1. LECTURE CONNECTIONS 14 | RNA Molecules and RNA Processing © 2009 W. H. Freeman and Company

2. In eukaryotic cells, RNA molecules are often extensively modified after transcription. Different proteins are produced from the same DNA sequence. RNA undergoes alternative processing.

3. 14.1 Many Genes Have Complex Structures Genes encode proteins. Proteins are made of amino acids, so a gene contains the nucleotides that specify the amino acids of a protein. Amino acids have a variety of roles in metabolism. The chemical properties of the amino acids of proteins determine the biological activity of the protein.

4. Gene Organization The concept of - colinearity: there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein. Bacteria and many viruses. - noncolinearity Eukaryotic cells contain far more DNA than is required to encode proteins. Nuclear RNAs undergo some type of change before they are exported to the cytoplasm. Regions of DNA might not be transcribed.

7. Gene Organization Exons: coding regions Introns: noncoding regions All the introns and the exons are initially transcribed into RNA but, after transcription, the introns are remove by splicing.

8. The coding sequences of many eukaryotic genes are disrupt by noncoding regions.

9. The Concept of the Gene The gene includes DNA sequence that codes for all exons, introns, and those sequences at the beginning and end of the RNA that are not translated into a protein, including the entire transcription unit – the promoter, the RNA coding sequence, and the terminator.

10. 14.2 mRNAs are modified after transcription in eukaryotes The structure of messenger RNA: A mature mRNA contains 5′ untranslated region (5′ UTR, or leader sequence) Shine–Dalgarno consensus sequence in bacteria Protein coding region: codons that specify the aa sequence of the protein. Start codon and stop codon 3′ untranslated region (3’UTR or trailer): affects the stability of the mRNA and the translation of the mRNA protein-coding sequence.

11. Three primary regions of mature mRNA in bacteria.

12. Concept Check 1 Which region of mRNA contains the Shine–Dalgarno sequence? a.5′ UTR b.3′ UTR c.Protein coding region d.All three regions

13. Pre-mRNA processing The addition of the 5′ cap: - An extra nucleotide is added to the 5’ end and - Methylation to the base of new nucleotide and to the 2’-OH group of the sugar of one or more nucleotides at the 5’end. The addition of the poly(A) tail: 50 ~ 250 adenine nucleotides are added to the 3′-end of the mRNA by polyadenylation.

15. Pre-mRNA processing RNA splicing: removal of introns in the nucleus Consensus sequences: –5′ splice site: GU and end with AG –3′ consensus sequence: CAGG –Branch point: the adenine “A”: 18 ~ 40 nucleotides upstream of 3′-splicing site Spliceosome: 5 RNA molecules + 300 proteins The process of splicing

17. Concept Check 2 If a splice site were mutated so that splicing did not take place, what would the effect be on the protein encoded by the mRNA? a.It would be shorter than normal. b.It would be longer than normal. c.It would be the same length but would have different amino acids.

18. Intron removal, mRNA processing, and transcription take place at the same site in the nucleus. Self-splicing introns happen in some rRNA genes in protists and in mitochondria genes in fungi. There are alternative processing pathways for processing pre-mRNA.

20. The Dscam gene of Drosophila can produce 38,016 different types of proteins by alternative nRNA splicing The Drosophyla genome is thought to contain only 14,000 genes, but here is a single gene that encodes three times that number of proteins.

22. RNA editing: The coding sequence of an mRNA molecule is altered after transcription. Insertion or deletion of nucleotides or the conversion of one base into another. gRNAs (guide RNAs) contain sequences that are partially complementary to segments of the pre- edited RNA. After the mRNA is anchored to the gRNA, the mRNA undergoes cleavage and nucleotides are added, deleted, or altered according to the template provided by gRNA. RNA editing

24. Concept Check 3 Alternative 3′ cleavage sites result in: a.multiple genes of different length. b.multiple genes of pre-mRNA of different length. c.multiple mRNAs of different length. d.all of the above.