CH 17 p. 1: Transcription, RNA Processing, and Translation: Mechanisms and Comparisons

Transcription, RNA Processing, and Translation

Overview: Information Flow in Cells

This chapter explores how genetic information is transcribed from DNA to RNA and subsequently translated into proteins. The central dogma of molecular biology describes this flow: DNA → RNA → Protein. The process involves transcription, RNA processing (in eukaryotes), and translation.

Transcription: DNA to RNA (Section 17.1)

Central Dogma and DNA Strands

Transcription is the process by which an RNA copy of DNA information is made. The template strand of DNA is transcribed, while the non-template (coding) strand is not. The coding strand has the same sequence as the RNA (except T is replaced by U).

RNA Polymerase Function

RNA polymerase catalyzes the synthesis of RNA by adding nucleoside triphosphates (NTPs) to the 3' end of the growing RNA chain. In bacteria, there is one type of RNA polymerase; in eukaryotes, there are at least three, each producing different kinds of RNA.

Transcription Initiation in Bacteria

Transcription begins when RNA polymerase is activated by binding to a sigma protein, forming a holoenzyme. Sigma proteins recognize and bind to the promoter region upstream of the gene, which acts as a regulatory sequence.

Promoter Structure and Regulation

Promoters contain conserved sequences, notably the -10 box and -35 box, which are recognized by sigma proteins. Different sigma proteins recognize different promoters, allowing regulation of gene expression in response to environmental changes.

Initiation Phase: Template Strand Selection

The orientation and position of sigma protein binding to the promoter determine which DNA strand is used as the template. Sigma must bind both the -10 and -35 boxes for transcription to initiate.

Steps of Initiation

• Sigma binds promoter

• RNA polymerase unwinds and unzips DNA

• RNA polymerase adds NTPs complementary to the template strand

• Sigma protein is released

RNA Polymerase Structure and Channels

RNA polymerase contains multiple channels for the DNA template, incoming NTPs, and the exiting RNA transcript, facilitating efficient transcription.

Elongation and Termination Phases

During elongation, RNA polymerase continues to add NTPs. Termination occurs when a transcription-termination signal in the DNA is transcribed, causing the RNA to fold into a hairpin structure, which disrupts the interaction with RNA polymerase and releases the RNA.

Comparison: Bacterial vs. Eukaryotic Transcription

While the basic steps are similar, there are key differences:

• Location: Bacteria (cytoplasm), Eukaryotes (nucleus)

• RNA polymerases: Bacteria (one type), Eukaryotes (multiple types)

• Promoter diversity: Bacteria (-10 and -35 boxes), Eukaryotes (TATA box, more diversity)

• Proteins recognizing promoters: Bacteria (sigma), Eukaryotes (basal transcription factors)

• Termination: Bacteria (hairpin), Eukaryotes (poly(A) signal)

• Product: Bacteria (mature mRNA), Eukaryotes (pre-mRNA, requires processing)

RNA Processing in Eukaryotes (Section 17.2)

Genes-in-Pieces Hypothesis

Eukaryotic genes are not continuous; they consist of exons (coding regions) and introns (non-coding regions). Introns are removed from the primary transcript, and exons are joined to form mature mRNA.

RNA Splicing Mechanism

Splicing is catalyzed by small nuclear ribonucleoproteins (snRNPs), which assemble into a spliceosome. The process involves binding snRNPs to exon-intron boundaries and a branch point, cutting the intron, forming a lariat, and joining exons.

• snRNPs bind to 5' and 3' exon-intron boundaries and branch point

• Spliceosome forms

• Intron is cut and forms a lariat

• Exons are joined together

Adding Caps and Tails to mRNA

The 5' cap (modified guanine triphosphate) is added early in transcription. The poly(A) tail is added to the 3' end after cleavage at the poly(A) signal. These modifications are not coded by the DNA template.

Mature mRNA Transcript

Mature mRNA has a continuous coding region (introns removed), untranslated regions (UTRs) at both ends, a 5' cap, and a 3' poly(A) tail. UTRs stabilize mRNA and regulate translation; the cap and tail aid ribosome binding and protect against degradation.

Translation: RNA to Protein (Section 17.3)

Ribosomes and Protein Synthesis

Translation occurs at the ribosome, where mRNA is decoded into a specific amino acid sequence. In bacteria, translation can begin before transcription ends, as both processes occur in the cytoplasm.

Polyribosomes

Multiple ribosomes can translate a single mRNA simultaneously, forming polyribosomes and increasing protein synthesis efficiency.

Translation: Bacteria vs. Eukaryotes

Both share most steps and molecules, but in eukaryotes, mRNA must be exported from the nucleus before translation, and initiation is more complex.

How mRNA Specifies Amino Acids

Translation is the process of converting the nucleotide sequence of mRNA into the amino acid sequence of a protein. Two hypotheses explain how mRNA codons specify amino acids:

• Direct interaction: Amino acids interact directly with mRNA codons.

• Adaptor molecule: An intermediary (such as tRNA) binds both amino acids and mRNA codons.

Summary Table: Transcription, RNA Processing, and Translation

Process	Bacteria	Eukaryotes
RNA polymerases	One	Three, each produces a different class of RNA
Promoter structure	Typically contains a -10 box and -35 box	More variable and larger; often includes a TATA box about -30 from the start site
Proteins that associate with promoters	Sigma; different versions of sigma bind to different promoters	Many general transcription factors
RNA processing	Rare	Extensive; several processing steps occur in the nucleus before RNA is exported
Translation (initiation, elongation, termination)	Initiation and termination less elaborate; elongation similar to eukaryotes	Initiation and termination more complex; elongation similar to bacteria