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                     MICROBIOLOGY 101/102 INTERNET TEXT



                          Updated: 10/22/99




                      MICROBIOLOGY | GENETICS | MEDICAL


                          THE YEAR IN MICROBIOLOGY

                                  Why Sex?

                 Evolution of Antibiotic Resistant Bacteria

                  Genes that Affect Personality: Depression



   * Introduction To Genetic Lectures
        o Chemistry of Love
        o Recent History of Genetics
             + Gregor Mendel
             + History from Mendel to Transformation
             + Transformation
             + One Gene, One Enzyme
             + Structure of DNA
                  + Chemistry of genes; review
   * Basic Genetic Terminology
        o What is The Science of Genetics
   * DNA Replication
   * The Genetic Code
   * Introduction to Mutation
   * Alleles
   * Mutagens and Carcinogens
   * Importance of Studying Mutants
        o Dominant and Recessive Genes
   * Diploid Sex
        o Recombination
   * Microbial Sex
   * Transcription and Translation
        o RNA Polymerase
        o Promoter
        o Sense Strand
        o Stop Signal
        o Translation
             + Ribosome
             + Transfer RNA
             + Anticodon
   * Control of Protein Synthesis
   * Gene Regulation by control of protein synthesis.
        o Introduction to regulation; basic principles.
        o E. coli and the Foundations of Regulation
   * Lactose Operon
        o Lac-Mutants
        o Constitutive Lactose Mutants
   * Hypothesis of Lac-Regulation.
        o Induction of Lactose Utilization
        o Regulatory Gene
        o Lactose Structural Genes
        o Lactose Repressor Protein
   * Repressible Proteins
   * Self Test


 The universal principle of molecular recognition. A typical cell contains a
number of molecules exposed to the environment and in communication with it.
These molecules act as the "eyes, ears and nose" of a cell. They contain, as
 part of each molecule, specific portions called RECEPTORS or BINDING SITES.
    Other molecules in the environment contain specific components called
    LIGANDS. Ligands are sections or regions of a molecule that have the
   characteristic of binding or attaching (docking) specifically to unique
receptors on the cells. Following this attachment a message is passed to the
    interior of each cell involved as to the situation it has found. This
 information, in turn, triggers the COMMAND CENTER of each cell to carry out
  a series of preprogrammed responses based on the data it has received. We

  will discuss some of these responses throughout the course. Permission to
             use this cartoon was granted by Sigma Chemical Co.




We are voyagers in an informational revolution sea. This revolution is
composed of a PHYSICAL and a BIOLOGICAL component. The electronic
informational portion utilizes computers, vast data storage capacity and
speed-of-light data exchange technology. The biological revolution consists
of nothing less than an ultimate understanding of the MECHANISTIC nature of
life. Alone, each of these technologies is bringing about the most rapid
changes humans have ever experienced. Combined, they form an explosive
potential for change that is far greater than the sum of their separate
effects. Either revolution is capable of changing the human condition beyond
anything previously imagined, but together the ultimate possibilities are
impossible to grasp. (Sci. Am. Sept. 1995)

Even a person with only a basic
understanding of these technologies and
a feeble imagination can conjure up the
reasonable possibility of our
prolonging human life indefinitely by
techniques of gene and organ
transplantation or tissue regeneration
(Sci Am. Oct 1995). After all, tissue
growth is simply a matter of turning on
& off the correct genes. Whereas,
transplantation merely requires a
knowledge of how to regulate the immune


Articles in Nature Oct. 12, 1995, report that scientists can now: For an
overview of the field of genetics visit this site.

CONTROL PLANT FLOWERING. This means that we will be able to grow tropical
plants in cold climates because we can turn on their flowering genes for
fruit production whenever we want. The fact that such control has been
achieved in plants suggests that control of animal genes is not far behind.

The first cases of gene replacement therapy have been underway for several
years now and there are journals dedicated solely to this form of treatment
(TIME Mag.: Oct 9 1995, pg. 62) .The growth of complete higher animals in
vitro is probably no more than 10 to 20 years in our future and it requires
no leap of brilliance to realize that what can be done for the cow or dog
can also be done for the HUMAN.

   How do you feel about that possibility? Should we do it when we can or
                           should we leave it be?


The cloning of a sheep from one of its cells in 1997 and of mice and cattle
in 1998 suggests the possibility that this technology may be a high school
biology lab demonstration by the year 2010. Almost weekly reports of new
cancer genes appear in the news and, less well reported are gains in our
understanding of gene regulation. Within 20 years many hereditary diseases
will yield to our growing knowledge and by the year 3000, such diseases are
likely to be footnotes in medical history CDs (books).

Scientists are carefully, but nervously, teasing
apart the relationship between genes and  behavior.
(TIME Oct 2, 1995 & SCI AM. Oct 1995; Consilience by
E. O. Wilson). The first to yield will probably be
conditions like shyness, manic depression, and
schizophrenia. Once the chemical causes and cures of
these inheritable diseases are discovered, the
unraveling of the chemical nature of intelligence
itself, as well as the chemical bases of emotions
will surely follow. The temptation to improve one's
own and that of one's children's intelligence will
prove irresistible to the rich and powerful (read the
ED-book "Remaking Eden" which is all about this). The
wild dash into the future of biological knowledge is
fueled by the parallel growth in an ability to
transmit, find and organize this flood of new
information (e.g., the Internet) which, in turn, fertilizes creative minds
and spurs the further growth of knowledge. If you're interested in a
discussion of the ethics involved. see Science 274:488(1996).

                        EXTRA CREDIT COMMENTARY 8A:
      How many of you know someone who suffers from migraines or manic
    depression? If so ask them if they could cure a human fetus of these
              disorders, would they do it? What would you do?


It is not unreasonable to consider that the electronic and biological
revolutions will eventually merge to create ELECTRONICALLY LINKED HUMANS
(e.g.  the movie FIRST CONTACT) able to gather, think and exchange
information at the speed of light using the entire reservoir of human
knowledge. After all, nerve impulses are only a type of electrical current
and there is no reason why the additional growth of brain cells can't
ultimately be controlled.

Whether you view such a future with HORROR or JOYFUL ANTICIPATION, without
knowledge you will be helpless to influence the direction it takes and the
type of world it produces. Educated people must be available to help read an
ethical compass to find direction in this stormy technological sea and the
knowledge-challenged (ignorant) will be in NO position to do this. As we
embark on the beginnings of our knowledge journey consider the following
sample ETHICAL QUESTIONS, for they are here now and can not be avoided.
Note---when I first came up with some of these suggestions they were only in
my imagination, yet in only ~3 years many of them have become realities:

                        EXTRA CREDIT COMMENTARY 8B:
     Pick any one of the scenarios below and express your views on its
   ethics and whether it should be legal or illegal. A strictly religious
     argument is not acceptable although you may bring in the impact of
                 religion on a society's view of morality.


   Mike Carter

   SCENARIO A. For women who are infertile, but have a functional uterus,
   and for those parents carrying known or unknown genetic defects.

   My personal view on this is one of acceptance. I am a male and I have
   never had a child or went through the process of raising a child. I
   feel that if you are unable to have children, you should be given that
   opportunity. I had a teacher in high school (I attended a catholic
   high school) that was having a very bad time getting pregnant. She had
   gotten pregnant before and lost the child. All of her students saw the
   struggle that she went through and it was horrible. Finally she had a
   child and she adored this child, even though this child was deformed
   which also makes it hard. This child?s parents showed so much love for
   him and raised him in a wonderful home. They wanted this child so bad
   that it did not matter if the child was purple this couple would of
   loved it just as much. I feel that if you have to resort to human
   embryos to get a child, you and your spouse are obviously serious
   about a child and ready to do whatever it takes.


 HUMAN EMBRYOS for sale.

SCENARIO A. For women who are infertile, but have a functional uterus, and
for those parents carrying known or unknown genetic defects.

   * TV spot advertising the THE PERFECT EMBRYO EMPORIUM:  Our motto is "We
     test every one of our embryos for all 433 currently known genetic
     diseases;-with us YOU KNOW WHAT YOU'RE GETTING!":
        o Commercial: Well dressed smiling woman ordering an embryo: "I'll
          take a white, male embryo. Put it on my Credit card please.
          Deliver it to the 'Happy Mom' Implantation Clinic next Monday at 9
          AM. My name is.........".
        o We also test your own embryos for genetic defects before
          implantation to insure that you have the HEALTHY child every
          person deserves. Inquirer today about our "Defect-Free Embryo
   * NEW BUSINESS OPPORTUNITIES. "Are you a healthy young woman who wants to
     make $5,000 for that new car, new outfit or to pay off your college
     loans? If your heredity qualifies you, your eggs or embryo may be worth
     BIG BUCKS! Give us a call at "Embryos 'R Us" at 555-BABY.
        o 2/17/1999: Advertisement in Daily Evergreen offering $2500-5000 to
          be an egg donor by a company in Spokane, WA.
        o A few weeks later a couple offered $50,000 for an egg from a tall
          female with a 1400 or better SAT score; any takers in the

SCENARIO B. What about those parents who are just TOO BUSY to be pregnant?

   * NEW BUSINESS OPPORTUNITIES. "Are you and your husband too busy to have
     a baby? Are your jobs too demanding and too important to give you time
     off to become the great Mom & Pop you know you can be? If so, visit us
     at SURROGATE RENT-A-WOMB INC; we guarantee a first class womb for your
     little angel. Our wombs are all between the optimal bearing years of 20
     to 25." Our motto: "You Provide the EMBRYO and We Provide the Womb
     Worthy of your Little Prince or Princess".

SCENARIO C. For those of you whose genes just TOO FANTASTIC for the world to
lose?: Visit CLONE WORLD!

   * Are your genes too great to DIE? Does the world need more people like
     YOU? Is there just not enough of you to go around!
     800-EGO-TRIP. We'll take care of it all; the cloning and surrogates.
     Ask about our discount deal on five or more "fantastic me" clones.

SCENARIO D. What about the embryos that don't "move" or go out of style?

   * TV Spot:
          OTHER BARGAINS".
   * "On the way out George, could you dump these embryos in the trash
     please? We need space for the NEW SUMMER LINE of Leonardo DiCaprio
     embryos (with this one we're going to "sink" the competition)".

Click here or here for a discussion on genetics and ethics.


                             CHEMISTRY OF LOVE

It appears that even LOVE is a tool of the genes. Data is accumulating that
the behavior we call love is stimulated (induced) by a group of CHEMICALS.
What is the evolutionary SURVIVAL ADVANTAGE of having a love-chemical that
kicks in when you see babies?

        EXTRA CREDIT COMMENTARY 8C: Future letter to "dear Abbie":
    "I'm going with the nicest person who tells me they LOVE ME and want
   to get married, but they are taking LOVE HORMONE replacement treatment
    (see 6A in Chap 6 before answering this). Can I be sure they really
           means it. Signed Puzzled In Love". Dear Puzzled....:



                        MODERN HISTORY OF GENETICS

                               GREGOR MENDEL

Considering the problem between religion and genetics (evolution), it is
ironic that the history of modern genetics began in the 1860s with an
AUGUSTINIAN MONK named Gregor Mendel. Mendel, who lived in an Austrian
monastery, was in charge of the monastery gardens. He noticed that certain
physical characteristics of the peas could be predicted in the offspring by
knowing the characteristics of the parent plants. So to amuse himself Mendel
performed a series of controlled genetic crosses of pea plants. That is, he
carefully collected the pollen (sperm) of plants with certain physical
characteristics and fertilized other plants with characteristics differing
from the pollen donor. He collected the seeds from these crosses, planted
them and recorded the characteristics of the resulting plants. He determined
how these characteristics related both quantitatively and qualitatively to
those of the parents and concluded the following:

 That INVISIBLE MARKERS carry physical traits from parents to

 That TWO MARKERS exist for each trait.

 That some markers are DOMINANT over other forms of a marker.

 That each parent's reproductive cells carried ONE OF EACH SET of
markers that come together in the new plants.

Mendel's observations, published in an obscure journal, lay unnoticed for
about 40 years. You can read some of Mendel's work if you are into that:
Click here, and then follow URL to Mendel's paper (Adobe Acrobat required).


In the early 1900s other biologists began to study heredity and Mendel's
results were rediscovered, repeated and verified. By the 1920's the word
GENE, referring to UNITS OF INHERITANCE, had been coined. But the chemical
nature of these units remained unknown. It was clear that heredity was
complex, so genes must be complex. The years between 1910 and 1930 were
years of great discoveries about PROTEINS and #ENZYMES. As work on proteins
showed them to be composed of combinations of the 20 different amino acids,
this complexity made proteins candidates for carriers of genetic
information. In the late 1800s the events that occur when cells divide had
been seen and studied and the nucleus was assumed to have some major role in
cell life. By the late 1920s the nucleus of cells had been thoroughly
studied, its basic chemical composition determined from isolated nuclei,
chromosomes and the MITOTIC EVENTS (the organized movement and arrangement
that chromosomes undergo during cell division) had been defined and the idea
that the nucleus seemed to be where genes resided was taking hold within the
scientific community. So it was puzzling that nuclei CONTAINED LITTLE
PROTEIN, and in fact the major nuclear chemical component of nuclei seemed
to be a rather simple polymeric molecule, DNA. The air of the scientific
meetings of this period were rent with violent arguments over the nature and
action of genes.


                         RECENT HISTORY OF GENETICS

Modern or MOLECULAR GENETICS begins in 1928 with
an experiment performed by FRED GRIFFITH in
England using the bacterium Streptococcus
pneumonia in mice. Prior to antibiotics S.
pneumonia was a major cause of death in humans.
Because this bacterium is also lethal to mice
Griffith was studying it in mice in hopes of
shedding some light on the human form of the
disease. It was known that a mutation in the
bacteria that caused it to lose its prominent
#capsule would render it AVIRULENT (or unable to
cause the disease in mice). Thus when living
capsulated and the non-capsulated forms were
injected into mice only the mice that had
received the former died (Fig. 1). However, if
the encapsulated bacteria were first killed by
gentle heating the mice also survived. Reasoning
that the capsule was crucial to pathogenicity,
Griffith decided to see if injecting a MIXTURE
of dead-encapsulated bacteria with living
non-encapsulated mutants would kill the mice.
This mixture killed the mice, which was
surprising since none of the components,
including isolated bacterial capsule were
lethal. When Griffith isolated bacteria from the
dead mice (#Koch's Postulates) he found that
they had been TRANSFORMED into stable
encapsulated virulent forms. That is, the
isolated cells passed the ability to produce
capsules on to their daughter cells. Three other
scientists took up the task of figuring out the
nature of the change in virulence. They verified
that capsular material itself did not killed the
mice, BUT LIVING BACTERIA that had gained the
genetic ability to now make CAPSULE were the lethal agent. Further, their
studies indicated that the genetic nature of the capsulated-bacteria that
were recovered from the dead mice had been changed; or that the DEAD
capsulated forms had "risen from the dead". The material that caused the
change was named "THE TRANSFORMING PRINCIPLE". Once it was realized that the
transforming principle was a gene, the study took on a new intensity. But
the crucial question remained: "What is a gene made of?". At first most
scientists concluded that the transforming principle must be protein since
only protein was COMPLEX enough to contain the mass of necessary genetic
information needed for life. After 10 years of work, the   transforming
principle was separated away from all other cellular components, including
proteins. They found that transforming principle appeared to be composed
only of DNA. However, even when transforming principle seemed to be PROTEIN
FREE other scientists claimed that DNA, could not be the STUFF OF GENES
because it was "just too simple". The definitive experiments involved
showing that the transforming principle was not destroyed by enzymes that
DIGESTED PROTEINS (PROTEASES) but that it was destroyed by a newly isolated
enzyme, DNase, that degraded DNA. Their announcement in 1944, as to the
chemical nature of genes, marks the beginning of the era of molecular


    [no image available] CRITICAL THINKING QUESTIONS: Can you relate the
  discovery of transformation in mice to Pasteur's observation that "Chance
                         favors the Prepared Mind"?

The above is an example of "PURE or BASIC SCIENCE" can you tell someone what
     those terms mean in the context of this story?   How does the term
                     "serendipity" relate to this story?



In the 1940s, emerging data was showing that the TOOLS of a cell were
enzymes and genetic experiments had verified  MENDELIAN genetics that there
was a 1:1 effect between mutations and the visible changes they induced. G.
Beadle, working on the genetics of mold mutants, reasoned that each enzyme
must be made by ONLY ONE GENE; he called this the "ONE-GENE-ONE-ENZYME"
concept. This data, combined with the finding that the transforming
principle was DNA (i.e. genes were composed of DNA) began to focus peoples
thoughts on just how this large, but chemically simple, molecule containing
only four bases (NUCLEOTIDES) and sugar and phosphate could contain the
genetic information required to code for protein synthesis. Although we now
know that many enzymes are composed of the protein products of 2 or more
genes that associate together to produce a functional "enzyme", Beadle's
basic theory remains correct, although somewhat modified to read:


                       THE FINAL PIECE OF THE PUZZLE

The final piece of evidence fell into place in 1953, when a brash young
American and an equally brash young Englishman (J. Watson & F. Crick
respectively), using data from other people's labs, built a model of DNA.
This model involved PAIRING the nucleotides bases adenine with thymine and
cytosine with guanine. In one of those dramatic moments that change the
course of history, they realized the significance of their findings, for it
elegantly & simply explained the basic workings of genetics. They showed
that the fundamental unit of DNA involves the helical intertwining of two
chains held together by #HYDROGEN BONDS through the pairings of A-T and G-C.
One of many ironies of Watson & Crick's discovery was that they beat L.
Pauling, who had won the Nobel Prize for discovering the HYDROGEN BOND, and
who was also working on the structure of DNA to the correct model because
Pauling made a simple beginning-student's mistake in molecular modeling. As
in the Olympics, the Gold goes to those who win by the smallest of margins.
To earn extra credit view the film "The Double Helix" available in SLIC.



                      REVIEW OF THE CHEMISTRY OF GENES

 The general structures of the FIVE bases, the pentose sugars and
phosphate in DNA and RNA are seen in the accompanying pictures.
[eyescan.gif (247 bytes)] Click here to see the AT & GC base pairing.

 DNA contains phosphate, the pentose sugar deoxyribose and the four
bases adenine, thymine, guanine and cytosine.

 RNA contains phosphate, the pentose sugar ribose and the four bases
adenine, uracil, guanine and cytosine.

 The nucleotide bases pair up in DNA A-T and G-C and in RNA A-U and
G-C. The base pairs are held together by hydrogen bonds. Two HB between A-T
and three between G-C. The two strands are said to be COMPLEMENTARY.

  DNA usually exists as a double stranded molecule whereas RNA is
often single stranded as well as double stranded.
[eyescan.gif (247 bytes)] Click here, & here (Chime views) and here for
other views of the double helix.

 DNA is always genetic material, whereas RNA may have OTHER FUNCTIONS
than that of carrying genetic information. [eyescan.gif (247 bytes)] Click
here to see a comparison of DNA and RNA.

 The chains are composed of alternating sugar-phosphate units (the
SUGAR-PHOSPHATE BACKBONE) with the bases attached to the sugars.

 In the double stranded form the chains exist mostly as a helix, with
the backbone on the outside and the bases facing each other on the inside.
This helix is flexible and can be packaged very tightly.

 The units of RNA and DNA that carry the genetic information in long
LINEAR CHAINS, STRANDS, are called the CHROMOSOMES and the total genetic
complement of an organism is called its GENOME.

 Each daughter cell of an organism receives a complete GENOME from
its parent.



The way genetics effects our lives is a controversial subject. It is
frightening to many people to think that genes control their destiny,
particularly in the area of personality and behavior. The controversy
surrounding the effects of NURTURE (the effect of environment) vs. NATURE
(the effect of heredity) on what kind a person one becomes, is ancient. Many
people believe passionately that their environment is the most critical
factor in their development. For example, if a child goes "bad" the cause is
often attributed to the way his/her parents raised them (nurture), i.e., if
they were taken to church, if they were punished (or not punished) at the
proper times and in the proper way, if they had poor or good parental role
models etc. We jail criminals as a way of "rehabilitating" them, by making
them "change" their behavior to conform that which is acceptable to society.
Yet we are frustrated by the FREQUENT FAILURE of this action to achieve the
intended results; i.e., child molesters often continue to molest children,
some thieves continue to rob, children from "good families" commit terrible
crimes etc. Why does such nurturing-treatment fail so often? Do you have any

All humans become furious if someone suggests that they are genetically
"inferior" because of their race or ethnic origin. Yet paradoxically,
prejudice based on heredity is common; the lack of a gene for empathy
perhaps? We glibly declare that our relatives resemble each other; i.e.,
they "have aunt June's nose; uncle Harry's chin etc.". But, none of us like
to be told we "behave" like another relative; "he has his grandfather's
temper" (grandfather having died before "he" was born). Throughout history
the occupants of countries carefully studied the personalities of the sons
of THEIR RULERS to see if they "inherited" their father's good or bad
personality characteristics, even if the father died when the prince was
young. Thus there is a RELUCTANT RECOGNITION (often unspoken) that genes
play a role in both our physical and behavioral characteristics. The
argument that rages today is HOW MUCH influence do the genes have on our
personalities? What do you think? Are you controlled by your GENES? Do you
have a personality like a near relative?

One reason for the nurture vs. nature controversy is the problem people have
in relating biological evolution to social evolution. The complex social
system evolved by our primitive human ancestors, like that of the chimps and
other hominids of today, had its base in biological evolution. That is, it
was (and is) "instinctive" (in the genes) rather than being reasoned. The
complex social arrangements in human societies that have developed, mainly
since humans collected in settlements in the last 8,000 to 10,000 years,
have evolved ON TOP OF the biologically evolved ones; they have NOT REPLACED
them. This is difficult for most people to accept. For example, one may
train a lion or tiger to be a family pet that lies around the living room
letting the kids crawl over it, but it would be foolish in the extreme to
think that the genetically driven instincts to hunt and kill for food or
mates had been replaced or superceded by the superficial training and a FULL
STOMACH ("Dear, have you seen Tommy? He was playing with our pet TIGER a
while ago."). Rather, the animal has been conditioned to behaved in a
"civilized" way by intensive and constantly reinforced training. This
training is a thin veneer that can easily be torn away by minor changes to
allow the powerful genetic programming to assert itself. If you doubt this,
consider the amount of effort every parent puts into "civilizing" their
children and imagine how the children would develop if left to develop while
totally isolated from human society; it is not a pretty picture.


                      WHAT IS THE SCIENCE OF GENETICS?

GENETICS is the science of heredity. A GENETICIST studies:

 How genes work

 How genes are transferred

 How genes are regulated

 How genes are changed or mutated

As discussed above, humans have known for 1,000s of years that
characteristics could be inherited. Clearly children were observed to
physically RESEMBLE THEIR PARENTS. Further, physical characteristics have
long played an important role in mate selection. Men selected women whose
families had a history of producing strong children and women, in turn,
selected mates who had physical characteristics that indicated an ability to
provide for a family. Farmers, from the inception of agriculture, selected
animals and crops based on desired physical qualities which they expected to
be passed on to their offspring. Our farmer ancestors soon learned to BREED
animals and plants to IMPROVE (select) desired qualities. Thus the practical
SEEDS of genetics have been around for a very long time.

Recent studies have shown that all humans consider physical qualities in
prospective mates that signal "good health" (e.g skin tone, bright/clear
eyes, luxurious hair, physical symmetry) as being beautiful (desirable as
breeding partners). Evolution presumably has taught us that it is important
that our mates be as "robust" as possible because that improves the chances
of the survival of any offspring and hence the survival of "OUR GENES" into
the future.

                        EXTRA CREDIT COMMENTARY 8D:
   Give me your views on how big a part hereditary plays in your behavior
    and personality, and which is more important in making a person what
             they are: nature (genes) or nurture (environment)


   Mike Carter

   I believe that genes play a large part in a person?s personality. But
   I think that the environment you were raised in plays a larger part.
   If you had a bad temper and your parents and friends would let you get
   mad and out of control. Then you would grow up thinking that it was
   expectable to do that. On the other hand if you are scalded every time

   You lose your temper and are out of control you are going to realize
   that there is a negative action that takes place every time you lose
   your temper. Sooner or later you are going to get tired of always
   getting in trouble, yelled at or in some cases hit. Then you will
   think twice before you fly off the handle and lose your temper.
   Another reason that I think environment is important, goes with the
   saying like father like son. I have friends who have been raised
   watching their fathers. In one case he always watched his father be
   disrespectful to his mother, now he has a girlfriend and is very
   disrespectful to her. Another case is the son watched his father show
   his family respect and now this man is 23 and treats his own family
   that he has with a lot of respect. I believe humans can be
   conditioned. How many times have you been dating someone and a friend
   approaches you and says, " you sure have changed since you and Suzie Q
   have been dating" you may have changed for the worse or for better. I
   believe the environment you were raised is the environment was you are
   going to represent, try to find, and feel the most comfortable in that
   environment. I have read research done on the nourishment of babies.
   Babies that have had close relations with their mother were heavier,
   healthier and grew faster than the babies that had minimal contact
   with their mother. Environment is very important.





                              DNA REPLICATION

Although Watson and Crick realized that the double stranded nature of DNA
explained how genes could be copied, the details of replication still are
not fully understood. In considering DNA replication the following points
must be borne in mind:

 DNA replication occurs at a breakneck pace in a bacterium that
divides every 20 minutes; the DNA unwinding at the rate of 20,000 turns/min,
with 300 bases added to the new strands every second. Click here for
excellent images on replication.

 Since mistakes are usually BAD, there must be "PROOFREADING" to see
that the base pairings are correct.

 However, mistakes, called #MUTATIONS, are necessary for evolution to
occur, so NATURE needs some mistakes to happen; but not too many.

 DNA replication occurs "Like two porcupines making LOVE; very


 The first step must involve DNA STRAND SEPARATION in order to allow
the bases on each strand to be exposed for copying.

 The second step involves the pairing up of the proper bases so as to
insure FIDELITY or accuracy of base pairing.

 The third step involves the bonding between the various components
of the NEWLY SYNTHESIZED STRAND. Click here for a site on DNA replication
showing all the major proteins involved.

In the first step an enzyme, DNA POLYMERASE,  binds to the starting point of
replication on the DNA and causes it to SPREAD APART. This allows the
nucleotides (the bases A, T, G, C) to pair up with their complementary bases
on the old parental strands. Then an enzyme, LIGASE, chemically links the
phosphate-sugar backbone components together. The DNA polymerase also has
PROOFREADING ability, in that it checks to see that the base pairing is
correct. If an incorrect base pair (e.g. A-G) is found the DNA polymerase
replaces it with the correct one. This mini-description of DNA replication
is a very ABBREVIATED version of the process; it is far more complex than
this, involving a number of special proteins and additional enzymes.

Once Watson & Crick had defined the basic structure of DNA they, and
everyone else, saw that the sequences of the base pairs could comprise a
linear GENETIC CODE, just as any child realizes that they can make their own
"secret codes" out of combinations of letters and numbers. It also followed
that a GENE then was simply a CODE for a protein and since proteins were
composed of amino acids, the various amino acids must be coded for by at
least 20 DIFFERENT bp sequences. However, determining the exact nature of
the general code and each individual amino acid code word proved to be a
daunting task that was not solved until 1963.

It had been found that proteins had other roles in cells than enzymes. Some
proteins are structural components of the cell (e.g. the #flagella & pili),
other were receptors for chemical signals (i.e., they were the sensing
organs or "noses" of the cells) and still other proteins had a regulatory
role in determining the timing of cellular events. Thus it became clear to
geneticists of the 1950s and 1960s that there had to be genes that coded for
these four types of proteins; ENZYMES, STRUCTURAL, SENSORY and REGULATORY.

It also was clear in the 1960s that the
chromosomes of cells were composed of
further apparent that since each cell
contains the entire complement of an
organism's genes, and these genes
clearly are not expressed (functioning)
in every cell all the time, that there
had to be ways of regulating the process
of protein synthesis.

Prokaryotic cells generally have only a
chromosome contains ONE GENE for each
characteristic; such an arrangement is
said to be HAPLOID. However, eukaryotic cells contain two or more duplicates
of each chromosome, thus each cell has at least TWO copies of each gene. The
eukaryotic cells are said to be DIPLOID. Prokaryotic cells like E. coli
contain about 4,720 genes, but eukaryotic cells can contain over 100,000
genes. The smallest bacteria (Mycoplasma genitalium) so far sequenced
contains 476 genes. Of these, 176 can be inactivated one-at-a-time without
affecting the organism's ability to grow and reproduce. Two mycoplasma
species have 300 genes IN COMMON, so the question arises "HOW MANY GENES ARE
ESSENTIAL FOR LIFE?". To see the circular chromosome or genome of a
prokaryotic cell click here (Java site) and click on the various regions to
see the genes in them.


[no image available]CRITICAL THINKING QUESTION: What types of bacteria might
you predict would have the fewest genes and which type the most? Hint, think


                              THE GENETIC CODE

During the late 1950s and the early 1960s additional facts became clear
about the process of protein synthesis and the genetic code. Data
accumulated to support the proposal that the genetic code was a THREE LETTER
OR TRIPLET CODE. For one thing, there had to be a MINIMUM OF 20 CODE WORDS
for the 20 amino acids. Further, the code had to contain PUNCTUATION, that
is STOP and START code words, otherwise proteins could not be made in
FUNCTIONAL LENGTHS. A simple math calculation shows that a three letter code
was a minimum since the four bases could be arranged in 64 groups of 3 (4 x
4 x 4 = 64). The code could be based on more than a three letter codon, but
as nature is ruthlessly efficient, it appeared unlikely that more than 3
letters would be used. Another piece of the puzzle was the discovery of a
TRANSITORY form of RNA that was in very HIGH CONCENTRATION during peak
protein synthesis. It was proposed that this RNA carried the MESSAGE of a
protein's code from DNA to the protein synthesizing machinery. This RNA was
named MESSENGER RNA or mRNA. Finally, it was noted that cells active in
protein synthesis contain huge quantities of large molecular aggregates
called RIBOSOMES and that these ribosomes were always associated with newly
made protein and mRNA. This became known as the CENTRAL DOGMA. Click here to
see the CENTRAL DOGMA illustrated. Click here and here to see the entire
genetic code.


                           THE ART OF BEING LUCKY

A young postdoc, M. Nirenberg, of apparent average research skills, working
at the National Institutes of Health on a routine enzyme characterization
problem in the early 1960s, attended a seminar in which he heard the #mRNA
theory discussed. Working in the same group as Dr. Nirenberg was a team
studying a RNase that was able to synthesize RNA molecules rather than break
them down if the environment was manipulated properly. The group studying
this RNase had made a number of RNA polymers using controlled combinations
of the four bases in RNA. For example, if you gave the enzyme only uracil it
would make an RNA polymer consisting only of uracil etc. Dr. Nirenberg
reasoned that if the idea of "mRNA" was correct then these RNA polymers
sitting on the shelf of his coworker's labs contained mRNA of KNOWN
COMPOSITION. Since their composition was known and since mRNA coded for
amino acids, one should be able to determine the amino acid code using these
artificial mRNAs to direct protein synthesis in the test tube. When Dr.
Nirenberg took his idea to his boss at the time he was kindly told to
"Forget it, stick to your simple project that is guaranteed to get you an
easy job in some university". Dr. Nirenberg didn't take that advice and
recruited another graduate student (Mrs. Matthaei) to work with him. Within
a short time, using a crude protein synthesizing system from E. coli, they
obtained proteins whose COMPOSITION was DETERMINED by the ARTIFICIAL mRNA
added to the mixture. Following the initial reports of success there was a
"FEEDING FRENZY" of research using this general approach and by 1966 the
entire genetic code was unambiguously known. Dr. Nirenberg subsequently won
the Nobel prize for "sticking to his idea".

[eyescan.gif (247 bytes)] Click here to look at the genetic code, but don't
learn it. Study the code until you understand the term "DEGENERATE".  Which
amino acid has the fewest codons? Which one has the most?

  PERSONAL NOTE: I know this story to be true, because I heard it

from Nirenberg's Boss at the time of his discovery at NIH, with whom I
worked from 1962 to 1964. For a source of pictures of nucleic acids click
the picture.



             We now know the following about the GENETIC CODE:

 The original theory of mRNA carrying the information from DNA


 It is, with a couple of small exceptions, UNIVERSAL.

 It is DEGENERATE, referring to the fact that because of the EXCESS
of code words some amino acids are coded for by more than one 3-letter

 It contains start and stop CODONS (punctuation). There are three
stop codons (PERIODS) and one major start (CAPITAL) codon, although other
codons can be utilized for starting in some systems.

The importance of this discovery can not be overstated. With this
information, man will ultimately be able to "write" any genetic code he
wants for any life form, INCLUDING HIS OWN. An analogy might be that knowing
how to write a language, you can write any story you're capable of imagining
. The universality of this system also supports the #evolutionary concept.



  "What the devil determines each variation?" Written by Charles Darwin in
                        1847 to a fellow scientist.

Although the Sci-Fi movies have given mutants a bad name, WE ARE ALL MUTANTS
and we are walking around with these large brains because of mutations.
Mutations are the events that DRIVE evolution. Evolution occurs because
nature loves VARIATION. Variation is required for survival in a constantly
changing environment. However, the problem with mutations is that they are
random events; a sort of "genetic lottery". Most mutations are BAD, MEAN and
UGLY, but, like the lottery, once in a great while a winner comes up.
Mutations have the following characteristics:

 They are the result of a CHANGE IN THE BASE PAIR SEQUENCE in a
genome DNA or RNA strand. For simplicity I will confine the explanation to
DNA. When the DNA replicates that base pair change is INHERITED by the
daughter cell. If the daughter cell is a "germ cell" (egg/sperm) that is
involved in the formation of an offspring, then a mutation may be passed on
to the children.

 The vast majority of mutations are HARMFUL, although a few are

 Most mutations are harmful because they result in a CHANGE in the
genetic code which results in a change in the PRIMARY AMINO SEQUENCE in a
protein, which results in a change in the protein's ABILITY TO DO WHAT IT
WAS ORIGINALLY MADE TO DO. For example, if you meant to say to your
"significant other", "I didn't love Lou", but you mutate the statement to "I
don't love You", I'll wager you will be in deep Doo Doo.

     Another example of meaning changes by small "mutations":

          The men wrote: "A woman, without her man, is nothing."

          The women wrote: "A woman: without her, man is nothing."

 Mutations are generally RANDOM EVENTS. The RATE of mutations can be
increased by MUTAGENIC AGENTS including UV-light, X-rays, atomic radiation,
and chemicals like benzene etc. However, using molecular biology techniques
today we can DESIGN mutations in DNA; that is, we can change particular base
pairs to alter individual amino acids within a protein chain and then see
how this change affects the function of the protein.

 Mutations may involve a SINGLE base pair or LARGE FRAGMENTS of
chromosomes carrying MANY genes. The principle is only that there is an
INHERITABLE CHANGE IN THE BASE SEQUENCE. For example, in a base sequence of
AATGGCAAT all the following changes (indicated in RED) in that sequence are

loss of a base or bases)

A modification that exchanges one codon for another that codes for the SAME
amino acid (#DEGENERACY) is a TRUE mutation, even though it doesn't have any
obvious effect. However, in the molecular biology section we will see how
such a change can CHANGE your GENETIC FINGERPRINT (#Chap. X). Mutations that
change one amino acid for another amino acid with a VERY SIMILAR CHEMISTRY,
may not cause a significant effect on the protein's function and thus may be
functionally neutral, but it may change the protein's chemistry so that it
reacts differently under different conditions; like changing the brand of
tires on your car or changing from snow tires to regular tires.

The names of some of the various categories of mutations are listed below:

 Wild type = the base pair (bp) sequence of a gene as INITIALLY found
in nature: ONE cat ate its rat END.

 Point and missense = ONE bp change creating a different amino acid:
ONE hat ate its rat END.

 Deletion = one or more bp REMOVED: ONE ate its rat END.

 Reversion = bp sequence of two or more bases REVERSED: ONE cat aet
its rat END.

 Nonsense = bp change results in a STOP CODON being put where it
doesn't belong: ONE END ate its rat END.

 Frameshift = the removal or addition of bases so that the
three-letter reading is OUT OF FRAME: ONE tat eit sra tEN D ...., or ONE cca
tat eit ....... Note these are also point mutations. If you have the
addition or deletion of three bases, it is NOT a frameshift mutation.

In haploid organisms a mutation is much more serious than it is in a diploid
because diploids have a SPARE GENE for each characteristic; except in for
certain genes in the sex chromosomes. Thus if one gene is lost by mutation
the remaining gene can often (but not always) fill in and do the job of the
missing gene.

An example of a harmful mutation is that of SICKLE CELL ANEMIA where a
change from GAG to GTG in a gene produces the disease. The mechanics of a
simple point mutation is illustrated in Fig. 3 below:

                       [FixMutation.gif (10085 bytes)]
                    Figure 3. Fixation of a mutation into
                     the DNA as a permanent part of the
                       inheritance. On the top, DNA is
                      undergoing replicated, however a
                     MISTAKE has occurred and T has been
                    paired with G. If that mispairing is
                     NOT CORRECTED before the NEXT ROUND
                      of REPLICATION, when the strands
                     containing the mismatched G-T pair
                      are copied, one of them (middle)
                    contains the "correct" base sequence
                      of TGT and the newly synthesized
                     strand copied from it becomes ACA .
                    Whereas the top strand of the middle
                    fig., which contains the "incorrect"
                     sequence ATA, is copied in the new
                     strand as TAT. The bottom strand of
                    the middle figure continues producing
                      "CORRECT" new DNA strands. If the
                    TEMPLATE or SENSE STRAND in this DNA
                        is the TOP STRAND in each DNA
                     molecule, then mRNA would be copied
                    from the ACA in the correct strand to
                      give a mRNA codon of UGU for the
                      amino acid CYSTEINE. However, the
                     template strand of the mutated DNA
                    yields a mutant mRNA with a UAU codon
                        for the amino acid TYROSINE.
                        Following the second round of
                     replication the ERROR (MUTATION) is
                    "FIXED"; in both strands of the cell
                          that contains that DNA.

                         ALLELES: GENETIC VARIANTS

When a wild type gene mutates
it forms an ALLELE or
ALTERNATIVE of that gene.
Since the number of potential
mutations in a gene is MINIMALLY the number of bp in any gene, many alleles
are possible (many human hair and skin colors). Most mutations result in a
gene producing a protein with no activity at all, but in some cases the
activity is increased or not subject to normal regulation, or is regulated
by a different #allosteric molecule. In rare cases the allele has a
different catalytic activity, perhaps by chemically acting less
specifically. If you take characteristics like skin or hair color it is easy
to see that there are many alleles that affect these characteristics.



A MUTAGEN is something that increases the RANDOM number of mutations over
time. A CARCINOGEN is something that increases the number of random
mutations that LEAD TO CANCER. You may wonder, what is the difference
between the two and I can only advise you to stay away from BOTH as much as
you can. The most COMMON CARCINOGEN we all encounter is the UV from our
benefactor the SUN. You may have been told that there are wavelengths of UV
light that don't increase the cancer risk; this information is WRONG. The
most common form of cancer is skin cancer and the most common place for skin
cancer to occur is on the face. The quantity of UV reaching the earth would
be FATAL to all life on the surface if most of that UV was not BLOCKED by a
form of oxygen known as the OZONE LAYER that lies at the outer edge of our
atmosphere. Good scientific data is currently available to indicate that the
ozone layer is being destroyed by man-made chemicals (It rated a Nobel
Prize). There is solid evidence that a hole in the protective ozone layer
above the Antarctic has opened up in the last few years and that it is
enlarging. There are people who argue that the data is wrong, or that
man-made materials are not involved. However, in the meantime the level of
skin cancer is growing world wide and particularly in those areas under the
"ozone hole". The problem with obtaining solid #epidemiological data on the
relationship between UV exposure, the ozone hole and cancer, is the delay
between exposure and the onset of the cancer. The data indicate that it
usually takes 30 to 40 years for the UV-exposed tissue to turn cancerous,
and in the meantime the individual may have smoked, worked in a chemical
factory and eaten a lot of fatty foods. How many of you know relatives who
have had skin cancer?

Some other known or suspected carcinogens are X-rays, cosmic rays, many
different man-made chemicals, and cigarette smoke. There are several reasons
why we can't always identify mutagens/carcinogens. These include the LONG
TIME between exposure and cancer formation, the fact that most new chemicals
that are produced are NOT TESTED for mutagenicity or carcinogenicity, test
animals don't always react to a potential carcinogen the SAME WAY humans do
and that there are many NATURAL CARCINOGENS we come into contact with.

   *  The carcinogen story is amply illustrated with the sorry tale
     of the Radium Watch Painters and Patent Medicines (Sci. Am. Aug. 1993
     pg. 94). In the early part of this century radium, a RADIOACTIVE
     element, was used to make watches whose numbers glowed in the dark and
     in patent medicines. The watch dials were hand painted by young poor,
     working-class women using tiny brushes. To produce a sharp point on the
     brushes the women were taught to roll the brushes ON THEIR TONGUES
     between strokes, thus washing traces of the radioactive paint into
     their mouths. Within a few years these young women began to develop,
     and to die from, cancers of the mouth, throat and intestines. However,
     despite warnings from the FDA, which had NO LEGAL POWER in that day,
     the practice continued and, the use of radium laced homeopathic "radium
     therapy" for numerous ills grew. Only with the horrible death of E.M.
     Byers (in 1932, a yr. before my birth), a PROMINENT RICH SOCIALITE,
     from radium-containing patent medicine, was the commercial use of
     radium stopped.
                           EXTRA CREDIT COMMENTARY 8E:
      Do you think the Federal government should regulate the commercial use
       of radioactive materials in consumer goods or should it be up to the
       consumer to decide if they want to use products with radium in them?
        Do you think that the FDA has TOO MUCH POWER and that it interferes
       with the free flow of commerce? Should we weaken the power of the FDA
        so that potentially useful medicines and treatments can be applied
       quickly to the treatment of diseases as many are suggesting? Explain
                              your answer for credit.

     [no image available] CRITICAL THINKING QUESTIONS: Should all newly
 synthesized chemicals be tested for their cancer-causing ability and if so,
     who (the companies or the tax payers) should pay for that testing.



Mutations are a way of "SEEING" how genes
work since genes determine the (potential)
physical appearance and what can or can not
be done biochemically. The way a living
organism naturally looks is called its
PHENOTYPE. For example, our hair, eye and
skin colors are all examples of phenotypic
characteristics determined by genes. The
differences in these characteristics are the
results of ALLELES in the respective genes
produced by mutations.

Before going further the idea of #DOMINANCE and RECESSIVENESS in genes must
be understood. You already know that the PRODUCTS OF GENES are made to DO
SOMETHING and that most mutations damage a gene so that it can no longer
make the product or does the job that it was designed to do. Thus if you
have two alleles (two cars) in a genome and one is the wild-type (a car
which runs) and the other is a mutation (a car which doesn't run), the
product of the former will WORK as designed and the product of the mutant
allele will NOT. Even if they both make a protein, the mutant protein
usually doesn't work so it is like a car that doesn't run. Reason tells you
that the product that does something will DOMINATE over the one that does
NOTHING; thus one gene is DOMINANT over the other, which is said to be
RECESSIVE. Some consequences of this follow naturally. The total of all out
genes, both dominant and recessive, is called our GENOTYPE.

 The dominant gene is always "SEEN" when it is present in a genome.

 A recessive gene is HIDDEN when a dominate allele IS PRESENT, so you
can't tell if a recessive gene is even around.

 In a haploid organisms every gene is EFFECTIVELY or FUNCTIONALLY
DOMINANT. Therefore, if you want to be sure of observing the EFFECTS of a
particular mutation of a gene, it is easiest to study that gene in a haploid
where it can not escape detection. Consider the circumstance of a naked
person in a stadium full of people as opposed to that naked person being the
ONLY ONE in the stadium.

 Dominance can best be studied in diploid organisms and recessiveness
in haploid organisms.

Geneticists usually begin a genetic investigation with a WILD-TYPE
(dominant) form of a gene and then examine its phenotypic or biochemical
VARIANTS to get some idea of how it works. Someone studying eye color in
humans would first try to determine how many different eye color variants
existed in the species. Then the frequency and distribution of these colors
in populations and in offspring would be carefully quantitated. This
information would tell you which were dominate and which were recessive
alleles. For example, I and my full brother both have BROWN EYES, but my
half brother has BLUE EYES. What does that tell you about the dominance of
brown vs. blue and my father's and my mother's and step mother's allelic
makeup regarding eye-color genes?


[no image available] CRITICAL THINKING QUESTION: Can you identify a physical
characteristic in your own family that is dominant? How do you know it is?


                       HAVE AN EVOLUTIONARY PURPOSE?

  "A gene's meaning is context-dependent........the climate in which a gene
   has to survive consists largely of the other genes of the species." R.
                   Dawkins in Climbing Mount Improbable.

When you consider human sex objectively (if that is possible), it must be
viewed as being a lot of trouble, a major complicating part of life, and a
messy process at best. Further, considering the many variations in nature on
the sexual life style, it could be argued that many other systems make a lot
more sense than the jury-rigged scheme humanoids have evolved. For example,
in many organisms the male is a tiny parasite living in the female's body
and when required he is poked with the hormone equivalent of a sharp stick
to kick out some sperm. In other cases the female mates with several males
during an orgy of DNA exchange and then she stores the sperm for the rest of
her long life, metering it out to fertilize her eggs as necessary, while the
happy (but stupid) males quickly die so they won't waste anymore food. In
other cases, the male is eaten after or even during the mating process (not
a pretty picture if you are male), which puts an interesting twist on the
ideal of "feeding one's children". So why did nature, evolution or God, if
you will, produce this thing that takes up an inordinate amount of our time
and energy (or is that just my problem?)?

Although there is still argument about exactly how sex evolved, the
following describes the current theory. It turns out that the evidence
indicates that while mutation is the basic driving force of evolution, it is
NOT ENOUGH to produce the variation nature apparently requires to deal with
the ever changing environment. Since genes really don't work independently,
it is important that nature TESTS DIFFERENT COMBINATIONS of alleles of each
gene with the alleles of all the other genes. A good metaphor is that sex is
like the game of poker. If the genes are the individual cards, the hands of
the other players represent the environment (of the particular hand) and the
pot is SURVIVAL, then it is easy to see the value of shuffling the deck
frequently and passing out NEW HANDS. Just as the shuffling of cards and the
dealing of new hands allows different card combinations the possibility of
WINNING against an ever changing environment (the hands in each game), so
does sex. That is, sex is nature's way of SHUFFLING THE GENETIC DECK.


                                DIPLOID SEX

In a diploid organism each parent contributes
offspring (= hand). Since many of the gene pairs
are #alleles of each other, the offspring
carries a large variety of genetic potential.
During the formation of the germ cells the
MATERNAL and PATERNAL chromosome pairs undergo a
process called RECOMBINATION in which EQUIVALENT
REGIONS of the two chromosome are EXCHANGED.
This results in paternal genes being mixed with
(shuffled) maternal genes on each chromosome,
thus forming chromosomes with new combinations
of genes (new hands). These newly RECOMBINED
CHROMOSOMES subsequently form the egg and sperm
which contain only ONE COPY OF EACH RECOMBINED
CHROMOSOME (haploid). Only after the egg is
fertilized does the diploid situation reoccur.
The new individual now carries not only a mixture of the original parental
genes from each egg and sperm, but this new mixture now can interact in ways
never seen before. Sex allows nature to constantly test the SURVIVAL
POTENTIAL of infinite gene combinations. In Fig. 4, each of the smaller
rectangular PATTERNS represents A GENE. A pair (diploid) of chromosomes
composed of 4 genes each, is shown on the left. This pair is composed of
parental chromosomes which can RECOMBINE in any number of ways when
producing sex cells, in this case sperm, producing of a wide variety of gene
combinations. Visit this site for an excellent discussion of recombination
with pictures.

For example, when the Europeans came to the American continent they found
that the Indians were EXTREMELY SUSCEPTIBLE to a variety of Europeans
diseases including measles, smallpox, chickenpox etc. In the case of these
diseases the mortality rate of the Indians was much higher than that of the
Europeans. Indeed it was so high that some Europeans even traded the Indians
blankets from the European Smallpox Wards, knowing that the disease would
kill them. Yet some Indians survived, although often entire tribes did
perish, and the survivors were more resistant to these "European" diseases.
You are now asking yourself "what does this have to do with sex?". The
evolutionary theory predicts that within the Indian population a few Indians
had, PURELY BY CHANCE, received gene combinations (WINNING HANDS) that
allowed them to survive the European diseases. You might say that nature is
a pessimist that plays a "WHAT IF" game; what if smallpox appears?, what if
measles appears?, what if AIDS appears etc.?, I'd better have a few people
around who can survive these diseases to insure the survival of the species.
It is perhaps distressing to learn, but nature cares LITTLE FOR INDIVIDUALS,
but very much for POPULATIONS. A corollary to this is that as the Europeans
bred with the Indians they mixed their resistance genes into the Indian
population, thus aiding in their survival--so sex is right in the middle of
this survival game, in several ways.



It turns out that we don't need to feel sorry for the microbes when it comes
to efficiency of DNA exchange (that's a SCIENTIFIC WAY of saying "sex"). Not
only can prokaryotic cells engage in DNA exchange, but they make humans look
like a bunch of celibate priests; in fact the term "promiscuous" doesn't
even come close to describing their frisky activities. But before we can
discuss exactly what the microbes are up to, you must understand PROTEIN
SYNTHESIS. In #Chapter IX you will see how bacteria exchange DNA. Take a
look at the central dogma before going on.




                      Figure 5. Transcription Process.

The process of protein synthesis is divided into two parts for convenient
discussion. The first step is called TRANSCRIPTION. In the process of
TRANSCRIPTION the instructions stored in the DNA are transferred to RNA. It
is not clear why this is necessary, but it may be that RNA was around before
DNA or maybe if DNA had been used for this step there would have just been
too much DNA around and things would have gotten confusing. What ever the
case, DNA is COPIED into mRNA. The process of copying the DNA is carried out
by an enzyme named, appropriately enough, RNA POLYMERASE. The basic steps

 The RNA polymerase finds its way to a START SITE on the DNA. This
site is called the PROMOTER SITE and every gene or groups of genes has one.
You might consider the PS and RNA polymerase as being two pieces of Velcro.
Once the RNA polymerase finds the PS it binds to it.

Actually by now you should know that I'm talking about a specific #ACTIVE
SITE on the RNA polymerase that recognizes a bp sequence on the DNA as it

 Once on the promoter, RNA polymerase opens up the DNA so that it can
copy one of the strands. But how does it know which strand to copy? That
information is built into the active site and the strand it COPIES is called
the SENSE or TEMPLATE STRAND while the one it doesn't copy is called the
NONSENSE STRAND. You may well ask; "why do I have to learn 'nonsense
strand'?" The answer is (are you seated?), because they can use nonsense
strands to TREAT DISEASES and to make tomatoes last longer on the store

As you see in the accompanying figure, the RNA polymerase moves down the DNA
double strand and synthesizes a COMPLEMENTARY copy of mRNA from the template
strand. Now if I were to give you the sequence of the template strand could
you identify the mRNA strand made from it? What about vice versa? If you
think the sun is going to come up in the east tomorrow you'd better be able
to do this as I'm totally addicted to asking various forms of this question
on exams.

                                     The copying proceeds until the RNA
                                     polymerase comes to a STOP SIGNAL at
                                     which point the mRNA falls off the
                                     DNA/RNA polymerase complex. This mRNA
                                     now can be used as a template from
which protein can be made. The process of making protein from mRNA is called
TRANSLATION. Translation is a complex process, but I'm going to give you the
abridged 101-version. For lots of other animations of biological processes
visit this site, but again be prepared to spend a long time down loading

There are several players in TRANSLATION. One component, called the
RIBOSOME, is the FACTORY upon which the protein is made. The ribosome is
composed of two subunits that are made from ~40 proteins and several small
RNA molecules. The two subunits only come together on the mRNA, otherwise
they float around in the cytoplasm as two separate pieces. A second type of
RNA, transfer-RNA (tRNA), brings the individual amino acids to the
appropriate codons on the mRNA-Ribosome complex where the amino acids are
bonded together in linear chains.

    [Ribosome Structure (5299 bytes)]
    Figure 7. Ribosome structure. The
     remaining components are the 20
    amino acids and a molecule called
     TRANSFER RNA or tRNA. The entire
      process takes a lot of energy,
     mostly in the form of #ATP. The       [Transfer RNA (3543 bytes)]
     mRNA in prokaryotes doesn't last   Figure 8. Transfer RNA. Each tRNA
   long since life is so fast paced in   carries a particular amino acid
     the prokaryotic world that they       on one end that MATCHES the
    need to be able to shift gears in     appropriate anticodon on the
   microseconds and old mRNA just gets       other. The anticodon is
    in the way. There is a UNIQUE tRNA   complementary to the amino acid
    for each codon and hence for EACH      codon on the mRNA. Thus the
    AMINO ACID because the tRNAs carry  matching mRNA codon would be UUA.
    the respective amino acids to the
     correct codons on the mRNA. The
     region on the tRNA that binds to
       the mRNA codon is called the


   Figure 9. RNA polymerase is shown moving along a series of 3 structural
    genes and transcribing mRNA (purple). Ribosomes bind to the mRNA and
        translates it into 3 proteins (orange, green & dark purple).

The individual step in translation are:

 The two components of the ribosome BIND to the mRNA at the START

 Then the first tRNA-amino acid complex binds to the CODON
immediately following the start codon.


                 [101TranslationAnimation.gif (88329 bytes)]

                      Summary Animation of Translation

 The mRNA moves over ONE 3-LETTER codon on the ribosome.

 The next tRNA with its
attached amino acid BINDS TO THE NEXT
EMPTY mRNA CODON, thus bringing the
two amino acids together so that an
ENZYME can form a PEPTIDE bond between
the two adjacent amino acids

 The mRNA moves over to the next codon and the first, now empty, tRNA
FALLS OFF ready to be loaded again with a fresh amino acid molecule. Click
here to see relationship between tRNA and genetic code.

 The next loaded tRNA binds to its appropriate codon on the mRNA and
its amino acid is COVALENTLY BOUND to the previous one and the protein chain
grows by one more amino acid.

The process continues down the length of mRNA, the protein growing one amino
acid at time until it arrives at a STOP CODON. At this point the ribosome
FALLS OFF, falls into two parts which go looking for a NEW START CODON on
another mRNA molecule. Actually, the ribosomes line up at the START CODON
and proceed daisy-chain-like down the mRNA, each ribosome producing a
COMPLETE PROTEIN as it moves along the mRNA. We know this to be the case as
we've seen these chains of ribosomes and proteins in various stages of being
made all attached to mRNA in the electron microscope.

For another illustration of the process of transcription and translation
click here and view Fig. 5. Click here for an animation of protein
synthesis; click on "Protein Synthesis" button. For an animation of
translation load the   "Translation Animation" movie (this may
take a hour to load but it is a terrific way to learn the process).




As promised when the regulation of #pre-formed enzymes was discussed, we
will now see how enzymes are regulated by controlling their synthesis.
Remember that every cell contains a complete set of genes, but only a few of
those genes are active at any given time. The E. coli bacterium has ~4,720
genes, but only about 1,000 different enzymes in its cytoplasm at any one
time. The cells in our bodies each contain ~100,000 genes but at any one
moment they only make enzymes needed for hands, or eyes or noses etc. This
is quite a trick for a MULTICELLULAR creature like ourselves as the genes
must know at all time WHERE THEY ARE in the body so as to make only the
enzymes needed there. Consider what happens when we injure our hand and we
have to make new tissue. This means making only new "hand cells". Why don't
we make eye cells instead? If that were the case you wouldn't need a mirror
to look at a pimple on your back , you'd only have to hold the finger with
the eye growing out of it behind you. But this scenario doesn't happen
because of 3 billion years of testing and perfecting (#evolution).

Therefore the ultimate regulation in a cell is controlling WHERE and WHEN, a
gene's product is made. Since #energy conservation is crucial for survival,
it is INEFFICIENT to expend limited resources to make an unneeded molecule.
Conversely, it is equally important that a cell manufactures only that which
is required at a specific POINT IN TIME and LOCATION. Being too early or too
late is not just socially unacceptable, it is usually LETHAL to a
multicellular organism. Since gene regulation is a requirement in all cells,
it follows that regulatory mechanisms developed VERY EARLY in the evolution
of life. It also ensures that multicellular organisms required far more
multicellular organisms cells become differentiated as to their duties
within the organism and each distinct responsibility requires that a UNIQUE
SET OF GENES be regulated. As a multicellular organism develops from a
single fertilized egg each of its cells remains aware of its physical
location within the embryo mass, and what it is to do in that local and when
to do it relative to the multitudinous other activities occurring throughout
the embryo. This requires that each cell has an elaborate #SENSING SYSTEM
that tells it not only WHERE IT IS relative to the other cells, but WHAT IS
HAPPENING biochemically with those other cells at every moment. The
unraveling of the complex mystery of regulation remains one of the last
major challenges to our understanding of the MECHANICS OF LIFE. Our first
steps in this understanding, as well as many additional ones, came from
studies done on prokaryotes. A basic principle of life is that as living
organism became more complex, rather than inventing entirely new mechanisms
of regulation, nature found new ways to combine and use the original
mechanisms developed in ancestral cells. An analogy is a basic wheel and
shaft combination being modified into things like clocks, automobiles and
jet planes; i.e., energy is transferred through increasingly elaborate
combinations of wheels and shafts to carry out ever more complex operations.



As you will learn in #lab, the test for human or animal FECAL POLLUTION in
water is the detection of the common gut bacterium E. coli. Since this
relationship was first recognized and E. coli was chosen as the INDICATOR
ORGANISM for fecal pollution, almost every city has had a lab for testing
for the presence of E. coli in its water supply. In addition, every
microbiologist trained in approximately the last 70 years has grown E. coli.
Further, every lab has the medium for growing this organism and
biochemically characterizing it. One characteristic that made E. coli useful
as the fecal indicator organism was its RARE ABILITY to utilize the sugar
LACTOSE. Thus E. coli has become the most studied bacterium in the world. As
a consequence of this, its genetics, physiology and biochemistry are better
understood than those of any other bacterium. You might say that POOP WAS

Because of E. coli's RARE ability to utilize the sugar LACTOSE early
investigators developed a simple #DIAGNOSTIC MEDIUM containing lactose that
would grow many different bacteria, but only those bacteria (usually E.
coli) that utilized lactose would take up certain dyes in the medium and
form DEEP BLUE COLONIES; all other bacterial colonies remained uncolored
(white or light pink). It was soon observed that mutations that resulted in
E. coli losing its ability to utilize lactose could be detected easily by
their COLORLESS COLONIES on the indicator medium.

LACTOSE is a DISACCHARIDE composed of the sugar glucose and galactose. The
enzyme that is responsible for the breaking the bond between these two
sugars is known as BETA-GALACTOSIDASE. Sensitive colormetric procedures that
allowed a few molecules of this enzyme to be detected were subsequently
developed, making simple, inexpensive and rapid experiments on lactose
metabolism possible. Over many years the genes responsible for lactose
metabolism were identified, and their function and regulation determined.

As I've repeatedly emphasized, the cell is very economical and efficient in
an energy and nutrition-limited world. They follow the basic principle of
"IF IT ISN'T NEEDED, DON'T MAKE IT". The challenge is how do cells inform a
gene when to make something and when to hold off. This simple question
embodies the key to life for it determines the organization necessary for
life. The lactose regulatory system, discovered in E. coli, is still our
model for understanding gene regulation. But first a little history.

                              THE LAC OPERON


 Figure 10. The lactose operon. For more discussions/explanations of the Lac
              Operon [eyescan.gif (247 bytes)] here and here.

Through intense investigation of the physiology and genetics of E. coli,
particularly as it involved the metabolism of lactose, a picture of gene
regulation emerged by the early 1960s, culminating in a Nobel prize for
three French scientists in 1965. The picture they described took the
following form. The enzymes involved in lactose utilization were found to be
chemical analogs of lactose. Further, once the inducer, lactose, was
removed, the synthesis of the lactose enzymes CEASED within seconds. The
cluster of genes that controlled the utilization of lactose functioned as a
COORDINATED UNIT.(like a football team). This unit was given the name the
LAC OPERON. A physical plan of the lac operon is in Fig. 10.



A large number of mutants that effected the regulation of the lactose
enzymes were discovered between 1940 and 1960. Certain mutants, showed that
a REGULATORY GENE was responsible for REPRESSING the synthesis of the
lactose enzymes and that lactose RELIEVED that repression. Mutations in the
regulatory gene were of two opposing types.

   * With one type of mutant synthesis of the lactose enzymes NEVER turned
     off, that is they were said to be CONSTITUTIVE or made all the time.
   * Whereas, other mutants of the regulatory gene became NONIDUCIBLE. That
     is, lactose did not turn on the synthesis of the lac operon enzymes.
   * With yet other mutants, even if the regulatory gene was functioning
     perfectly, the system was rendered NON-RESPONSIVE to the repressor gene
     product even in the absence of lactose; that is, the lactose enzymes
     were again constitutive (on all the time).
   * Another groups of mutants which did not lie physically near any of the
     above mutations, completely PREVENTED the synthesis of the lactose


As the list of characterized mutants grew, a REGULATORY PICTURE began to
emerge out of the fog of data.

 The group of regulated lactose genes, the