1. Genetics: Analysis and Principles Robert J. Brooker CHAPTER 13 TRANSLATION OF mRNA

2. INTRODUCTION The translation of the mRNA codons into amino acid sequences leads to the synthesis of proteins A variety of cellular components play important roles in translation –These include proteins, RNAs and small molecules In this chapter we will discuss the current state of knowledge regarding the molecular features of mRNA translation

3. Kinds of RNA  The class of RNA found in ribosomes is called ribosomal RNA (rRNA). During polypeptide synthesis, rRNA provides the site where polypeptides are assembled.  Transfer RNA (tRNA) molecules both transport the amino acids to the ribosome for use in building the polypeptides and position each amino acid at the correct place on the elongating polypeptide chain. Human cells contain about 45 different kinds of tRNA molecules.  Messenger RNA (mRNA) molecules are long strands of RNA that are transcribed from DNA and that travel to the ribosomes to direct precisely which amino acids are assembled into polypeptides.

4. The Genetic Code  The essential question of gene expression is, “How does the order of nucleotides in a DNA molecule encode the information that specifies the order of amino acids in a polypeptide?”  The answer came in 1961, through an experiment led by Francis Crick.  That experiment was so elegant and the result so critical to understanding the genetic code that we will describe it in detail.

5. Proving code words have only three letters  Crick and his colleagues reasoned that the genetic code most likely consisted of a series of blocks of information called codons.  They further hypothesized that the information within one codon was probably a sequence of three nucleotides specifying a particular amino acid.  They arrived at the number three, because a two-nucleotide codon would not yield enough combinations to code for the 20 different amino acids that commonly occur in proteins.  With two DNA nucleotides (G, C, T, and A), only 32 = 16, different pairs of nucleotides could be formed.

6.  However, these same nucleotides can be arranged in 64, different combinations of three, more than enough to code for the 20 amino acids.  When they made a single deletion or two deletions near each other, the reading frame of the genetic message shifted, and the downstream gene was transcribed as nonsense.  However, when they made three deletions, the correct reading frame was restored, and the sequences downstream were transcribed correctly.  They obtained the same results when they made additions to the DNA consisting of one, two, or three nucleotides.

7. The code is practically universal  For example, the codon AGA specifies the amino acid arginine in bacteria, in humans, and in all other organisms whose genetic code has been studied.  Because the code is universal, genes transcribed from one organism can be translated in another; the mRNA is fully able to dictate a functionally active protein.  Similarly, genes can be transferred from one organism to another and be successfully transcribed and translated in their new host.  Many commercial products such as the insulin used to treat diabetes are now manufactured by placing human genes into bacteria, which then serve as tiny factories to turn out prodigious quantities of insulin.

9. But Not Quite  In 1979, investigators began to determine the complete nucleotide sequences of the mitochondrial genomes in humans, cattle, and mice.  It came as something of a shock when these investigators learned that the genetic code used by these mammalian mitochondria was not quite the same as the “universal code” that has become so familiar to biologists.  In the mitochondrial genomes, what should have been a “stop” codon, UGA, was instead read as the amino acid tryptophan; AUA was read as methionine rather than isoleucine; and AGA and AGG were read as “stop” rather than arginine.  Thus, it appears that the genetic code is not quite universal.

10. Activating Enzymes  Activating enzymes called aminoacyl-tRNA synthetases, one of which exists for each of the 20 common amino acids.  Therefore, these enzymes must correspond to specific anticodon sequences on a tRNA molecule as well as particular amino acids.  Some activating enzymes correspond to only one anticodon and thus only one tRNA molecule.  Others recognize two, three, four, or six different tRNA molecules, each with a different anticodon but coding for the same amino acid.

11. Figure 13.11 Aminoacyl tRNA Synthetase Function The amino acid is attached to the 3’ OH by an ester bond

12. Wobble position and base pairing rules Figure 13.12 tRNAs charged with the same amino acid, but that recognize multiple codons are termed isoacceptor tRNAs

13. “Start” and “Stop” Signals  There is no tRNA with an anticodon complementary to three of the 64 codons: UAA, UAG, and UGA.  These codons, called nonsense codons, serve as “stop” signals in the mRNA message, marking the end of a polypeptide.  The “start” signal that marks the beginning of a polypeptide within an mRNA message is the codon AUG, which also encodes the amino acid methionine.  The ribosome will usually use the first AUG that it encounters in the mRNA to signal the start of translation.

14. Initiation  Initiation in eukaryotes and prokaryotes is similar, although it differs in two important ways: 1.First: in eukaryotes, the initiating amino acid is methionine rather than N -formylmethionine. 2.Second: the initiation complex is far more complicated than in bacteria, containing nine or more protein factors, many consisting of several subunits.

15. Figure 13.13 (a) Bacterial cell Prokaryotic Ribosomes

16. Figure 13.13 Eukaryotic Ribosomes

17. C G A U C A A U A CC G A U C A A U G C G codon codon codon The ribosome attaches to the RNA and scans for AUG,the start codon The ribosome reads the mRNA three nucleotides at a time Each group of three nucleotides is a single codon Each codon specifies an particular amino acid Start codon

18. 16S rRNA binds to an mRNA at the ribosomal-binding site or Shine-Dalgarno box 16S rRNA Figure 13.17 Prokaryotic Ribosome-mRNA Recognition 7 nt

19. (actually 9 nucleotides long) Figure 13.16 Prokaryotic Translation Initiation 16S RNA

20. Figure 13.16 The tRNA i Met is positioned in the P site All other tRNAs enter the A site Prokaryotic Translation Initiation

21. Eukaryotic Translation Initiation Initiation factors bind to the 5’ cap in mRNA & to the polyA tail These recruit the 40S subunit, tRNA i met The entire assembly scans along the mRNA until reaching a Kozak’s consensus Once right AUG found, the 60S subunit joins Translation intitiates Start codon G C C (A/G) C C A U G G -6 -5 -4 -3 -2 -1 +1 +2 +3 +4 Most important positions for codon selection

22. Elongation  When a tRNA molecule with the appropriate anticodon appears, proteins called elongation factors assist in binding it to the exposed mRNA codon at the A site.  When the second tRNA binds to the ribosome, it places its amino acid directly adjacent to the initial methionine, which is still attached to its tRNA molecule, which in turn is still bound to the ribosome.  The two amino acids undergo a chemical reaction, catalyzed by peptidyl transferase, which releases the initial methionine from its tRNA and attaches it instead by a peptide bond to the second amino acid.

23. Translocation  In a process called translocation the ribosome now moves (translocates) three more nucleotides along the mRNA molecule in the 5´ →3´ direction.  This movement relocates the initial tRNA to the E site and ejects it from the ribosome, repositions the growing polypeptide chain to the P site, and exposes the next codon on the mRNA at the A site.

24. Termination  Elongation continues in this fashion until a chain- terminating nonsense codon is exposed (for example, UAA).  Nonsense codons do not bind to tRNA, but they are recognized by release factors, proteins that release the newly made polypeptide from the ribosome.

25. Release factors Initiator tRNA Stages of Translation Figure 13.15

26. U C A G C A A G A C Met U C A G U A A U G U C Anti-codon tRNA Amino acid This continues until the ribosome reaches a STOP codon, which indicates the end of the gene The ribosome & last tRNA fall off the mRNA & the amino acid chain is complete! TRANSLATION ELONGATION

27. Protein Folding Begins while Protein is still being synthesized Guided by and made more efficient by molecular chaperones

28. The amino acid chain folds up into a 3-dimensional structure dictated by the order of the amino acids. This unique structure gives the protein its unique function and allows it to do its work Every protein has a unique order of amino acids

29. Proteins have many functions

30. Protein example: Antibiotics Some antibiotics are peptides, others glycopeptides, others are amino acid derivatives Inhibitors of prokaryotic translation, allowing for discrimination between prokaryotic and eukaryotic cells Examples: Tetracycline, Streptomycin, Chloramphenicol, Erythromycin