IMMUNOLOGY

Immunology is the study of our protection from foreign macromolecules or invading organisms and our responses to them. These invaders include viruses, bacteria, protozoa or even larger parasites. In addition, we develop immune responses against our own proteins (and other molecules) in autoimmunity and against our own aberrant cells in tumor immunity.

Our first line of defense against foreign organisms are barrier tissues such as the skin that stop the entry of organism into our bodies. If, however, these barrier layers are penetrated, the body contains cells that respond rapidly to the presence of the invader. These cells include macrophages and neutrophils that engulf foreign organisms and kill them without the need for antibodies. Immediate challenge also comes from soluble molecules that deprive the invading organism of essential nutrients (such as iron) and from certain molecules that are found on the surfaces of epithelia, in secretions (such as tears and saliva) and in the blood stream. This form of immunity is the innate or non-specific immune system that is continually ready to respond to invasion.

A second line of defense is the specific or adaptive immune system which may take days to respond to a primary invasion (that is infection by an organism that has not hitherto been seen). In the specific immune system, we see the production of antibodies (soluble proteins that bind to foreign antigens) and cell-mediated responses in which specific cells recognize foreign pathogens and destroy them. In the case of viruses or tumors, this response is also vital to the recognition and destruction of virally-infected or tumorigenic cells. The response to a second round of infection is often more rapid than to the primary infection because of the activation of memory B and T cells. We shall see how cells of the immune system interact with one another by a variety of signal molecules so that a coordinated response may be mounted. These signals may be proteins such as lymphokines which are produced by cells of the lymphoid system, cytokines and chemokines that are produced by other cells in an immune response, and which stimulate cells of the immune system.

RNA vs DNA

Why is DNA our genetic material and
not RNA. What characteristics of RNA strip it from preferential
characteristics that DNA has?


The main reason DNA is better for 'safe' storage of information is its
stability. There are several different ways DNA resists change more than
RNA; here are some:

First, as you noted, the deoxyribose sugar in DNA is less reactive than the
ribose sugar. In general C-H bonds are less reactive than C-OH (hydroxyl).
Also, RNA is not very stable in alkaline conditions, while DNA is.

More broadly speaking, the double-strand DNA (dsDNA) has relatively small
'grooves' where damaging enzymes can attach, which makes it harder for them
to 'attack' the DNA. Double-stranded RNA (dsRNA) has much larger grooves, so
it would more subject to being broken down.

Second, the connection between the strands of dsDNA is tighter than dsRNA --
it's easier to 'unzip' dsRNA than it is to unzip dsDNA.

Overall, it's easier (faster, requires less energy) to break down and reform
RNA than DNA -- since we want our genetic material to be stable, we want the
substance that's harder to break down.

As an interesting side note, it is well known that DNA can be damaged by UV,
but RNA is actually more resistant to damage by UV. Also, the sequence of
DNA and its physical conformation (the shape the strands are folded into)
seems to play a role as well.

This might be a chicken-egg point, but it's important to note that the body
actively destroys enzymes that cleave DNA (called nucleases) -- when it
needs to cleave DNA, it makes its own specific enzymes. It's one of several
ways DNA is protected against damage. The body can actually "identify"
foreign DNA and destroy it, and not destroy its own DNA.

Unlike DNA, RNA strands are continually made, broken down, and reused. If
you add up the chemical stability, the energy it takes to break or make DNA
and RNA bonds, and the availability of enzymes to do this work, a compelling
case for DNA over RNA can be made.

Hope this helps,
Burr
====================================================================
This is a very interesting question. RNA and DNA are chemical cousins, RNA
(ribonucleic acid) has an additional 2' OH group on its ribose sugar (which
is why DNA is called deoxyribonucleic acid) and uses uracil instead of
thymine (which differ only by a CH3 group). Like DNA, RNA can form a double
helix structure and can store information because like DNA it is constructed
from four bases along a sugar phosphate backbone.

One of the main reasons RNA is less stable than DNA is that the 2' OH group
of RNA can react with the molecule's backbone in flexible regions, causing
the molecule to cleave. Since long strands of RNA are therefore chemically
less stable, organisms which evolved to use DNA instead of RNA to protect
their biological code probably had a selective advantage. This may explain
why almost all of life uses DNA as its genetic code (an exception to this
are certain viruses which use RNA).

An important discovery by Tom Cech of the University of Colorado showed that
RNA can actually adopt complex structures and can act as an enzyme (a
molecule that catalyzes a reaction). Because RNA can encode biological
information, many scientists speculate that life may have originated from an
RNA molecule which contained the information to copy itself and the
enzymatic ability to do so. This is known as the "RNA World hypothesis."

Ethan Greenblatt
Ph.D. Candidate
Stanford Department of Chemistry
====================================================================

REPLICATION OF DNA

DNA replication begins with a partial unwinding of the double helix at an area known as the replication fork. This unwinding is accomplished by an enzyme known as DNA helicase. This unwound section appears under electron microscopes as a "bubble" and is thus known as a replication bubble.


--------------------------------------------------------------------------------

As the two DNA strands separate ("unzip") and the bases are exposed, the enzyme DNA polymerase moves into position at the point where synthesis will begin.

But where does the DNA polymerase enzyme know where to begin synthesis? Is there some sort of marker, a start point?

YES; the start point for DNA polymerase is a short segment of RNA known as an RNA primer. The very term "primer" is indicative of its role which is to "prime" or start DNA synthesis at certain points. The primer is "laid down" complementary to the DNA template by an enzyme known as RNA polymerase or Primase.

The DNA polymerase (once it has reached its starting point as indicated by the primer) then adds nucleotides one by one in an exactly complementary manner, A to T and G to C.

How does the polymerase "know" which base to add?

DNA polymerase is described as being "template dependent" in that it will "read" the sequence of bases on the template strand and then "synthesize" the complementary strand. The template strand is ALWAYS read in the 3' to 5' direction (that is, starting from the 3' end of the template and reading the nucleotides in order toward the 5' end of the template). The new DNA strand (since it is complementary) MUST BE SYNTHESIZED in the 5' to 3' direction (remember that both strands of a DNA molecule are described as being antiparallel). DNA polymerase catalyzes the formation of the hydrogen bonds between each arriving nucleotide and the nucleotides on the template strand.


--------------------------------------------------------------------------------

In addition to catalyzing the formation of Hydrogen bonds between complementary bases on the template and newly synthesized strands, DNA polymerase also catalyzes the reaction between the 5' phosphate on an incoming nucleotide and the free 3' OH on the growing polynucleotide (what we know is called a phosphodiester bond!). As a result, the new DNA strands can grow only in the 5' to 3' direction, and strand growth must begin at the 3' end of the template, right? Again, note that a phosphodiester bond is formed between the 3' OH group of the sugar and the 5' phosphate group of the incoming nucleotide.


--------------------------------------------------------------------------------

Because the original DNA strands are complementary and run antiparallel, only one new strand can begin at the 3' end of the template DNA and grow continuously as the point of replication (the replication fork) moves along the template DNA. The other strand must grow in the opposite direction because it is complementary, not identical to the template strand. The result of this side's discontiguous replication is the production of a series of short sections of new DNA called Okazaki fragments (after their discoverer, a Japanese researcher). To make sure that this new strand of short segments is made into a continuous strand, the sections are joined by the action of an enzyme called DNA ligase which LIGATES the pieces together by forming the missing phosphodiester bonds!
The last step is for an enzyme to come along and remove the existing RNA primers (you don't want RNA in your DNA now that the primers have served their purpose, do you?) and then fill in the gaps with DNA. This is the job of yet another type of DNA polymerase which has the ability to chew up the primers (dismantle them) and replace them with the deoxynucleotides that make up DNA. Here is a link with a diagram of the overall process of DNA replication of Okazaki Fragments.



--------------------------------------------------------------------------------

Since each new strand is complementary to its old template strand, two identical new copies of the DNA double helix are produced during replication. In each new helix, one strand is the old template and the other is newly synthesized, a result described by saying that the replication is semi-conservative. This process is shown schematically below. Crick described the DNA replication process and the fitting together of two DNA strands as being like a hand in a glove. The hand and glove separate, a new hand forms inside the old glove, and a new glove forms around the old hand. As a result, two identical copies now exist.

DNA

Components of DNA
DNA is a polymer. The monomer units of DNA are nucleotides, and the polymer is known as a "polynucleotide." Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base. The four nucleotides are given one letter abbreviations as shorthand for the four bases.

A is for adenine
G is for guanine
C is for cytosine
T is for thymine
Purine Bases
Adenine and guanine are purines. Purines are the larger of the two types of bases found in DNA

PHASE OF BACTERIAL GROWTH

Bacteria, when transferred from one medium to another, shows characterstic growth curve.
It shows four distinct phase of growth.
Lag phase
Log or exponential phase
Stationary phase
Decline or death phase

Lag phase :- When the bacteria are transferred from one medium to another they do not show sudden growth as they may be depleted of energy. The nutrients may be different in two media. Organisms synthesize new enzymes to utilize new nutrients. Organisms increase in size but show no change in number.
Log phase :- In this phase bacteria divide exponentially. The graph shows curve which means not all the bacteria multiply simultaneously. After some time period the no. of division fall down.
Stationary phase :- In this phase bacterial population does not change with time - No. of bacteria born are same as no. of bacteria died.
Decline phase :- In this phase bacteria die exponentially. Bacterial population fall down as inverse of log phase. This phase come due to accumulation of waste products and depletion of nutrients

rhizosphere

the root system of higher plant is not only associated with the organic and inorganic substances but also with metabolically active micro organisms called RHIZOSPHERE.