Gene Expression: From Gene to Protein

Overview of Gene Expression

Gene expression is the process by which information encoded in a gene is used to direct the synthesis of a protein. This process involves two main stages: transcription (the synthesis of RNA from DNA) and translation (the synthesis of protein from RNA). The flow of genetic information follows the central dogma of molecular biology: DNA → RNA → Protein.

• Transcription: The process of copying a gene's DNA sequence to make an RNA molecule.

• Translation: The process where the RNA sequence is used to build a protein.

• Central Dogma: Information flows from DNA to RNA to protein and not in reverse from protein to nucleic acid.

Genes Specify Proteins via Transcription & Translation

RNA: The Bridge Between DNA and Protein Synthesis

RNA acts as the intermediary between DNA and protein synthesis. It is chemically similar to DNA but has several key differences:

• RNA contains the sugar ribose instead of deoxyribose.

• RNA uses the base uracil (U) instead of thymine (T).

• RNA is usually single-stranded.

Prokaryotic vs. Eukaryotic Gene Expression

Gene expression differs between prokaryotes and eukaryotes, primarily due to the presence of a nucleus in eukaryotes.

• Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm.

• Eukaryotes: Transcription occurs in the nucleus, and the resulting RNA is processed before being exported to the cytoplasm for translation.

Transcription: DNA to RNA

Initiation of Transcription

Transcription begins at specific DNA sequences called promoters, where RNA polymerase binds and starts RNA synthesis. In eukaryotes, transcription factors are required for RNA polymerase to bind to the promoter.

• Promoter: DNA sequence where transcription starts.

• RNA Polymerase: Enzyme that synthesizes RNA from the DNA template.

• Terminator: DNA sequence signaling the end of transcription.

Elongation of Transcription

During elongation, RNA polymerase moves along the DNA, unwinding the double helix and synthesizing RNA in the 5’ to 3’ direction. The RNA sequence is complementary to the DNA template strand and nearly identical to the coding strand (except U replaces T).

• RNA is synthesized from 5’ to 3’.

• Multiple RNA polymerases can transcribe a gene simultaneously.

Termination of Transcription

Transcription ends when RNA polymerase reaches the terminator sequence. In prokaryotes, this results in the release of the RNA transcript. In eukaryotes, the transcript (pre-mRNA) requires further processing.

• Prokaryotes: RNA is ready for translation immediately after transcription.

• Eukaryotes: Pre-mRNA undergoes processing before translation.

RNA Processing in Eukaryotes

RNA Processing and Splicing

In eukaryotes, pre-mRNA undergoes several modifications before becoming mature mRNA:

• 5’ Cap: Addition of a modified guanine nucleotide to the 5’ end.

• Poly-A Tail: Addition of a string of adenine nucleotides to the 3’ end.

• RNA Splicing: Removal of noncoding regions (introns) and joining of coding regions (exons).

These modifications help export mRNA from the nucleus, protect it from degradation, and assist in ribosome binding during translation.

RNA Splicing

Splicing removes introns and joins exons to produce mature mRNA. The spliceosome is a complex responsible for this process. Alternative splicing allows a single gene to code for multiple proteins.

• Introns: Noncoding sequences removed from pre-mRNA.

• Exons: Coding sequences expressed in the final mRNA.

• Alternative Splicing: Different combinations of exons can be joined to produce different proteins from one gene.

Types of RNA

Major Types of RNA and Their Functions

• Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes for protein synthesis.

• Ribosomal RNA (rRNA): Forms the core of ribosome structure and catalyzes protein synthesis.

• Transfer RNA (tRNA): Brings amino acids to the ribosome and matches them to the coded mRNA message using anticodons.

The Genetic Code

Properties of the Genetic Code

The genetic code is a set of rules by which the sequence of nucleotides in mRNA is translated into the sequence of amino acids in a protein.

• Codon: A sequence of three mRNA nucleotides that codes for a specific amino acid.

• Redundant: More than one codon can specify the same amino acid.

• Not ambiguous: Each codon specifies only one amino acid.

Translation: RNA to Protein

Overview of Translation

Translation is the process by which ribosomes synthesize proteins using the sequence of codons in mRNA. tRNA molecules bring amino acids to the ribosome, where they are joined together to form a polypeptide chain.

• Ribosome: Molecular machine composed of rRNA and proteins; has large and small subunits.

• tRNA: Each tRNA has an anticodon that pairs with a codon on the mRNA and carries a specific amino acid.

Ribosome Structure and Function

Ribosomes have three binding sites for tRNA:

• A site (Aminoacyl-tRNA site): Holds the tRNA carrying the next amino acid.

• P site (Peptidyl-tRNA site): Holds the tRNA with the growing polypeptide chain.

• E site (Exit site): Where discharged tRNAs leave the ribosome.

Steps of Translation

• Initiation: The small ribosomal subunit binds to mRNA and the initiator tRNA. The large subunit then binds, forming the complete initiation complex. The start codon (AUG) signals the beginning of translation.

• Elongation: Amino acids are added one by one to the growing polypeptide chain. The ribosome moves along the mRNA, reading codons and matching them with tRNA anticodons.

• Termination: When a stop codon is reached, release factors bind to the ribosome, causing the release of the polypeptide and disassembly of the translation complex.

Mutations and Their Effects on Proteins

Types of Mutations

Mutations are permanent changes in the DNA sequence. They can affect gene expression and protein function in various ways:

• Point Mutations: Change in a single nucleotide pair. Can be silent (no effect), missense (change one amino acid), or nonsense (introduce a stop codon).

• Insertions and Deletions: Addition or loss of nucleotide pairs, which can cause frameshift mutations, altering the reading frame and usually resulting in nonfunctional proteins.

Mutations can be spontaneous or induced by environmental factors (mutagens) and are a source of genetic diversity.

Summary Table: Key Differences in Gene Expression