Chemistry Chapter 13 - Transcription

What is the Central Dogma of Molecular Genetics?

The Directional Flow of Genetic Information From DNA to RNA to Protein

What are Promoters?

Specific DNA Sequences Located Upstream of the Gene/DNA Where RNA Polymerase Binds

What is RNA Pol Holoenzyme?

Composed of Multiple Subunits (α₂ββ’ωσ)

What is the Core Enzyme for Prokaryotic Transcription?

RNA Pol Holoenzyme Without Sigma (σ)

What Subunit Recognizes the Promoter?

Sigma (σ)

Is Primer Required for Initiation?

No

What is the Transcription Start Site +1?

The Exact DNA Location Where RNA Pol Begins Synthesis

What is the -35 Sequence (TTGACA)?

Specific DNA Sequence in Prokaryotic Transcription That Helps RNA Pol Locate the Promoter and Assists in DNA Unwinding

What is the -10 Sequence/Pribnow Box (TATAAT)

Specific DNA Sequence in Prokaryotic Transcription That Interacts With the Sigma (σ) Factor For Promoter Recognition

What is the First Step of Prokaryotic Transcription?

Initiation: RNA Pol Holoenzyme Binds to Promoter (Two Sequences) and Initiates Transcription

What is the Second Step of Prokaryotic Transcription?

Elongation: Core Enzyme Remains After Sigma (σ) is Released. RNA is Synthesized 5’→3’ Using NTPs

What is the Second Part of Elongation in Prokaryotic Transcription?

RNA Pol Reads the Antisense Strand (3’→5’) as a Template. The Resulting RNA is Complementary to the Antisense Strand, Except U Replaces T.

What is the Third Step of Prokaryotic Transcription?

Termination: RNA Pol Continues Along the Gene Until it Reaches a Termination Sequence

What is Intrinsic (Rho-Independent) Termination in Prokaryotic Transcription?

1. RNA Forms a GC-Rich Hairpin Followed by a Stretch of U’s

2. This Destabilizes the RNA-DNA Hybrid, Causing RNA Pol to Release the Transcript

What is Rho-Dependent Termination in Prokaryotic Transcription?

1. Rho Protein Binds to a Specific Site “Rut” on RNA and Moves Along Using ATP

2. When Rho Catches Up to RNA Pol, it Helps Dissociate the RNA Transcript From DNA

What’s the Difference in Eukaryotic Transcription?

1. Occurs Within the Nucleus; mRNA Must Exit the Nucleus for Translation

2. Chromatin Remodeling

3. RNA Pol Relies on Transcription Factors

4. Enhancers and Silencers Regulate Transcription

What is RNA Pol I?

Transcribes rRNA Genes in Eukaryotic Transcription

What is RNA Pol II?

Transcribes mRNA and Some snRNA in Eukaryotic Transcription

What is RNA Pol III?

Transcribes tRNA and Some Other Small RNAs in Eukaryotic Transcription

What are Cis-Acting Elements?

Non-Coding DNA Regions That Regulate Transcription of Nearby Genes by Acting as Binding Sites for Trans-Acting Elements

What are Examples of Cis-Acting Elements?

Promoters, Enhancers, Silencers, and TATA Box

What are Trans-Acting Elements?

Typically Proteins That Regulate the Expression of Genes by Binding to Cis-Elements

What are Examples of Trans-Elements?

RNA Polymerase, Transcription Factors, Activators, Repressors

What is the First Step of Eukaryotic Transcription?

Initiation: RNA Pol II Binds to the Core Promoter (TATA Box)

What is the Second Step of Eukaryotic Transcription?

Elongation: RNA Pol II Synthesizes mRNA 5’→3’ Using A, C, G, and UTP

What is the Third Step of Eukaryotic Transcription?

Termination: Stops at Termination Site (Polyadenylation Site) and Releases RNA

What is the Core Promoter in Eukaryotic Transcription?

The Minimal DNA Sequence Required for Transcription Initiation

What are the Two Components of the Core Promoter in Eukaryotic Transcription?

TATA Box and TSS (+1)

What is the TATA Box?

A Conserved DNA Sequence ~25-30bp Upstream of the TSS; TATA-Binding Protein (TBP) Binds to TATA Box, Determining Transcription Initiation

What is the Proximal Promoter?

Located Upstream of the Core Promoter (Often Close); Contains TF Binding Sites That Regulate Transcription Efficiency

What is the Distal Promoter?

Regulatory Sequences Often Found Upstream or at a Distance From the Gene

What are Examples of Proximal Promoters?

CAAT Box and GC Box

What are Examples of Distal Promoters?

Enhancers and Silencers

What are Enhancers?

Cis-Acting Element That Increases Transcription by Promoting TF and RNA Pol II Activity

What are Silencers?

Cis-Acting Element That Decreases Transcription by Inhibiting TF or RNA Pol II Binding

What are Transcription Factors (TFs)?

Proteins That Bind to Cis-Acting Elements to Regulate Transcription

What are General Transcription Factors (GTFs)?

Essential For Transcription Initiation. Binds to Promoter and Assembles With RNA Pol II to Form the Holoenzyme

What are Activators?

Trans-Element That Bind to Enhancers to Enhance Transcription of Target Genes

What are Repressors?

Trans-Element That Binds to Silencers to Inhibit Transcription by Blocking RNA Pol II or TF Binding

What is RNA Processing?

In Eukaryotic Transcription, mRNA Undergoes Capping, Splicing, and Poly-A Tail Addition Before Export From the Nucleus

What is Capping in mRNA Processing?

A Modified Guanine Nucleotide is Added to the 5’ End of Eukaryotic mRNA. Protects mRNA from Degradation by Exonucleases and Facilitates Binding of Ribosomes During Translation Initiation

What is Poly-A Tail Addition in mRNA Processing?

A Stretch of Adenine Nucleotides is Added to the 3’ End of the mRNA After Transcription

What is Splicing/Intron Removal?

Non-Coding Introns are Removed; Coding Exons are Joined to Form Continuous mRNA

Why Does mRNA in Eukaryotes Need to be Processed?

Because Prokaryotic mRNAs Usually Lack Introns and are Ready For Translation Immediately, Unlike Eukaryotic mRNA

What is Self-Splicing RNA?

Group I and II Introns That Can Remove Introns and Join Exons Without Proteins

What are the Two Transesterification Reactions of Self-Splicing RNA?

1. The 3’-OH of a Free Guanosine Attacks the 5’ Splice Site, Cleaving the Exon-Intron Junction

2. The 3’-OH of the Upstream Exon Then Attacks the 3’ Splice Site, Joining the Exons and Releasing the Exon

What is a Ribozyme?

An RNA Acting as an Enzyme

What is a Spliceosome?

Removes Introns from Pre-mRNA

What is the Mechanism of Splicing With Spliceosome?

1. U1 Binds to 5’ SS; U2 Binds BPS

2. U4/5/6 Join → Spliceosome Forms, Looping Intron into Lariat

3. BP Attacks 5’ Site → Intron Excised

4. 3’ OH of Exon Attacks 3’ SS → Exons Ligated