Gene Expression: From Gene to Protein (Transcription and Translation)

Gene Expression: From Gene to Protein

Transcription and Translation: Definitions and Overview

Gene expression is the process by which information encoded in DNA is used to direct the synthesis of proteins. This process occurs in two main stages: transcription and translation.

• Transcription: The synthesis of RNA from a DNA template. The enzyme RNA polymerase catalyzes this process, producing a complementary RNA strand (mRNA) from the DNA template strand.

• Translation: The synthesis of a polypeptide (protein) from an mRNA template. This process occurs at the ribosome and involves tRNAs and ribosomal RNA (rRNA).

• Reactants and Products:

  • Transcription: Reactants – DNA template, RNA nucleotides; Product – mRNA

  • Translation: Reactants – mRNA, amino acids, tRNAs, ribosome; Product – polypeptide

Flow of Genetic Information: DNA → RNA → Protein

The central dogma of molecular biology describes the directional flow of genetic information:

• DNA (gene) is transcribed into mRNA.

• mRNA is translated into a protein.

• The template strand of DNA is read by RNA polymerase to synthesize a complementary mRNA strand. The non-template (coding) strand has the same sequence as the mRNA (except T is replaced by U).

• The sequence of codons in mRNA determines the sequence of amino acids in the protein.

Directionality of Transcription and Translation

• Transcription: RNA polymerase reads the DNA template strand in the 3' → 5' direction and synthesizes mRNA in the 5' → 3' direction.

• Translation: Ribosomes read the mRNA in the 5' → 3' direction, synthesizing the polypeptide from the amino (N) terminus to the carboxyl (C) terminus.

Using the Codon Table

• Each group of three nucleotides (codon) in mRNA specifies one amino acid.

• The start codon (AUG) signals the beginning of translation and codes for methionine.

• Translation proceeds in the 5' → 3' direction along the mRNA.

• To translate an mRNA sequence:

  1. Identify the start codon (AUG).

  2. Read codons in sets of three nucleotides.

  3. Use the codon table to determine the corresponding amino acids.

Predicting mRNA and Polypeptide Sequences

• Given a DNA template strand, transcribe the complementary mRNA (replace A with U, T with A, C with G, G with C).

• Given a non-template (coding) strand, the mRNA sequence is the same except T is replaced by U.

• Translate the mRNA sequence into a polypeptide using the codon table, starting at the start codon.

Gene Expression in Bacteria vs. Eukaryotes

Feature	Bacteria	Eukaryotes
Location of Transcription	Cytoplasm	Nucleus
Location of Translation	Cytoplasm	Cytoplasm
mRNA Processing	None	5' cap, 3' poly-A tail, splicing
Coupling of Transcription & Translation	Yes	No

Mutations and Their Effects

• Mutation: A change in the DNA sequence that can affect gene function.

• Mutations can alter the genotype and potentially the phenotype.

• Types of mutations:

  • Silent: No change in amino acid sequence.

  • Missense: Changes one amino acid.

  • Nonsense: Introduces a stop codon, truncating the protein.

  • Frameshift: Insertion or deletion shifts the reading frame.

• Many mutations have no effect on phenotype due to redundancy in the genetic code or because they occur in non-coding regions.

Major Events in Transcription

• Initiation: RNA polymerase binds to the promoter region of DNA, unwinds the DNA, and begins RNA synthesis.

• Elongation: RNA polymerase moves along the DNA, synthesizing RNA in the 5' → 3' direction.

• Termination: RNA polymerase reaches a terminator sequence and releases the newly made RNA transcript.

• All steps are directed by the DNA sequence.

RNA Processing in Eukaryotes

• 5' Capping: Addition of a modified guanine nucleotide to the 5' end for stability and ribosome recognition.

• 3' Polyadenylation: Addition of a poly-A tail to the 3' end for stability and export from the nucleus.

• Splicing: Removal of non-coding introns and joining of exons by the spliceosome.

• If these processes fail, mRNA may be unstable, not exported, or not translated correctly.

Alternative Splicing

• Allows a single gene to produce multiple protein variants by including or excluding different exons during splicing.

• Increases protein diversity without increasing the number of genes.

tRNAs and Ribosomes: Structure and Function

• tRNA: Small RNA molecules that carry specific amino acids to the ribosome. Each has an anticodon that pairs with a codon on mRNA.

• Ribosome: A complex of rRNA and proteins that facilitates the coupling of tRNA anticodons with mRNA codons during protein synthesis.

Major Events in Translation

• Initiation: The small ribosomal subunit binds to mRNA and the initiator tRNA (carrying methionine) binds to the start codon. The large subunit then joins.

• Elongation: tRNAs bring amino acids to the ribosome, where peptide bonds are formed between amino acids, extending the polypeptide chain.

• Termination: When a stop codon is reached, release factors promote the release of the completed polypeptide and disassembly of the ribosome.

tRNA Movement and Amino Acid Addition

• tRNAs move through the ribosome's three sites: A (aminoacyl), P (peptidyl), and E (exit).

• At the A site, a new tRNA enters; at the P site, the growing polypeptide is held; at the E site, tRNAs exit the ribosome.

• Amino acids are added to the C-terminus of the growing polypeptide.

Codons, Anticodons, and Directionality

• Codons are read in the 5' → 3' direction on mRNA.

• Anticodons on tRNA are complementary and antiparallel to mRNA codons (written 3' → 5').

• To predict the anticodon for a codon, write the complementary bases in the opposite direction.

Post-Translational Modifications

• The initial polypeptide may require folding, cleavage, or chemical modifications (e.g., phosphorylation, glycosylation) to become functional.

• Some proteins are targeted to specific cellular locations after translation.

Visualizing Directionality in Transcription and Translation

• DNA is read 3' → 5' during transcription; mRNA is synthesized 5' → 3'.

• During translation, the ribosome moves along mRNA 5' → 3', synthesizing the polypeptide from N-terminus to C-terminus.

• Recently initiated transcripts or polypeptides are shorter than those that have been elongating longer.

Additional info: For diagrams, always label the 5' and 3' ends of nucleic acids and the N- and C-termini of proteins. Directionality is crucial for understanding the flow of genetic information.