BSC 219

RNA

10/18/12

Gene Organization

Introns

Regions of RNA that are not reflected in protein sequence

INTervening sequences

Exons

Regions of RNA that are reflected in protein sequence

EXpressed sequences

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.

14.2 Messenger RNAs, Which Encode the Amino Acid Sequences of Proteins, 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 sequence

Protein coding region

3′ untranslated region

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:

50 ~ 250 adenine nucleotides are added to the 3′-end of the mRNA.

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 + 300 proteins

The process of splicing

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.

RNA editing: The coding sequence of an mRNA molecule is altered after transcription.

Guide RNA is used to serve as template for RNA editing

14.3 Transfer RNAs, Which Attach to Amino Acids, Are Modified after Transcription in Bacteria and Eukaryotic Cells

The Structure of Transfer RNA

Rare modified RNA nucleotide bases

Ribothymine

Pseudouridine

Common secondary structure – the cloverleaf structure

The Structure of Transfer RNA

Transfer RNA gene structure and processing

Multiple steps

Cleavage from larger precursor is common

Addition of 3’ sequence CCA

Modification of bases into rare bases across structure

The Structure of the Ribosome

Large ribosome subunit

Small ribosome subunit

Both comprise RNA and small proteins

rRNA is methylated at Carbon 2 at multiple locations

Ribosomal RNA Gene Structure and Processing

14.5 Small RNA Molecules Are Present Extensively in Eukaryotes and Participate in a Variety of Functions

RNA interference: limits the invasion of foreign genes and censors the expression of their own genes

siRNA and miRNA-small interfering RNA and microRNA

both make ds RNA structure

siRNA makes hairpin upon self

miRNA anneals to complementary mRNA

Enzyme Dicer cuts ds RNA into fragments of approximately 22 bases

Fragmented ds RNA then interacts with protein complex to form RISC

RNA-Induced Silencing Complex

RISC aligns RNA with complementary sequence on mRNA

Complex either causes mRNA to be degraded or halts translation

14.5 Small RNA Molecules Are Present Extensively in Eukaryotes and Participate in a Variety of Functions

BSC 219

Gene Organization

Introns

Regions of RNA that are not reflected in protein sequence

INTervening sequences

Exons

Regions of RNA that are reflected in protein sequence

EXpressed sequences

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.

14.2 Messenger RNAs, Which Encode the Amino Acid Sequences of Proteins, 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 sequence

Protein coding region

3′ untranslated region

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:

50 ~ 250 adenine nucleotides are added to the 3′-end of the mRNA.

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 + 300 proteins

The process of splicing

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.

RNA editing: The coding sequence of an mRNA molecule is altered after transcription.

Guide RNA is used to serve as template for RNA editing

14.3 Transfer RNAs, Which Attach to Amino Acids, Are Modified after Transcription in Bacteria and Eukaryotic Cells

The Structure of Transfer RNA

Rare modified RNA nucleotide bases

Ribothymine

Pseudouridine

Common secondary structure – the cloverleaf structure

The Structure of Transfer RNA

Transfer RNA gene structure and processing

The Structure of the Ribosome

Large ribosome subunit

Small ribosome subunit

Ribosomal RNA Gene Structure and Processing

14.5 Small RNA Molecules Are Present Extensively in Eukaryotes and Participate in a Variety of Functions

RNA interference: limits the invasion of foreign genes and censors the expression of their own genes

14.5 Small RNA Molecules Are Present Extensively in Eukaryotes and Participate in a Variety of Functions

Model Genetic Organism – the Nematode Worm