BIO181- 5.2: Gene Function (Unit 5: Genetic Principles)

Gene Function

Historical Foundations of Gene Function

The concept of gene function has evolved through key experiments in genetics and molecular biology. Early work by Gregor Mendel established that hereditary information is passed in discrete units called genes. Later, experiments by Griffith, Avery et al., and Hershey et al. demonstrated that DNA is the hereditary molecule.

• Phenotype: The observable traits of an organism, determined by its genotype.

• Genotype: The genetic makeup of an organism, encoded in its DNA.

• Key question: How do genes (DNA) specify phenotype, and what is the link between genes and proteins?

One-Gene, One-Enzyme Hypothesis

In 1941, George Beadle and Edward Tatum used the bread mold Neurospora crassa to study gene function by creating genetic mutants. Their work led to the one-gene, one-enzyme hypothesis, which states that each gene contains the information needed to make a single enzyme.

• Knock-out mutants (null mutants): Organisms with genes mutated to non-functional alleles.

• Careful analysis of mutant phenotypes showed that genes are responsible for the synthesis of specific enzymes.

• Later, it was understood that genes code for all proteins, not just enzymes.

Genetic Screens and Arginine Synthesis

In 1944, Adrian Srb and Norman Horowitz performed genetic screens for N. crassa mutants unable to synthesize the amino acid arginine. Their studies revealed that arginine is synthesized via a multi-step metabolic pathway requiring multiple enzymes, each encoded by a different gene.

• Genetic screen: A technique for identifying mutants with specific defects from a large population.

• Arginine synthesis involves conversion from ornithine to citrulline to arginine, each step catalyzed by a separate enzyme.

Precursor	Enzyme 1	Ornithine	Enzyme 2	Citrulline	Enzyme 3	Arginine

Example: Mutants unable to grow unless supplemented with a specific intermediate revealed which enzyme (and thus which gene) was defective.

Link Between DNA and Protein

DNA as an Information Storage Molecule

Francis Crick proposed that DNA is a code, with its sequence of bases specifying the 20 amino acids found in proteins. In eukaryotes, DNA is located in the nucleus, while protein synthesis occurs in the cytoplasm.

• RNA is present in both the nucleus and cytoplasm and acts as an intermediary.

• Information in DNA is not directly translated into protein sequence; RNA serves as the messenger.

Messenger RNA (mRNA) and the Flow of Genetic Information

François Jacob and Jacques Monod proposed that messenger RNA (mRNA) carries genetic information from DNA in the nucleus to ribosomes in the cytoplasm, where proteins are synthesized.

• mRNA acts as a link between genes and ribosomes.

• Protein synthesis takes place in the cytoplasm.

Transcription: DNA to RNA

Experiments showed that a single strand of DNA can serve as a template for RNA synthesis via complementary base pairing. RNA polymerase is the enzyme responsible for synthesizing RNA from ribonucleotide building blocks.

• Prediction: RNA strand will be produced containing bases complementary to the DNA template.

• Result: Information is transferred from DNA to RNA via complementary base pairing.

Central Dogma of Molecular Biology

Concept and Flow of Genetic Information

The central dogma summarizes the flow of genetic information in cells:

• DNA is transcribed to messenger RNA (mRNA).

• mRNA is translated to protein.

Equation:

$\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

Genes ultimately code for proteins, which determine cellular structure and function.

Implications for Heredity

According to the central dogma, an organism's genotype is determined by its DNA sequence, and its phenotype is a product of the proteins it produces.

• Alleles of the same gene differ in DNA sequence, leading to differences in protein sequence and function.

• Many genes code for RNA molecules (e.g., rRNA, tRNA) that are not translated into proteins but perform essential cellular functions.

• Changes in genotype may lead to changes in phenotype.

The Genetic Code

Definition and Role

The genetic code is the set of rules that specifies the relationship between the sequence of nucleotide bases in DNA or RNA and the sequence of amino acids in a protein.

• Each codon consists of three nucleotide bases and codes for a specific amino acid.

Mathematical Basis for Codons

George Gamow predicted that a three-base codon is necessary to encode the 20 amino acids, given only four different bases in RNA.

• Number of possible codons: $4 \times 4 \times 4 = 64$

• Three-base codons provide more than enough combinations to specify all amino acids.

Experimental Verification of the Triplet Code

Francis Crick and colleagues confirmed the triplet nature of the genetic code by creating mutations in viral DNA. Only deletions or insertions in multiples of three restored the correct reading frame and functional protein.

• Reading frame: The way codons are grouped for translation; mutations can disrupt or restore the frame.

Mutation Type	Ornithine	Citrulline	Arginine
No growth	GROWTH	GROWTH	GROWTH
Ornithine only	GROWTH	No growth	No growth
Citrulline only	No growth	GROWTH	No growth
Arginine only	No growth	No growth	GROWTH

Conclusion: Codons are read in groups of three bases.

Properties of the Genetic Code

The genetic code has several key properties that ensure accurate translation of genetic information:

• Predictive: The amino acid sequence encoded by a DNA or RNA sequence can be predicted using the genetic code.

• Start codon: AUG signals the start of translation.

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

• Redundancy: Many amino acids are encoded by more than one codon.

• Unambiguous: Each codon specifies only one amino acid.

• Universal: With few exceptions, the genetic code is the same in all living organisms.

Codon	Amino Acid
AUG	Methionine (Start)
UAA, UAG, UGA	Stop
UUU, UUC	Phenylalanine
UUA, UUG, CUU, CUC, CUA, CUG	Leucine
Additional info: See standard genetic code table for all 64 codons.

Example: The codon UUU always codes for phenylalanine, regardless of the organism.

Additional info: The notes cover topics from Ch. 15 (DNA and the Gene: Synthesis and Repair), Ch. 16 (How Genes Work), and Ch. 17 (Transcription, RNA Processing, and Translation) of a General Biology textbook.