BLOCK 3: MBG: (3.5) RNA AND GENE REGULATION

Gene Regulation

• Prokaryotic Gene Regulation is either turning on genes that are off (Positive regulation) or turning off genes that are on (Negative regulation).
• Inducer molecules induce expression of a gene. They either block repression or enable activation.
• Repressor molecules bind to DNA and prevent transcription.
• Co-repressors molecules bind to repressors creating a repressor complex that blocks transcription.
• Inhibitors prevent the association of key transcriptional machinery to DNA.
• Operon Model involves a key sequence that binds to and blocks the promoter.
• Energy Efficiency drives gene regulation. It is more efficient to only produce what is needed.
• Environmental Changes necessitate responses for bacteria, e.g. lack of food.
• Eukaryotic Gene Regulation is more complex. It involves multiple promoters, enhancers, and transcription factors.
• Transcription Factors bind to specific sequences and recruit and orient RNA polymerase to the promoter.
• Enhancers can be located on the same chromosome or even on a different chromosome, influencing gene expression through bending or massive complexes.
• Regulation of transcription controls the level of association of RNA polymerase to the promoter.
• Eukaryotic Gene Regulation predominantly occurs at the level of transcription.
• Organization of the genetic material plays a key role in eukaryotic gene regulation.

DNA vs. RNA

• DNA contains deoxyribose and RNA contains ribose
• DNA exists as a double-stranded helix and RNA exists as a single-stranded helix
• DNA uses thymine (T), but RNA uses uracil (U)
• DNA is used as a template for RNA synthesis
• RNA acts as a primer to initiate DNA synthesis at origins of replication

RNA Structure

• RNA can form higher order structures based on its single-stranded nature
• RNA can fold back on itself to form stem-loop structures or other complex shapes
• RNA can form intramolecular base pairings involving hydrogen bonds

Types of RNA

• Ribosomal RNA (rRNA) is the primary component of ribosomes which are responsible for protein synthesis
• Messenger RNA (mRNA) carries genetic information from DNA to the ribosomes
• Transfer RNA (tRNA) brings amino acids to the ribosomes to make proteins
• Small nuclear RNA (snRNA) is transcribed from protein-coding genes and is involved in processing RNA

Polycistronic mRNA

• Polycistronic mRNA is a messenger RNA molecule that encodes multiple proteins
• Polycistronic mRNA is found in prokaryotes and allows for the coordinated expression of genes involved in the same pathway
• Eukaryotes typically have monocistronic mRNA, where one mRNA molecule codes for one protein

Transcription

• Transcription is the process of converting DNA into RNA. It involves three main steps: initiation, elongation, and termination.
• Sense strand: the DNA strand that has the same sequence as the mRNA, but contains T instead of U.
• Antisense strand: the DNA strand that is the template for RNA synthesis. It has the complementary sequence to mRNA.
• The promoter is the sequence of DNA that indicates the start of a gene. It is where the RNA polymerase binds to initiate transcription.
• Transcription factors are proteins that help RNA polymerase bind to the promoter and initiate transcription.

Prokaryotic Transcription

• Prokaryotes use a single RNA polymerase for all types of RNA synthesis
• The promoter typically contains a TATA box (-10) and a consensus sequence at -35 (TTGACA)
• Transcription initiation and termination are simpler than in eukaryotes

Eukaryotic Transcription

• Eukaryotes have three distinct RNA polymerases: RNA polymerase I, II, and III
• RNA polymerase I transcribes rRNA genes
• RNA polymerase II transcribes protein-coding genes and snRNAs
• RNA polymerase III transcribes tRNA and 5S rRNA genes
• Eukaryotic promoters are more complex than those in prokaryotes
• Transcription initiation involves multiple transcription factors
• Termination is more complex than in prokaryotes, with distinct mechanisms for each polymerase.

Transcription Termination

• Transcription termination is controlled by termination sequences in DNA and specific proteins
• RNA polymerase I uses a protein called TTFI as a termination factor
• RNA polymerase II uses a variety of termination factors, including the CTD domain of the polymerase, Xrn2 exonuclease, and termination sequences.
• RNA polymerase III termination mechanisms are less characterized.

Impact of Changes in Sequence

• Changes in DNA or RNA sequence can affect transcription, RNA structure, and protein function
• Changes in the promoter sequence can affect RNA polymerase binding and transcription activity.
• Changes in the termination sequences can result in the production of mRNAs of incorrect lengths
• Changes in RNA sequence can affect mRNA structure, stability, and translation efficiency.

This quiz covers key concepts in gene regulation, including mechanisms of prokaryotic and eukaryotic gene expression. Topics include the roles of inducers, repressors, co-repressors, and the operon model, as well as the impact of environmental changes. Test your understanding of how gene regulation contributes to cellular efficiency.