RNA Molecules and RNA Molecules and RNA ProcessingRNA Processing

Functions and ModificationsFunctions and Modifications of RNA Molecules of RNA Molecules

DNA

Information Flow From DNA

initial transcript RNA

transcription

Proteintranslation

replication

processing

mature RNA

Types of RNA ProducedTypes of RNA Produced by Transcription by Transcription

• Messenger RNAMessenger RNA

Contains the code words for the Contains the code words for the sequence of amino acids in a specific sequence of amino acids in a specific proteinprotein

CODON = group of three nucleotidesCODON = group of three nucleotidesacting as a code word for an amino acidacting as a code word for an amino acid

Arrangement of Arrangement of Codons on mRNACodons on mRNA

Types of RNA Produced by TranscriptionTypes of RNA Produced by Transcription • Transfer RNATransfer RNA

– ““Translates” the message by bringing a Translates” the message by bringing a specific amino acid into the correct position specific amino acid into the correct position on the growing protein chainon the growing protein chain

– Has ANTICODON = a group of three Has ANTICODON = a group of three nucleotides on a tRNA that recognizes a nucleotides on a tRNA that recognizes a mRNA codonmRNA codon

– Has amino acid attachment siteHas amino acid attachment site

anticodonanticodon

Types of RNA Produced by TranscriptionTypes of RNA Produced by Transcription • Ribosomal RNARibosomal RNA

One of the structural components of the One of the structural components of the ribosomeribosome

Ribosome = organelle where protein Ribosome = organelle where protein synthesis occurs synthesis occurs

Has sites to bind both mRNA and tRNAHas sites to bind both mRNA and tRNA

Interrupted Genes Interrupted Genes Eukaryotic Genes have interruptions within Eukaryotic Genes have interruptions within regions coding for protein regions coding for protein

intron = interrupting sequenceintron = interrupting sequenceexon = portion of coding regionexon = portion of coding region

Processing of the pre-mRNA is required Processing of the pre-mRNA is required to remove introns and join exons. to remove introns and join exons.

intron 1intron 1 intron 2intron 2Exon 1Exon 1 Exon 2Exon 2 Exon 3Exon 3

Coding RegionCoding RegionExon 1Exon 1 Exon 2Exon 2 Exon 3Exon 3

Translated to Produce Protein Translated to Produce Protein

mRNA ProcessingmRNA ProcessingDNADNA

Add 5’ capAdd 5’ cap

Remove IntronsRemove IntronsSplice Exons Splice Exons together together

Cleave at 3’ endCleave at 3’ endAdd 3’ poly-A tailAdd 3’ poly-A tail

Transcription Transcription

Pre mRNAPre mRNA

Mature mRNA leaves for cytoplasmMature mRNA leaves for cytoplasm

In nucleusIn nucleus

5’5’ 3’3’intron 1intron 1 intron 2intron 2Exon 1Exon 1 Exon 2Exon 2 Exon 3Exon 3

m7m7G-P-P-P-G-P-P-P-intron 1intron 1 intron 2intron 2Exon 1Exon 1 Exon 2Exon 2 Exon 3Exon 3

AAAAAA…..AAAAAA…..m7m7G-P-P-P-G-P-P-P-intron 1intron 1 intron 2intron 2Exon 1Exon 1 Exon 2Exon 2 Exon 3Exon 3

AAAAAA……AAAAAA……m7m7G-P-P-P-G-P-P-P-Exon 1Exon 1 Exon 2Exon 2 Exon 3Exon 3

Start Codon

Stop Codon

Untranslated Region (UTR)

UTR with consensus sequence

Protein-coding RegionProtein-coding Region

Applying Your KnowledgeApplying Your Knowledge

Which of the following molecules lacks Which of the following molecules lacks introns? introns?

1.1. Pre-mRNAPre-mRNA

2.2. DNADNA

3.3. Mature messenger RNAMature messenger RNA

4.4. All of these lack intronsAll of these lack introns

5.5. None of these lack intronsNone of these lack introns

Intron Removal for Ovalbumin mRNAIntron Removal for Ovalbumin mRNA

Addition of a Addition of a 5’-Methyl 5’-Methyl

Guanine CapGuanine Cap

Cleavage and Polyadenylation of 3’ endCleavage and Polyadenylation of 3’ end

1.1. Pre-mRNA is cleaved 11-30 nucleotides Pre-mRNA is cleaved 11-30 nucleotides downstream of the AAUAAA consensus downstream of the AAUAAA consensus sequence. (Rat1 will attach to 5’ end to terminate sequence. (Rat1 will attach to 5’ end to terminate transcription.)transcription.)

2.2. 50-200 Adenine nucleotides are added 50-200 Adenine nucleotides are added enzymatically to the resulting 3’ end.enzymatically to the resulting 3’ end.

Identifying Sites for Intron RemovalIdentifying Sites for Intron Removal

Steps in SplicingSteps in Splicing

Alternative SplicingAlternative Splicing

Multiple 3’ Cleavage SitesMultiple 3’ Cleavage Sites

RNA Editing

Applying Your KnowledgeApplying Your Knowledge

A poly-A tail (repeating sequence of A poly-A tail (repeating sequence of adenine nucleotides) is added to adenine nucleotides) is added to _____ of the primary transcript. _____ of the primary transcript.

1.1. The 3’ end The 3’ end 2.2. The 5’ endThe 5’ end3.3. Either the 3’ end or the 5’ endEither the 3’ end or the 5’ end4.4. Both the 3’ end and the 5’ endBoth the 3’ end and the 5’ end5.5. Neither the 3’ end nor the 5’ endNeither the 3’ end nor the 5’ end

Applying Your KnowledgeApplying Your Knowledge

Which molecule contains the information Which molecule contains the information for assembling the amino acids in the for assembling the amino acids in the correct order in the protein? correct order in the protein?

1.1. rRNArRNA2.2. tRNAtRNA3.3. mRNAmRNA4.4. All of theseAll of these5.5. None of theseNone of these

tRNA ProcessingtRNA Processing

Cleavage SplicingNucleotide Addition

NucleotideModification

rRNA ProcessingrRNA Processing

RNA InterferenceRNA Interference(RNAi)(RNAi)

• Process by which small Process by which small RNA molecules regulate RNA molecules regulate gene expressiongene expression

• Types of small RNAsTypes of small RNAs– Micro RNAs (miRNAs)Micro RNAs (miRNAs)– Small Interfering RNAsSmall Interfering RNAs

(siRNAs)(siRNAs)

• Protein componentsProtein components– DicerDicer– Protein + RNA = RISCProtein + RNA = RISC

(RNA-Induced Silencing Complex)(RNA-Induced Silencing Complex)

Producing Small RNAsProducing Small RNAs

Interfering with RNA FunctionInterfering with RNA Function

Interfering with DNA Interfering with DNA FunctionFunction

• Some siRNAs can Some siRNAs can inhibit transcriptioninhibit transcription

• Protein componentsProtein components– Protein + RNA = RITSProtein + RNA = RITS

(RNA-Induced (RNA-Induced Transcriptional Silencing)Transcriptional Silencing)

– Methylating EnzymeMethylating Enzyme• Changes the chemical Changes the chemical

characteristics of DNA or characteristics of DNA or chromatin histone chromatin histone proteins to silence proteins to silence transcriptiontranscription

siRNAs

Fro

m d

iffer

ent R

NA

mol

ecul

es

Gene Silencing by RNA InterferenceGene Silencing by RNA Interference

Extra genes for a protein involved in Extra genes for a protein involved in pigment production were introduced pigment production were introduced into petunia plants. Silencing of both into petunia plants. Silencing of both the native and newly-introduced genes the native and newly-introduced genes led to white flower coloration. led to white flower coloration.

Processes Affected by RNAiProcesses Affected by RNAi

• Genomic “Immunity”- protection from viral Genomic “Immunity”- protection from viral and transposon genes observed in plants and transposon genes observed in plants and invertebratesand invertebrates

• Regulation of gene expression related to Regulation of gene expression related to – Development --miRNAs involved in the Development --miRNAs involved in the

timing of morphogenesis and maintenance of timing of morphogenesis and maintenance of stem cell populationsstem cell populations

– Cell fate and proliferation Cell fate and proliferation – Cancer Cancer – Cell deathCell death