1. RNA and Protein Synthesis DNA, RNA, Protein Synthesis & GENES

2. Essential Idea Information transferred from DNA to mRNA is translated into an amino acid sequence Copyright Pearson Prentice Hall

3. Understandings Initiation of translation involves assembly of the components that carry out the process. Synthesis of the polypeptide involves a repeated cycle of events. Disassembly of the components follows termination of translation. Free ribosomes synthesize proteins for use primarily within the cell. Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes. Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane. Copyright Pearson Prentice Hall

4. Translation Nucleus mRNA Messenger RNA is transcribed in the nucleus, and then enters the cytoplasm where it attaches to a ribosome.

5. IB Assessment Statement Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA, using ATP for energy. Copyright Pearson Prentice Hall

6. A C C A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf

7. LE 17-14a Amino acid attachment site Hydrogen bonds 3 5 Two-dimensional structure Anticodon Amino acid attachment site 3 5 Hydrogen bonds Anticodon Symbol used in this book Three-dimensional structure 35 Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule tRNA is roughly L-shaped

8. LE 17-14a Amino acid attachment site Hydrogen bonds 3 5 Two-dimensional structure Anticodon Amino acid attachment site 3 5 Hydrogen bonds Anticodon Symbol used in this book Three-dimensional structure 35 Similar to DNA, t RNA has a 3’ end and a 5’ end. The 3’ end forms a site where the amino acid attaches. ATP is needed for the attachment of the amino acid to the tRNA 3’ end.

9. LE 17-14b Hydrogen bonds Amino acid attachment site 5 3 35 Anticodon Symbol used in this book Anticodon Three-dimensional structure

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11. Activation of tRNA a) Amino acid which is specific to each tRNA. (b) CCA base sequence to which the amino acid is attached by the 'Activating Enzyme'. (c) Complementary base pairing sequence. Helical in shape. (d) 8 free bases non- pairing giving one loop of RNA.

12. Activation of tRNA (e) 7 free bases non-pairing giving second loop of RNA. (f) Small open loop of RNA which is variable in shape between different tRNA. (g) Anti-codon (3 bases) which binds to the mRNA codon (3 bases) this is specific to the amino acids being carried. The anti- codon is complementary to the sense DNA

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15. tRNA activation http://www.phschool.com/science/biology_ place/biocoach/translation/addaa.html Copyright Pearson Prentice Hall

16. IB ASSESSMENT STATEMENT Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites. Copyright Pearson Prentice Hall

17. Ribosome structure Proteins and Ribosomal RNA combine in the structure Large sub-unit and a small sub- unit Large sub-unit has three binding sites for tRNA molecules ( E, P and A site). Small sub-unit has a binding site for mRNA Copyright Pearson Prentice Hall

18. Ribosome Function Ribosomes are enzymes. The catalyse the translation of mRNA into a polypeptide. Their substrate is mRNA. Each ribosome can catalyse the transcription of different mRNA. Copyright Pearson Prentice Hall

20. Accurate translation requires two steps: 1.First step: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl- tRNA synthetase 2.Second step: a correct match between the tRNA anticodon and an mRNA codon

21. LE 17-15 Amino acid Aminoacyl-tRNA synthetase (enzyme) Pyrophosphate Phosphates tRNA AMP Aminoacyl tRNA (an “activated amino acid”)

22. Translation Lysine tRNA Phenylalanine Methionine Ribosome mRNA Start codon The ribosome binds new tRNA molecules and amino acids as it moves along the mRNA.

23. Ribosomes Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)

24. LE 17-16a tRNA molecules Exit tunnel Growing polypeptide Large subunit mRNA 3 Computer model of functioning ribosome Small subunit 5 E P A

25. A ribosome has three binding sites for tRNA: 1.The P site holds the tRNA that carries the growing polypeptide chain 2.The A site holds the tRNA that carries the next amino acid to be added to the chain 3.The E site is the exit site, where discharged tRNAs leave the ribosome

26. LE 17-16b P site (Peptidyl-tRNA binding site) E site (Exit site) mRNA binding site A site (Aminoacyl- tRNA binding site) Large subunit Small subunit Schematic model showing binding sites EPA

27. LE 17-16c Amino end mRNA 5 3 Growing polypeptide Next amino acid to be added to polypeptide chain tRNA Codons Schematic model with mRNA and tRNA E

28. Amino end mRNA 5 3 Growing polypeptide Next amino acid to be added to polypeptide chain tRNA Codons Schematic model with mRNA and tRNA E Translation occurs in a 5’→ 3’ direction. During translation, the ribosome moves along the mRNA towards the 3’ end. The start codon is nearer to the 5’ end.

29. Translation Protein Synthesis tRNA Ribosome mRNA Lysine Translation direction 3’3’3’3’ 5’5’5’5’

30. Protein Synthesis (building a polypeptide): Ribosomes are the site of polypeptides synthesis. This involves linking amino acids together through condensation (dehydration) reactions.

31. Building a Polypeptide The three stages of translation (building a polypeptide) on the ribosomes: 1.Initiation 2.Elongation 3.Termination

32. 7.4.3 Stages of translation. Initiation: In which the ribosome, tRNA and mRNA come together to begin the translation of the mRNA. Elongation: tRNA molecules attach to the mRNA based on the codon-anticodon recognition. Amino acids are brought together and polymerised into the primary structure of the polypeptide. Termination: mRNA and the ribosomes detach from one another. The polypeptide is released and the tRNA return to be charged with more amino acid.

33. Initiation: – The initiation stage of translation brings together mRNA and a tRNA with the first amino acid, and the two ribosomal subunits First, a small ribosomal subunit binds with mRNA and a special initiator tRNA Met GTP Initiator tRNA mRNA 5 3 mRNA binding site Small ribosomal subunit Start codon P site 5 3 Translation initiation complex E A Large ribosomal subunit GDP Met

34. Initiation: – Then the small subunit moves along the mRNA until it reaches the start codon (AUG) Proteins called initiation factors bring in the large subunit so the initiator tRNA occupies the P site Met GTP Initiator tRNA mRNA 5 3 mRNA binding site Small ribosomal subunit Start codon P site 5 3 Translation initiation complex E A Large ribosomal subunit GDP Met

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36. Elongation of the Polypeptide Chain During the elongation stage, amino acids are added one by one to the preceding amino acid A peptide bond is formed between the amino acids. Animation: Translation Animation: Translation

37. The process continues until the ribosome reaches a stop codon. Polypeptide Ribosome tRNA mRNA

38. Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome The polypeptide, and the translation assembly then comes apart and is released

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40. 3 The release factor hydrolyzes the bond between the tRNA in the P site and the last amino acid of the polypeptide chain. The polypeptide is thus freed from the ribosome. The two ribosomal subunits and the other components of the assembly dissociate. Release factor Stop codon (UAG, UAA, or UGA) 5 3 5 3 5 Free polypeptide When a ribosome reaches a stop codon on mRNA, the A site of the ribosome accepts a protein called a release factor instead of tRNA.

41. IB Assessment Statement: State that translation occurs in a 5’→ 3’ direction. Copyright Pearson Prentice Hall

42. Translation Direction Translation of the mRNA takes place from the 5' free end to the free 3' end. Ribosomes move along the mRNA in this direction. The genetic code is translated from the 5' free end to the 3' free end. Copyright Pearson Prentice Hall

43. IB Assessment Statement Draw and label a diagram showing the structure of a peptide bond between two amino acids. Copyright Pearson Prentice Hall

44. Peptide Bond formation 1.During translation amino acids are joined together to form polypeptides. 2.The specific sequence of amino acids is called the primary structure. 3.Between each amino acid a peptide bond forms to join them together. Copyright Pearson Prentice Hall

45. Peptide Bond formation 4.In this example the amino acids are both Alanine in which the R group is a single hydrogen. 5.The carboxyl acid end on the first amino acid is orientated to the amino group of the second amino acid. 6.The -OH group and -H are removed to form water (condensation reaction ). Copyright Pearson Prentice Hall

46. Peptide Bond formation 7.The bond forms between the terminal carbon on the first amino acid and the nitrogen on the second amino acid. 8.The backbone of the molecule has the sequence N-C-C-N-C-C 9.Polypeptides maintain this sequence no matter how long the chain. 10.The R groups project from the backbone. 11.As the amino acids are added in translation the polypeptide folds up into it specific shape. Copyright Pearson Prentice Hall

47. Click here for translation animation http://www.stolaf.edu/people/giannini/flashanim at/molgenetics/translation.swf

48. The Roles of RNA and DNA The cell uses the DNA “master plan” to prepare RNA “blueprints.” The DNA stays in the nucleus. The RNA molecules go to the protein building sites in the cytoplasm—the ribosomes.

49. Genes and Proteins Genes contain instructions for assembling proteins. Many proteins are enzymes, which catalyze and regulate chemical reactions. Proteins are each specifically designed to build or operate a component of a living cell.

50. Genes and Proteins The sequence of bases in DNA is used as a template for mRNA. The codons of mRNA specify the sequence of amino acids in a protein. Codon mRNA Alanine Arginine Leucine Amino acids within a polypeptide Single strand of DNA

51. IB ASSESSMENT STATEMENT Explain the process of translation, including ribosomes, polysomes, start codons and stop codons. Copyright Pearson Prentice Hall

52. INITIATION OF TRANSLATION (more detailed) The tRNA charged with Methionine has the anti- codon UAC. This is complementary to the start codon (mRNA) of AUG. The small sub unit of the ribosome associates with the Methionine tRNA. The small unit of the ribosome moves over the START codon. The large unit of the ribosome moves over the mRNA. Copyright Pearson Prentice Hall

53. INITIATION OF TRANSLATION (more detailed) There are three binding sites for tRNA on the large sub unit. A-(Amino acid) is the position which the new tRNA codon- anticodon binds making sure that the correct amino acid is in position. P-(Polypeptide) is the position in which the amino acid on the tRNA adds to the polypeptide. E-( Exit) is the position the tRNA (without amino acid) locates and is the released from the ribosome to become re- activated. Copyright Pearson Prentice Hall

54. INITIATION OF TRANSLATION (more detailed) The START codon (AUG) occupies the P site. The A site is free for the complementary tRNA to bind. Specificity is maintained by the codon-anticodon binding which is a major feature of the ribosome function. Copyright Pearson Prentice Hall

55. Elongation OF TRANSLATION (more detailed) In this sequence the A site has the codon CCG. The tRNA anticodon GGC which carried Proline hydrogen bonds with the codon bases. The codon -anticodon binding has placed the two amino acids methionine and proline beside each other. Copyright Pearson Prentice Hall

56. Elongation OF TRANSLATION (more detailed) (a)The bond between the tRNA and methionine is broken. This releases free energy. (b)The free energy is used to form the peptide bond between methionine and proline. The large sub-unit then moves to three bases (one codon) towards the 3' end of the mRNA. Copyright Pearson Prentice Hall

57. Elongation OF TRANSLATION (more detailed) Both units of the ribosome are now located over the second and third codons (a) The tRNA for methionine is on the E site and is released from the ribosome. It will beceom recharged with methionine in the cell cytoplasm. The tRNA for proline is in the P site. (b) The A site for the next tRNA is free and holds the codon base sequence GCU. The tRNA for Alanine has the anti- codon CGA which is complementary to the codon on the A site. Copyright Pearson Prentice Hall

58. Elongation OF TRANSLATION (more detailed) The anticodon tRNA for Alanine complementary base pairs with the A site codon. The ribosome checks that this is the correct tRNA and therefore amino acid. The bond between the tRNA and Proline is broken. Free energy is released. A peptide bond is formed between Proline and Alanine. The peptide chain will be folding and shaping. Copyright Pearson Prentice Hall

59. Termination OF TRANSLATION (more detailed) The end of the codon sequence in mRNA has been reached. The ribosome encounters a termination sequence signaling the end of translation. The ribosome moves the alanine tRNA to the P site. The polypeptide is released from the translation process. The ribosome has no new codons read. The two sub units move and separate. The protein will now be further modified in either the endoplasmic reticulum, golgi or secreted in a vesicle. Copyright Pearson Prentice Hall

60. IB Assessment Statement State that free ribosomes synthesize proteins for use primarily within the cell, and that bound ribosomes synthesize proteins primarily for secretion or for lysosomes. Copyright Pearson Prentice Hall

61. Free vs. Bound Ribosomes Free ribosomes in the cytoplasm are associated with the synthesis of proteins for internal use in the cell. Ribosomes which are attached to the wall of the endoplasmic reticulum are associated with proteins which will ne placed into vesicles and secreted form the cell. Copyright Pearson Prentice Hall

63. Animations about Transcription/ Translation https://www.youtube.com/watch?v=NJxobgkPEAo http://www.medschool.lsuhsc.edu/biochemistry/images/protein%20synthesi s_1.swf http://bio3400.nicerweb.com/med/Vid/Klug8e/ch14/14_2_3a_00i.swf http://ihome.cuhk.edu.hk/~z045513/virtuallab/animation/Translation.swf Copyright Pearson Prentice Hall

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