Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
Lecture 1:
The Molecular Structure of DNA and RNA
The famous X-ray Diffraction “Photograph 51” taken by Rosalind Franklin in 1952. James Watson
and Francis Crick used the information from this photograph, as well as information from several
other experiments (none of which they performed themselves), to build their double-helical model
of DNA in 1953. http://fig.cox.miami.edu/~cmallery/150/gene/DNAdiscovery.htm
I.
DNA IS THE GENETIC MATERIAL
A.
A “Big Picture” Question
Genetics is the study of the structure, function and transmission of genes. As
such, it is really a science about life information: how it is stored, how it directs
the activities of living organisms, and how it is passed from one generation to the
next.
Page 1
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
Only living organisms have genes, and genes are found only in living organisms.
Therefore, in order to really understand what genetics is all about, we must first
ask what life is all about.
What characteristics define living organisms as different from inanimate
objects?
What is it about a tree that makes it fundamentally different
from the soil in which its roots are embedded and derive nutrients?
How do we know that a seagull is alive but the air through which it
flies is not?
As an upper-division student of biology or biochemistry, ask yourself:
What are the basic criteria for being alive?
As you ponder this question, try to think in the very broadest terms. Perhaps Earth
isn’t the only planet that sustains life. How would we recognize life elsewhere in
the universe if we came across it? What basic properties would those alien
organisms have to possess, and share in common with terrestrial organisms, for us
to categorize them as “alive”?
This “big picture” question is designed to encourage you to place genetics in its
largest context before studying the minute details of the nature and transmission
of genes. Once you have answered the question, you will be in a better position to
understand what it is that living organisms need to accomplish, and what role the
genome plays in helping organisms meet their needs (or, more accurately, the needs
of their genes).
You will probably also discover that there are really only a very few basic criteria
for life and an almost infinite variety of ways that these needs can (or could) be
met. The fact that all terrestrial life forms meet them in essentially the same way
is one of the most powerful arguments that life probably arose only once on earth,
and therefore all terrestrial organisms are related to one another, even if only as
distant cousins.
B. Information, Entropy, and Solla Sollew
Page 2
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
In contemplating the criteria that set living organisms apart from nonliving
objects, you probably included some kind of information molecule on your list. This
makes sense, since living organisms clearly have to maintain an orderly system in a
surrounding environment that is essentially chaotic and disorderly, and this
requires some kind of “blueprint” or plan.
In Zen Buddhism, this tension between life forms and their
environment is referred to as “dukha”, or a “wheel out of kilter”. If
you are a living organism there is always something wrong, something
that needs to be attended to or fixed (as we all experience on a daily
basis). The advertising industry not withstanding, there will never
come a time in life when all problems are solved (even if you buy
that new BMW convertible), and life is simply a progression of problems, one
following on the heels of another. Every day, you get hungry and need to eat (which
is how you direct a stream of negative entropy upon your body to sustain order),
you get tired and go to sleep, something breaks down that needs to be fixed, you’re
unable to register into your classes and have to try to add them, and so on and so
on.
Dr. Suess’s book I Had Trouble in Getting to Solla Sollew (“Where they never have
troubles! At least, very few”) is a wonderful expose of tendency we have to think
there is a final destination where our problems will disappear. In the end, his
mythical creature cannot reach Solla Sollew and decides to turn around and face
his problems, one day at a time.
The fundamental problem is that life is negatively entropic (i.e. ordered), while the
Universe’s energy cascades the other way (towards disorder). Even more
fundamentally, life forms are really just the vehicles by which proteins compete
with one another, and those proteins that compete best survive to compete in
subsequent generations. So it is actually the fact that proteins must harness
negative entropy in order to out-compete one another that life forms must also do
so.
UNIVERSE
(entropy)
LIFE (GENES)
(negative entropy)
Page 3
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
Information is necessary to create molecules (proteins in terrestrial life forms)
that can harness negative entropy. And on earth, that information is carried by
genes, which are themselves comprised of DNA (deoxyribonulecic acid), a large
polymer made up of linked subunits called nucleotides. Most genes code for
proteins, which is how the whole circle is connected.
Thus, the source of all life’s “problems” is entropy, and the solutions lie in the
information provided by DNA. Therefore, genetics is perhaps most
fundamentally a study of how life forms store, express, and transmit the
information required for proteins to effectively harness the negative entropy
required to compete with each other for limited environmental resources.
C. Information and DNA
Biologists first became aware that life requires an information molecule that
carries the blueprint for a life form and its proteins in the early 1900s. They also
realized that it must be replicable and transmittable, since each life form clearly
passes on specific information to its descendents (e.g. Dogs give birth to puppies,
not kittens, and oaks beget other oak trees, not pines).
Clues to the biochemical nature of this information molecule came from Gregor
Mendel’s discovery of the laws governing the transmission of inherited traits from
one generation to the next (1850s – 1860s), the detailed descriptions of the
behavior of chromosomes during mitosis and meiosis by cell biologists in the late
1800s, and studies that inventoried the biochemical contents of eukaryotic nuclei.
From these discoveries, biologists deduced that the information molecule must be
closely associated with chromosomes, the protein-rich, thread-like structures
located within the nuclei of eukaryotic cells. They also realized that the genetic
information molecule must have the following characteristics:

It must contain, in a stable form, all the information for an organism’s
cell structure, function, development, and reproduction. In particular, it
must tell a cell how and when to make proteins, because proteins are the
“work horses” of the cell and largely determine the physical characteristics
of the cells and organisms in which they reside.
Page 4
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1

It must be able to replicate accurately so that all progeny cells will
contain the same genetic information as the parent cell from which they
are derived. Without this basic ability, the information for how to make the
an organism’s proteins would be lost from one generation to the next and the
ability to create and sustain order could not be perpetuated.

It must be capable of variation. Without variation (which we now know is
caused by changes in the sequence or location of genes), there would have
been nothing for natural selection to work upon and evolution would never
have happened. (In other words, we’d all still be primitive molecules floating
around in the primordial soup. The fact that some proteins compete better
than others for limited resources requires that there be variation in the
activity and/or structure of proteins, and this requires that the information
molecule be capable of change.)
The science of biochemistry was much more advanced than the science of
molecular biology in the early 1900s. Biochemists study all biomolecules, but they
are most interested in proteins because proteins are the most ubiquitous
structural molecules in cells, and proteins are also the catalysts that drive most
cellular processes. Collagen, keratin, actin, myosin, antibodies, growth hormones,
amylase, insulin, phosphatases, and kinases are just a few examples of common
proteins that are made by most animals. They were often abundant and easily
purified, and are fascinating to biochemists because of their rich and complex
chemistries. Therefore, most biochemists simply assumed that the information
molecule must be some type of protein.
Much less was known about DNA, a homogeneous and chemically inert molecule that
co-purifies with proteins when chromosomes are extracted from nuclei. Unlike
proteins, all DNA molecules have the same 3-D conformation (long, thin rods) and
are negatively charged with the same charge to mass ratio. Moreover, there are
only 4 different types of subunits (adenine, thymine, guanine, and cytosine) that
differ only in the form of their nitrogenous bases, which are chemically similar to
one another and extremely non-reactive. In fact, it was difficult to get DNA to
Page 5
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
react with anything but strong acids, and few biochemists paid it much attention
until several seminal experiments performed between 1928 and 1952 showed that
it was almost certainly the molecule that carries the genetic information.
D. Genetic Information is Digital
Moreover, genetic information could theoretically be held as either an analog or
digital form. However, analog information breaks down over time as it is copied,
while digital information does not. (When you Xerox a copy of a copy of a copy
you’ll eventually get just a bunch of gray blur.) This is why most of our technology
(from telephones to stereos to computers) is now running on the
basis of digitally held information.
Indeed, Richard Dawkins, who wrote a seminal book entitled
The Selfish Gene in the 1970s, argues that life is simply a
stream of digital information that changes over time!
II.
MOLECULAR GENETICS
Molecular Genetics is the study of the structure and function of genes at their
most fundamental level: as sequences of deoxyribonucleic acid (DNA).





The field began in 1953 with the discovery of the 3-D structure of DNA and
has rapidly advanced in the past 50 years
1960s: Discovery of messenger RNA and the genetic code
1970s: Birth of recombinant DNA technology
1980s: The ability to “amplify” target sequences of DNA by the polymerase
chain reaction (PCR)
1990s-present: Genome sequencing, molecular medicine, human DNA
identification
III. EARLY EXPERIMENTS TO FIND THE GENETIC MOLECULE
A. Frederick Griffith’s Experiments with Streptococcus pneumoniae
(1928)
Page 6
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1

Griffith studied a bacterium (Diplococcus pneumoniae) now known as
Streptococcus pneumoniae

S. pneumoniae comes in two strains
o S  Smooth
 Secrete a polysaccharide capsule
 Protects bacterium from the immune system of animals
 Produce smooth colonies on solid media
o R  Rough
 Unable to secrete a capsule
 Produce colonies with a rough appearance
 In addition, the capsules of two smooth strains can differ significantly in
their chemical composition
 Rare mutations can convert a smooth strain into a rough strain, and vice
versa.

Griffith conducted experiments using two strains of S. pneumoniae: type
IIIS and type IIR
Page 7
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
1. Inject mouse with live type IIIS bacteria:
 Mouse died
 Type IIIS bacteria recovered from the mouse’s blood
2. Inject mouse with live type IIR bacteria
 Mouse survived
 No living bacteria isolated from the mouse’s blood
3. Inject mouse with heat-killed type IIIS bacteria
 Mouse survived
 No living bacteria isolated from the mouse’s blood
4. Inject mouse with live type IIR + heat-killed type IIIS cells
 Mouse died
 Type IIIS bacteria recovered from the mouse’s blood
See Figure 9.2, Brooker

Griffith concluded that something from the dead type IIIS was
“transforming” type IIR into type IIIS
o He called this process transformation

The substance that allowed this to happen was termed “the transformation
principle”, but Griffith did not know what it was

However, his experiments proved that “the transforming principle” was not
sensitive to heat, suggesting that the genetic material was NOT a protein, as
many biochemists had assumed up to that point
o Proteins are notoriously heat-sensitive
o DNA is very resistant to damage by heat

After Griffith published his work, the nature of the transforming principle
was exlpored further by using experimental approaches that incorporated
various biochemical techniques
B. The Experiments of Avery, MacLeod and McCarty (1940s)
Page 8
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1

Avery, MacLeod and McCarty realized that Griffith’s observations could be
used to identify the genetic material

By the 1940s, it was known that DNA, RNA, proteins and carbohydrates are
major constituents of living cells

They therefore prepared cell extracts from type IIIS cells containing each
of these macromolecules
o Only the extract that contained purified DNA was able to convert
type IIR into type IIIS
o Therefore, they concluded that DNA is is “the transforming principle”
See Figure 9.3, Brooker
C. Hershey and Chase Experiment with Bacteriophage T2 (1952)


In 1952, Alfred Hershey and Marsha Chase provided further evidence that
DNA is the genetic material
They studied the bacteriophage T2
o It is relatively simple since its composed of only two macromolecules,
DNA and protein
Inside the
capsid
Made up
of protein
Page 9
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
See Figure 9.5, Brooker
The Hershey and Chase experiment can be summarized as follows:

Used radioisotopes to distinguish DNA from proteins
 32P labels DNA specifically
 35S labels protein specifically

Radioactively-labeled phages were used to infect nonradioactive Escherichia
coli cells
o After allowing sufficient time for infection to proceed, the residual
phage particles were sheared off the cells
 Phage “ghosts” and E. coli cells were separated
 Radioactivity was monitored using a scintillation counter

Their hypothesis was that only the genetic material of the phage is injected
into the bacterium and that the location of the isotope labeling at the
conclusion of the experiment would therefore reveal which type of molecule
(protein or DNA) is the genetic material.
See Figure 9.6, Brooker
IV. THE STRUCTURE OF NUCLEIC ACIDS
DNA is a large macromolecule with several levels of complexity
1.
2.
3.
4.
Nucleotides form the repeating units
Nucleotides are linked to form a strand
Two strands can interact to form a double helix
The double helix folds, bends and interacts with proteins resulting in a
3-D structures known as chromosomes
Page 10
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
Three-dimensional structure
The nucleotide is the repeating structural unit of DNA and RNA. It has three
components
 A phosphate group
 A pentose sugar
 A nitrogenous base
See Figure 9.8 and 9.9, Brooker



Nucleotides are covalently linked together by phosphodiester bonds
o A phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon
of another
Therefore the strand has directionality
o 5’ to 3’
The phosphates and sugar molecules form the backbone of the nucleic acid
strand and the bases project inward from the backbone
See Figure 9.11, Brooker
Page 11
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
A Few Key Events Led to the Discovery of the Structure of DNA:

In 1953, James Watson and Francis Crick discovered the double helical
structure of DNA

The scientific framework for their breakthrough was provided by other
scientists including:
o Linus Pauling
 In the early 1950s, he proposed that
regions of protein can fold into a
secondary structure called an a-helix
 To elucidate this structure, he built
ball-and-stick models
o Rosalind Franklin and Maurice Wilkins
 She worked in the same laboratory as
Maurice Wilkins
 She used X-ray diffraction to study
wet fibers of DNA
The diffraction pattern is
interpreted
(using mathematical
theory)

She made marked advances in X-ray diffraction techniques with
DNA
Page 12
Modified from http://www.mhhe.com/brooker
BIO 184

Fall 2006
LECTURE 1
The diffraction pattern she obtained suggested several
structural features of DNA:
 Helical
 More than one strand
 10 base pairs per complete turn
o Erwin Chargaff
 Chargaff pioneered many of the biochemical techniques for the
isolation, purification and measurement of nucleic acids from
living cells
 It was already known then that DNA contained the four bases:
A, G, C and T
 He postulated that an analysis of the base composition of DNA
in different species may reveal important features about the
structure of DNA
 He performed an analysis of the nucleotide composition of the
cells of many different species and always found that the
amount of cytosines = guanine and the amount of adenine =
thymine. A small sample of his data is shown in the table below.

This observation became known as Chargaff’s rule
o It was crucial evidence that Watson and Crick used to
elucidate the structure of DNA
Page 13
Modified from http://www.mhhe.com/brooker
BIO 184

Fall 2006
LECTURE 1
Familiar with all of these key observations, Watson and Crick set out to
solve the structure of DNA
 They built ball-and-stick models that incorporated all known
experimental observations and finally hit on the correct
structure in 1953
 Watson, Crick and Maurice Wilkins were awarded the Nobel
Prize in 1962
o Rosalind Franklin died in 1958 (at the age of 39 from
leukemia, probably induced by exposure to X-rays), and
Nobel prizes are not awarded posthumously
The Watson-Crick Double-helical Model of DNA:


Two strands are twisted together around a common axis
o There are 10 bases per complete twist
o The two strands are antiparallel
 One runs in the 5’ to 3’ direction and the other 3’ to 5’
o The helix is right-handed
 As it spirals away from you, the helix turns in a clockwise
direction
The double-bonded structure is stabilized by
1. Hydrogen bonding between complementary bases
 A bonded to T by two hydrogen bonds
 C bonded to G by three hydrogen bonds
2. Base stacking
 Within the DNA, the bases are oriented so that the
flattened regions are facing each other

There are two asymmetrical grooves on the outside of the helix
1. Major groove
2. Minor groove

Certain proteins can bind within these grooves and can thus interact with
a particular sequence of bases
Page 14
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
Page 15
Modified from http://www.mhhe.com/brooker
BIO 184

Fall 2006
LECTURE 1
To fit within a living cell, the DNA double helix must be extensively
compacted into a 3-D conformation
o This is aided by DNA-binding proteins
RNA Structure

The primary structure of an RNA strand is much like that of a DNA
single strand of DNA

RNA strands are typically a few dozen to several thousand nucleotides in
length
Page 16
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1

In RNA synthesis, only one of the two strands of DNA is used as a
template

Although usually single-stranded, RNA molecules can form short doublestranded regions
o This secondary structure is due to complementary base-pairing
 A to U and C to G
o This allows short regions to form a double helix
Different types of RNA secondary structures are possible

Page 17
Modified from http://www.mhhe.com/brooker
BIO 184
Fall 2006
LECTURE 1
Noncomplementary regions
Have bases projecting away
from double stranded regions
Also called
hair-pin
Complementary regions
Held together by
hydrogen bonds

Many factors contribute to the tertiary structure of RNA including:
o Base-pairing and base stacking within the RNA itself
o Interactions with ions, small molecules and large proteins
The tertiary structure of tRNAphe, the
transfer RNA that carries phenylalanine
Page 18