Nucleic Acids and Gene Structure

Transcription stops due to specific sequences in the transcript, not a stop codon. Examples include rho-dependent and terminator structures.

Eukaryotic genes contain introns (non-coding) and exons (coding), where introns are removed. They also have regulation sequences and multiple promoters that can lead to multiple mRNAs.

Eukaryotic cells have three types of RNA polymerases: Pol I (rRNA), Pol II (mRNA), and Pol III (small non-coding RNAs).

The promoter for ribosomal RNA (rRNA) synthesis contains an upstream control element (UCE) and a core promoter element (CPE).

Coding sequences within a gene. The ORF closest to the promoter is typically transcribed more often.

Some eukaryotic genes have multiple promoters, leading to the production of multiple different mRNAs from a single gene.

Genes are organized in clustered, repeated units, often found in rRNA genes.

The third base of a codon can sometimes have flexibility in pairing with a tRNA anticodon, allowing for redundancy in amino acid codons.

The wider groove in a DNA double helix, exposing more information about the base pairs.

The narrower groove in a DNA double helix, exposing less information about the base pairs.

A protein's ability to recognize and bind to a specific DNA sequence.

A protein that binds to the TATA box in promoters, crucial for initiating transcription.

Assists TFIID in positioning RNA polymerase II correctly for accurate transcription initiation.

A protein complex that bridges enhancers and promoters, mediating long-range transcriptional regulation.

DNA sequences that increase the rate of transcription of target genes, often located far from the gene itself.

DNA sequences that decrease the rate of transcription of target genes.

DNA sequences that prevent the effects of enhancers and silencers from spreading inappropriately, allowing for their specific action on neighboring genes.

Enhancers and silencers that work on the same DNA strand.

TFIII-C is a transcription factor specifically for RNA polymerase III. It recruits TFIII-B, which then recruits RNA Polymerase III to the promoter. TFIII-B remains bound to the DNA to quickly re-initiate transcription, while TFIII-C is removed.

RNA polymerase II promoters show a wide range of complexity due to the need to regulate gene expression in different ways. Some genes need to be constantly expressed, others need to be turned on and off rapidly, and some are only expressed during specific developmental stages.

RNA Pol II is a complex enzyme with 12 subunits, some of which share similarities with bacterial RNA polymerases. One important feature is the C-terminal domain (CTD), a tail that can be modified by phosphorylation.

The CTD is a series of repeating amino acid sequences at the tail of RNA Pol II. It's the site of phosphorylation, which plays a crucial role in controlling the polymerase's activity, like switching it on or off and coordinating transcription.

The efficiency of transcription initiation depends on several factors, including the strength of the core promoter in recruiting general transcription factors and additional specific transcription factors, as well as the accessibility of DNA sequence (histones/chromatin).

The core promoter is a sequence of DNA that recruits RNA Polymerase II to the start of transcription. Key elements include the TATA box, INR (Initiator), and DPE (Downstream Promoter Element) along with the RE (TFIIB Recognition Element). Promoters don't always have all the elements, but more elements means more likely it is to be transcribed.

The entire process of transcription is divided into 5 stages: 1) Recruitment/Assembly, 2) Initiation, 3) Elongation, 4) Termination, and 5) Recycling. Each stage involves specific factors and modifications to the RNA polymerase.

TFIIA helps stabilize the binding of TFIID and TFIIB, making the complex more robust, and promotes the interaction of the two factors by bringing them together

TFIIB helps orient RNA Polymerase II correctly on the DNA strand for transcription and helps stabilize the binding of the polymerase to the DNA.

TFIIF helps stabilize the binding of TFIIB and RNA Polymerase II. It also ushers in RNA Polymerase II to the promoter, acting sort of like a chaperone.

TFIIE stabilizes TFIIH and help regulate its activity.

TFIIH is a key player in transcription initiation. It has two main roles: 1) unwinding DNA to expose the template strand (helicase activity) and 2) activating the RNA Polymerase by phosphorylating its CTD tail (kinase activity).

The PIC is formed when TFIID binds to the DNA at the promoter sequence. The TBP component of TFIID specifically binds to the TATA box, causing a bend in the DNA. Not all promoters have a TATA box, and those that do only make up 1/4 of promoters.

Introns are non-coding sequences within a gene that are removed during RNA processing. They are like filler text in a book, not part of the final story.

Some eukaryotic genes have multiple promoters, which allows them to produce different versions of mRNA from the same gene. It's like having multiple entry points in a book leading to different stories.

Genes are organized in clusters where multiple copies of the same gene are arranged in a row. It's like having many identical books stacked together.

The third base of a codon (three bases that code for an amino acid) can sometimes have flexibility in pairing with a tRNA anticodon. This allows for redundancy in the genetic code.

Pol I is a type of RNA polymerase that produces ribosomal RNA (rRNA) which are essential for protein synthesis. It's like a factory that builds the machines for protein production.