNA Models

  21. Genetic codon • Nature • Deciphering • Feature • Effect of mutation • Universality • ORFs • Overlapping genes

  22. Nature 1.Genetic codeis a triplet code (three nucleotide encode one amino acid) The way in which the nucleotide sequence in nucleic acids specifies the amino acid sequence in proteins. The triplet codons arenonoverlappingandcomma-less. ---UCU UCC CGU GGU GAA---

  23. 2. Genetic code is degenerate : Only 20 amino acids are encoded by 4 nucleotides in triplet codons (43 =64 of amino acids could potentially be encoded). Therefore, more than one triplet are used to specify a amino acids, and the genetic code is said to be degenerate, or to have redundancy.

  24. Deciphering System A: cell-free protein synthesizing systemfrom E. coli • cell lysate treated by DNase to prevent new transcription • Add homopolymeric synthetic mRNAs [poly(A)] + 19 cold (non-labeled) and one labeled aminoacids • In vitro translation • Analyze the translated polypeptides

  25. poly(U) ---UUU--- polyphenylalanine poly(C) ---CCC--- polyproline poly(A) ---AAA--- polylysine poly(G) --- did not work because of the complex secondary structure Random co-polymers (e.g. U and G in the same RNA) were used as mRNAs in the cell-free system to determine the codon for many amino acids.

  26. Features Synonymous codons: 18 out of 20 amino acids have more than one codon to specify them, causing the redundancy of the genetic code. the third position: pyrimidine ----synonymous (all cases) purine ----synonymous (most cases) the second position: pyrimidine ----hydrophobic amino acids purine -----polar amino acids

  27. Effect of Mutation 1. Transition: the most common mutation in nature changes from purine to purine, or pymidine to pymidine At third position: no effect except for Met  Ile; Trp  stop second position: results in similar chemical type of amino acids.

  28. 2. Transversions: purine  pymidine At third position: over half have no effect and result in a similar type of amino acid. (Example: Asp  Glu) At second position: change the type of amino acid.

  29. In the first position, mutation (both transition and transvertion) specify a similar type of amino acid, and in a few cases it is the same amino acid. Thus, natural triplet codons are arranged in a way to minimize the harmful effect of an mutation to an organism.

  30. Summary • 简并性:64种密码子决定20种氨基酸,重复,同义密码子 • 摆动性(变偶性):反密码子的3个碱基与密码子反向互补,前两个碱基严格互补,第三个可以摆动 • 普遍性:生物体普遍适用 • 偏爱性:不同生物体(线粒体)使用何种同义密码子有偏爱

  31. Universality • The standard codons are true for most organisms, but not for all.

  32. ORFs Open reading frames (ORFs) are suspected coding regions starting with ATG and end with TGA,TAA or TAG identified by computer. When the ORF is known to encode a certain protein, it is usually referred as a coding region.

  33. I coupled with U,A and C Which codon can be recognized by Anticodon IGC?

  34. m7G加在5,端: 免受酶切 促进启始蛋白质合成 Processing of RNA Only the mature RNA could be translated. The precursor of mRNA is called heterogeneous nuclear RNA, (hnRNA), which needs be processed. Processing:Capping in 5,end Poly A in 3,end Cutting intron Linked exon