Overview

1. Overview • Analyzed SME KBs representing textbook section 7.1.5 • Did not analyze the pump priming KBs • Did not analyze the KE’s KBs • Form of analysis results: • Prose descriptions of content of SME KBs • Comparison of KB content with textbook content • What’s missing • What’s incorrect • What’s there and correct

2. Textbook Section 7.1.5 • RNA processing • Bacterial RNA Processing • Eucaryotic RNA processing • mRNA processing • “processing of other types of RNA” • Steps in eucaryotic mRNA processing: • RNA capping – The 5’ end is capped by the addition of … a guanine (G) nucleotide with a methyl group attached. Capping usually occurs just after the RNA polymerase has synthesized the 5’ end of the primary transcript and before it has completed transcribing the whole gene. • Polyadenylation – The 3’ ends of eucaryotic RNAs are first trimmed by an enzyme that cuts the RNA chain at a particular sequence of nucleotides and is then finished off by a second enzyme that adds a series of repeated adenine (A) nucleotides (a poly(A) tail) onto the cut end. The poly(A) tail is generally a few hundred nucleotides long.

3. (iflu) mRNA-Processing • Eucaryotic-mRNA-Processing • A kind of scenario • Subevents in sequence: • a Eucaryotic-Transcription • a Eukaryotic-mRNA-Processing • Subevents in sequence: • a Capping • a Polyadenylation • a Move-Out-Of • a Eucaryotic-Translation

4. (iflu) mRNA-Processing • Eucaryotic-mRNA-Processing • A kind of scenario • Missing: a kind of RNA-processing (which is a kind of scenario) • Subevents in sequence: • a Eucaryotic-Transcription • a Eukaryotic-mRNA-Processing • Subevents in sequence: • a Capping • a Polyadenylation • a Move-Out-Of • a Move-Out-Of ? • a Eucaryotic-Translation The text refers to “RNA processing” as occurring before the RNA exits the nucleus.

5. (iflu) Eucaryotic-Transcription • Eucaryotic-Transcription • A kind of scenario No other description in the KB. • Eucaryotic-mRNA-Processing • Subevents in sequence: • a Eucaryotic-Transcription Result is a Primary—Transcript (call it PT1) Missing: Eucaryotic transcription takes place in the nucleus. • a Eukaryotic-mRNA-Processing • Subevents in sequence: • a Capping • a Polyadenylation • a Move-Out-Of • a Eucaryotic-Translation

6. (iflu) Capping • Capping A compound action with an associated Attach No other description in the KB. • Eucaryotic-mRNA-Processing … • a Capping Base is PT1, Object is a CAP, Result is a Capped-Eucaryotic-mRNA, Site is the site of the following Polyadenylation, Enables the subsequent Move-Out-Of Missing: • That capping involves “a modification of the 5’ end of the primary transcript” • That capping “usually occurs just after the RNA polymerase has synthesized the 5’ end of the primary transcript and before it has completed transcribing the whole gene” • Description of class Capped-Eucaryotic-mRNA (other than being a subclass of Primary—Transcript) Note the result of Capping is still a Primary--Transcript (Error?) …

7. (iflu) Polyadenylation • Polyadenylation A compound action with an associated Attach No other description in the KB. • Eucaryotic-mRNA-Processing … • a Polyadenylation Site is the site of the following Move-On, object is a Poly-A-Tail, enables the following Move-Out-Of, result is an Eucaryotic-MRNA • Missing: • That the “polyadenylation provides most newly transcribed mRNAs with a special structure at their 3’ end”. • That in the Polyadenylation “the 3’ ends of eucaryotic RNAs are first trimmed by an enzyme that cuts the RNA chain at a particular sequence of nucleotides and is then finished off by a second enzyme that adds a series of repeated adenine (A) nucleotides (a poly(A) tail) onto the cut end.” • Nothing is said about the fact that “the poly(A) tail is generally a few hundred nucleotides long.” …

8. (iflu) Move-Out-Of • Move-Out-Of Described only in pump priming KB. • Eucaryotic-mRNA-Processing … • a Move-Out-Of The Eucaryotic-MRNA resulting from the Polyadenylation moves out of the site of the preceding Polyadenylation to the site of the following Eucaryotic-Translation on a Nuclear-Pore path. The text says that the mRNA “must be transported out of the nucleus through small pores in the nuclear envelope”, where as the description simply says that the path is a Nuclear-Pore. The description is correct, but is ambiguous as to whether the path is a single Nuclear-Pore or multiple Nuclear-Pores, as the text would suggest. …

9. (iflu) Eukaryotic-mRNA-Processing • Eucaryotic-mRNA-Processing • Subevents in sequence: • a Eucaryotic-Transcription • a Eukaryotic-mRNA-Processing • Subevents in sequence: • a Capping • a Polyadenylation • a Move-Out-Of Nothing is said about the purpose of Eukaryotic-mRNA-Processing. In particular, the textbook says: • These two modifications are thought to increase the stability of the mRNA molecule and to aid its export from the nucleus to the cytoplasm. • They are also used later by the protein-synthesis machinery as an indication that both ends of the mRNA are present and that the message is therefore complete. • a Eucaryotic-Translation

10. (ttaylor) Overview • RKF-eukaryotic-transcription • RKF-rna-processing • Stages: • RKF-rna-capping • Polyadenylation • RKF-rna-splicing • RKF-transport-of-eukaryotic-mrna-across-nuclear-membrane

11. (ttaylor) RKF-Rna-Processing • Rna processing is a scripted event that is a kind of biochemical synthesis and a kind of processing. It has three stages: rna capping followed by Polyadenylation, followed by rna splicing. It is done by a capping enzyme in a cell nucleus. A pre RNA is destroyed, a eucaryotic mRNA is output, and a poly a tail is transferred. An rna cap is a primary moving object. A poly a polymerase is an actor. • RNA capping and Polyadenylation occur only in the processing of primary transcripts destined to become mRNA molecules that are in eucaryotic cells. Neither of those provisos are in this description of rna processing. • RNA processing is done on a “primary transcript”. There is no mention of a primary transcript in this KB. • Rna splicing is included in Rna processing, which differs from the text.

12. (ttaylor) RKF-Rna-Capping • Rna capping is a kind of biochemical synthesis. It produces rna caps and is similar to Polyadenylation • Missing: • “RNA capping involves a modification of the 5’ end of the primary transcript” • “The 5’ end is capped by the addition of an atypical nucleotide – a guanine (g) nucleotide with a methyl group attached.” • “Capping usually occurs just after the RNA polymerase has synthesized the 5’ end of the primary transcript and before it has completed transcribing the whole gene.”

13. (ttaylor) RKF-Polyadenylation • Polyadenylation is a kind of biochemical synthesis that produces poly a tails. • Missing: • “the 3’ ends of eucaryotic RNAs are first trimmed by an enzyme that cuts the RNA chain at a particular sequence of nucleotides” • “and is then finished off by a second enzyme that adds a series of repeated adenine (A) nucleotides (a poly(A) tail) onto the cut end.” • “The poly(A) tail is generally a few hundred nucleotides long.”

14. RKF-transport-of-eukaryotic-mrna-across-nuclear-membrane • A transport-of-eukaryotic-mrna-across-nuclear-membrane is a scripted event that is a kind of “passing through a portal” and a kind of transporting. It occurs after an “rna processing”. It occurs at a nuclear membrane, the actor is a nuclear pore, and the primary moving object is a processed mRNA.

15. (ttaylor) RKF-Eukaryotic-Transcription • A eukaryotic-transcription is a kind of transcription. It occurs in a eucaryotic cell and in a cell nucleus. Pre RNAs are produced. • A transcription is a type of scripted event and a type of stuff that is a kind of a duplication of an information bearing thing and a kind of genetic information transfer. It has a ribonucleotide bonding as a sub-event, rna polymerization as a stage, and a phosphodiester bond formation as a subprocess. It produces MRNAs, has rna polymerase as a catalyst, has efficiency, has a DNA molecule as a genetic template. During a transcription, adenine deoxyribonucleotides and uracil ribonucleotides, guanine ribonucleotides and cytosine deoxyribonucleotides, cytosine ribonucleotides and guanine deoxyribonucleotides, and adenine ribonucleotides and thymine deoxyribonucleotides are correctly base paired. One gene is repeatedly copied in every transcription. Not all transcriptions are equal in efficiency, and not every transcription has a nucleolytic proofreading as a sub-event.

16. (iflu) CAP and Poly-A-Tail • CAP • A Nucleotide-Sequence Parts are a 5-Prime-Nucleotide, a 3-Prime-Nucleotide, and a Methyl-Guanosine • Methyl-Guanosine • A Nucleoside Parts a pentose and a Guanine • Poly-A-Tail • A Nucleotide-Sequence Basic-structural-units are a 5-Prime-Nucleotide and a Adenosine-phosphate