# 13.4 GENE EXPRESSION Gene expression is the process by which the genetic information stored in DNA is used to direct the synthesis of a functional gene product, typically a protein. This process acts as the link between an organism's genetic makeup (*genotype*) and its observable characteristics (*phenotype*). The core principle governing this flow of information is the **central dogma of molecular genetics**: DNA is transcribed into RNA, which is then translated into protein. ### Transcription: DNA to RNA Transcription is the synthesis of an RNA molecule from a DNA template. This is the first step of gene expression and occurs in the G₀, G₁, and G₂ phases of the cell cycle. The primary enzyme involved is **RNA polymerase**. #### 1. Initiation Phase This is the beginning of transcription, where RNA polymerase binds to the DNA. - **Promoter Region:** A specific DNA sequence where RNA polymerase attaches. The location of these sequences is described relative to the transcription start site. | Organism | Promoter Sequences | Location (approx. nucleotides before start site) | | :--- | :--- | :--- | | **Prokaryotes** | TATAAT ("-10 sequence")
TTGACA ("-35 sequence") | -10
-35 | | **Eukaryotes** | TATA box
CAAT box
GC-rich box | -25
-80
-90 | - **RNA Polymerase:** - In prokaryotes, it consists of a **core enzyme** (two α, two β subunits) and a **sigma (σ) factor**. Together they form the **holoenzyme**, which recognizes the promoter. The sigma factor detaches after initiation. - Unlike DNA polymerase, RNA polymerase *does not require a primer*. - **Types of RNA Polymerase:** | Organism | Types | Function | | :--- | :--- | :--- | | **Prokaryotes** | One type | Synthesizes all RNA types | | **Eukaryotes** | Three types | **RNA Pol I:** Synthesizes rRNA
**RNA Pol II:** Synthesizes mRNA
**RNA Pol III:** Synthesizes tRNA | - **Transcription Bubble:** Once bound, RNA polymerase unwinds the DNA duplex, creating a "bubble" where the template strand is exposed. #### 2. Elongation Phase The RNA strand is synthesized. - RNA polymerase moves along the DNA, adding ribonucleotides (rNTPs) complementary to the **template strand** (also called the *antisense strand*). - The newly synthesized RNA is created in the **5' to 3' direction**. - The other DNA strand is known as the **coding strand** or *sense strand* because its sequence is similar to the mRNA transcript (with T instead of U). #### 3. Termination Phase This is the end of transcription. - Synthesis stops when RNA polymerase reaches a **terminator region** on the DNA. - This region consists of GC-rich sequences followed by AT-rich sequences. - The transcribed RNA forms a stable **GC hairpin loop**, which causes the RNA polymerase to pause and detach from the DNA template, releasing the new RNA molecule. ### Post-Transcriptional Modification (Eukaryotes) In eukaryotic cells, the initial RNA transcript (*pre-mRNA*) must be processed before it can be translated. This occurs in the nucleus. 1. **5' Capping:** A modified guanine nucleotide (7-methyl GTP) is added to the 5' end of the pre-mRNA. This protects the mRNA from degradation and helps it bind to the ribosome. 2. **3' Polyadenylation (Tailing):** A **poly-A tail** (a chain of 30-500 adenine nucleotides) is added to the 3' end. This also protects the mRNA and aids in its export from the nucleus. 3. **RNA Splicing:** - Eukaryotic genes contain non-coding regions (*introns*) interspersed with coding regions (*exons*). - **Spliceosomes** (large RNA-protein complexes) remove the introns. - **RNA ligase** joins the remaining exons together to form the mature, functional mRNA. ### The Genetic Code The set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins. - **Codon:** A sequence of three nucleotides on an mRNA molecule that specifies a particular amino acid or signals termination. There are 4³ = 64 possible codons. - **Start Codon:** **AUG**, which codes for Methionine and initiates translation. - **Stop Codons:** **UAA, UAG, UGA**. They signal the end of translation and do not code for an amino acid (*nonsense codons*). - **Sense Codons:** The other 61 codons that specify amino acids. - **Characteristics of the Genetic Code:** - ***Degeneracy:*** Most amino acids are coded for by more than one codon. - ***Universality:*** The code is nearly the same in all organisms, from bacteria to humans (with minor exceptions, e.g., in mitochondria). - ***Non-punctuated:*** The code is read continuously, with no gaps or spaces between codons. - ***Non-overlapping:*** Each nucleotide is part of only one codon. The sequence is read in successive, distinct triplets. ### Translation: RNA to Protein Translation is the process where a ribosome decodes an mRNA message to produce a specific polypeptide chain (protein). #### 1. Activation of Amino Acids - An amino acid is attached to its corresponding tRNA molecule by the enzyme **aminoacyl-tRNA synthase**. - This forms an **aminoacyl-tRNA complex** and requires energy (ATP). #### 2. Formation of Initiation Complex - The small ribosomal subunit binds to the 5' end of the mRNA. - The initiator tRNA (carrying methionine in eukaryotes, N-formyl methionine in prokaryotes) binds to the start codon (AUG) at the **P site** (peptidyl site) of the ribosome. - The large ribosomal subunit then joins to form the complete initiation complex. The ribosome has three key sites: - **A site (Aminoacyl):** Where the next aminoacyl-tRNA binds. - **P site (Peptidyl):** Holds the tRNA with the growing polypeptide chain. - **E site (Exit):** Where the uncharged tRNA leaves the ribosome. #### 3. Polypeptide Elongation A repeating cycle builds the polypeptide chain: 1. **Codon Recognition:** An incoming aminoacyl-tRNA with the complementary anticodon binds to the mRNA codon at the A site. 2. **Peptide Bond Formation:** The enzyme **peptidyl transferase** catalyzes the formation of a peptide bond between the new amino acid at the A site and the growing polypeptide chain at the P site. The chain is transferred to the tRNA at the A site. 3. **Translocation:** The ribosome moves one codon down the mRNA (in the 5'→3' direction). The tRNA from the P site moves to the E site and exits; the tRNA from the A site (now holding the polypeptide) moves to the P site. The A site is now free for the next tRNA. #### 4. Termination - Elongation ends when a stop codon (UAA, UAG, UGA) enters the A site. - A **release factor** (a protein) binds to the stop codon instead of a tRNA. - This triggers the release of the polypeptide from the tRNA, and the entire complex (ribosomal subunits, mRNA, tRNA) disassembles. ### Comparison of Translation in Prokaryotes vs. Eukaryotes | Feature | PROKARYOTES | EUKARYOTES | | :--- | :--- | :--- | | **Ribosome Size** | **70S** (50S + 30S subunits) | **80S** (60S + 40S subunits) | | **Location** | Cytosol | Cytosol and Rough Endoplasmic Reticulum (RER) | | **Initiating Amino Acid**| N-formyl methionine (modified) | Methionine (not modified) | | **Initiation Factors** | One type | More than one type | | **Release Factors** | Two types | One type | ### Biological Significance Gene expression is the fundamental process that allows a cell to respond to its environment, differentiate into specialized cell types, and carry out all life functions. It is the molecular basis of heredity and connects an organism's genotype to its phenotype. For more on how cells utilize these proteins, see and .