Monday, March 21, 2011


Medical research

Biomedical research (or experimental medicine), in general simply known as medical research, is the basic research, applied research, or translational research conducted to aid and support the body of knowledge in the field of medicine. Medical research can be divided into two general categories: the evaluation of new treatments for both safety and efficacy in what are termed clinical trials, and all other research that contributes to the development of new treatments. The latter is termed preclinical research if its goal is specifically to elaborate knowledge for the development of new therapeutic strategies. A new paradigm to biomedical research is being termed translational research, which focuses on iterative feedback loops between the basic and clinical research domains to accelerate knowledge translation from the bedside to the bench, and back again

What Is the Procedure for DNA Testing?

There are various ways to test DNA. One very common method used in various settings, including forensic and paternity testing labs, is polyermase chain reaction, or PCR. Using this method, DNA is extracted from sample cells and primers are used to locate the sequence of interest on the DNA strand. This sequence is then amplified to create many million and even billions of copies, according to University of Washington professor Donald E. Riley. 

In the case of paternity testing, somatic, or body, cells from the possible father are obtained by taking a swab of the inner lining of the suspected father's mouth. The DNA is extracted from the cells and is then amplified, creating many copies. 

These copies are then compared to those of the offspring to see whether there is a close match, according to one Buzzle writer. As stated by professor Riley, although PCR is less time-consuming and cheaper than another method called RFLP, it is very susceptible to contamination and care must be exercised during the entire testing process. 

In RFLP, or Restriction Fragment Length Polymorphism, a restriction enzyme is used. Obtained by bacteria that can "cut" DNA at a particular location, restriction enzymes cut many copies of the DNA sequence of interest. The sequence is then separated according to size using gel electrophoresis. Next, "blotting" is performed in which a film is applied to the gel and stained allowing the different bars, representing different sequences, to be seen. This prevents any further migration of the DNA sequences in the gel. A DNA probe is then attached to the sequence of interest. 

As in PCR, the DNA copies are compared to others in the population to determine if there is a "match." Rather than just one person's DNA, in the case of paternity testing, DNA from a large population needs to be used in order to effectively compare the lab sample to those in the population. This, along with the increased cost and time required, is the reason that RFLP is no longer widely used as it had been.

DNA profiles for forensic use

Each of the chromosomes in your cells contains sections of non-coding DNA — DNA that does not code for a protein. Non-coding DNA contains areas called short tandem repeats (STRs), made up of repeats of short base sequences, such as CATG in the sequence CATGCATGCATG. 

If the DNA of two people was analysed for 10 different STRs on different chromosomes, there is only one chance in a million that they would have the same number of repeats in all of these STRs. Identical twins are the only exception — they have identical DNA and identical STRs.

If a crime suspect's DNA profile for 10 STRs matches the STR profile of a sample found at the crime scene, there is a very high probability that both lots of DNA are from the same person. However, if the profiles differ for even one STR, this cannot be assumed. 

DNA is used as evidence in court, but it is considered ‘circumstantial' evidence, and can only be used as proof with other supporting evidence. However, it has proven useful in establishing the innocence of suspects.

What is a gene?


A gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases. The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes.

Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people. Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.

What is Genetic Engineering?

We find it mixed in our food on the shelves in the supermarket--genetically engineered soybeans and maize. We find it growing in a plot down the lane, test field release sites with genetically engineered rape seed, sugar beet, wheat, potato, strawberries and more. There has been no warning and no consultation. 

It is variously known as genetic engineering, genetic modification or genetic manipulation. All three terms mean the same thing, the reshuffling of genes usually from one species to another; existing examples include: from fish to tomato or from human to pig. Genetic engineering (GE) comes under the broad heading of biotechnology. 

But how does it work? If you want to understand genetic engineering it is best to start with some basic biology. 

What is a cell? A cell is the smallest living unit, the basic structural and functional unit of all living matter, whether that is a plant, an animal or a fungus.Some organisms such as amoebae, bacteria, some algae and fungi are single-celled - the entire organism is contained in just one cell. Humans are quite different and are made up of approximately 3 million cells -(3,000,000,000,000 cells). Cells can take many shapes depending on their function, but commonly they will look like a brick with rounded comers or an angular blob - a building block.Cells are stacked together to make up tissues, organs or structures (brain, liver, bones, skin, leaves, fruit etc.). 

In an organism, cells depend on each other to perform various functions and tasks; some cells will produce enzymes, others will store sugars or fat; different cells again will build the skeleton or be in charge of communication like nerve cells; others are there for defence, such as white blood cells or stinging cells in jelly fish and plants. In order to be a fully functional part of the whole, most cells have got the same information and resources and the same basic equipment. 

A cell belonging to higher organisms (e.g. plant or animal) is composed of: 
• a cell MEMBRANE enclosing the whole cell. (Plant cells have an additional cell wall for structural reinforcement.) 
• many ORGANELLES, which are functional components equivalent to the organs in the body of an animal e.g. for digestion, storage, excretion. 
• a NUCLEUS, the command centre of the cell. It contains all the vital information needed by the cell or the whole organism to function, grow and reproduce. This information is stored in the form of a genetic code on the chromosomes, which are situated inside the nucleus. 

Proteins are the basic building materials of a cell, made by the cell itself. Looking at them in close-up they consist of a chain of amino-acids, small specific building blocks that easily link up. Though the basic structure of proteins is linear, they are usually folded and folded again into complex structures. Different proteins have different functions. They can be transport molecules (e.g. oxygen binding haemoglobin of the red blood cells); they can be antibodies, messengers, enzymes (e.g. digestion enzymes) or hormones (e.g. growth hormones or insulin). Another group is the structural proteins that form boundaries and provide movement, elasticity and the ability to contract. Muscle fibres, for example, are mainly made of proteins. Proteins are thus crucial in the formation of cells and in giving cells the capacity to function properly. 

Chromosomes means "coloured bodies" (they can be seen under the light microscope, using a particular stain). They look like bundled up knots and loops of a long thin thread. Chromosomes are the storage place for all genetic - that is hereditary - information. This information is written along the thin thread, called DNA. "DNA" is an abbreviation for deoxyribo nucleic acid, a specific acidic material that can be found in the nucleus. The genetic information is written in the form of a code, almost like a music tape. To ensure the thread and the information are stable and safe, a twisted double stranded thread is used - the famous double helix. When a cell multiplies it will also copy all the DNA and pass it on to the daughter cell. 

The totality of the genetic information of an organism is called genome. Cells of humans, for example, possess two sets of 23 different chromosomes, one set from the mother and the other from -the father. The DNA of each human cell corresponds to 2 meters of DNA if it is stretched out and it is thus crucial to organise the DNA in chromosomes, so as to avoid knots, tangles and breakages. The length of DNA contained in the human body is approximately 60,000,000,000 kilometres. This is equivalent to the distance to the moon and back 8000 times! 

The information contained on the chromo-somes in the DNA is written and coded in such a way that it can be understood by almost all living species on earth. It is thus termed the universal code of life. In this coding system, cells need only four symbols (called nucleotides) to spell out all the instructions of how to make any protein. Nucleotides are the units DNA is composed of and their individual names are commonly abbreviated to the letters A, C G and T These letters are arranged in 3-letter words which in turn code for a particular amino acid - as shown in the flow diagram 1. The information for how any cell is structured or how it functions is all encoded in single and distinct genes. A Gene is a certain segment (length) of DNA with specific instructions for the production of commonly one specific protein. The coding sequence of a gene is, on average about 1000 letters long. Genes code for example for insulin, digestive enzymes, blood clotting proteins, or pigments.

How does a cell know when to produce which protein and how much of it? In front of each gene there is a stretch of DNA that contains the regulatory elements for that specific gene, most of which is known as the promoter. It functions like a "control tower," constantly holding a "flag" up for the gene it controls. Take insulin production (which we produce to enable the burning of the blood sugar). When a message arrives in the form of a molecule that says, 'more insulin", the insulin control tower will signal the location of the insulin gene and say "over here". The message molecule will "dock in" and thus activate a "switch" to start the whole process of gene expression. 

How does the information contained in the DNA get turned into a protein at the right time? As shown in picture 2, each gene consists of 3 main components: a "control tower" (promoter), an information block and a polyA signal element. If there is not enough of a specific protein present in the cell, a message will be sent into the nucleus to find the relevant gene. If the control tower recognises the message as valid it will open the "gate" to the information block. Immediately the information is copied - or transcribed - into a threadlike molecule, called RNA. RNA is very similar to DNA, except it is single stranded. After the copy is made, a string of up to 200 "A"-type nucleotides - a polyA tail - is added to its end (picture 2). This process is called poly-adenylation and is initiated by a polyA signal located towards the end of the gene. A polyA tail is thought to stabilise the RNA message against degradation for a limited time. Now the RNA copies of the gene leave the nucleus and get distributed within the cell to little work units that translate the information into proteins. 

No cell will ever make use of all the information coded in its DNA. Cells divide the work up amongst one other - they specialise. Brain cells will not produce insulin, liver cells will not produce saliva, nor will skin cells start producing bone. If they did, our bodies could be chaos! 

The same is true for plants: root cells will not produce the green chlorophyll, nor will the leaves produce pollen or nectar. Furthermore, expression is age dependent: young shoots will not express any genes to do with fruit ripening, while old people will not usually start developing another set of teeth (exceptions have been known). 

All in all, gene regulation is very specific to the environment in which the cell finds itself and is also linked to the developmental stages of an organism. So f I want the leaves of poppy plants to produce the red colour of the flower petals I will not be able to do so by traditional breeding methods, despite the fact that leaf ells will have all the genetic information necessary. There is a block that prevents he leaves from going red. This block may be caused by two things: 
• The "red" gene has been permanently shut down and bundled up thoroughly in all leaf cells. Thus the information cannot be accessed any more. 
• The leaf cells do not need the colour red and thus do not request RNA copies of this information. Therefore no message molecule is docking at the "red" control tower to activate the gene. 

Of course - you might have guessed - there is a trick to fool the plant and make it turn red against its own will. We can bring the red gene in like a Trojan horse, hidden behind the control tower of a different gene. But for this we need to cut the genes up and glue them together in a different form. This is where breeding ends and genetic engineering begins. 

BREEDING is the natural process of sexual reproduction within the same species. The hereditary information of both parents is combined and passed on to the offspring. In this process the same sections of DNA can be exchanged between the same chromosomes, but genes will always remain at their very own and precise position and order on the chromosomes. A gene will thus always be surrounded by the same DNA unless mutations or accidents occur. Species that are closely related might be able to interbreed, like a donkey and a horse, but their offspring will usually be infertile (e.g. mule). This is a natural safety devise, preventing the mixing of genes that might not be compatible and to secure the survival of the species.

Genetic Engineering.


Genetic engineering (GE) is used to take genes and segments of DNA from one species, e.g. fish, and put them into another species, e.g. tomato. To do so, GE provides a set of techniques to cut DNA either randomly or at a number of specific sites. Once isolated one can study the different segments of DNA, multiply them up and splice them (stick them) next to any other DNA of another cell or organism. GE makes it possible to break through the species barrier and to shuffle information between completely unrelated species; for example, to splice the anti-freeze gene from flounder into tomatoes or strawberries, an insect-killing toxin gene from bacteria into maize, cotton or rape seed, or genes from humans into pig. 

Yet there is a problem - a fish gene will not work in tomato unless I give it a promoter with a "flag" the tomato cells will recognise. Such a control sequence should either be a tomato sequence or something similar. Most companies and scientists do a shortcut here and don't even bother to look for an appropriate tomato promoter as it would take years to understand how the cell's internal communication and regulation works. In order to avoid long testing and adjusting, most genetic engineering of plants is done with viral promoters. Viruses - as you will be aware - are very active. Nothing, or almost nothing, will stop them once they have found a new victim or rather host. They integrate their genetic information into the DNA of a host cell (such as one of your own), multiply, infect the next cells and multiply. This is possible because viruses have evolved very powerful promoters which command the host cell to constantly read the viral genes and produce viral proteins. Simply by taking a control element (promoter) from a plant virus and sticking it in front of the information block of the fish gene, you can get this combined virus/fish gene (known as a "construct') to work wherever and whenever you want in a plant. 

This might sound great, the drawback though is that it can't be stopped either, it can't be switched off. The plant no longer has a say in the expression of the new gene, even when the constant involuntary production of the "new" product is weakening the plant's defences or growth. 

And furthermore, the theory doesn't hold up with reality. Often, for no apparent reason, the new gene only works for a limited amount of time and then "falls silent". But there is no way to know in advance if this will happen. 

Though often hailed as a precise method, the final stage of placing the new gene into a receiving higher organism is rather crude, seriously lacking both precision and predictability. The "new" gene can end up anywhere, next to any 
gene or even within another gene, disturbing its function or regulation. If the "new" gene gets into the "quiet" non-expressed areas of the cell's DNA, it is likely to interfere with the regulation of gene expression of the whole region. It could potentially cause genes in the "quiet" DNA to become active. 

Often genetic engineering will not only use the information of one gene and put it behind the promoter of another gene, but will also take bits and pieces from other genes and other species. Although this is aimed to benefit the expression and function of the "new" gene it also causes more interference and enhances the risks of unpredictable effects.

How to get the gene into the other cell.

There are different ways to get a gene from A to B or to transform a plant with a "new" gene. A VECTOR is something that can carry the gene into the host, or rather into the nucleus of a host cell. Vectors are commonly bacterial plasmids (see below and next page) or viruses (a). Another method is the "SHOTGUN TECHNIQUE" also known as "bio-ballistics," which blindly shoots masses of tiny gold particles coated with the gene into a plate of plant cells, hoping to land a hit somewhere in the cell's DNA (b).

What is a plasmid?

PLASMIDS can be found in many bacteria and are small rings of DNA with a limited number of genes. Plasmids are not essential for the survival of bacteria but can make life a lot easier for them. Whilst all bacteria - no matter which species - will have their bacterial chromosome with all the crucial hereditary information of how to survive and multiply, they invented a tool to exchange information rapidly. If one likens the chromosome to a bookshelf with manuals and handbooks, and a single gene to a recipe or a specific building instruction, a plasmid,could be seen as a pamphlet. Plasmids self-replicate and are thus easily reproduced and passed around. Plasmids often contain genes for antibiotic resistance. This type of information which can easily be passed on, can be crucial to bacterial strains which are under attack by drugs and is indeed a major reason for the quick spread of antibiotic resistance.

Working with plasmids.

Plasmids are relatively small, replicate very quickly and are thus easy to study and to manipulate. It is easy to determine the sequence of its DNA, that is, to find out the sequence of the letters (A, C, G and 1) and number them. Certain letter combinations -such as CAATTG - are easy to cut with the help of specific enzymes (see proteins). Ilese cutting enzymes, called restriction enzymes, are part of the Genetic Engineering "tool-kit" of biochemists. So if I want to splice a gene from fish into a plasmid, I have to take the following steps: I place a large number of a known plasmid in a little test tube and add a specific enzyme that will cut the plasmid at only one site. After an hour I stop the digest, purify the cut plasmid DNA and mix it with copies of the fish gene; after some time the fish gene places itself into the cut ring of the plasmid. I quickly add some "glue" from my "tool-kit" - an enzyme called ligase - and place the mended plasmids back into bacteria, leaving them to grow and multiply. But how do I know which bacteria will have my precious plasmid? For this reason I need MARKER GENES, such as antibiotic resistance genes. So I make sure my plasmid has a marker gene before I splice my fish gene into it. If thA I plasmid is marked with a gene antibiotic resistance I can now add specific antibiotic to the food supply of the bacteria. All those which do not have the plasmid will die, and all those that do have the plasmid will multiply.

Unanswered Questions and Inherent Uncertainties

What's wrong with Genetic Engineering ? 

Genetic Engineering is a test tube science and is prematurely applied in food production. A gene studied in a test tube can only tell what this gene does and how it behaves in that particular test tube. It cannot tell us what its role and behaviour are in the organism it came from or what it might do if we place it into a completely different species. Genes for the colour red placed into petunia flowers not only changed the colour of the petals but also decreased fertility and altered the growth of 
the roots and leaves. Salmon genetically engineered with a growth hormone gene not only grew too big too fast but also turned green. These are unpredictable side effects, scientifically termed pleiotropic effects. 

We also know very little about what a gene (or for that matter any of its DNA sequence) might trigger or interrupt depending on where it got inserted into the new host (plant or animal). These are open questions around positional effects. And what about gene silencing and gene instability? How do we know that a genetically engineered food plant will not produce new toxins and allergenic substances or increase the level of dormant toxins and allergens? How about the nutritional value? And what are the effects on the environment and on wild life? All these questions are important questions yet they remain unanswered. Until we have an answer to all of these, genetic engineering should be kept to the test tubes. Biotechnology married to corporations tends to ignore the precautionary principle but it also igpores some basic scientific principles.

Friday, March 4, 2011

THE BIOCHEMICAL REACTIONS

  • DNA replication begins with the "unzipping" of the parent molecule as the hydrogen bonds between the are broken.
  • Once exposed, the sequence of bases on each of the separated strands serves as a template to guide the insertion of a complementary set of bases on the strand being synthesized.
  • The new strands are assembled from 
  • Each incoming nucleotide is covalently linked to the "free" 3' carbon atom on the pentose (figure) as
  • the second and third phosphates are removed together as a molecule of (PPi).
  • The nucleotides are assembled in the order that complements the order of bases on the strand serving as the template.
  • Thus each C on the template guides the insertion of a G on the new strand, each G a C, and so on.
  • When the process is complete, two DNA molecules have been formed identical to each other and to the parent molecule.

THE ENZYMES

  • A portion of the double helix is unwound by a
  • A molecule of aDNA polymerasebinds to one strand of the DNA and begins moving along it in the 3' to 5' direction, using it as a template for assembling aleading strand of nucleotides and reforming a double helix. In eukaryotes, this molecule is called DNA polymerase delta (δ).
  • Because DNA synthesis can only occur 5' to 3', a molecule of a second type of DNA polymerase (epsilon, ε, in eukaryotes) binds to the other template strand as the double helix opens. This molecule must synthesize discontinuous segments of polynucleotides (calledfragments). Another enzyme, then stitches these together into the 
DNA Replication is Semiconservative
When the replication process is complete, two DNA molecules — identical to each other and identical to the original — have been produced. Each strand of the original molecule has
  • remained intact as it served as the template for the synthesis of
  • a complementary strand.
This mode of replication is described as semi-conservative: one-half of each new molecule of DNA is old; one-half new. Watson and Crick had suggested that this was the way the DNA would turn out to be replicated. Proof of the model came from the experiments of Meselson and Stahl. [

Bacteria

The single molecule of DNA that is the genome contains 4.7 x 106nucleotide pairs. DNA replication begins at a single, fixed location in this molecule, the proceeds at about 1000 nucleotides per second, and thus is done in no more than 40 minutes. And thanks to the precision of the process (which includes a "proof-reading" function), the job is done with only about one incorrect nucleotide for every 109 nucleotides inserted. In other words, more often than not, the E. coli genome (4.7 x 106) is copied without error! 

Eukaryotes

The average human chromosome contains 150 x 106 nucleotide pairs which are copied at about 50 base pairs per second. The process would take a month (rather than the hour it actually does) but for the fact that there are many places on the eukaryotic chromosome where replication can begin. Replication begins at some replication origins earlier in S phase than at others, but the process is completed for all by the end of S phase. As replication nears completion, "bubbles" of newly replicated DNA meet and fuse, finally forming two new molecules. 
With their multiple origins, how does the eukaryotic cell know which origins have been already replicated and which still await replication? 
An observation: When a cell in G2 of theis fused with a cell in S phase, the DNA of the G2 nucleus does not begin replicating again even though replication is proceeding normally in the S-phase nucleus. Not until mitosis is completed, can freshly-synthesized DNA be replicated again. 
Two control mechanisms have been identified — one positive and onenegative. This redundancy probably reflects the crucial importance of precise replication to the integrity of the genome. 


In order to be replicated, each origin of replication must be bound by:
  • an OriginRecognition Complex of proteins (ORC). These remain on the DNA throughout the process.
  • Accessory proteins called licensing factors. These accumulate in the nucleus during G1 of the cell cycle. They include:
    • Cdc-6 and Cdt-1, which bind to the ORC and are essential for coating the DNA with
    • MCM proteins. Only DNA coated with MCM proteins (there are 6 of them) can be replicated.
Once replication begins in S phase, 
  • Cdc-6 and Cdt-1 leave the ORCs (the latter by and destruction in 
  • The MCM proteins leave in front of the advancing replication fork.


G2 nuclei also contain at least one protein — called geminin — that prevents assembly of MCM proteins on freshly-synthesized DNA (probably by blocking the actions of Cdt1). 
As the cell completes mitosis, geminin is degraded so the DNA of the two daughter cells will be able to respond to licensing factors and be able to replicate their DNA at the next S phase.

DNA Translation


Translation occurs in the cytoplasm where the ribosomes are located. Ribosomes are made of a small and large subunit which surround the mRNA.
Transfer RNA (tRNA) molecules are 75 - 95 nucleotides long and have four arms and three loops. True to its name, tRNA transfers amino acids to the site of the growing protein chain (polypeptide). Each tRNA molecule (in red below) recognises a specific, three base-pair mRNA code or codon (the DNA form of a codon is called a triplet and the sequence on the tRNA is called an anticodon). Since there are three bases and four possible nucleotides, there can be up to 64 (4x4x4) possible tRNA molecules. Three of these tRNA molecules recognise "stop" or termination codons which have been named amber (UAG), opal (UGA) and ochre (UAA).
The codon indicates which amino acid is to be added and the amino acid is attached to the tRNA molecule at the acceptor arm. As we can see from the table below, most amino acids are represented by more than one codon. This means that the expected protein can still be synthesised, even when a degree of mutation occurs in the DNA or mRNA.
There are 20 essential amino acids, however they can be combined in any order, just like the four nucleotides. This permits the production of the many different proteins which let organisms grow and function.
Name
1-Letter Nickname
Triplet
3-Letter Nickname
Glycine
G
GGT,GGC,GGA,GGG
Gly
Alanine
A
GCT,GCC,GCA,GCG
Ala
Valine
V
GTT,GTC,GTA,GTG
Val
Leucine
L
TTG,TTA,CTT,CTC,CTA,CTG
Leu
Isoleucine
I
ATT,ATC,ATA
Ileu
Serine
S
TCT,TCC,TCA,TCG,AGT,AGC
Ser
Threonine
T
ACT,ACC,ACA,ACG
Thr
Cysteine
C
TGT,TGC
Cys
Methionine
M
ATG
Met
Glutamic Acid
E
GAA,GAG
Glu
Aspartic Acid
D
GAT,GAC,AAT,AAC
Asp
Lysine
K
AAA,AAG
Lys
Arginine
R
CGT,CGC,CGA,CGG,AGA,AGG
Arg
Asparagine
N
AAT,AAC
Asn
Glutamine
Q
GAA,GAG
Gln
Phenylalanine
F
TTT,TTC
Phe
Tyrosine
Y
TAT, TAC
Tyr
Tryptophan
W
TGG
Trp
Unknown
X
 
xxx
Proline
P
CCT,CCC,CCA,CCG
Pro
Terminator
*
TAA,TAG,TGA
End


INITIATION
When the large ribosmal subunit,small ribosomal subunit, mRNA and the tRNA carrying a methionine come together in the cytoplasm, the ribosome becomes active and the synthesis of a polypeptide, or "translation", is initiated. The AUG codon binds at theprotein binding site (P) of the ribosome and AUG is always the first codon of an mRNA.





The next complementary tRNA will bind at theattachment binding site(A) of the ribosome. The adjacent amino acids are then joined by a peptide bond via a peptidaseenzyme. Thus the polypeptide chain begins to grow and as it does, it is passed to the next tRNA currently occupying the A site.






ELONGATION
The ribosome then moves 1 codon down the mRNA in a 5' to 3' direction. This is achieved by atranslocase enzyme. As the process of ribosome translocation continues, the "old" tRNA is released to bind another amino acid and go in search of a new codon. The binding of a new aminoacid is mediated by an enzyme called amino-acyl-tRNA synthase






TERMINATION
The process continues along the mRNA until a stop codon is reached. While there is no tRNA for a stop codon, there is an enzyme calledrelease factor which cleaves the polypeptide chain resulting in a new protein.





Finally, the entire complex is disrupted, the ribosome separates and the mRNA is released to be used again or degraded. Translation occurs at multiple sites along an mRNA so that many ribosomes can be seen by electron microscopy bound to a single mRNA strand with many polypeptide chains forming from each.

Introduction to DNA Structure

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. Structures are shown below:

Structure of A and G

The 9 atoms that make up the fused rings (5 carbon, 4 nitrogen) are numbered 1-9. All ring atoms lie in the same plane.

PYRIMIDINE BASES

Cytosine and thymine are pyrimidines. The 6 stoms (4 carbon, 2 nitrogen) are numbered 1-6. Like purines, all pyrimidine ring atoms lie in the same plane.

Structure of C and T

DEOXYRIBOSE SUGAR

The deoxyribose sugar of the DNA backbone has 5 carbons and 3 oxygens. The carbon atoms are numbered 1', 2', 3', 4', and 5' to distinguish from the numbering of the atoms of the purine and pyrmidine rings. The hydroxyl groups on the 5'- and 3'- carbons link to the phosphate groups to form the DNA backbone. Deoxyribose lacks an hydroxyl group at the 2'-position when compared to ribose, the sugar component of RNA.

Structure of deoxyribose

NUCLEOSIDES

A nucleoside is one of the four DNA bases covalently attached to the C1' position of a sugar. The sugar in deoxynucleosides is 2'-deoxyribose. The sugar in ribonucleosides is ribose. Nucleosides differ from nucleotides in that they lack phosphate groups. The four different nucleosides of DNA are deoxyadenosine (dA), deoxyguanosine (dG), deoxycytosine (dC), and (deoxy)thymidine (dT, or T).

Structure of dA

In dA and dG, there is an "N-glycoside" bond between the sugar C1' and N9 of the purine.

NUCLEOTIDES

A nucleotide is a nucleoside with one or more phosphate groups covalently attached to the 3'- and/or 5'-hydroxyl group(s).

DNA BACKBONE

The DNA backbone is a polymer with an alternating sugar-phosphate sequence. The deoxyribose sugars are joined at both the 3'-hydroxyl and 5'-hydroxyl groups to phosphate groups in ester links, also known as "phosphodiester" bonds.

Example of DNA Backbone: 5'-d(CGAAT):

Features of the 5'-d(CGAAT) structure:

  • Alternating backbone of deoxyribose and phosphodiester groups
  • Chain has a direction (known as polarity), 5'- to 3'- from top to bottom
  • Oxygens (red atoms) of phosphates are polar and negatively charged
  • A, G, C, and T bases can extend away from chain, and stack atop each other
  • Bases are hydrophobic

DNA DOUBLE HELIX

DNA is a normally double stranded macromolecule. Two polynucleotide chains, held together by weak thermodynamic forces, form a DNA molecule.

Structure of DNA Double Helix

FEATURES OF THE DNA DOUBLE HELIX

  • Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral
  • The two polynucleotide chains run in opposite directions
  • The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the railing of a sprial staircase
  • The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a spiral staircase.

BASE PAIRS

Within the DNA double helix, A forms 2 hydrogen bonds with T on the opposite strand, and G forms 3 hyrdorgen bonds with C on the opposite strand.

Example of dA-dT base pair as found within DNA double helix

Example of dG-dC base pair as found within DNA double helix

  • dA-dT and dG-dC base pairs are the same length, and occupy the same space within a DNA double helix. Therefore the DNA molecule has a uniform diameter.
  • dA-dT and dG-dC base pairs can occur in any order within DNA molecules

DNA HELIX AXIS

The helix axis is most apparent from a view directly down the axis. The sugar-phosphate backbone is on the outside of the helix where the polar phosphate groups (red and yellow atoms) can interact with the polar environment. The nitrogen (blue atoms) containing bases are inside, stacking perpendicular to the helix axis.

View down the helix axis


What is DNA?


Deoxyribonucleic acid (/diˌɒksiˌraɪbɵ.njuːˌkleɪ.ɨk ˈæsɪd/  ( listen)), or DNA, is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms, with the exception of some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.



DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

Within cells, DNA is organized into long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed

A DNA Spray Keeps Burglars at Bay




That gadget was  a canister loaded with a harmless solution containing synthetic DNA. If a criminal attempts to burgle a premises fitted with the device, an employee can hit a panic button that alerts police to a crime in progress and simultaneously shoots out a fine mist covering everyone in the room, including the robber. And as each batch of the spray -- which glows blue under ultraviolet light -- has a unique DNA signature, police can connect the robber to the scene of the crime.
A company-provided picture shows how the DNA spray fingers a burglar under ultraviolet light.


Criminally minded readers might now be thinking, "Well, if I robbed a shop, I'd just scrub myself clean when I got home." But as Andrew Knights, managing director of SelectaDNA, explains, the solution isn't so easy to remove. "It will come off within a number of hand washes," he told AOL News. "But if you run through a spray it'll accumulate on the inside of your nostrils and ears and under the fingernails; areas that are difficult to get off." And, he notes, if a criminal doesn't have an ultraviolet light, he won't know where the liquid is lurking.

Hundreds of sprays have been deployed at retailers and banks across the U.K.,and New Zealand; Knights' company, part of Britain's Selectamark security group, is also in talks with U.S. companies.

Knights says the sprays can reduce crime levels, but he admits the unique DNA evidence they offer has yet to be used in a prosecution. 

That's not a sign of failure, though. If a suspect is scanned with a UV light at a police station (almost everyone arrested in the U.K now undergoes this procedure, no matter what crime the person is suspected of) and starts to glow, he says, "They'll generally plead guilty. The criminal knows it's better to make a plea bargain, rather than annoy the police even further by forcing them to go through the DNA testing."

That's exactly what happened when an 18-year-old burglar from the town of Rawtenstall -- some 20 miles east of Preston in northwestern England -- was hauled in for questioning last month. When he walked under a UV light at the station, his arms started to shine, explains Police Constable Phil Buck, a crime-prevention coordinator in the northern English county of Lancashire. The young offender picked up the glow when he broke into a garden center whose roof had been smeared in another crime-fighting substance: SelectaDNA Gel. "He held up his brightly glowing hands and confessed," says Buck, adding that the teen admitted breaking into the gardening store three times.

However, the main aim of the SelectaDNA spray isn't to capture criminals but to scare them away. "Retailers are investing in this technology because they want to move the crime on somewhere else," Knights says. "They are just out to protect their property and staff." That's why every business that uses a SelectaDNA spray also prominently displays a bright yellow sign in their window showing a stick man with a bag of swag being hit by the mist. "Warning," the sign reads. "SelectaDNA spray installed here."

What is RNA?

Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate.
RNA comes in a variety of different shapes. Double-stranded DNA is a staircase-like molecule.

RNA is very similar to  but differs in a few important structural details: in the cell, RNA is usually single-stranded, while  is usually double-stranded; RNA nucleotides contain ribose while  contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than that is present in 
Ribonucleic acid (RNA) has the bases adenine (A), cytosine (C), guanine (G), and uracil (U).
Ribonucleic acid (RNA) has the bases adenine (A), cytosine (C), guanine (G), and uracil (U). Image Credit: National Institute of General Medical Sciences
RNA is transcribed from by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which are expressed, but also as the genomes of most
RNA and  are both nucleic acids, but differ in three main ways. First, unlikewhich is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Second, while contains ''deoxyribose'', RNA contains ''ribose'' (there is no hydroxyl group attached to the pentose ring in the 2' position in These hydroxyl groups make RNA less stable than  because it is more prone to hydrolysis. Third, the complementary base to adenine is not as it is in  but rather uracil, which is an unmethylated form of  For instance, determination of the structure of the ribosome—an enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA.

What is DNA?

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and molecules. The DNA segments that carry this genetic information are called  but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.
Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid in a process called transcription.
DNA Structure
Within cells, DNA is organized into long structures called  Theseare duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.