Transcription

Topic 2: Transcription

Reading: Chapter 2 (61-78)

Exceptions and Nuances to the Central Dogma

  • RNA information can flow to DNA (e.g., reverse transcriptase)

  • RNA can be modified after its transcription

  • DNA expression can depend on its physical location within the chromosome

Types of RNAs

  • mRNA (messenger RNA)

    • Encodes the amino acid sequence for proteins

  • tRNA (transfer RNA)

    • Reads the information encoded in mRNA and transfers the appropriate amino acid to the growing polypeptide chain

  • rRNA (ribosomal RNA)

    • Components of ribosomes, essential for protein synthesis

RNA Precursors

  • Structure of ribonucleotides:

    • Note the hydroxyl (-OH) group on the 2' carbon of the sugar

    • Bases: adenine, guanine, cytosine, uracil (for RNA) while DNA has thymine (T)

    • Nucleoside Triphosphates (NTPs): building blocks for RNA

RNA vs. DNA

Characteristic

DNA

RNA

Composed of

Nucleotides

Nucleotides

Type of sugar

Deoxyribose

Ribose

Presence of 2'-OH

No

Yes

Bases

A, C, G, T

A, C, G, U

Nucleotides joined by

Phosphodiester bonds

Phosphodiester bonds

Structure

Usually double stranded (ds)

Usually single stranded (ss)

Stability

Quite stable (double helix)

Easily degraded

DNA & RNA Structure

  • 5' End:

    • DNA and RNA both have a 5' end.

  • 3' End:

    • Both structures can extend from the 5' to the 3' end.

  • Primary Structure: Refers to the sequence of nucleotides.

RNA Secondary Structure

  • ssRNA (single-stranded RNA) can fold upon itself, forming double-stranded (ds) regions.

  • All types of RNA, including mRNAs, likely possess some form of secondary structure, such as wobble base pairing, leading to tertiary structures.

Tertiary Structure of RNA

  • Defined three-dimensional shape of the RNA molecule which contributes to increased stability.

  • Recognized by interacting proteins.

RNA Modifications and Processing

  • RNA modifications can include changes to sugar or base (i.e., methylation).

  • RNA processing encompasses:

    • Cutting RNA into smaller segments

    • RNA editing (rearranging RNA sequences)

    • Removal of terminal phosphates and other variations

DNA & RNA Synthesis: Comparison

  • Both require polymerases and utilize templates.

  • Nucleotides for RNA synthesis include ribonucleotides: ATP, CTP, GTP, and UTP.

  • The template can be a double-stranded DNA, but only one strand is utilized.

  • RNA synthesis can start from scratch (de novo); it does not require a primer.

  • The enzyme for RNA synthesis is RNA polymerase.

  • Transcript can involve one origin with multiple promoters.

Bacterial RNA Polymerase

  • In bacteria, there exists one RNA polymerase responsible for synthesizing mRNA, tRNA, and rRNA, but not primers.

  • In E. coli, the holoenzyme is structured as α2ββ'ω while the core enzyme is α2ββ'ω without the sigma factor.

  • The σ factor is crucial for initiation and subsequently cycles off.

  • Notes on prokaryotic vs. archaeal RNA polymerase:

    • Various differences and the archaea core RNA polymerase is more akin to eukaryotic RNA Pol II

Template Strand vs. Coding Strand

  • Conventions indicate that gene sequences are generally expressed as sequences from the coding (non-template) strand.

Steps in Transcription

  1. Initiation: Holoenzyme recognizes a promoter region and binds to it, initiating the transcription process.

  2. Elongation: RNA polymerase synthesizes RNA while adding one nucleotide at a time; a transcription bubble opens as DNA and RNA hybrids form (8-9 base pairs long).

  3. Termination: RNA polymerase releases the DNA template and RNA transcript upon reaching a terminator.

Promoter Recognition and Isomerization

  • The specific sequence where RNA polymerase binds is significant for transcription initiation.

  • Sigma factor enables the recognition of promoter sequences like the Pribnow box.

  • Details on promoter regions (upstream/downstream) are critical for understanding regulatory mechanisms in transcription.

Transcription Termination Signals

  • Two types of termination for transcription:

    • Factor-dependent: Involves the Rho protein, which binds to the RNA and facilitates release of RNA polymerase and transcript.

    • Factor-independent: Utilizes structural formations such as hairpins in RNA to stall and effectively terminate transcription.

RNA Processing

  • The primary transcript refers to the newly synthesized RNA which must undergo processing.

  • Enzymatic cleavage occurs to produce smaller RNA components like rRNA and tRNA.

  • There is a noteworthy distinction between functionally processed RNA (mature RNA) and primary transcripts.

Structure of Mature tRNA

  • Components include:

    • Acceptor arm

    • Anticodon

    • Variable loop and other defining segments.

RNA Degradation

  • The stability and longevity of different RNA types vary significantly; for example, tRNA and rRNA are generally more stable than mRNA, which typically has a half-life of only 1-3 minutes.

  • Enzymes (RNases) play essential roles in the degradation and processing of RNA.