2. Chapter 7 Genetic code

3. 7.1 THE GENETIC CODE 7.2 tRNA STRUCTURE AND FUNCTION

4. THE GENETIC CODE  Nature  Deciphering ( 破译 )  Feature  Effect of mutation  Universality  ORFs  Overlapping genes

5. Nature 1. Genetic code is 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 are nonoverlapping （ 不重叠） and comma-less （无逗号）. ---UCU UCC CGU GGU GAA---

6. 2. Genetic code is degenerate （简并性） : Only 20 amino acids are encoded by 4 nucleotides in triplet codons (4 3 =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 （有丰余）.

7. Deciphering System A: cell-free protein synthesizing system from E. coli 1.cell lysate treated by DNase to prevent new transcription 2.Add homopolymeric synthetic mRNAs [poly(A)] + 19 cold (non-labeled) and one labeled aminoacids 3.In vitro translation 4.Analyze the translated polypeptides

8. 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.

9. System 2: Synthetic trinucleotides (late 1960s) could assign specific triplets unambiguously to specific amino acids. Synthetic trinucleotides attach to the ribosome and bind their corresponding aminoacyl-tRNAs from a mixture. Upon membrane filtration, the trinucleotides bound with ribosome and aminoacyl-tRNA would be retained. Deciphering

10. 密码子的破译 遗传密码的破译是六十年代分子生物学最辉煌的成就。 50 年代的数学推理过程和 61-65 的实验研究阶段。 1954 年 物理学家 George Gamov 根据 DNA 中的 4 种核 苷酸，在蛋白中存在 20 种氨基酸的对应关系。 4 1 =4; 4 2 =16 少于 20 。 那么 4 3 =64 ； 4 4 =256 随后的实验证明了他的假设是正确的。

11. ①在体外无细胞蛋白合成体系中加入人工合成的 polyU (1961, Nirenberg, Matthaei) 密码子的破译 ②混合共聚物实验 - 对密码子中碱基组成的测定 —polyAC 8 种不同的密码子（ 1963 ， Speyer, Ochoa) ③ AA-tRNA 与确定的密码子结合（ 1964 ， Nirenberg, 和 Leder) ④用重复共聚物破译密码（ Nishimura,Jones 和 Khorana ）用有机化学合成法合成特定的重复序列。

12. Fig(1)

13. 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 ----hydrophilic amino acids purine -----polar amino acids

14. Effect of Mutation 1. Transition （转换） : 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.

15. 2. Transversions （颠换） : 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.

16. 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.

17. Universality （通用性） The standard codons are true for most organisms, but not for all. Codon Usual meaning Alternative Organelle or organism AGA AGG ArgStop,Ser Some animal mitochondria AUAIleMetMitochondria CGGArgTrp Plant mitochondria CUNLeuThr Yeast mitochondria AUU GUG UUG Ile Val Leu Start Some protozoans UAA UAG StopGlu Some protozoans UGAStopTrpMitochondria,mycoplasma

18. ORFs （可读框） 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.

19. Overlapping genes Generally these occur where the genome size is small (viruses in most cases) and there is a need for greater information storage density. More than one start codons in a DNA sequence are used for translate different proteins. A way to maximize the coding capability of a given DNA sequence.

20. 重叠基因：是指一个基因的编码区部分或 全部与另一个基因的编码区重叠。 ATG GTC GGG GAC CGA TGT TTG GAA ATG TTT GGA

21. tRNA STRUCTURE AND FUNCTION  tRNA primary structure  tRNA secondary structure  tRNA tertiary structure  tRNA function  Aminoacylation of tRNAs  Aminoacy-tRNA synethetases  Proofreading tRNAs charging

22. tRNA are the adaptor molecules that deliver amino acids to the ribosome and decode the information in mRNA.

23. Linear length: 60-95 nt (commonly 76) Residues: 15 invariant and 8 semi-invariant.The position of invariant and semi-variant nucleosides play a role in either the secondary and tertiary structure. tRNA primary structure Modified bases:Modified bases: Sometimes accounting for 20% of the total bases in one tRNA molecule.Over 50 different types of them have been observed. Sometimes accounting for 20% of the total bases in one tRNA molecule.Over 50 different types of them have been observed.

24. tRNA secondary structure The cloverleaf structure is a common secondary structural representation of tRNA molecules which shows the base paring of various regions to form four stems (arms) and three loops.

25. tRNA secondary structure D loop T loop Anticodon loop

26. The 5 ’ -and 3 ’ - end are largely base-paired to form the amino acid acceptor stem which has no loop. Amino acid acceptor stem:Amino acid acceptor stem:

27. Composed of 3 or 4 bp stem and a loop called the D- loop (DHU-loop) usually containing the modified base dihydrouracil （ 二氢尿嘧啶）. D-arm and D-loopD-arm and D-loop

28. Consisting of a 5 bp stem and a 7 residues loop in which there are three adjacent nucleosides called the anticodon which are complementary to the codon sequence (a triplet in the mRNA) that the tRNA recognize. Anticodon loop:

29. Variable arm and T-arm:Variable arm and T-arm: Variable arm: 3 to 21 residues and may form a stem of up to 7 bp. T-arm is composed of a 5 bp stem ending in a loop containing the invariant residues GT  C.

30. tRNA tertiary structure Formation: 9 hydrogen bones (tertiary hydrogen bones) to help the formation of tRNA tertiary structure, mainly involving in the base paring between the invariant bases.

31. Hydrogen bonds: Base pairing between residues in the D- and T-arms fold the tRNA molecule over into an L-shape, with the anticodon at one end and the amino acid acceptor site at the other. The base pairing is strengthened by base stacking interactions.

32. tRNA function When charged by attachment of a specific amino acid to their 3 ’ -end to become aminoacyl-tRNAs, tRNA molecules act as adaptor molecules in protein synthesis.

33. Aminoacylation of tRNAs Reaction step:Reaction step: First, the aminoacyl- tRNA synthetase attaches AMP to the- COOH group of the amino acid utilizing ATP to create an aminoacyl adenylate intermediate. Then, the appropriate tRNA displaces the AMP.

34. Nomenclature of tRNA-synthetases and charged tRNAs catalyze amino acid-tRNA joining reaction which is extremely specific. Amino acid: serine Cognate tRNA: tRNA ser Cognate aminoacyl-tRNA synthetase: seryl-tRNA synthetase Aminoacyl-tRNA: seryl-tRNA ser Aminoacyl-tRNA synthetases

35. The synthetase enzymes are either monomers, dimers or one of two types of tetramer.They contact their cognate tRNA by the inside of its L-shape and use certain parts of the tRNA, called identity elements, to distinguish these similar molecules from one another.

36. Proofreading Proofreading occurs at step 2 when a synthetase carries out step 1 of the aminoacylation reaction with the wrong, but chemically similar, amino acid. Synthetase will not attach the aminoacyl adenylate to the cognate tRNA, but hydrolyze the aminoacyl adenylate instead.

37. Fig （ 1 ） Modified nucleosides in tRNA Modified nucleosides in tRNA

38. fig(3) tRNA tertiary structure

39. Fig(4) Identity elements in various tRNA moleculesIdentity elements in various tRNA molecules Identity element: They are particular parts of the tRNA molecules.These are not always the anticodon sequence,but base pair in the acceptor stem.If these are swapped between tRNAs then the synthetases enzymes can be tricked into adding the amino acid to the wrong tRNA

40. P1 The genetic code Universality Modifications of the genetic code Codon Usual meaning Alternative Organelle or organism AGA AGG A rg Stop,Ser Some animal mitochondria AUAIleMetMitochondria CGGArgTrpPlant,mitochondria CUNLeuThr Yeast mitochondria AUU GUG UUG Ile Val Leu Start Some protozoans UAA UAG StopGlu Some protozoans UGAStopTrp Mitochondria,mycoplas ma

41. The universal genetic code First position (5’end) Second position Second position Third positi on(3’e nd) UCAG UPhePheLeuLeuUUUUUCUUAUUGSerSerSerSerUCUUCCUCAUCGTyrTyrStopstopUAUUACUAAUAGCysCysStopTrpUGUUGCUGAUGG U C A G CLeuLeuLeuLeuCUUCUCCUACUGProProProProCCUCCCCCACCGHisHisGlnGlnCAUCACCAACAGArgArgArgArgCGUCGCCGACGG U C A G AIleIleIleMetAUUAUCAUAAUGThrThrThrThrACUACCACAACGAsnAsnLysLysAAUAACAAAAAGSerSerArgArgAGUAGCAGAAGG U C A G GValValValValGUUGUCGUAGUGAlaAlaAlaAlaGCUGCCGCAGCGAspAspGluGluGAUGACGAAGAGGlyGlyGlyGkyGGUGGCGGAGGG U C A G

42. Figure 6 tRNA tertiary structure

43. Figure 7 tRNA tertiary structure

46. Anti-codon 及其两侧碱基修饰对密码子 解读的生物学意义 Xo 5 U (5- 羟基尿苷 ) Cmnm 5 U (5- 羧甲基氨甲基尿苷 ) mCm 5 U (5- 甲氧基羰甲基尿苷 ) Xm 5 s 2 U (5- 甲基 -2 硫代尿苷 ) K 2 C (2- 赖氨酸胞苷 ) Com 5 U (5(2)- 羟羧甲基尿苷 ) I (Inosine 次黄嘌呤 ) m 7 G (7- 甲基尿苷 ) m 5 C (5- 甲基胞苷 ) m 6 A (6- 甲基腺苷 ) s 2 C (2- 硫代胞苷 ) ψ ( 假尿苷 ) Um (2’-O- 甲基尿苷 ) Q (Queuosine) a) Methylated Nt at anti-codon and flanked

47. b) 被修饰的 Nt 34 的配对能力 Nt 1 of anti-codon  Nt 3 of codon U (mt, ct) A,U,C,G CmO 5 U (5(2)- 羟羧甲基尿苷 ) A,G,U Cmnm 5 U (5- 羧甲基氨甲基尿苷 ) A,G mCm 5 U (5- 甲氧基羰甲基尿苷 ) A,G Um (2’-O- 甲基尿苷 ) A,G Xm 5 S 2 U (5- 甲基 -2 硫代尿苷 ) A Q (Queuosine) U,C I (Inosine ） U,C,A U* （ 4 硫代尿苷） G,A