1. RNA Molecules and RNA Processing
Benjamin A. Pierce
GENETICS
A Conceptual Approach
SIXTH EDITION
CHAPTER 14
RNA Molecules and RNA Processing
© 2017 W. H. Freeman and Company

2. The family of Tsar Nicholas Romanov II of Russia.

3. Gene Organization The concept of colinearity and noncolinearity
Number of nucleotides in a gene should be proportional to the number of amino acids in the encoded protein
DNA much longer than mRNA; demonstrated through hybridization

4. 14.1 The concept of colinearity suggests that a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein.

5. 14.2 The noncolinearity of eukaryotic genes was discovered by hybridizing DNA and mRNA.

6. Gene Organization
Introns
Exons

7. 14.3 The coding sequences of many eukaryotic genes are disrupted by noncoding introns.

8. TABLE 14.1 Major types of introns Type of Intron Location
Splicing Mechanism
Group I
Genes of bacteria, bacteriophages, and eukaryotes
Self-splicing
Group II
Genes of bacteria, archaea, and eukaryotic organelles
Nuclear pre- mRNA
Protein-encoding genes in the nucleus of eukaryotes
Spliceosomal
tRNA
tRNA genes of bacteria, archaea, and eukaryotes
Enzymatic
Note: There are also several types of minor introns, including group III introns, twintrons, and archaeal introns.

9. The Concept of the Gene The gene includes
DNA sequences that code for all exons and introns
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
The terminator

10. The Structure of Messenger RNA
A mature mRNA contains a 5′ untranslated region (5′ UTR, or leader sequence)
Shine–Dalgarno sequence
Protein-coding region
3′ untranslated region

11. 14.5 Three primary regions of mature mRNA are the 5′ untranslated region, the protein-coding region, and the 3′ untranslated region.

12. Pre-mRNA Processing The addition of the 5′ cap:
A nucleotide with 7-methylguanine; 5′-5′ bond is attached to the 5′ end of the RNA.
The addition of the poly(A) tail:
~ adenine nucleotides are added to the 3′ end of the mRNA.

13. Posttranscriptional modifications to eukaryotic pre-mRNA
TABLE 14.2
Posttranscriptional modifications to eukaryotic pre-mRNA
Modification
Function
Addition of 5' cap
Facilitates binding of ribosome to 5' end of mRNA, increases mRNA
3' cleavage and addition of poly(A) tail
Increases stability of mRNA, facilitates binding of ribosome to mRNA
RNA splicing
Removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing
RNA editing
Alters nucleotide sequence of mRNA

14. 14. 6 Most eukaryotic mRNAs have a 5′ cap
14.6 Most eukaryotic mRNAs have a 5′ cap. The cap consists of a nucleotide with 7-methylguanine attached to the pre-mRNA by a unique 5′–5′ bond (shown in detail in the bottom box).

15. 14.7 Most eukaryotic mRNAs have a 3′ poly(A) tail.

16. Pre-mRNA Processing RNA splicing: Consensus sequences:
5′ consensus sequence: GU A/G AGU: 5′ splice site
3′ consensus sequence: CAGG
Branch point: the adenine “A”: ~18-40 nucleotides upstream of 3′-splicing site
Spliceosome: five RNA molecules proteins
The process of splicing

17. 14. 8 Splicing of pre-mRNA requires consensus sequences
14.8 Splicing of pre-mRNA requires consensus sequences. Critical consensus sequences are present at the 5′ splice site and the 3′ splice site. A weak consensus sequence (not shown) exists at the branch point.

18. 14.9 The splicing of nuclear introns requires a two-step process.

19. 14. 10 RNA splicing takes place within the spliceosome
14.10 RNA splicing takes place within the spliceosome. The spliceosome assembles sequentially.

20. Concept Check 1 It would be shorter than normal.
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?
It would be shorter than normal.
It would be longer than normal.
It would be the same length but would have different amino acids.

21. Concept Check 1 It would be shorter than normal.
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?
It would be shorter than normal.
It would be longer than normal.
It would be the same length but would have different amino acids.

22. Pre-mRNA Processing Nuclear organization
Intron removal, mRNA processing, and transcription take place at the same site in the nucleus.
Minor splicing
Self-splicing introns in some rRNA genes in protists and in mitochondria genes in fungi
Alternative processing pathways for processing pre-mRNA

23. 14.11 Group I and group II introns fold into characteristic secondary structures.

24. Eukaryotic cells have alternative pathways for processing pre-mRNA. (a) With alternative splicing, pre-mRNA can be spliced in different ways to produce different mRNAs. (b) With multiple 3′ cleavage sites, there are two or more potential sites for cleavage and polyadenylation; use of the different sites produces mRNAs of different lengths.

25. 14.13 Pre-mRNA encoded by the gene for calcitonin undergoes alternative processing.

26. Concept Check 2 Alternative 3′ cleavage sites result in _____.
multiple genes of different lengths
multiple genes of pre-mRNA of different lengths
multiple mRNAs of different lengths
All of the above

27. Concept Check 2 Alternative 3′ cleavage sites result in _____.
multiple genes of different lengths
multiple genes of pre-mRNA of different lengths
multiple mRNAs of different lengths
All of the above

28. RNA Editing
RNA editing: coding sequence altered after transcription. Guide RNAs play a role.

29. 14. 14 Trypanosoma brucei causes African sleeping sickness
14.14 Trypanosoma brucei causes African sleeping sickness. Messenger RNA produced from mitochondrial genes of this parasite (in purple) undergoes extensive RNA editing. [David Spears/Last Refuge Ltd./Phototake.]

30. 14. 15 RNA editing is carried out by guide RNAs
RNA editing is carried out by guide RNAs. The guide mRNA has sequences that are partly complementary to those of the preedited mRNA and pairs with it. After pairing, the mRNA undergoes cleavage and new nucleotides are added, with sequences in the gRNA serving as a template. The ends of the mRNA are then joined together.

31. Mature eukaryotic mRNA is produced when pre-mRNA is transcribed and undergoes several types of processing.

32. 14.17 This representation of the nucleotide sequence of the gene for human interleukin 2 includes the TATA box, transcription start site, start and stop codons, introns, exons, poly(A) consensus sequence, and 3′ cleavage site.

33. The Structure of Transfer RNA
Rare modified RNA nucleotide bases
Ribothymine
Pseudouridine
Common secondary structure—the cloverleaf structure
Anticodon

34. 14. 18 Two of the modified bases found in tRNAs
Two of the modified bases found in tRNAs. All the modified bases in tRNAs are produced by the chemical alteration of the four standard RNA bases.

35. All tRNAs possess a common secondary structure, the cloverleaf structure. The base sequence in the flattened model is for tRNAAla.

36. Transfer RNAs are processed in both bacterial and eukaryotic cells. Different tRNAs are modified in different ways. One example is shown here.

37. Concept Check 3 Encoded by guide RNAs
How are rare bases incorporated into tRNAs?
Encoded by guide RNAs
By chemical changes in one of the standard bases
Encoded by rare bases in DNA
Encoded by sequences in introns

38. Concept Check 3 Encoded by guide RNAs
How are rare bases incorporated into tRNAs?
Encoded by guide RNAs
By chemical changes in one of the standard bases
Encoded by rare bases in DNA
Encoded by sequences in introns

39. The Structure of the Ribosome
Large ribosome subunit
Small ribosome subunit

40. Composition of ribosomes in bacterial and eukaryotic cells
TABLE 14.3
Composition of ribosomes in bacterial and eukaryotic cells
Cell Type
Ribosome Size
Subunits
rRNA Component
Proteins
Bacterial
70S
Large (50S)
23S (2900 nucleotides), 5S (120 nucleotides) 31
Small (30S)
16S (1500 nucleotides) 21
Eukaryotic
80S
Large (60S)
28S (4700 nucleotides), 5.8S (160 nucleotides), 5S (120 nucleotides) 49
Small (40S)
18S (1900 nucleotides) 33
Note: The letter “S” stands for “Svedberg unit.”

41. Numbers of rRNA genes in different organisms
TABLE 14.4
Numbers of rRNA genes in different organisms
Species
Number of Copies of rRNA Genes per Genome
Escherichia coli 7
Yeast
100–200
Human
280
Frog
450

42. Ribosomal RNA is processed after transcription
Ribosomal RNA is processed after transcription. Prokaryotic rRNA (a) and eukaryotic rRNA (b) are produced from precursor RNA transcripts that are methylated, cleaved, and processed to produce mature rRNAs. Eukaryotic 5S rRNA is transcribed separately from a different gene.

43. Concept Check 4 Methylation of bases Cleavage of bases
What types of changes take place in rRNA processing?
Methylation of bases
Cleavage of bases
Nucleotides trimmed from the ends of rRNAs
All of the above

44. Concept Check 4 Methylation of bases Cleavage of bases
What types of changes take place in rRNA processing?
Methylation of bases
Cleavage of bases
Nucleotides trimmed from the ends of rRNAs
All of the above

45. 14.5 Small RNA Molecules Participate in a Variety of Functions
RNA interference: limits the invasion of foreign genes and censors the expression of their own genes
Types of small RNAs
Processing and function of microRNAs

46. 14.22 Small interfering RNAs and microRNAs are produced from double-stranded RNAs.

47. Differences between siRNAs and miRNAs
TABLE 14.5
Differences between siRNAs and miRNAs
Feature
siRNA
miRNA
Origin
mRNA, transposon, or virus
RNA transcribed from distinct gene
Cleavage of
RNA duplex or single-stranded RNA that forms long hairpins
Single-stranded RNA that forms short hairpins of double-stranded RNA
Size
21–25 nucleotides
Action
Degradation of mRNA, inhibition of transcription, chromatin modification
Degradation of mRNA, inhibition of translation, chromatin modification
Target
Genes from which they were transcribed
Genes other than those from which they were transcribed

48. CRISPR RNAs function in defense against invasion of foreign DNAs, such as DNA from bacteriophage and plasmids.