The second midterm exam to be held on Tuesday, April 1 in class. It covers from the February 13 through the March 25 lecture. This corresponds to pages 174 to 334 (end of chapter 9) in the text. There will be a question and answer session from 4 to 6 PM on Friday, March 28 in Heald Auditorum.
This lecture dealt primarily with translation, the process of protein synthesis based on an mRNA code. Translation in prokaryotes is often coupled with transcription, meaning that the two take place in close proximity to each other (see Fig. 9.32). In contrast, in eukaryotes, transcription takes place in the nucleus and translation takes place in the cytoplasm.
The main components of translation are: (1) Messenger RNA, (2) Ribosomes (composed of RNA and protein), (3) Transfer RNA (a small RNA about 70-90 bases long, when "activated" has an attached amino acid, binds to the mRNA codon through a three base anti-codon) (4) Aminoacyl tRNA synthetases (enzymes which join specific amino acids to specific tRNAs), (5) Initiation, elongation and termination factors (proteins involved in the mechanics of translation).
The process of translation involves: (a) mRNA binding to small subunit of ribosome, (b) activated tRNA (with amino acid) binding to large subunit of the ribosome while pairing through anticodon to initiation codon in mRNA (c) A second activated tRNA comes into position on the ribosome, pairing with the second codon. (d) A peptide bond is formed between the two amino acids (e) Translocation occurs, with the ribosome moving three bases down the mRNA and the first tRNA being moving into an "ejection" position on the ribosome (f) Steps 3 through 5 are successively repeated.
There are some differences between translation in prokaryotes and eukaryotes. Prokaryotes may have "polycistronic messages" which can code for more than one polypeptide and allow "coordinate regulation" of related genes. Recognition of start of translation is by ribosome binding sites on mRNA in prokaryotes and by 5’ cap in eukaryotes.
The genetic code was worked out in a variety of experiments and was basically established by the 1960s. Francis Crick played a key role in several of the studies. Genetic code properties are as follows: (1) Triplet code. Inferred because at least three bases would be needed to code for 20 different amino acids (4 X 4 X 4 = 64, which is greater than 20, while 4 X 4 = 16).This was confirmed experimentally using frameshift mutants in the rII locus of phage T4. Combining three insertions, or three deletions together often resulted in a wild type phenotype. (2) Non-overlapping. An overlapping code would have been expected to usually result in multiple amino acid changes for each mutation, which was very rarely observed. An overlapping code was also expected to result in a specific pattern of amino acids in proteins. (3) Redundant / degenerate. This means that most amino acids are coded by more than one codon. The specifics of the genetic code were worked out by doing "in vitro" translation with artificial messenger RNAs or short triribonucleotides and cell-free extracts. (4) Nearly universal. The few exceptions are seen in protozoa, mitochondria and chloroplasts. Changes from a genetic code, once established, would be extremely damaging, which may account for why the principal code has been so well-preserved. (5) Three stop codons (UAA, UAG, UGA) and one initiation codon (AUG). (6) "Wobble" is an explanation for how there can be more codons for amino acids than there are tRNAs. Evidently some tRNAs can pair with more than one codon because the first base in the anti-codon (which pairs with the third base in the codon) can pair with more than one base due to their configuration or structure. . Some bases in the anticodon are modified or unusual bases.
In some viruses and transposable elements, one stretch of DNA may code for more than one protein by using different reading frames during translation. The bacterial virus Phi-X 174 is an example of this form of genetic economy. (end chapter 9).