Chapter 1

The Beginnings of Molecular Biology

The double helical, base-paired structure of DNA is a scientist’s dream―simple, elegant, and universal for all organisms. [In the words of Watson] “The structure was too pretty not to be true.”

Harrison Echols, Operators and Promoters: The Story of Molecular Biology and Its Creators (2001), p. 8

1.1 Introduction

What is molecular biology?

The study of biological phenomena at the molecular level, in particular the study of:

• the molecular structure of DNA and the information it encodes;

• the biochemical basis of gene expression and regulation.

• Captivates Hollywood and the general public.• Excites scientists and science fiction writers.• Inspires artists.• Challenges society with emerging ethical

issues.

Deoxyribonucleic acid (DNA)

Three lines of research led to the discovery that DNA is the

hereditary material

• The nature of genes.• The behavior of chromosomes during

mitosis.• The chemical composition of DNA.

DNA is the hereditary material: each chromosome is a single molecule of DNA, and genes are sequences of DNA.

1.Some great discoveries are not appreciated or communicated to a wide audience until years after the discoverers are dead and their discoveries are “rediscovered.”

2.A combined approach of in vivo and in vitro studies has led to significant advances.

Six important principles of scientific discovery

3. The study of mutations is a driving force in genetics and in modern molecular biology.

4. Major breakthroughs often follow technological advances.

5. Progress in science may result from competition, collaboration, and the tenacity and creativity of individual investigators.

Six important principles of scientific discovery

6. All research in biology during the last 150+ years has developed within the framework of evolution.

Six important principles of scientific discovery

1.2 Insights into the nature ofthe heredity material

• The transmission of characteristics from parent to offspring by means of genes.

Heredity

“The more deeply … we penetrate into the phenomena of heredity, the more firmly are we convinced that something of the kind [germ-plasm or hereditary substance] does exist, for it is impossible to explain the observed phenomena by means of much simpler assumptions. We are thus reminded afresh that we have to deal not only with the infinitely great, but also with the infinitely small…”August Weismann, Germ-Plasm: a Theory of Heredity (1893)

Mendel’s laws of inheritance

• The law of segregation.

• The law of independent assortment.

• The law of dominance.

Mendel’s report was greeted by a disinterest that lasted 36 years…

The law of segregation

• During the formation of gametes, the paired hereditary determinants separate (segregate) in such a way that each gamete is equally likely to contain either member of the pair.

The law of independent assortment

• Segregation of the members of any pair of hereditary determinants is independent of the segregation of other pairs in the formation of gametes.

The law of dominance

• For each physical trait, one member of any pair of hereditary determinants is dominant so that the physical trait that it specifies appears in a 3:1 ratio.

• The alternative form is recessive.

Incomplete dominance

• A form of intermediate inheritance in which one allele for a specific trait is not completely dominant over the other allele.

• This results in a combined phenotype.

The chromosome theory of inheritance

• A unifying theory stating that inheritance patterns can be explained by assuming the genes are located in specific sites on chromosomes.

Meiosis explains Mendel’s law of segregation

• Homologous chromosomes separate during meiosis I.

• Alleles (alternative forms of a gene) are segregated into different gametes during meiosis II.

Meiosis explains Mendel’s law of independent assortment

• Nonhomologous chromosomes assort independently during meiosis I.

• Thus, genes for different traits assort independently.

The transforming principle is DNA

• In vivo experiments

1928: Frederick Griffith described a transforming principle that transmitted the ability of bacteria to cause pneumonia in mice.

• Griffith’s model of genetic transformation was met with almost universal skepticism.

• He was so shy that he had trouble even reading his papers in front of a small audience.

The transforming principle is DNA

• In vitro experiments

1944: Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that purified DNA was sufficient to cause transformation.

The transforming principle is DNA

Creativity in approach leads to the one gene-one enzyme hypothesis

1941: George Beadle and Edward Tatum were the first to demonstrate a link between a gene and a step in a metabolic pathway catalyzed by an enzyme.

Instead of working out the chemistry of known genetic differences…

• Beadle and Tatum worked backwards. • They selected mutants of the pink bread

mold, Neurospora crassa, in which known chemical reactions were blocked.

The importance of technological advances: the Hershey-Chase

experiment

•1952: Alfred Hershey and Martha Chase demonstrated that the genetic material of a virus that infects bacteria, bacteriophage T2, is DNA.

•Their findings suggested that DNA could be the universal hereditary material.

1.3 A model for the structure of DNA: the DNA double helix

•1953: James Watson and Francis Crick proposed the double helix as a model for the structure of DNA.

•Their discovery was based, in part, on X-ray diffraction analysis performed by Rosalind Franklin in Maurice Wilkin’s lab

Other scientific findings at the time provided the context for the proposed structure of DNA

1. The proposed helical secondary structure of proteins by Linus Pauling in 1951

2. The disproving of Phoebus Levene’s tetranucleotide hypothesis by Erwin Chargaff

1.4 The central dogma of molecular biology

The Central Dogma was summarized by Francis Crick as follows:

“Once information has passed into protein it cannot get out again”… Crick’s choice of the word “dogma” was not a call for blind faith in what was really a central hypothesis. According to Horace Judson in his book The Eighth Day of Creation, it was because Crick had it in his mind that “a dogma was an idea for which there was no reasonable evidence.” Crick told Judson “I just didn’t know what dogma meant… Dogma was just a catch phase.”

• Replication: The process of making an exact copy of DNA from the original DNA.

• Transcription: The process of DNA being copied to generate a single-stranded RNA identical in sequence to one strand of the double-stranded DNA.

• Translation: The process of the RNA nucleotide sequence being converted into the amino acid sequence of a protein.

• Reverse transcription: the process of a single-stranded DNA copy being generated from a single-stranded RNA.

1.5 An evolutionary framework for heredity

On the Origin of Species

• 1859: Darwin concluded that evolution occurs when heritable variation leads to differential success in reproduction.

• Darwin’s theory of evolution by natural selection implied that all organisms are related by common ancestry.

Last Universal Common (Cellular) Ancestor (LUCA)

• A first simple life-form that existed on Earth more than 4 billion years ago.

• All life evolved from LUCA.

Selectionist (neo-Darwinian) theory

• Natural selection is the force that gradually shapes the adaptation of organisms, acting on individuals in populations and affecting their ability to survive and reproduce.

• Evolution is a change in the characteristics of a population over time.

• Advantageous changes are passed on in offspring by Darwinian (positive) selection

• Deleterious changes tend to disappear by purifying (negative) selection

• Neutral changes may be fixed or may disappear in a population over time.

The nearly neutral theory of molecular evolution

• Late 1960s: Motoo Kimura proposed that the main cause of evolutionary change at the molecular level is random fixation of selectively neutral or nearly neutral mutations.

• How much genetic variation is adaptive and maintained by natural selection and how much is neutral and maintained by genetic drift?

• Genetic drift: random changes in gene frequencies of a population from generation to generation.

The nearly neutral theory of molecular evolution

• Positive selection of adaptive mutations is not the dominant mode of selection.

• The dominant mode of selection is purifying selection that eliminates deleterious mutations while allowing random fixation of nearly neutral mutations.