1. Transcription

• One of the two strands of DNA is used as a template to make a single strand of RNA - messenger RNA (mRNA). Each gene, which codes for a single protein chain, makes a separate strand of mRNA. (look).
• RNA polymerase binds to a promoter region on the DNA to begin unwinding the DNA helix and manufacture the RNA strand. (look) , (look)
• Note that while DNA replication must occur on both strands of DNA - requiring Okazaki fragments - translation to form a single strand of RNA need occur only on one strand of DNA, thus eliminating the need for Okazaki fragments or other complications of copying the "lagging strand". Transcription to a single strand of RNA starts just as formation of the RNA primer in DNA replication and then just continues to copy the information on one strand of the DNA until a stop signal (3 base codon) is found.
• In bacteria, mRNA is produced directly from the DNA and that mRNA binds to ribosomes with protein synthesis occuring directly. This can happen because the DNA is exposed to the cytosol and the ribosomes and other components necessary for protein synthesis are right there!
• But, in eukaryotes, transcription to produce the primary transcript of RNA occurs in the nucleus while protein synthesis is located in the cytosol. And, eukaryotes have introns, non-coding sequences of DNA, in between exons, the coding sequences. Specific nucleotide sequences signal the beginning and end of an intron on the primary transcript and a splicing mechanism (by snRNAs - small nuclear RNAs - pronounced "snurps") removed the sequences coded for by introns. (look) The complex of snRNAs is called a splicosome.
• Some introns are self-splicing, giving a hint of the mechanism and evolution of the splicosome.
• The complete process of transcription in eukaryotes and a comparison with the same process in prokaryotes is summarized in this figure - (look)

2. Translation

• Proteins are coded for by triplets of nucleotide bases on the RNA. (look)
• Transfer RNA (tRNA) binds to mRNA to bring in the correct amino acid to be added to a growing protein chain. Here is another view of the a tRNA. Note that some bases are unusual - Greek letter "psi" is pseudouridine, I is inosine, and D is dihydrouridine.
• The ribosome is the "factory" which contains many proteins and some ribosomal RNA and which facilitates the entire process of binding to the mRNA and polymerizing the growing protein chain. Protein synthesis proceeds from the N-terminal to the C-terminal.
• Many ribosomes may be bound to a single mRNA molecule at any given time.
• The decoding of the a codon on mRNA to specify which amino acid is to be added to the growing protein chain is done by aminoacyl-tRNA synthetases. There is one specific aminoacyl-tRNA synthetase for each of 20 amino acids.
• There are 61 codons in the genetic code and 20 amino acids. However, there are fewer than 61 tRNAs and many more than 20 tRNAs. This is explained by nonstandard base pairing - wobble pairs - between codons on the mRNA and anticodons on the tRNA. The first two bases on the codon generally pair exactly, but the third base can participate in wobble pairing. Inosine is particularly useful in this regard, as it can pair with A, C, or U in the third base position. Thus, inosine appears often in the tRNA anticodons that pair with redundant codons on the mRNA.
• A report (summary in "Nature" Vol 431, Sept. 30, 2004, pp 520-521) has shown for a bacterial ribosome, the presence of a chaparone-like trigger factor that protects hydrophobic groups on a growing protein chain. ("What is the function of the trigger factor on ribosomes? What other protein component, discussed in a much earlier lecture, is similar in function to the trigger factor?)
• Translation may be regulated by microRNA (miRNA) a 22 nucleotide piece of RNA that binds to mRNA and stops translation. The miRNA is similar in function to another small RNA called inhibitory RNA (iRNA). However, miRNA stops translation while iRNA labels a piece of mRNA for degradation.

3. Origin of life

• It is thought that RNA preceded both DNA and protein. RNA can not only carry information but also catalyze reactions. (look)
• The "RNA first hypothesis" is shown in this figure.
• And, you will remember that DNA replication uses an RNA precursor, indicating that DNA may have appeared after RNA.

All text and images, not attributed to others, including course examinations and sample questions, are Copyright, 2009, Thomas J. Herbert and may not be used for any commercial purpose without the express written permission of Thomas J. Herbert.