Chapter 1: The Origins of Molecular Biology: A Mendelian and Darwinian View
of the World
I. Introduction
A. Introduction: The Big Question
1. Q: Why did the field of Molecular Biology come into being?
2. A: The simplest answer is that the field of Molecular Biology
came into being as a way to explain mechanistically how heredity
works!
a. For example, you may want to know how eye color is
inherited
b. You may want to know how, on a molecular level, eye
color forms (How the pigment is actually produced)
B. Introduction: Molecular Biology Pre-History
1. If Molecular Biology studies how heredity works, and how
traits are expressed then the field of Molecular Biology must
have its roots in Genetics
2. How old is the field of genetics? How long have humans been
studying heredity?
3. How old is the field of genetics? How long have humans been
studying heredity?
4. About 10,000-12,000 years ago humans began to manipulate
animals and plants, to domesticate them
a. Plants include wheat, barley, lentils, peas
b. Animals include dogs, sheep and goats
5. Humans were able to quickly understand the concept of
heredity (create breeds that were better suited to agricultural
production by mating individual organisms with desirable traits)
6. In terms of crops, humans have selected for varieties with
significantly better viability
a. Crop variants that produce more fruit/vegetable
b. Crops that are more resistant to pests
7. Using Molecular Biology:
a. Clone genes that allow for pest resistance etc.
b. Genetic Modification: Insert that into the genome of a
plant using Agrobacterium (round-up ready/Bt crops)
8. Besides domestication, understanding how heredity works
also is extremely important for public health
9. Humans have known for long periods of time that inbreeding
generally results in expression of deleterious traits (generally
due to more efficient transmission of deleterious gene variants)
10. Example: The Romanov’s and the Royals of Europe
a. Tsar Nicholas Romanov II was the Czar of Russia from
b. The family included his wife Alexandria as well as four
daughters
11. On August 12, 1904 Tsar Nicholas II and Alexandria had their
first son, Alexis
12. Alexis was clumsy as a young child and fell often. When he
cut or scraped himself, he bled profusely, and bruises caused
uncontrollable internal bleeding
13. Alexis was suffering from a disease called hemophilia, which
ran through the Royal Families of Europe through the 19th
century
14. At the time of the Romanov’s, it was known that the disorder
ran in within families
a. It was unknown what the mechanism of inheritance of
the disease was
b. It was unknown what genes were implicated
15. Today, through Molecular Biology, we know that
hemophiliacs contain a defective variant of the Clotting Factor
VIII gene on the X chromosome
16. Today, hemophilia is not a life threatening disease and that
blood transfusions are unnecessary
17. Today, using molecular biology in vitro, we can produce the
Clotting Factor VIII protein, which can be given to patients
C. Introduction: The General Definition of Molecular Biology
1. The term Molecular Biology was coined by Dr. Warren Weaver
in 1938
2. Warren Weaver was a civil engineer and mathematician by
trade
3. Weaver was a great advocate for science and was responsible
for supporting grants for genetics and molecular biology
4. He defined molecular biology as the study of biological
phenomena at the molecular level (Initial Definition)
a. This definition covers a wide range of phenomena
b. This definition is inaccurate in that it does not explain
5. Molecular Biology: Study how the processes of heredity,
evolution as well as how basic cellular functions work (More
Modern Definition)
6.Heredity can be defined as the study of the passage of traits
from parent to offspring
a. Abstract Concepts of Genetics
b. Eye color
c. Hair color
d. Body pattern
e. Disease or Disease predisposition
7. Evolution can be defined as the development of more complex
organisms from less complex organisms
a. Abstract Concepts of Evolution
b. Development of antibiotic resistance in bacteria
c. Humans developing from lesser primates apes
8. There are other processes that also fall under molecular
biology that are not considered part of the process of gene
expression
a. DNA replication
b. Membrane biosynthesis
c. Cellular respiration
9. Our Main Focus in Molecular Biology: Molecular basis of gene
expression
10. Specifically, if one wants to study gene expression
mechanistically on the molecular level, then one follows the
different molecules that allow for expression of a gene as well as
the molecules that carry out the function of a gene
a. Structure of DNA and the hereditary information it
encodes
b. Structure and function of RNA
c. Structure and function proteins
d. Mechanisms of DNA replication before cell division
D. Introduction: The Beginnings of Molecular Biology
1. Molecular Biology as a way to explain how genetics and
evolution work
a. Answers important biological questions of who we are
b. Answers important biology questions of where we come
from
2. At the most fundamental level, Genetics is the study of heredity
3. Heredity can be defined as the study of the passage of traits
from parent to offspring
a. Eye color
b. Hair color
c. Body pattern
d. Disease or Disease predisposition
4. Evolution can be defined as the development of more complex
organisms from less complex organisms
a. Development of antibiotic resistance in bacteria
b. Humans developing from lesser primates apes
E. Introduction: A History Leading To the Development of Molecular
Biology
1. Before Molecular Biology, the fields of genetics and evolution
were very abstract fields
2. Abstract Cconcepts of Genetics
a. Over time geneticists became easily able to follow, and
the predict how certain traits where inherited
b. However, they did not know how these traits were
inherited in the way they predicted and why they did not
know why their predictions were never quite perfect
3. Abstract Concepts of Evolution
a. They were able to develop extensive fossil/anatomical
records and make important comparisons between known
living or extinct species
b. They were able to make important predictions about
transitional species
c. As with the geneticists, they also had no idea why some
species were so similar and others so different
4. In each case, Molecular Biology was able to provide the
mechanistic basis of how the processes of heredity and evolution
work
II. Historical Perspectives on Heredity
A. Historical Perspectives on Heredity: An Introduction
1. The study of heredity is not just limited to the modern era, but
started over 2000 years ago
2. The study of heredity asks one of the fundamental questions of
life, how do we have the traits we have?
3. The study of heredity has captured the imagination of many
scientists through out history
4. The study of heredity started long ago in ancient Greece with
Aristotle (384-322 BC)
a. Aristotle proposed the theory of pangenesis
b. Pangenesis: Hereditary characteristics are transmitted
by gemmules from individual body cells
5. Robert Hooke (1635-1703) developed the first microscope in
1665 and allowed humans to see cells for the first time
6. The use of microscopes allowed for the visualization of sperm
and eggs
7. Performationism: Inside the sperm or egg exists a miniature
adult (a homunculus) which enlarges during development
8. Note: performationism meant that all traits would be inherited
from one parent
B. Historical Perspectives on Heredity: The Age of Mendel
1. It was not until the 1860s that mechanisms of heredity started
to become truly understood
2. The person responsible for determining the mechanism of
heredity was the Austrian monk Gregor Mendel
3. Gregor Mendel was born in 1822 in what is now considered the
Czech Republic to a family of farmers
4. Although his family had little money, he still received a
substantial education during his childhood
5. In 1843, Mendel was admitted to the Augustinian Monastery in
Brno, where he was trained as a priest
6. Mendel later went on the become a teacher and scholar
7. Later he went on to further his education at the University of
Vienna from 1851-1853, where he took courses in Math,
Chemistry, Paleontology, Botany and Plant Physiology
8. Most scientists during the middle-late 1800s sought to follow
human traits as they thought (without evidence) that each
organism inherited traits in much different manners than other
organism
9. The other scientists of that time who did follow human traits
followed those that generally are inherited in a more complex
manner
a. Traits may involve many genes
b. These genes may have strong interactions with
environmental factors
10. Mendel took a different approach because he decided he
could not use people as a system for studying inheritance, he
instead bred pea plants
11. Mendel was easily able to isolate different strains of pea plant
with very distinct characteristics
a. Seed shape
b. Seed color
c. Pod shape
d. Stem length
12. Through his work with pea plants he was able to determine
how each of these individual traits were inherited from parent to
offspring
13. Each trait was controlled by a pair of factors
14. From Mendel’s study of the different traits, and their multiple
factors, came his law of Independent Segregation (Mendel’s
second law)
a. Each trait is determined by different factors
b. Each organism must inherit two factors for each trait
(one from each parent)
c. Each parent then must segregate his/her two factors
into separate gametes
15. In Mendel’s experiments, he noticed that certain factors are
dominant to others, which led to postulate a Concept of
Dominance
16. Today, we find that each trait is determined by a gene and
that each gene can exist in multiple forms (factors) called alleles
17. Mendel extended his breeding experiments such that he
could follow more than one trait at a time
18. From the results of these experiments he postulated the law
of independent assortment (Mendel’s first law),
19. The first law states that for each trait, the factors will assort
independently from one another during gamete formation
a. Each gamete will have one factor for each trait
b. The presence of a specific factor for one gene will have
no influence on which factor will be present for another
gene
20. Upon union of two gametes, each trait will again be
represented by two factors
21. Mendel performed his work generally outside the scientific
community, and thus, his work although published was not
exactly viewed favorably (36 years)
22. His work sat idle until 1900 when Hugo DeVries, Karl Correns
and Erich Von Tschermak independently recreated his work
23. Although Mendel was able to determine how different traits
were inherited he had no idea how traits were encoded
a. Had no idea that traits were determined by genes
b. Had no idea what genes were composed of
24. During the early 1900’s, many other scientists determined
the mechanisms of inheritance for a large number of traits in a
variety of different organisms
25. In the early 1900’s Thomas Hunt Morgan postulated sexlinkage for which he won a Nobel Prize
C. Historical Perspectives on Heredity: The Chromosomal Theory of
Heredity
1. One of the main difficulties in the acceptance of Mendel’s work
is the lack of actual physical evidence
2. August Weisman (1893) was one of the first scientists to link
behavior of chromosomes to heredity
3. When studied segregation of chromosomes, he noticed that the
number of chromosomes in the nuclei of germ cells is halved.
Therefore, he postulated that the material of heredity (genetic
information) is located in the nucleus
4. From this, Weisman postulated that The Germ-plasm theory
a. States that cells in the reproductive organs carry a
complete set of genetic information, and that this
information is passed along to the egg and sperm
b. Perhaps this information is present in the chromosomes
5. In 1903 Walter Sutton published his paper “The Chromosomes
in Heredity
a. Paper focused on the principles in Meiosis
b. Sutton saw that there appeared to be two copies for
each chromosome
c. During meiosis, each gamete receives only one member
of the chromosome pair, which appropriately follows
Mendel’s law of independent assortment
6. Sutton’s Conclusions
a. Chromosomal movement explains Mendel’s second law
(independent segregation)
b. Proposal of the Chromosomal Theory of Heredity
7. Sutton assumed that genes are part of the chromosome
a. Assumed that the seed color gene is found on one pair of
chromosomes
b. Explains the 3:1 ratio when crossing heterozygotes
c. He also assumed that seed shape genes were found on
another pair of chromosomes from the seed color genes,
which allow for the observed 9:3:3:1 ratio
8. Sutton’s results were important for two reasons
a. Most importantly suggested (but did not prove) physical
evidence for Mendel’s rules regarding segregation
b. Linked the study of Genetics to the study of cytology and
would drive the development of the field of Molecular
Biology
9. With the work of Sutton and the Chromosomal Theory of
Heredity two questions remained
a. What were the chromosomes composed of?
b. What material carried the information of heredity?
10. Given that the chromosomes appeared to segregate according
to Mendel’s laws of independent segregation, then the
material(s) that compose chromosomes must also be responsible
for heredity
III. The Beginnings of Molecular Biology
A. The Beginnings of Molecular Biology: Friedrich Meischer’s
Contributions To Determining Which Molecule Holds Genetic
Information
1. At about the same time that Mendel was working on his pea
plants, Friedrich Meischer (1868) was embarking on studying
the chemical makeup of cells
2. Meicher theorized that to determine the material of heredity
one must understand the chemical nature of cells
3. Meicher, in order to determine the material of heredity
studied the chemistry of pus
4. Pus includes bacteria, which cause an infection, as well as
many white blood cells, which are called on to fight the infection
5. Meicher took the white blood cells and isolated their nuclei to
study what was inside
6. Upon analysis, he expected to find protein inside the nucleus,
however, he found the ratios of carbon and nitrogen to be
inconsistent the presence of protein
7. As well, he found that the material was slightly acidic and
importantly was high in phosphorus-he called this material
nuclein
8. With further analysis of nuclein, he found that the three main
components of nuclein were phosphate, sugar and a nitrogen
containing base
B. The Beginnings of Molecular Biology: The Controversy Between DNA
and Protein Carrying the Information of Heredity
1. In the early 20th Century the controversy raged which molecule
contained the information of heredity
a. Nucleic Acid (DNA)
b. Protein
2. Due to the chemical nature of each molecule, it was thought
that proteins contained the information of heredity
a. Proteins are composed of a possible 20 different amino
acids
b. Each amino acid has its own chemical properties
c. Within a cell there could be many different variations of
protein
3. DNA was thought to be much less complex than protein and
thus could not be the material of heredity
a. Composed of only four different nitrogenous bases
b. Only a few structural variations
C. The Beginnings of Molecular Biology: Fredrick Griffith’s
Contributions To Molecular Biology
1. Next Griffith treated Type S bacteria with heat, thus killing
them
2. When he injected the heat killed type S bacteria, he found that
the mice remained healthy
3. The last experiment he did was he mixed the heat killed type S
bacteria with the live type R bacteria
4. He then injected this mixture, and found that the mice became
sick and died
5. He concluded that there was a transfer of some component
from the dead pathogenic (Type S) bacteria to the live nonpathogenic Type R bacteria to make it become pathogenic
6. He called this component the transforming principle, that
when transmitted from the dead S to the live R bacteria allowed
them to become pathogenic
7. Griffith was not able to determine the true chemical nature of
the transforming principle
D. The Beginnings of Molecular Biology: In vitro Experiments Based on
Griffith’s work
1. In 1931, Henry Dawson showed that the mouse was not needed
for transformation
a. He heat killed the pathogenic type S bacteria and then
mixed it with the live type R bacteria
b. Instead of injecting the mixture into mice, he plated the
mixture on agar plates
c. He found some type R colonies and some type S colonies
on his plates
2. In 1933, Lionel Alloway showed that a cell-free extract
prepared from broken type S bacteria could also be used for
transformation of live type R cells to type S cells
3. In 1941 Oswald Avery, Colin MacLeod and Maclyn McCarty
took Griffith’s experiment further to determine the true chemical
nature of the transforming principle
4. Purified protein, DNA, and RNA from type S bacteria
a. They then treated live type R cells with either the DNA,
RNA or the protein
b. They found that the DNA led to transformation of the
live type R to type S bacteria, whereas the other two did
not
5. The Beginnings of Molecular Biology: In vitro Experiments
Based on Griffith’s work (Supplemental Figure)
D. The Beginnings of Molecular Biology: The Hershey-Chase Experiment
1. Even with the results of Avery, MacLeod and McCarty, the
controversy about whether DNA or protein contained the
information of heredity, was still raging
2. Hershey and Chase performed what is now recognized as the
sentinel experiment, which put the controversy to rest
3. In order to determine whether protein or DNA was being
inserted into the host cell, Hershey and Chase needed to find a
way to label each type of molecule
4. Hershey and Chase used the T2 bacteriophage, in their
experiments
5. T2 bacteriophage is a virus that infect E. coli. Viruses are
unable to reproduce on their own, they need to reproduce use a
host cell
6. At the time, it was known that a virus had an outer protein
coat, and inside this protein coat was DNA
7. When a T2 bacteriophage infects and E. coli, it attaches to the
outside, and then injects its genetic material into the E. coli cell.
Once injected, the cell uses this genetic material to make new
virus
8. What Hershey and Chase wanted to do was to figure out what
got inserted into the host cell because that must be the genetic
material
9. They knew protein contained sulfur, whereas DNA did not and
DNA contained phosphorus whereas proteins did not
10. They labeled proteins with a radioactive form of sulfur (S35)
11. They labeled DNA with a radioactive form of phosphorus
(P32)
12. Next they created Bacteriophage that had either their DNA
labeled with P32 or their protein labeled with S35
13. They then took their phage that either contained radioactive
protein or radioactive DNA and infected E. coli with them
14. Upon infection, the viruses would bind to the outside of the E.
coli cell and insert their genetic material
15. Next, they took their mixture containing infected E. coli and
used a blender to lightly shear off whatever was left that was
bound to the outside of the cell
16. They then centrifuged their sample to pellet the bacteria.
This leaves any part of the phage that was not inserted into the
cell left in solution (supernatant)
17. When they looked at sample in which the phage contained
radioactive protein (35S), they found that the radioactivity was
found in the supernatant and not in the bacterial pellet
18. This suggests that protein is not inserted into the host cell,
and thus protein would not be the genetic material
19. In contrast, when they looked at the sample in which the
phage contained radioactive DNA (32P), they found that the
radioactivity was found in the bacterial pellet and not in the
supernatant
20. This suggests that DNA is being inserted into the host cell, and
thus, DNA would be the genetic material
E. The Beginnings of Molecular Biology: A Model For the Structure of
DNA
1. Previously, it had been shown that DNA is composed of three
different components
a. Sugar
b. Phosphate
c. Nitrogenous bases
2. It was known that there were four nitrogenous bases
a. Adenine
b. Thymine
c. Cytosine
d. Guanine
3. Quantitative methods by Erwin Chargaff had shown that the
number of [A] = [T] and the amount of [G] =[C] (However, [G+C]
does not equal [A+T]
4. Based off of this work, and by X-ray diffraction analysis on DNA
by Maurice Wilkins and Rosalind Franklin, James Watson and
Francis Crick were able to determine the 3-D structure of DNA
a. Found that the shape of DNA is in the form of a helix of
constant diameter
b. Found that the nitrogenous bases were stacked towards
the interior of the molecule, with the backbone containing
sugar (deoxyribose) and phosphate
c. They were able to determine the distance between the
stacked bases
5. The Beginnings of Molecular Biology: A Model For the
Structure of DNA (Supplemental Figure)
IV. The Gene Is The Basic Unit of Heredity
A. The Gene Is The Basic Unit of Heredity: Introduction
1. As Mendel worked with his pea plants he had no concept of
what a gene was
2. Instead he was only following hereditary characteristics
a. Seed shape
b. Seed color
c. Plant size
3. In 1889 Hugo de Vries tried to explain Mendel’s factors in his
book “Intracellular Pangenesis”
4. De Vries stated that the pangen is “smallest particle
representing one hereditary characteristic”
5. About 20 years late Wilhelm Johannsen coined the term gene
by shortening the word pangen
6. Be aware neither scientist understood physically what a gene
was, they only knew that it encoded a specific hereditary
characteristic
B. The Gene Is The Basic Unit of Heredity: The Molecular Identity of a
Gene
1. Over time, it was determined that the genes were located on
chromosomes, which were composed of primarily DNA and
associated proteins
2. As early as 1910, Thomas Hunt Morgan and his research group
at Columbia University started mapping the exact positions of
each discovered gene within the genome
a. Morgan and his group worked with Drosophila
melanogaster
b. Produced mutant flies with different characteristics
(mutant strains)
3. Morgan and his group were able to map their positions by
using a series of genetic crosses using his different mutant
strains
a. Mapped each new gene with respect to known genes
b. Were able to map each gene by determining which
genes were linked (on the same chromosome)
4. By 1913 Alfred Sturtyvant, student in Morgans’s lab, produced
the first ever physical map locating each known gene of an
organism’s genome (Drosophila)
5. At this point in time, a gene was being better defined as a unit
that encodes a specific inherited trait
C. The Gene Is The Basic Unit of Heredity: Determining What A Gene
Encodes on a Molecular Level
1. As the field of molecular biology started to develop,
researchers wanted to develop a better molecular definition of a
gene
a. What the structure of a gene looks like
b. More importantly, what a gene actually encodes
2. In 1941, George Beadle and Edward L. Tatum were the first to
demonstrate the link between a gene and a step in a metabolic
pathway which is catalyzed by an enzyme
3. Beadle and Tatum worked backwards using specific mutants of
the pink bread mold, Neurospora crassa in which specific
chemical reactions were blocked
4. Beadle and Tatum followed the biochemical pathway for niacin
biosynthesis
a. Considered a water soluble vitamin
b. Niacin is a precursor to NADPH
5. They induced mutations into the Neurospora by using Xirradiation and then plated them on minimal medium
6. As long as a metabolic step is not affected by the X-irradiation,
the Neurospora should grow on the minimal media
7. However, failure to grow on the media indicates that a
mutation has occurred leading to a growth defect
8. These mutants need media with specific supplemented
compounds (usually amino acids) to grow-these mutant strains
of Neurospora are known as auxotrophs
9. In the Beadle and Tatum experiment, they studied the pathway
of niacin synthesis (See Figure 1.5)
10. One can determine the specific nature of the auxotroph by
placing the auxotrophic strain supplemented with various
intermediates in the pathway of niacin synthesis (Figure out
which enzyme within the pathway has been affected)
11. Beadle and Tatum observed a one-to-one correspondence
between the genetic mutations and the lack of a specific enzyme
required in a biochemical pathway, and they dubbed this the
“One Gene – one enzyme hypothesis”
D. The Gene Is The Basic Unit of Heredity: Determining What A Gene
Encodes on a Molecular Level (Modern)
1. Eventually, the one gene-one enzyme hypothesis was amended
based on several other discoveries in addition to that of Beadle
and Tatum
a. The discovery that DNA holds the genetic information by
Avery, Macleod and McCarty as well as Hershey and Chase
b. The discovery of the DNA double helix by Watson and
Crick
2. Watson and Crick further proposed that a gene encodes a
protein
a. Not all genes encoding proteins encode enzymes
b. Some genes encode structural proteins, signaling
proteins as well as others
3. This hypothesis has been amended further, because there are
some genes that do not even encode polypeptides, they encode
RNAs
4. Today through the work of many Molecular Biologists the
actual structure of the gene has been determined
5. In 1972, Walter Fiers and his colleagues were the first to
sequence an entire gene