The Protein Synthesis Process

Now let's look at the order of events in the synthesis of our protein from our sample mRNA :

• A ribosome binds to mRNA with the AUG codon in the P-site and the UUU codon in the A-site.
• An amino acyl-tRNA (anti-codon = UAC) with an attached methionine comes in to the P-site of the ribosome
• An amino acyl-tRNA (anti-codon = AAA) with an attached phenylalanine comes in to the A-site of the ribosome
• A chemical bond forms between the methionine and phenylalanine (in a protein, this covalent bond is called a peptide bond).
• The methionine-specific tRNA leaves the P-site and goes off to collect another methionine
• The ribosome shifts so that the P-site now contains the UUU codon with the attached phenyl-alanine tRNA and the next codon (ACA) now occupies the A-site.
• An amino acyl-tRNA (anti-codon) with an attached threonine comes in to the A-site of the ribosome.
• A peptide bond forms between the phenylalanine and the threonine.
• The phenylalanine-specific tRNA leaves the P-site and goes off to find another phenylalanine.
• The ribosome shifts down codon so that the cease sequence is now in the A-site. On encountering the cease sequence:
• The ribosome detaches from the mRNA and splits in to its parts
• The threonine-specific tRNA releases its threonine and leaves
• The new protein floats away
• Several ribosomes can attach to a molecule of mRNA after another and start making proteins. So several proteins can be made from mRNA. In fact, in E. coli bacteria, translation of the mRNA begins even before transcription is completed.

Building a Protein: Transcription

Building proteins is much like building a house:

1. The master blueprint is DNA, which contains all of the information to build the new protein (house).
2. The working copy of the master blueprint is called messenger RNA (mRNA), whic­h is copied from DNA.
3. The construction site is either the cytoplasm in a prokaryote or the endoplasmic reticulum (ER) in a eukaryote.
4. The building materials are amino acids.
5. The construction workers are ribosomes & transfer RNA molecules.

Let's look at each phase of the new construction more closely.
       In a eukaryote, DNA never leaves the nucleus, so its information must be copied. This copying method is called transcription & the copy is mRNA. Transcription takes place in the cytoplasm (prokaryote) or in the nucleus (eukaryote). The transcription is performed by an enzyme called RNA polymerase. To make mRNA, 


RNA polymerase :

               Binds to the DNA strand at a specific sequence of the gene called a promoter Unwinds & unlinks the strands of DNA. Makes use of the DNA strands as a guide or template

               Matches new nucleotides with their complements on the DNA strand (G with C, A with U -- keep in mind that RNA has uracil (U) in lieu of thymine (T)). Binds these new RNA nucleotides together to form a complementary copy of the DNA strand (mRNA). Stops when it encounters a termination sequence of bases (cease codon) mRNA is happy to live in a single-stranded state (as against DNA's desire to form complementary double-stranded helixes). In prokaryotes, all of the nucleotides in the mRNA are part of codons for the new protein. However, in eukaryotes only, there's additional sequences in the DNA & mRNA that don't code for proteins called introns.

This mRNA is then further processed : 

               Introns get cut out

               The coding sequences get spliced together

               A special nucleotide "cap" gets added to finish

               A long tail consisting of 100 to 200 adenine nucleotides is added to the other finish

               No knows why this processing occurs in eukaryotes. Finally, at any moment, plenty of genes are being transcribed simultaneously according to the cell's needs for specific proteins.

The working copy of the blueprint (mRNA) must now go the construction site where the workers will build the new protein. If the cell is a prokaryote such as an E. coli bacterium, then the site is the cytoplasm. If the cell is a eukaryote, such as a human cell, then the mRNA leaves the nucleus through giant holes in the nuclear membrane (nuclear pores) & goes to the endoplasmic reticulum (ER).

How does DNA encode the information for a protein?

How does DNA encode the information for a protein? 

      ~~> There's only DNA bases, but there's twenty amino acids that can be used for proteins. So, groups of nucleotides form a word (codon) that specifies which of the twenty amino acids goes in to the protein (a 3-base codon yields 64 feasible patterns (4*4*4), which is over to specify twenty amino acids. Because there's 64 feasible codons & only twenty amino acids, there is some repetition in the genetic code. Also, the order of codons in the gene specifies the order of amino acids in the protein. It may need anywhere from 100 to one,000 codons (300 to four,000 nucleotides) to specify a given protein. Each gene also has codons to designate the beginning (start codon) & finish (cease codon) of the gene.

What DNA Does

           DNA carry all of the information for your physical characteristics, which are fundamentally determined by proteins. So, DNA contains the instructions for making a protein. In DNA, each protein is encoded by a gene (a specific sequence of DNA nucleotides that specify how a single protein is to be made). Specifically, the order of nucleotides within a gene specifies the order and types of amino acids that must be put together to make a protein.  A protein is made of a long chain of chemicals called amino acids.
Proteins have lots of functions :
        Enzymes that over out chemical reactions (such as digestive enzymes)
        Structural proteins that are building materials (such as collagen and nail keratin)
        Transport proteins that over substances (such as oxygen-carrying hemoglobin in blood)
        Contraction proteins that cause muscles to compress (such as actin and myosin)
        Storage proteins that hold on to substances (such as albumin in egg whites and iron-storing ferritin in your spleen)
Hormones - chemical messengers between cells (including insulin, estrogen, testosterone, cortisol, et cetera)
Protective proteins - antibodies of the immune process, clotting proteins in blood
Toxins - poisonous substances, (such as bee venom and snake venom)

The particular sequence of amino acids in the chain is what makes protein different from another. This sequence is encoded in the DNA where gene encodes for protein.

DNA Replication

• DNA carries the information for making all of the cell's proteins. These proÃ�­teins implement all of the functions of a living organism & decide the organism'Ã�­s characteristics. When the cell reproduces, it's pass all of this information on to the daughter cells.

• Before a cell can reproduce, it must first replicate, or make a replica of, its DNA. Where DNA replication occurs depends on whether the cells is a prokaryote or a eukaryote (see the RNA sidebar on the earlier page for more about the categories of cells). DNA replication occurs in the cytoplasm of prokaryotes & in the nucleus of eukaryotes. Irrespective of where DNA replication occurs, the basic method is the same.

• The structure of DNA lends itself basically to DNA replication. Each side of the double helix runs in opposite (anti-parallel) directions. The beauty of this structure is that it can unzip down the middle & each side can serve as a pattern or template for the other side (called semi-conservative replication). However, DNA does not unzip entirely. It unzips in a small area called a replication fork, which then moves down the whole length of the molecule.

Let's look at the details:

1. An enzyme called DNA gyrase makes a nick in the double helix & each side separates
2. An enzyme called helicase unwinds the double-stranded DNA
3. Several small proteins called single strand binding proteins (SSB) temporarily bind to each side & keep them separated
4. An enzyme complex called DNA polymerase "walks" down the DNA strands & adds new nucleotides to each strand. The nucleotides pair with the complementary nucleotides on the existing stand (A with T, G with C).
5. A subunit of the DNA polymerase proofreads the new DNA
6. An enzyme called DNA ligase seals up the fragments in to long continuous strand
7. The new copies automatically wind up again

Different types of cells replicated their DNA at different rates. Some cells constantly divide, like those in your hair & fingernails & bone marrow cells. Other cells go through several rounds of cell division & cease (including specialized cells, like those in your brain, muscle & heart). Finally, some cells cease dividing, but can be induced to divide to repair injury (such as skin cells & liver cells). In cells that do not constantly divide, the cues for DNA replication/cell division come in the kind of chemicals. These chemicals can come from other parts of the body (hormones) or from the environment.

Fitting Inside a Cell

         DNA is a long molecule. For example, a typical bacterium, like E. coli, has DNA molecule with about six,000 genes (A gene is a specific sequence of DNA nucleotides that codes for a protein. We'll speak about this later). If drawn out, this DNA molecule would be about one millimeter long. However, a typical E. coli is only six microns long (six one-thousandths of a millimeter).So to fit inside the cell, the DNA is highly coiled and crooked in to circular chromosome.

        Complex organisms, like plants and animals, have 50,000 to 100,000 genes on lots of different chromosomes (humans have 46 chromosomes). In the cells of these organisms, the DNA is crooked around bead-like proteins called  histones. The histones are also coiled tightly to form chromosomes, which can be present in the nucleus of the cell. When a cell reproduces, the chromosomes (DNA) get copied and distributed to each offspring, or daughter, cell. Non-sex cells have copies of each chromosome that get copied and each daughter cell receives copies (mitosis). In the coursework of meiosis, precursor cells have copies of each chromosome that gets copied and distributed equally to sex cells. The sex cells (sperm and egg) have copy of each chromosome. When sperm and egg unite in fertilization, the offspring have copies of each chromosome (see How Sex Works).

DNA structure

        DNA is of the nucleic acids, information-containing molecules in the cell (ribonucleic acid, or RNA, is the other nucleic acid). DNA is present in the nucleus of every human cell. (See the sidebar at the bottom of the page for more about RNA & different types of cells). 

The information in DNA :        Guides the cell (along with RNA) in making new proteins that choose all of our biological traits
gets passed (copied) from generation to the next
The key to all of these functions is present in the molecular structure of DNA, as described by Watson & Crick.
        Although it may look complicated, the DNA in a cell is  a pattern made up of different parts called nucleotides. Imagine a set of blocks that has only shapes, or an alphabet that has only letters. DNA is a long string of these blocks or letters. Each nucleotide consists of a sugar (deoxyribose) bound on side to a phosphate group & bound on the other side to a nitrogenous base.

             There's classes of nitrogen bases called purines (double-ringed structures) & pyrimidines (single-ringed structures). The bases in DNA's alphabet are :
                                                                                      adenine (A) - a purine
                                                                                      cytosine(C) - a pyrimidine
                                                                                      guanine (G) - a purine
                                                                                      thymine (T) - a pyrimidine

             Watson & Crick discovered that DNA had sides, or strands, & that these strands were crooked together like a crooked ladder -- the double helix. The sides of the ladder comprise the sugar-phosphate portions of adjoining nucleotides bonded together. The phosphate of nucleotide is covalently bound (a bond in which or more pairs of electrons are shared by atoms) to the sugar of the next nucleotide. The hydrogen bonds between phosphates cause the DNA strand to twist. The nitrogenous bases point inward on the ladder & form pairs with bases on the other side, like rungs. Each base pair is formed from complementary nucleotides (purine with pyrimidine) bound together by hydrogen bonds. The base pairs in DNA are adenine with thymine & cytosine with guanine.

How DNA works

            Like the ring of power in Tolkien's "Lord of the Rings," deoxyribonucleic acid (DNA) is the master molecule of every cell. It contains vital information that gets passed on to each successive generation. It coordinates the making of itself as well as other molecules (proteins). If it is changed slightly, serious consequences may result. If it is destroyed beyond repair, the cell dies.
            Changes in the DNA of cells in multicellular organisms produce variations in the characteristics of a species. Over long periods of time, natural choice acts on these variations to evolve or alter the species.
The presence or absence of DNA facts at a crime scene could mean the difference between a guilty verdict & an acquittal. DNA is so important that the United States government has spent immense amounts of money to unravel the sequence of DNA in the human genome in hopes of understanding & finding cures for plenty of genetic diseases. Finally, from the DNA of cell, they can clone an animal, a plant or perhaps even a human being.
             But what is DNA? Where is it found? What makes it so special? How does it work? In this editorial, they will look deep in to the structure of DNA & report the way it makes itself & the way it determines all of your traits. First, let's look at how DNA was discovered.
             DNA is of a class of molecules called nucleic acids. Nucleic acids were originally discovered in 1868 by Friedrich Meischer, a Swiss biologist, who isolated DNA from pus cells on bandages. Although Meischer suspected that nucleic acids might contain genetic information, he could not confirm it.
So scientists had theorized about the informational role of DNA for a long time, but nobody knew how this information was encoded & transmitted. Plenty of scientists guessed that the structure of the molecule was important to this technique. In 1953, James D. Watson & Francis Crick discovered the structure of DNA at Cambridge University. The story was described in James Watson's book "The Double Helix" & brought to the screen in the film, "The Race for the Double Helix." Fundamentally, Watson & Crick used molecular modeling techniques & information from other investigators (including Maurice Wilkins, Rosalind Franklin, Erwin Chargaff & Linus Pauling) to solve the structure of DNA. Watson, Crick & Wilkins received the Nobel Prize in Medicine for the discovery of DNA's structure (Franklin, who was Wilkins' collaborator & provided a key piece of information that exposed the structure to Watson & Crick, died before the prize was awarded).
            In 1943, Oswald Avery & colleagues at Rockefeller University showed that DNA taken from a bacterium, Streptococcus pneumonia, could make non-infectious bacteria become infectious. These results indicated that DNA was the information-containing molecule in the cell. The information role of DNA was further supported in 1952 when Alfred Hershey & Martha Chase demonstrated that to make new viruses, a bacteriophage virus injected DNA, not protein, in to the host cell.

Silicon vs. DNA Microprocessors

• Silicon microprocessors have been the heart of the computing world for over 40 years. In that time, manufacturers have crammed increasingly electronic devices onto their microprocessors. In accordance with Moore's Law, the number of electronic devices put on a microprocessor has doubled every 18 months. Moore's Law is named after Intel founder Gordon Moore, who predicted in 1965 that microprocessors would double in complexity every years. Plenty of have predicted that Moore's Law will soon reach its finish, because of the physical speed & miniaturization limitations of silicon microprocessors.
• DNA computers have the potential to take computing to new levels, picking up where Moore's Law leaves off. There's several advantages to using DNA in lieu of silicon:
• As long as there's cellular organisms, there will always be a supply of DNA.The giant supply of DNA makes it an affordable resource.
• Unlike the poisonous materials used to make traditional microprocessors, DNA biochips can be made cleanly.
• DNA computers are plenty of times smaller than today's computers.DNA's key advantage is that it will make computers smaller than any computer that has come before them, while simultaneously holding more information. pound of DNA has the capacity to store more information than all the electronic computers ever built & the computing power of a teardrop-sized DNA computer, using the DNA logic gates, will be more powerful than the world's most powerful supercomputer. Over ten trillion DNA molecules can fit in to an area no larger than one cubic centimeter (0.06 cubic inches). With this small amount of DNA, a computer would be able to hold ten terabytes of information, & perform ten trillion calculations at a time. By adding more DNA, more calculations could be performed.

Unlike conventional computers, DNA computers perform calculations parallel to other calculations. Conventional computers operate linearly, taking on tasks separately. It is parallel computing that allows DNA to solve complex mathematical issues in hours, whereas it might take electrical computers hundreds of years to complete them.

The first DNA computers are unlikely to feature word processing, e-mailing & solitaire programs. In lieu, their powerful computing power will be used by national governments for cracking secret codes, or by airlines desirous to map more efficient routes. Studying DNA computers may also lead us to a better understanding of a more complex computer -- the human brain.

Success of the Adleman DNA computer

             The success of the Adleman DNA computer proves that DNA can be used to calculate complex mathematical issues. However, this early DNA computer is far from challenging silicon-based computers in terms of speed. The Adleman DNA computer created a group of feasible answers very quickly, but it took days for Adleman to narrow down the possibilities. Another drawback of his DNA computer is that it requires human assistance. The objective of the DNA computing field is to generate a device that can work independent of human involvement.

Years after Adleman's experiment, researchers at the University of Rochester developed logic gates made of DNA. Logic gates are a vital part of how your computer carries out functions that you command it to do. These gates convert binary code moving through the computer in to a series of signals that the computer makes use of to perform operations. Currently, logic gates interpret input signals from silicon transistors, and convert those signals in to an output signal that allows the computer to perform complex functions.

The Rochester team's DNA logic gates are the first step toward making a computer that has a structure similar to that of an electronic PC. In lieu of using electrical signals to perform logical operations, these DNA logic gates depend on DNA code. They detect fragments of genetic material as input, splice together these fragments and form a single output. For example, a genetic gate called the "And gate" links DNA inputs by chemically binding them so they are locked in an end-to-end structure, similar to the way Legos might be fastened by a third Lego between them. The researchers think that these logic gates might be combined with DNA microchips to generate a breakthrough in DNA computing.

DNA computer parts -- logic gates and biochips -- will take years to create in to a practical, workable DNA computer. If such a computer is ever built, scientists say that it will be more compact, correct and efficient than conventional computers. In the next section, we'll look at how DNA computers could surpass their silicon-based predecessors, and what tasks these computers would perform.

DNA computing technology

                 DNA computers cannot be found at your local electronics store yet. The know-how is still in development, and didn't even exist as an idea a decade ago. In 1994, Leonard Adleman introduced the idea of using DNA to solve complex mathematical issues. Adleman, a computer scientist at the University of Southern New york, came to the conclusion that DNA had computational potential after reading the book "Molecular Biology of the Gene," written by James Watson , who co-discovered the structure of DNA in 1953. In fact, DNA is similar to a computer hard drive in the way it stores permanent information about your genes.

                 Adleman is often called the inventor of DNA computers. His editorial in a 1994 issue of the journal Science outlined how to make use of DNA to solve a widely known mathematical issue, called the directed Hamilton Path issue, often known as the "traveling salesman" issue. The objective of the issue is to find the shortest route between lots of cities, going through each city only three times. As you add more cities to the issue, the issue becomes more difficult. Adleman chosen to find the shortest route between three cities.

You could probably draw this issue out on paper and come to a solution faster than Adleman did using his DNA test-tube computer.

Here are the steps taken in the Adleman DNA computer experiment :
         1.  Strands of DNA represent the three cities. In genes, genetic coding is represented by the letters A, T, C and G. Some sequence of these letters represented each city and feasible flight path.
         2.  These molecules are then mixed in a check tube, with some of these DNA strands sticking together. A chain of these strands represents a feasible answer.
         3.  Within a few seconds, all of the feasible combinations of DNA strands, which represent answers, are created in the check tube
         4.  Adleman eliminates the wrong molecules through chemical reactions, which leaves behind only the flight paths that connect all three cities.

How DNA computer's will work

               While still in their infancy, DNA computers will be able to storing billions of times more information than your personal computer. In this news story, you'll learn how scientists are using genetic material to generate nano-computers that might take the place of silicon-based computers in the next decade.

Even as you read this news story, computer chip manufacturers are furiously racing to make the next microprocessor that will topple speed records. Ultimately, though, this competition is bound to hit a wall. Microprocessors made of silicon will finally reach their limits of speed & miniaturization. Chip makers need a new material to produce faster computing speeds.

You won't think where scientists have found the new material they need to build the next generation of microprocessors. Millions of natural supercomputers exist inside living organisms, including your body. DNA (deoxyribonucleic acid) molecules, the material our genes are made of, have the potential to perform calculations plenty of times faster than the world's most powerful human-built computers. DNA might day be integrated in to a computer chip to generate a so-called biochip that will push computers even faster. DNA molecules have already been harnessed to perform complex mathematical issues.

DNA REPAIR

                DNA Repair provides a forum for the comprehensive coverage of cellular responses to DNA destroy in living cells. The journal publishes original observations on genetic, cellular, biochemical & molecular aspects of  DNA repair, mutagenesis, cell cycle regulation, apoptosis & other biological responses to cells exposed to genomic insult, as well as their relationship to human diseases.

                DNA Repair publishes Full-length research papers, Brief Document of Research, Invited minireviews, Letters to the Editor, Hot topics in DNA repair, Classics in DNA repair, Historical reflections, Book reviews & Meeting Reports. DNA Repair also welcomes Correspondence from the scientific community, as they relate to papers historically in the past published in the journal. These are handled directly by the Editor-in-Chief & may be accompanied by responses solicited papers are published every month. In addition, the journal will publish a smaller number of peer-reviewed Brief Reports on original research findings of special interest, as well as invited Mini-reviews on chosen topics that provide 'state-of-the-art' synopses of cellular responses to DNA destroy. Book reviews & meeting reports will be regularly featured & the Journal welcomes Correspondence from the scientific community, as they relate to papers historicallyin the past published in the journal. These are handled directly by the Editor-in-Chief & may be accompanied by responses solicited from relevant individuals.

BASIC RESEARCH ON DNA

Gregor Mendel
   ~~>  Gregor Mendel the "Father of Genetics" performed an experiement in 1857 that led to increased interest in the study of genetics. Mendel who became a monk of the Roman Catholic church in 1843, studied at the University of Vienna where he mastered arithmetic, & then later performed lots of scientific experiments. The greatest experiment that Mendel performed involved growing thousands of pea plants for 8 years. He was made to give up his experiment when he became abbot of the monastery because of the political issues of the time. He died in 1884, but has been recalled for the great contribution to science that he made. To learn about his experiment & what it led to read: Genetics.

Frederick Griffith
  ~~>   In 1928 a scientist named Frederick Griffith was working on a project that enabled others to point out that DNA was the molecule of inheritance. Griffith's experiment involved mice & types of pneumonia, a virulent as well as a non-virulent kind. He injected the virulent pneumonia in to a mouse & the mouse died. Next he injected the non-virulent pneumonia in to a mouse & the mouse continued to live. After this, he heated up the virulent disease to kill it & then injected it in to a mouse. The mouse lived on. Last he injected non-virulent pneumonia & virulent pneumonia, that had been heated & killed, in to a mouse. This mouse died.

•   Why? Griffith thought that the killed virulent bacteria had passed on a characteristic to the non-virulent to make it virulent. He thought that this characteristic was in the inheritance molecule. This passing on of the inheritance molecule was what he called transformation.

INFORMATION ON DNA

                     DNA consists of long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is of types of molecules called bases. It is the sequence of these 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 in to the related nucleic acid RNA, in a technique called transcription.

Deoxyribonucleic acid , 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 RNA 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 parts of cells, such as proteins and RNA molecules. The DNA segments that over this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

Within cells, DNA is organized in to long structures called chromosomes. These chromosomes are duplicated before cells divide, in a technique called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus as well as a number of their DNA in organelles, such as mitochondria or chloroplasts.[1] 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