CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The first pillar of life is a Program.

By program I mean an organized plan that describes both

the ingredients themselves and the kinetics of the
interactions among ingredients as the living system
persists through time. For the living systems we observe
on Earth, this program is implemented by the DNA that
encodes the genes of Earth's organisms and that is
replicated from generation to generation, with small
changes but always with the overall plan intact. The
genes in turn encode for chemicals--the proteins, nucleic
acids, etc.--that carry out the reactions in living systems.

It is in the DNA that the program is summarized and

maintained for life on Earth.”
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The second pillar of life is

IMPROVISATION.

Because a living system will inevitably

be a small fraction of the larger universe
in which it lives, it will not be able to
control all the changes and vicissitudes
of its environment, so it must have some
way to change its program. If, for
example, a warm period changes to an
ice age so that the program is less
effective, the system will need to change
its program to survive.

In our current living systems, such

changes can be achieved by a process of
mutation plus selection that allows
programs to be optimized for new
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The third of the pillars of life is

COMPARTMENTALIZATION.

All the organisms that we consider

living are confined to a limited
volume, surrounded by a surface
that we call a membrane or skin
that keeps the ingredients in a
defined volume and keeps
deleterious chemicals--toxic or
diluting--on the outside. Moreover,
as organisms become large, they
are divided into smaller
compartments, which we call cells
(or organs, that is, groups of cells),
in order to centralize and specialize
certain functions within the larger
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The fourth pillar of life is ENERGY.

Life as we know it involves movement--of chemicals, of the body, of

components of the body--and a system with net movement cannot be
in equilibrium. It must be an open and, in this case, metabolizing
system. Many chemical reactions are going on inside the cell, and
molecules are coming in from the outer environment--O2, CO2, metals,
etc. The organism's system is parsimonious; many of the chemicals are
recycled multiple times in an organism's lifetime (CO2, for example, is
consumed in photosynthesis and then produced by oxidation in the
system), but originally they enter the living system from the outside,
so thermodynamicists call this an open system. Because of the many
reactions and the fact that there is some gain of entropy (the
mechanical analogy would be friction), there must be a compensation
to keep the system going and that compensation requires a continuous
source of energy. The major source of energy in Earth's biosphere is
the Sun--although life on Earth gets a little energy from other sources
such as the internal heat of the Earth--so the system can continue
indefinitely by cleverly recycling chemicals as long as it has the added
energy of the Sun to compensate for its entropy changes.”
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The fifth pillar is REGENERATION.

Another system for regeneration is

the constant resynthesis of the
constituents of the living system
that are subject to wear and tear.
For example, the heart muscle of a
normal human beats 60 times a
minute--3600 times an hour,
1,314,000 times a year, 91,980,000
times a lifetime. No man-made
material has been found that would
not fatigue and collapse under such
use, which is why artificial hearts
have such a short utilization span.
The living system, however,
continually resynthesizes and
replaces its heart muscle proteins
as they suffer degradation; the
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The sixth pillar is ADAPTABILITY.

Improvisation is a form of adaptability, but is too slow

for many of the environmental hazards that a living
organism must face. For example, a human that puts a
hand into a fire has a painful experience that might be
selected against in evolution--but the individual needs
to withdraw his hand from the fire immediately to live
appropriately thereafter.

That behavioral response to pain (a reflex) is essential

to survival and is a fundamental response of living
systems that we call feedback.”
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“Finally, and far from the

least, is the seventh pillar,
SECLUSION.

By seclusion, in this
context, I mean something
rather like privacy in the
social world of our
universe.”
 CHEME 355
Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“At the present time the way in which mutation and

selection (survival of the fittest) has worked over
evolutionary time no longer seems to apply to Homo
sapiens. We have become more compassionate, less
demanding. Perhaps a newer approach--longer life
and deliberate changes in the program by a supreme
council of wise Solomons--could be substituted for the
cruder survival-of-the-fittest scenario.

I do not necessarily advocate such a drastic change in

the current mechanism of improvisation, which has
served us well over the centuries, but am only
pointing out that there is the possibility to change
particular mechanisms as long as we maintain the
pillars.”
 CHEME 355
Engineering/Technology

"All around I see evidence of the impact of science on

society. This is so obvious and so well known that
little more remains to be said about it. Science and
the technologies it has spawned form the basis of all
human activity, from the houses that we live in, the
food that we eat, the cars that we drive, to the
electronic gadgetry in almost every home that we use
to remain informed and entertained.”

Brenner, S. (1998) The impact of science on society.

Science 282: 1411-1412.
 CHEME 355
Genotype - Phenotype Correlation

The April 1998 issue of Life magazine

ran a cover story, complete with a
double-helix spanning the length of the
page, boldly titled "Were You Born That
Way?" The subtitle left no doubt about
the answer: "Personality, temperament,
even life choices. New studies show it's
mostly in your genes.”

Allen, G.E. (2001) Is a new eugenics

afoot? Science 294: 59-61.
 CHEME 355

Geneticist: A gene is a trait

Phenotype.
In the mid-1800s, a monk named Gregor Mendel,
working in Brno in the Czech Republic, observed
that the offspring of certain plants had physical
characteristics similar to the physical
characteristics of the plants' parents or
ancestors. Mendel set out to examine and
quantify the physical traits in pea plants (because
of their speedy reproductive cycles) in an attempt
to predict the traits that would occur in future
generations.

Mendel counted many thousands of instances of

seven different traits, including plant height,
flower color and position, seed color and shape,
and pod color and shape, and concluded that
certain particles or "factors" were being
transmitted from parent to offspring and so on,
thus providing a connection from one generation
to the next. Mendel suggested that these factors
were directly responsible for physical traits. His
interpretation of the experimental data further
suggested that each individual had not one, but
two factors for each trait, and that these factors
interacted to produce the final physical
 CHEME 355

Systems Biologist: A gene is a component in a network of reciprocal interactions

between cells and environment
 CHEME 355
Evolutionary Biologist: A gene is an agent of change
 CHEME 355

It is sequencing the genomes of

other animals to help biologists
better understand the construction
of the human genome.

These genome databases are new

frameworks for organizing all
biological and medical knowledge,
much as the periodic table of
elements organizes all of chemistry.

Humans have far fewer genes than

was generally expected to be the
case. The fruit fly has almost 14,000
genes, the roundworm 19,000, and
humans only 30,000 or so.
 CHEME 355

About the only thing humans have in

common with mice is that we are fellow
mammals.

Yet, of the 26,000 confirmed human

genes, only 300 had no counterpart in the
mouse.

On this basis, the chimpanzee, our closest

relative, is expected to have essentially
the same set of genes as humans.
 CHEME 355

Pathologist: A gene is a mutation

 CHEME 355
Gerontologist: Aging may be caused by genes wearing out
 CHEME 355

Biotechnology: A Gene is a Product to Manufacture at Scale

Recombinant DNA Technology.

A plasmid and the gene of interest are both
cut with the same restriction endonuclease.
The plasmid and gene now have
complementary "sticky ends." They
are incubated with DNA ligase, which
reforms the two pieces as recombinant
DNA.

Recombinant DNA is allowed to transform a

bacterial culture, which is then exposed to
antibiotics. All the cells except those which
have been encoded by the plasmid DNA
recombinant are killed, leaving a cell
culture containing the desired recombinant
DNA.

DNA cloning allows a copy of any specific

part of a DNA (or RNA) sequence to be
selected among many others and produced
in an unlimited amount. This technique is
the first stage of most of the genetic
engineering experiments: production of
DNA libraries, PCR, DNA sequencing, et al.
 CHEME 355
Intellectual Property

A gene is a proprietary product

(research university)
 CHEME 355
Society

A gene is a political issue

 CHEME 355

Genetic flow of information

 CHEME 355
Technological advances

The preceding fifty years has been a time of rapid and profound
technological change. Elucidation of the genetic flow of biological
information (i.e. information flow from DNA to RNA to protein) has
provided for:

development of recombinant DNA technology

rise of molecular cell biology
advent of intellectual property (in biology and medicine)
development of the biotechnology industry
development of transgenic technologies (including human gene
therapy)
elucidation of the modern definition of stem cells
advent of mammalian cloning technology
 CHEME 355

The Requirements of Genetic Material

Once it had been accepted that there was genetic transmission of
traits, the search began for the factor that carried the information. It
was established that the following characteristics were required of
genetic material:

It must be able to replicate, in order to be in each cell of a growing

organism.

It must be able to control expression of traits:

traits are determined by the enzymes and proteins that act within us;
these proteins are determined by their sequences;
therefore, the genetic material must be able to encode the sequence
of proteins.
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CHEME 355
The Search for Genetic Material

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 CHEME 355

Hereditary Material is Bound on Chromosomes

At the turn of the century, two developments in technology allowed scientists
to observe material inside the cell nucleus: the construction of increasingly
powerful microscopes and the discovery of dyes or stains that selectively
colored the various components of the cell. Long, thin, rod-like structures,
which tended to become colored when the cell was treated with certain stains,
called chromosomes were observed in the nucleus.

In addition:

• The number of chromosomes in any cell appeared to double immediately

prior to mitosis.

• Germ cells appeared to have exactly half of the number of chromosomes

found in somatic cells.

• The fertilization of an egg with a sperm cell produces a diploid cell called a
zygote, which has the same number of chromosomes as the somatic cells of
that organism.
 CHEME 355

Proof that the chromosomes were Mendel's hereditary factors did not come
until 1905. Microscopic observations discovered the sex chromosomes. These
chromosomes were named "X" and "Y." Gender was shown to be the direct
result of a specific combination of chromosomal material, and sex became the
first phenotype (physical characteristic) to be assigned a chromosomal
location - specifically the X and Y chromosomes.

Quantitative analysis of chromosomes showed a composition of about 40%

DNA and 60% protein. At first, it seemed that protein must be responsible for
carrying hereditary information, since not only is protein present in larger
quantities than DNA, but protein molecules are composed of twenty different
subunits while DNA molecules are composed of only four. It seemed clear that
a protein molecule could encode not only more information, but a greater
variety of information, because it possessed a substantially larger collection of
ingredients with which to work.
 CHEME 355
DNA is the genetic material, Avery et al. 1943

The Transforming
Principle - DNA Might be
the Genetic Material
DNA was first identified in 1868 by
Friedrich Miescher, a Swiss biologist.
He called the substance nuclein,
noted the presence of phosphorous,
and separated the substance into a
basic part (which we now know is
DNA) and an acidic part (a class of
acidic proteins that bind to basic DNA).

In 1943, Oswald Avery, Colin Macleod,

and Maclyn McCarty, at the Rockefeller
Institute, discovered that different
strains of the bacterium
Strepotococcus pneumonae could
have different effects on a mouse. One
virulent strain could kill an injected
mouse, and another avirulent strain
had no effect.
 CHEME 355
DNA is the genetic material, transfection
 CHEME 355
DNA is the genetic material, mutation
 CHEME 355
Genetic flow of information is carried out inside of cells
 CHEME 355
Genetic flow of information is carried out inside of cells
 CHEME 355
Chromosomal defects; point mutations
CHEME 355
Genotype-phenotype
 CHEME 355

Post-mortem
x-ray
OI type II

OSTEOGENESIS IMPERFECTA
Definition
Clinical syndromes
Demographics
Prominent phenotype
- bone weakness
- abnormal mineralization

Likely candidate for mutation?

Type I collagen!
 CHEME 355
Collagen structure & biosynthesis / biomineralization

Structure

Biosynthesis
 CHEME 355
Initial Studies

Penttinen, R.P., Lichtenstein, J.R., Martin, G.R., and McKusick, V.A. (1975)
Abnormal collagen metabolism in cultured cells in osteogenesis imperfecta.
Proc Natl Acad Sci U S A 72:586.

Barsh, G.S., and Byers, P.H.(1981)

Reduced secretion of structurally abnormal type I procollagen in a form of osteogenesis
imperfecta.
Proc Natl Acad Sci U S A 78:5142.

Barsh, G.S., David, K.E., and Byers, PH. (1982)

Type I osteogenesis imperfecta: a nonfunctional allele for pro alpha 1 (I) chains of type
I procollagen.
Proc Natl Acad Sci U S A 79:3838.

Chu, M.L., Williams, C.J., Pepe, G., Hirsch, J.L., Prockop, D.J., Ramirez, F. (1983)
Internal deletion in a collagen gene in a perinatal lethal form of osteogenesis
imperfecta.
Nature 304:78.
 CHEME 355

Two Classes of Mutation

Structural and Null

 CHEME 355

Glycine mutations are the most common structural mutations

Gly - X - Y - Gly - X - Y

Ala, Asp, Arg, Ser, Cyc, Trp, Val, Tyr, Term

Gly Asp

Asp
Gly

Gly Gly
Gly Gly

Normal Abnormal G A T C G A T C
CHEME 355
Inheritance patterns

New Accident
 CHEME 355
Inheritance patterns

OI IV

OI II

Somatic Mosaicism
 CHEME 355
Inheritance patterns

OI II OI II

Gonadal Mosaicism
 CHEME 355

Gly Asp

G A T C G A T C

Post-mortem x-ray image