Transcription and the Genetic Code

Transcription and the Genetic Code: Gene Expression

Understanding Gene Expression

• Definition: Gene expression is the process by which information in DNA is converted into RNA (transcription) and then used to assemble a specific protein (translation).

• Unit of Information: A gene is the fundamental unit of information within DNA.

• Central Dogma: Cells are governed by a cellular chain of command, known as the central dogma: DNA \rightarrow RNA \rightarrow protein.

• Genotype-Phenotype Link: Proteins serve as the crucial link between an organism's genotype (genetic makeup) and its phenotype (observable traits). Specific DNA sequences dictate protein synthesis, which in turn leads to specific traits.

Transcription: DNA to RNA

• Definition: Transcription is the synthesis of RNA under the direction of a DNA template. It produces messenger RNA (mRNA), which acts as the blueprint for a protein.

• Key Enzyme: RNA synthesis is catalyzed by RNA polymerase. This enzyme unwinds the DNA double helix by prying the strands apart and then links together RNA nucleotides complementary to the DNA template strand.

• Base-Pairing Rules: RNA synthesis follows the same base-pairing rules as DNA replication, with one key difference: uracil (U) substitutes for thymine (T).

  • Adenine (A) in DNA pairs with Uracil (U) in RNA.

  • Thymine (T) in DNA pairs with Adenine (A) in RNA.

  • Guanine (G) in DNA pairs with Cytosine (C) in RNA.

  • Cytosine (C) in DNA pairs with Guanine (G) in RNA.

Stages of Transcription

The process of transcription in both prokaryotes and eukaryotes involves three main stages: initiation, elongation, and termination.

1. Initiation

• Promoters: These are specific DNA sequences that signal the start of RNA synthesis and indicate where RNA polymerase should bind.

• Prokaryotic Initiation: In prokaryotes (e.g., bacteria), RNA polymerase is directly attracted to and binds to specific sequences within the promoter region, commonly including a sequence like TATAAT.

• Eukaryotic Initiation: In eukaryotes, the process is more complex:

  • Transcription Factors: DNA-binding proteins called transcription factors first bind to the promoter region.

  • Initiation Complex Formation: These transcription factors recruit RNA Polymerase II to the promoter.

  • Transcription Initiation Complex: The complete assembly of transcription factors and RNA polymerase II bound to a promoter is referred to as the transcription initiation complex.

  • TATA Box: A specific promoter DNA sequence called the TATA box is crucial in forming this initiation complex in eukaryotes.

2. Elongation

• Process: As RNA polymerase moves along the DNA template strand, it untwists the DNA double helix, exposing approximately 10 to 20 bases at a time for RNA synthesis.

• Directionality: RNA is synthesized in the 5' \text{ to } 3' direction.

• Rate: Transcription progresses at an approximate rate of 40 nucleotides per second in eukaryotes.

• Simultaneous Transcription: A single gene can be transcribed simultaneously by multiple RNA polymerase molecules, allowing for efficient production of many RNA copies.

3. Termination

• Mechanism Varies: The specific mechanisms of termination differ between bacteria and eukaryotes.

• Stem-Loop Structure: A common termination mechanism, particularly in bacteria, involves the formation of a stem-loop (hairpin) structure in the newly transcribed RNA. This structure forms due to complementary base pairing within the RNA molecule itself.

• Enzyme Release: The formation of the stem-loop structure physically nudges the backside of the RNA polymerase, leading to its dissociation from the DNA template and the release of the newly synthesized RNA transcript.

• DNA Characteristics: The template DNA region downstream of the stem-loop forming sequences is often rich in Adenine (A) and Thymine (T) bases.

Translation: RNA to Protein

• Definition: Translation is the synthesis of a polypeptide (protein) using the information encoded in mRNA.

• Location: Ribosomes are the cellular organelles responsible for the process of translation.

Prokaryotic vs. Eukaryotic Gene Expression Differences

• Prokaryotes: In prokaryotic cells, mRNA produced by transcription is immediately translated into protein without further processing. Since there is no nuclear envelope, transcription and translation can occur almost simultaneously in the cytoplasm.

• Eukaryotes: In eukaryotic cells, the nuclear envelope spatially separates transcription (which occurs in the nucleus) from translation (which occurs in the cytoplasm). Eukaryotic RNA transcripts undergo significant modification, known as RNA processing, before they are transported out of the nucleus to yield finished, mature mRNA.

Replication vs. Transcription Comparison

Eukaryotic RNA Processing (Post-Transcriptional Modification)

• Purpose: After transcription, primary RNA transcripts (pre-mRNA) in eukaryotes are modified by enzymes in the nucleus to prepare them for translation.

• Stages of Processing: During RNA processing, both ends of the primary transcript are altered, and internal segments of the molecule are typically removed and the remaining parts spliced together.

1. Alteration of mRNA Ends

• 5' Cap Addition: The 5' end of the pre-mRNA molecule receives a modified guanine nucleotide, known as the 5' cap.

• Poly-A Tail Addition: The 3' end receives a stretch of 50 \text{ to } 250 adenine nucleotides, called a poly-A tail.

• Functions of Modifications:

  • Export: They facilitate the export of the mature mRNA molecule from the nucleus to the cytoplasm.

  • Protection: They protect the mRNA from degradation by hydrolytic enzymes in the cytoplasm.

  • Ribosome Attachment: They help ribosomes recognize and attach to the 5' end of the mRNA during translation initiation.

2. RNA Splicing

• Introns: Most eukaryotic genes contain long noncoding stretches of nucleotides, called intervening sequences or introns, that lie between coding regions.

• Exons: The coding regions are called exons because they are eventually expressed, typically by being translated into amino acid sequences.

• Process: RNA splicing is the process that removes introns from the pre-mRNA and joins the exons together, creating an mRNA molecule with a continuous coding sequence ready for translation.

The Genetic Code

• Triplet Code (Codons): The flow of information from a gene to a protein is based on a triplet code. This means that a series of nonoverlapping, three-nucleotide words (codons) specify the amino acids.

  • Each codon (e.g., AGT on DNA, UCA on mRNA) specifies an amino acid to be placed at a corresponding position in the polypeptide chain.

  • A triplet code is the smallest unit of uniform length that can code for all 20 known amino acids (4^1=4, 4^2=16, 4^3=64 possible triplets).

• Template Strand and Codons:

  • Template Strand: During transcription, one of the two DNA strands, known as the template strand, provides the template for ordering the sequence of nucleotides in the RNA transcript.

  • Codons: During translation, the mRNA base triplets, or codons, are read by the translation machinery in the 5' \text{ to } 3' direction.

  • Each codon specifies which of the 20 amino acids is to be added to the growing polypeptide chain.

• Properties of the Genetic Code:

  • Deciphered: All 64 possible codons were deciphered by the mid-1960s.

  • Coding for Amino Acids: Out of the 64 triplets, 61 codons code for specific amino acids.

  • Stop Signals: The remaining 3 codons act as