Chapter 17: Gene Expression—REVIEW

Gene Expression: From Gene to Protein

Central Dogma of Molecular Biology

The Central Dogma describes the flow of genetic information within a biological system. It explains how the information in DNA is used to synthesize proteins, which perform most cellular functions.

• DNA is transcribed into RNA.

• RNA is translated into protein.

• This process is summarized as: DNA → RNA → Protein.

• Exceptions exist (e.g., some viruses use reverse transcription), but this is the general rule for cells.

Example: The gene for hemoglobin is transcribed into mRNA, which is then translated into the hemoglobin protein.

The Genetic Code and Codons

The genetic code is the set of rules by which information encoded in mRNA sequences is translated into proteins (amino acid sequences).

• A codon is a sequence of three mRNA nucleotides that specifies a particular amino acid.

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

• For example, both UUU and UUC code for phenylalanine.

• All codons specify either an amino acid or a stop signal.

Calculations:

• Each amino acid is coded by 3 nucleotides (1 codon).

• To code for a 218-amino acid polypeptide, minimum nucleotides needed: $218 \times 3 = 654$

• 18 codons code for 18 amino acids.

• 54 nucleotides can code for $54 \div 3 = 18$ amino acids.

• 936 nucleotides can code for $936 \div 3 = 312$ amino acids.

Transcription: Synthesis of RNA from DNA

Transcription is the process by which a DNA template is used to synthesize a complementary RNA molecule.

Key Molecules and Enzymes

• Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

• mRNA (messenger RNA): Carries genetic information from DNA to ribosomes.

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

• Transcription factors: Proteins that help RNA polymerase bind to the promoter (mainly in eukaryotes).

Stages of Transcription

1. Initiation: RNA polymerase binds to the promoter; DNA unwinds.

2. Elongation: RNA nucleotides are added to the 3' end of the growing RNA strand. RNA polymerase moves along the DNA template in the 3' to 5' direction, synthesizing RNA in the 5' to 3' direction.

3. Termination: RNA polymerase reaches a terminator sequence and releases the RNA transcript.

• Bonds: Hydrogen bonds form between DNA and RNA bases during transcription.

• The order of nucleotides in mRNA is determined by the DNA template strand.

RNA Processing in Eukaryotes

In eukaryotes, the primary RNA transcript (pre-mRNA) undergoes several modifications before becoming mature mRNA.

• 5' Cap: A modified guanine nucleotide is added to the 5' end to protect mRNA from degradation and assist in ribosome binding.

• Poly-A Tail: A string of adenine nucleotides is added to the 3' end for stability and export from the nucleus.

• Splicing: Removal of non-coding sequences (introns) and joining of coding sequences (exons).

• snRNA (small nuclear RNA): Component of spliceosomes, which catalyze splicing.

Example: The mature mRNA for beta-globin is shorter than the gene due to intron removal.

Translation: Protein Synthesis from mRNA

Translation is the process by which ribosomes synthesize proteins using the sequence of codons in mRNA.

Key Molecules and Enzymes

• Codon: Three-nucleotide sequence in mRNA specifying an amino acid.

• Anticodon: Three-nucleotide sequence in tRNA complementary to the mRNA codon.

• tRNA (transfer RNA): Brings amino acids to the ribosome.

• Ribosome: Site of protein synthesis; composed of rRNA and proteins.

• rRNA (ribosomal RNA): Catalyzes peptide bond formation; most abundant RNA in the cell.

• Stop codon: Signals termination of translation (e.g., UAA, UAG, UGA).

• Release factor: Protein that binds to the stop codon and releases the polypeptide.

Stages of Translation

1. Initiation: Small ribosomal subunit binds mRNA; initiator tRNA binds start codon (AUG) in the P site.

2. Elongation: Amino acids are added one by one to the C-terminus of the growing polypeptide; peptide bonds are catalyzed by rRNA (a ribozyme).

3. Termination: Stop codon enters the A site; release factor binds, and the completed polypeptide is released.

• Bonds: Peptide bonds join amino acids; hydrogen bonds hold codon-anticodon pairs together.

• The order of amino acids is determined by the sequence of codons in mRNA.

Order of Events in Translation:

1. Small ribosomal subunit associates with mRNA

2. Initiator tRNA in P position

3. Peptide bond formation

4. Stop codon in A position

5. Release factors bind

Comparison: Transcription, Translation, and DNA Replication

These processes are central to gene expression and inheritance, but have key differences and similarities.

Feature	RNA Polymerase	DNA Polymerase
Used in	Transcription	Replication
Synthesizes	RNA	DNA
Product strandedness	Single-stranded	Double-stranded
Primer needed?	No	Yes

Ribozymes

Ribozymes are RNA molecules with catalytic activity, capable of acting as enzymes.

• First discovered in the 1980s.

• Examples include:

  • rRNA in the ribosome (catalyzes peptide bond formation)

  • Self-splicing introns

Polyribosomes (Polysomes)

A polyribosome is a group of multiple ribosomes simultaneously translating a single mRNA molecule, increasing the efficiency of protein synthesis.

• In prokaryotes, transcription and translation can occur simultaneously because there is no nuclear envelope.

• In eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm, so these processes are separated.

Mutations: Types and Effects

Mutations are changes in the nucleotide sequence of DNA. Small-scale mutations can affect gene expression and protein function.

• Nucleotide-pair substitution: One base pair is replaced by another.

• Insertion: Addition of one or more nucleotide pairs.

• Deletion: Removal of one or more nucleotide pairs.

• Silent mutation: A change that does not alter the amino acid sequence (due to redundancy in the genetic code).

• Missense mutation: A change that results in a different amino acid.

• Nonsense mutation: A change that introduces a stop codon, truncating the protein.

• Frameshift mutation: Insertion or deletion not in multiples of three, altering the reading frame and usually resulting in a nonfunctional protein.

Example: Sickle-cell Disease

• Caused by a single nucleotide substitution in the beta-globin gene (Glu to Val).

• This missense mutation alters hemoglobin structure and function, leading to sickle-shaped red blood cells.

Frameshift mutations generally cause more severe effects than single base-pair changes because they alter the entire downstream amino acid sequence.

Additional Academic Context

• Promoter location: The promoter is upstream (5' direction) of the transcription start site on the DNA template strand.

• Start codon: AUG (methionine) is the universal start codon for translation.

• Stop codons: UAA, UAG, UGA signal the end of translation.