Chapter 17: Gene Expression – From Gene to Protein

Overview of Gene Expression

Gene expression is the process by which the information encoded in DNA is used to direct the synthesis of proteins, which ultimately determine an organism's traits. This chapter explores the molecular mechanisms underlying transcription and translation, the two main stages of gene expression.

• Genotype: The genetic makeup of an organism (DNA sequence).

• Phenotype: The observable traits of an organism, determined by protein function.

• Proteins are the links between genotype and phenotype.

• Gene expression includes two stages: transcription and translation.

• The one gene–one polypeptide hypothesis states that each gene codes for a single polypeptide.

• Example: A mutation in the gene for pigment synthesis can result in a dramatic change in appearance, such as the difference between brown and white fur in animals.

Transcription: DNA-Directed Synthesis of RNA

Basic Principles of Transcription

Transcription is the first stage of gene expression, where a segment of DNA is used as a template to synthesize messenger RNA (mRNA).

• RNA polymerase catalyzes RNA synthesis by joining RNA nucleotides complementary to the DNA template strand.

• RNA synthesis does not require a primer.

• Base-pairing rules: Adenine (A) pairs with Uracil (U) in RNA, and Cytosine (C) pairs with Guanine (G).

Stages of Transcription

• Initiation: RNA polymerase binds to the promoter region (often includes a TATA box in eukaryotes) with the help of transcription factors.

• Elongation: RNA polymerase unwinds the DNA and adds nucleotides to the growing RNA strand in the 5' to 3' direction.

• Termination: In bacteria, transcription ends at a terminator sequence; in eukaryotes, RNA polymerase II transcribes a polyadenylation signal, and the transcript is released.

RNA Processing in Eukaryotes

Modification of Pre-mRNA

Before mRNA can be translated, it undergoes several modifications in the nucleus.

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

• Poly-A Tail: Addition of 50–250 adenine nucleotides to the 3' end.

• These modifications facilitate mRNA export, protect it from degradation, and help ribosomes attach for translation.

RNA Splicing

• Introns: Noncoding regions that are removed from the pre-mRNA.

• Exons: Coding regions that are spliced together to form the mature mRNA.

• Spliceosomes: Complexes of proteins and small RNAs that catalyze splicing.

• Ribozymes: RNA molecules with catalytic activity, involved in splicing.

• Alternative RNA splicing: Allows a single gene to code for multiple polypeptides by varying which exons are included.

Translation: RNA-Directed Synthesis of Polypeptides

Molecular Components of Translation

Translation is the process by which the sequence of an mRNA molecule is used to build a polypeptide (protein).

• Transfer RNA (tRNA): Brings specific amino acids to the ribosome and matches them to the mRNA codon via its anticodon.

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

• Wobble: Flexible base pairing at the third position of the codon, allowing some tRNAs to bind to multiple codons.

Structure and Function of Ribosomes

• Ribosomes are made of ribosomal RNA (rRNA) and proteins.

• They have three binding sites for tRNA:

  • P site: Holds the tRNA carrying the growing polypeptide chain.

  • A site: Holds the tRNA carrying the next amino acid to be added.

  • E site: Exit site for discharged tRNAs.

Stages of Translation

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

• Elongation: Amino acids are added one by one to the growing chain through codon recognition, peptide bond formation, and translocation.

• Termination: Occurs when a stop codon is reached; a release factor binds, causing the polypeptide to be released.

Post-Translational Modifications and Protein Targeting

Protein Folding and Modifications

After translation, polypeptides fold into their functional three-dimensional shapes and may undergo further modifications.

• Folding: Spontaneous or assisted by chaperone proteins.

• Modifications: Glycosylation (addition of sugars), methylation (addition of methyl groups), and others.

Targeting Proteins to Specific Locations

• Free ribosomes: Synthesize proteins for use in the cytosol.

• Bound ribosomes: Synthesize proteins for the endomembrane system or secretion.

• Signal peptide: Directs the ribosome to the endoplasmic reticulum (ER) for further processing.

• Signal-recognition particle (SRP): Escorts the ribosome to the ER membrane.

Genetic Code and Codons

Triplet Code and Codons

The genetic code is based on codons, which are sequences of three nucleotides in mRNA that specify amino acids.

• There are 64 possible codons: 61 code for amino acids, 3 are stop signals.

• The code is redundant (more than one codon can specify the same amino acid) but not ambiguous (each codon specifies only one amino acid).

• Codons must be read in the correct reading frame for proper protein synthesis.

• The genetic code is nearly universal among organisms.

Mutations and Their Effects

Types of Mutations

Mutations are changes in the genetic material that can affect protein structure and function.

• Point mutations: Changes in a single nucleotide pair.

• Substitutions: One nucleotide is replaced by another.

  • Silent mutation: No effect on the amino acid sequence.

  • Missense mutation: Changes one amino acid to another.

  • Nonsense mutation: Changes an amino acid codon to a stop codon, leading to a truncated protein.

• Insertions and deletions: Addition or loss of nucleotide pairs, often causing frameshift mutations that alter the reading frame.

Causes of Mutations

• Spontaneous mutations: Errors during DNA replication or recombination.

• Mutagens: Physical or chemical agents that cause mutations; many are carcinogens (cancer-causing).

HTML Table: Types of Point Mutations

Key Equations and Concepts

• Central Dogma of Molecular Biology:

• Transcription:

• Translation:

• Genetic Code: