Gene Expression: Transcription, RNA Processing, and Translation

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Gene Expression: From Gene to Protein

Overview of the Central Dogma

The central dogma of molecular biology describes the flow of genetic information within a biological system. It states that genetic information is transcribed from DNA to RNA and then translated from RNA to protein. This process involves several key steps: transcription, RNA processing (in eukaryotes), and translation.

Transcription: Synthesis of RNA from DNA

Mechanism of Transcription

Transcription is the process by which RNA is synthesized from a DNA template. RNA polymerase reads the DNA template strand and synthesizes a complementary RNA strand in the 5' to 3' direction. Only one DNA strand (the template strand) is used for RNA synthesis, while the other (the coding strand) matches the RNA sequence except for uracil (U) replacing thymine (T).

Template strand: The DNA strand used by RNA polymerase to synthesize RNA.
Coding (non-template) strand: The DNA strand with the same sequence as the RNA (except T is replaced by U).
RNA polymerase: The enzyme that catalyzes RNA synthesis, does not require a primer.
Directionality: RNA is synthesized 5' to 3', reading the template 3' to 5'.

Diagram of transcription showing template and coding strands, RNA synthesis, and NTP addition

Structure of RNA Polymerase

RNA polymerase is a large, multi-subunit enzyme that binds to DNA and catalyzes the formation of phosphodiester bonds between ribonucleotides, forming the RNA strand.

Molecular structure of RNA polymerase bound to DNA

Stages of Transcription

Transcription occurs in three main stages: initiation, elongation, and termination.

Initiation: RNA polymerase binds to the promoter region of DNA, unwinds the DNA, and begins RNA synthesis.
Elongation: RNA polymerase moves along the DNA, adding ribonucleotides to the growing RNA strand.
Termination: RNA polymerase encounters a termination signal, releasing the RNA transcript.

Diagram showing initiation, elongation, and termination of transcription

Transcription in Eukaryotes

In eukaryotes, transcription is more complex and involves multiple RNA polymerases and a variety of promoter sequences, such as the TATA box. General transcription factors help RNA polymerase recognize and bind to promoters, forming the transcription initiation complex.

Eukaryotic transcription initiation with TATA box and transcription factors

Transcription Elongation and Termination

During elongation, RNA polymerase synthesizes RNA by adding nucleotides complementary to the DNA template. In eukaryotes, transcription continues until a polyadenylation signal (AAUAAA) is transcribed, after which the RNA transcript is cleaved and released as pre-mRNA.

RNA polymerase synthesizing RNA from DNA template

RNA Processing in Eukaryotes

Splicing: Removal of Introns

In eukaryotes, the initial RNA transcript (pre-mRNA) contains both exons (coding regions) and introns (non-coding regions). Introns are removed by RNA splicing, which is catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs) and other proteins. Splicing allows for the production of multiple proteins from a single gene through alternative splicing.

Exons: Sequences that remain in the mature mRNA.
Introns: Sequences removed during RNA processing.
Spliceosome: The complex responsible for splicing.

Diagram showing removal of introns and joining of exons during RNA splicing

5' Capping and 3' Polyadenylation

Pre-mRNAs are further processed by the addition of a 5' cap (a modified guanine nucleotide) and a 3' poly(A) tail (a stretch of adenine nucleotides). These modifications protect mRNA from degradation, aid in export from the nucleus, and are important for translation initiation.

5' cap: Facilitates ribosome binding and protects mRNA.
Poly(A) tail: Enhances stability and translation efficiency.
Untranslated regions (UTRs): Non-coding regions at both ends of mature mRNA.

Diagram of mature mRNA with 5' cap, coding region, and poly(A) tail

Translation: Synthesis of Proteins from mRNA

Overview of Translation

Translation is the process by which the sequence of bases in mRNA is converted into an amino acid sequence, forming a polypeptide. This process requires ribosomes, mRNA, and transfer RNAs (tRNAs).

Coupling of Transcription and Translation in Prokaryotes

In bacteria, translation can begin before transcription is complete, as both processes occur in the cytoplasm. Multiple ribosomes can simultaneously translate a single mRNA, forming a polyribosome (polysome).

Diagram of coupled transcription and translation in bacteria with polyribosomes

Structure and Function of tRNA

tRNAs are adapter molecules that match specific amino acids to codons in the mRNA. Each tRNA has an anticodon that base-pairs with a codon in mRNA and an amino acid attachment site. Aminoacyl-tRNA synthetases charge tRNAs with their corresponding amino acids using ATP.

Aminoacyl-tRNA: A tRNA linked to its amino acid.
Aminoacyl-tRNA synthetase: Enzyme that attaches the correct amino acid to its tRNA.

Base pairing within an aminoacyl tRNA Two- and three-dimensional structures of tRNA Charging of tRNA by aminoacyl-tRNA synthetase using ATP

Ribosome Structure and Function

Ribosomes are large complexes of rRNA and proteins, composed of a small and a large subunit. They facilitate the binding of tRNAs to mRNA and catalyze peptide bond formation. Ribosomes have three binding sites for tRNA: the A (aminoacyl), P (peptidyl), and E (exit) sites.

A site: Holds the tRNA carrying the next amino acid.
P site: Holds the tRNA with the growing polypeptide chain.
E site: Site from which tRNAs exit the ribosome.

Diagram of ribosome with A, P, and E sites Ribosome structure showing subunits and tRNA binding sites

Phases of Translation

Translation occurs in three phases: initiation, elongation, and termination.

Initiation: The small ribosomal subunit binds to mRNA, and the initiator tRNA binds to the start codon. The large subunit then assembles, forming the complete initiation complex.

Initiation of translation in bacteria

Elongation: Amino acids are added one by one to the growing polypeptide chain. Each cycle involves entry of an aminoacyl-tRNA into the A site, peptide bond formation, and translocation of the ribosome.

Elongation phase of translation

Termination: When a stop codon is encountered, a release factor binds, causing the polypeptide to be released and the ribosome to dissociate.

Termination of translation and release of polypeptide

Post-Translational Modification

After translation, most proteins undergo post-translational modifications, such as folding, cleavage, or addition of chemical groups, to become fully functional. These modifications occur in various cellular locations and are essential for proper protein function.

Summary Table: Key Steps in Eukaryotic Gene Expression

Step	Location	Main Events
Transcription	Nucleus	RNA polymerase synthesizes pre-mRNA from DNA template
RNA Processing	Nucleus	Splicing, 5' capping, 3' polyadenylation to produce mature mRNA
Translation	Cytoplasm	Ribosomes synthesize polypeptide from mRNA template
Post-Translational Modification	Various	Folding, cleavage, chemical modification of polypeptide

Key Terms and Concepts

Central Dogma: DNA → RNA → Protein
Transcription: Synthesis of RNA from DNA
RNA Processing: Modifications to pre-mRNA in eukaryotes
Translation: Synthesis of protein from mRNA
tRNA: Adapter molecule in translation
Ribosome: Molecular machine for protein synthesis
Polyribosome: Multiple ribosomes translating a single mRNA
Post-Translational Modification: Chemical changes to proteins after synthesis