Gene Expression I: The Central Dogma and Genetic Code

These 100 flashcards cover the key experiments, hypotheses, and definitions related to the discovery of the genetic code and the central dogma of molecular biology, including Beadle and Tatum's Neurospora experiments and the properties of codons.

Gene (Mendelian definition)

Units of heredity consisting of DNA sequences that encode a protein that can specify a trait.

Alleles

Different versions of a gene that arise from DNA mutations.

Neurospora crassa

Bread mold and an ideal model system because it is cheap, easy to grow, can be grown as a haploid, and growth medium can be manipulated.

Haploid (Neurospora context)

A state where organismal mutant alleles are not masked by a wild-type allele, which would occur in a diploid.

DNA Mutations

Changes in a given gene that create different alleles and affect the production or function of a protein product.

George Wells Beadle

Co-recipient of the 1958 Nobel Prize for discovering that genes act by regulating definite chemical events.

Edward Lawrie Tatum

Co-recipient of the 1958 Nobel Prize for research providing evidence that genes encode enzymes.

Joshua Lederberg

Recipient of half the 1958 Nobel Prize for discoveries concerning genetic recombination and the organization of bacterial genetic material.

X-rays

Used in the Neurospora experiments to generate DNA mutations.

Complete medium

A growth medium containing glucose, salts, vitamin (biotin), amino acids, and other nutrients.

Minimal medium

A growth medium containing only glucose, salts, and vitamin (biotin).

Wild-Type (WT) Neurospora

Can synthesize its own amino acids to support growth on minimal medium.

Nutrient mutants

Strains that cannot grow on minimal media unless it is supplemented with a specific missing nutrient like Amino acid X.

One-gene one-enzyme hypothesis

The proposal that each gene is responsible for producing a single specific enzyme required for a nutrient synthesis pathway.

Arginine

The specific amino acid whose synthesis was rescued in Beadle and Tatum's library of mutant Neurospora strains.

Srb and Horowitz

Researchers who extended Beadle and Tatum's work to identify biochemical pathways by testing metabolites like ornithine and citrulline.

Ornithine

A metabolite in the arginine synthesis pathway that rescues Class I mutants but not Class II or III mutants.

Citrulline

A metabolite that rescues both Class I and Class II mutants but not Class III mutants.

Enzyme A

The enzyme responsible for converting the precursor to ornithine; it is mutated in Class I mutants.

Enzyme B

The enzyme responsible for converting ornithine to citrulline; it is mutated in Class II mutants.

Enzyme C

The enzyme responsible for converting citrulline to arginine; it is mutated in Class III mutants.

Class I mutants

Mutant Neurospora strains that can grow on ornithine, citrulline, or arginine.

Class II mutants

Mutant Neurospora strains that can grow only on citrulline or arginine.

Class III mutants

Mutant Neurospora strains that require arginine specifically to grow.

Linear pathway

A biochemical pathway that requires the processing of a prior metabolite for each sequential step.

Refinement of the one-gene one-enzyme hypothesis

The realization that not all proteins are enzymes, some proteins have multiple polypeptides, and some genes encode RNA.

Polypeptide

A chain of amino acids; multiple chains may compose a single protein.

Sequence Hypothesis

Francis Crick's 1950s idea that the sequence of bases in nucleic acid is a simple code for the amino acid sequence of a protein.

Central Dogma

The conceptual framework for the flow of information from DNA to RNA to protein.

Genotype

Defined by an organism's DNA.

Phenotype

The physical traits of an organism, linked to the genotype by proteins.

Gene expression

The process whereby DNA directs RNA and protein synthesis.

Transcription

The process by which DNA is used as a template to produce messenger RNA (mRNA).

Translation

The process by which mRNA is used to synthesize a protein polypeptide.

Messenger RNA (mRNA)

The RNA molecule that carries genetic instructions from DNA to the sites of protein synthesis.

Codon

A non-overlapping unit of three nucleotides in DNA or mRNA that specifies a single amino acid.

4 nucleotides

The number of different building blocks (ATCG) in DNA, meaning $4^2=16$ was insufficient to code for 20 amino acids.

$$4^3 = 64$$

The number of possible triplet combinations of the four nucleotides, which is sufficient to specify all 20 amino acids.

Non-overlapping triplet code

A genetic code read as three-nucleotide units without sharing nucleotides between adjacent units.

Sydney Brenner

Collaborator with Francis Crick on experiments demonstrating that the genetic code is read in triplets.

T4 bacteriophage

The model system used by Crick and Brenner to use mutagens for adding or deleting nucleotides.

Reading frame

The system established at the start site that moves forward in triples; it must be maintained for a meaningful message.

Frameshift

A mutation caused by the insertion or deletion of nucleotides not in a multiple of 3, causing the message to become gibberish.

Fixed starting point

The specific location that sets the reading frame for non-overlapping triplet code translation.

Marshall Nirenberg

Scientist who helped solve the first codon, 'UUU', using E. coli lysates.

Heinrich Matthaei

Scientist who, with Nirenberg, synthesized an 'U' RNA to discover it produced only phenylalanines.

Cell-free lysate

E. coli solution used in Nirenberg's experiments that contained all components for protein synthesis but lacked endogenous DNA/RNA.

UUU

The first solved codon, which codes for the amino acid phenylalanine.

Codon table

A visual representation showing what every nucleotide triplet encodes, covering 64 combinations.

AUG

The codon that codes for methionine and serves as the 'start' signal for translation.

Stop signals

Codons that do not code for amino acids but terminate translation: UAA, UAG, and UGA.

Redundant

A property of the genetic code where many different codons specify the same amino acid.

Unambiguous

A property of the genetic code where each individual codon specifies only one single amino acid or stop signal.

Open reading frame (ORF)

A sequence of DNA containing an ATG start codon followed by more codons and ending with a stop codon.

ATG

The DNA version of the start codon sequence found in an Open Reading Frame.

Universal genetic code

The principle that the same codons specify the same amino acids in almost all organisms from bacteria to humans.

Green fluorescent protein (GFP)

A jellyfish gene used to demonstrate universality by being expressed in organisms like mosquito larvae.

Phenylalanine

The amino acid represented by the codon 'UUU'.

Amino acid X

Used as a generic label for a nutrient added to minimal medium to rescue mutant Neurospora growth.

Glucose and Salts

Basic components of minimal medium for Neurospora along with biotin.

Biotin

The specific vitamin included in both complete and minimal media for Neurospora growth.

61

The number of triplets out of 64 that specifically encode amino acids.

Methionine

The specific amino acid encoded by the start codon AUG.

UAA

One of the three stop codons used to terminate translation.

UAG

One of the three stop codons used to terminate translation.

UGA

One of the three stop codons used to terminate translation.

1956

The date on Francis Crick's unpublished note describing the flow of information from DNA to RNA to protein.

1944

The publication year of Srb and Horowitz's data on the ornithine cycle in Neurospora.

20

The total number of different amino acids found in proteins.

Agar

A substance mixed with growth medium to provide a solid support for Neurospora colonies.

Precursor (Arginine pathway)

The starting metabolite that Enzyme A converts into ornithine.

Exogenous

Originating from outside the organism, such as nutrients added to a growth medium.

Gibberish

The result of a reading frame shift where the once meaningful message becomes unreadable.

AAA

A homopolymer codon solved using biochemical experiments similar to the UUU discovery.

CCC

A homopolymer codon solved using biochemical experiments similar to the UUU discovery.

GGG

A homopolymer codon solved using biochemical experiments similar to the UUU discovery.

Protein function restoration

Occurs when a second mutation (like a deletion following an insertion) brings the sequence back into the correct reading frame.

Downstream message

The portion of the sequence following a mutation; it remains unchanged if exactly three nucleotides are deleted.

Transcription direction

Flow from DNA to RNA.

Translation direction

Flow from RNA to protein.

UACG

The 4 nucleotides present in an mRNA molecule.

Triple-nucleotide deletion

A mutation affecting a maximum of 2 codons where the downstream message beyond those codons remains the same.

2-nucleotide deletion

An alteration that can be restored by adding 1 nucleotide or deleting 1 additional nucleotide to reset the triplet frame.

Predicted protein-encoding gene

The definition of an Open Reading Frame (ORF) in genomic sequences.

Molecular Biology of the Cell (7th Edition)

The textbook source mentioned regarding the importance of understanding the reading frame.

Nitrogenous bases

Identify the specificity of nucleic acids according to the Sequence Hypothesis.

Genomic sequence

The complete set of DNA that requires a genetic code to make sense of.

Flower color

An example of a phenotypic trait specified by a gene.

Biotin (minimal medium)

The only vitamin required in minimal medium for wild-type Neurospora.

Neurospora colony

A visible growth of Neurospora on an agar plate.

Phenotypic Rescue

The process of restoring growth in a mutant by adding a bypassed metabolic product.

Downstream product

A metabolite occurring after a block in a biochemical pathway that can rescue mutant growth.

Redundancy illustration

Both UUU and UUC coding for Phe is an example of this genetic code property.

Triples

The unit groups of nucleotides in which the reading frame moves forward.

Starting signal

The point where the message begins, defined by start signals like AUG.

Stopping signal

The point where the message ends, defined by stop signals like UAA.

Jellyfish

The organism from which the green fluorescent protein gene used in mosquito larva studies originated.

Simple code

Crick’s description of the nucleic acid sequence as it relates to the amino sequence.

Sequence of bases

Solely expresses the specificity of a piece of nucleic acid in the Sequence Hypothesis.

Gene A -> RNA B

An example demonstrating that the final product of a gene can be RNA, not just a polypeptide.