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DNA

From Molecular Biology Wiki

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DNA

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DNA


DNA Model


Fourteen Stone


Ornamental Onion

DNA is composed of deoxyribonucleotide

DNA - DeoxyriboNucleic Acid

DNA is an acronym for DeoxyriboNucleic Acid, or usually 2'-deoxy-5'-ribonucleic acid.

Deoxyribonucleic acid (DNA) is a nucleic acid which carries the genetic instructions for the biological development of all cellular forms of life and many viruses.

Hereditary: Inheritance of DNA

DNA is sometimes referred to as the molecule of heredity as it is inherited and used to propagate traits. During reproduction, it is replicated and transmitted to offspring. Each person's DNA or genome is inherited in the form of chromosomes from both parents. Mitochondrial DNA is inherited from the mother, and twenty-three chromosomes from each parent combine to form the genome of a zygote, or the fertilized egg. Most human cells contain 23 pairs of chromosomes, together with the mitochondrial DNA inherited from the mother.


Central Dogma of Biology - Francis Crick


In bacteria and other simple cell organisms, DNA is distributed more or less throughout the cell. In the complex cells that make up plants, animals and in other multi-celled organisms, most of the DNA is found in the chromosomes, which are located in the cell nucleus. The energy-generating organelles known as chloroplasts and mitochondria also carry DNA, as do many viruses.


  1. Genes can be loosely viewed as the organism's "cookbook";
  2. A strand of DNA contains genes, areas that regulate genes, and areas that either have no function, or a function we don't know;
  3. DNA is organized as two complementary strands, head-to-toe, with bonds between them that can be "unzipped" like a zipper, separating the strands;
  4. DNA is encoded with four interchangeable "building blocks", called "bases", which can be abbreviated A, T, C, and G; each base "pairs up" with only one other base: A+T, T+A, C+G and G+C; that is, an "A" on one strand of double-stranded DNA will "mate" properly only with a "T" on the other, complementary strand;
  5. The order does matter: A+T is not the same as T+A, just as C+G is not the same as G+C;
  6. However, since there are just four possible combinations, naming only one base on the conventionally chosen side of the strand is enough to describe the sequence;
  7. The order of the bases along the length of the DNA is what it's all about, the sequence itself is the description for genes;
  8. Replication is performed by splitting (unzipping) the double strand down the middle via relatively trivial chemical reactions, and recreating the "other half" of each new single strand by drowning each half in a "soup" made of the four bases. Since each of the "bases" can only combine with one other base, the base on the old strand dictates which base will be on the new strand. This way, each split half of the strand plus the bases it collects from the soup will ideally end up as a complete replica of the original, unless a mutation occurs;
  9. Mutations are simply chemical imperfections in this process: a base is accidentally skipped, inserted, or incorrectly copied, or the chain is trimmed, or added to; all other basic mutations can be described as combinations of these accidental "operations".

Although sometimes called "the molecule of heredity", pieces of DNA as people typically think of them are not single molecules. Rather, they are pairs of molecules, which entwine like vines to form a double helix (see the illustration at the right).

Each vine-like molecule is a strand of DNA: a chemically linked chain of nucleotides, each of which consists of a sugar, a phosphate and one of four kinds of Aromatic hydrocarbon "bases". Because DNA strands are composed of these nucleotide subunits, they are polymers.

The diversity of the bases means that there are four kinds of nucleotides, which are commonly referred to by the identity of their bases. These are adenine (A), thymine (T), cytosine (C), and guanine (G).

In a DNA double helix, two polynucleotide strands can associate through the hydrophobic effect. Specificity of which strands stay associated is determined by complementary pairing. Each base forms hydrogen bonds readily to only one other -- A to T and C to G -- so that the identity of the base on one strand dictates the strength of the association; the more complementary bases exist, the stronger and longer-lasting the association.

The Structure of DNA

Although DNA is often termed "the molecule of heredity", DNA is not usually found in nature as a single molecule. DNA usually is found as a pair of complementary strands linked together to form a double helix.


DNA Structure Video:

DNA is a found in nature usually in the form of a double stranded helix with anti-parrallel strands. In DNA, either strand contains all the information essential for DNA replication. DNA double stranded state is actually its "resting state". During DNA relication and transcription, regions of DNA can exist as single stranded forms which are known as active regions.

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Double Helix


Anaconda!


DNA Blues


Fingerprints

The cell's machinery is capable of melting or disassociating a DNA double helix, and using each DNA strand as a template for synthesizing a new strand which is nearly identical to the previous strand. Errors that occur in the synthesis are known as mutations. The process known as PCR mimics this process in vitro in a nonliving system.

Because pairing causes the nucleotide bases to face the helical axis, the sugar and phosphate groups of the nucleotides run along the outside, and the two chains they form are sometimes called the "backbones" of the helix. In fact, it is chemical bonds between the phosphates and the sugars that link one nucleotide to the next in the DNA strand.


Image:DNA-detail.jpg
DNA structure in detail

The Hydrophobic Complimentary Core of Nucleotides

The interior portion "ladder" of DNA is composed of 4 nitrogenous bases: Adenine (A), Guanine (G), Thymine (T), and Cytosine (C). These bases are non-polar and are thus hyrdophobic (hydro Gk. water, and phobic fear or dislike).


Inside a DNA molecule these nucleotide bases pair up, A to T and C to G, forming hydrogen bonds that stabilize the DNA molecule. Because the interior bases pair up in this manner, we say the DNA double helix is complimentary. It is this sequence of bases inside the DNA double helix that we refer to as the genetic code.

Interestingly, humans are approximately 70% composed of water (similar to other life forms). For every DNA molecule in the cell, there are billions of water H2O molecules. A key question is how can you have two base pairs hydrogen bonding with each other and not to water molecules?

The first hydrogen bond "pays" the most entropic energy for the cost of the interaction.

The DNA Code: DNA Sequence

Within a gene, the sequence of nucleotides along a DNA strand defines a protein, which an organism is liable to manufacture or "express" at one or several points in its life using the information of the sequence. The relationship between the nucleotide sequence and the amino-acid sequence of the protein is determined by simple cellular rules of translation, known collectively as the genetic code. The genetic code is made up of three letter 'words' (termed a codon) formed from a sequence of three nucleotides (eg. ACT, CAG, TTT). These codons can then be translated with messenger RNA and then transfer RNA, with a codon corresponding to a particular amino acid. Since there are 64 possible codons, most amino acids have more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region.

In many species of organism, only a small fraction of the total sequence of the genome appears to encode protein. The function of the rest is a matter of speculation. It is known that certain nucleotide sequences specify affinity for DNA binding proteins, which play a wide variety of vital roles, in particular through control of replication and transcription. These sequences are frequently called regulatory sequences, and researchers assume that so far they have identified only a tiny fraction of the total that exist. "Junk DNA" represents sequences that do not yet appear to contain genes or to have a function.

Sequence also determines a DNA segment's susceptibility to cleavage by restriction enzymes, the quintessential tools of genetic engineering. The position of cleavage sites throughout an individual's genome determines one kind of an individual's "DNA fingerprint".


Separating the two Strands of a DNA double Helix

While the ratios of G to C and A to T in an organism’s DNA are fixed, the GC content (percentage of G +C) can vary considerably from one DNA to another.

When a DNA solution is heated enough, the non-covalent forces that hold the two strands together weaken and finally break. When this happens, the two strands come apart in a process known as DNA denaturation, or DNA melting. The tempereature at which the DNA strands are half denatured is called the melting temperature, or Tm. The amount of strand separation, or melting, is measured by the absorbance of the DNA solution at 260nm.


DNA molecules can twist and separate and can reassemble together again.


Nucleic acids absorb light at this wavelength because of the electronic structure in their bases, but when two strands of DNA come together, the close proximity of the bases in the two strands quenches some of this absorbance. When the two strands separate, this quenching disappears and the absorbance rises 30%-40%. This is called hyperchromic shift.

The GC content of DNA has a significant effect on its Tm. The higher a DNA’s GC content, the higher its Tm. Why should this be? One of the forces holding the two strands of DNA together is hydrogen bonding. Also G-C pairs form three hydrogen bonds, whereas A-T pairs have only two. It stands to reason, then that two strands of DNA rich in G and C will hold to each other more tightly than those of AT-rich DNA.


Heating is not the only way to denature DNA. Organic solvents such as dimethyl sulfoxide and formamide, or high pH, disrupt the hydrogen bonding between DNA strands and promote denaturation. Lowering the salt concentration of the DNA solution also aids denaturation by removing the ions that shield the negative charges on the two strands from one another. At low ionic strength, the mutually repulsive forces of the negative charges are strong enough to denature the DNA are a relatively low temperature. The GC content of DNA also affects its density.

Reuniting the Seperated DNA Strands

Once the two strands of DNA separate, they can, under the proper conditions, come back together again. This is called annealing or renaturation. Several factors contribute to renaturation efficiency.


Here are three of the most important:


1. Temperature: The best temperature for renaturation of a DNA is about 25° C below its Tm. This temperature is low enough that it does not promote denaturation, but high enough to allow rapid diffusion of DNA molecules and to weaken the transient bonding between mismatched sequences and short intra-strand base-paired regions. This suggests that rapid cooling following denaturation would frustrate renaturation. Indeed a common procedure to ensure that denatured DNA stays denatured is to plunge the hot DNA solution into ice. This is called quenching.


2. DNA concentration: The concentration of DNA in the solution is also important. Within reasonable limits, the higher the concentration, the more likely it is that two complementary strands will encounter each other within a given time. In other words the higher the concentration, the faster the annealing.


3. Renaturation time: Obviously the longer the time allowed for annealing, the more will occur. Britten and Kohne invented a term Cot, to encompass the latter two factors, DNA concentration and time. Cot is the product of the initial DNA concentration (Co) in moles of nucleotides per liter and time(t) in seconds. All other factors being equal, the extent of renaturation of complementary strands in a DNA solution will depend on Cot.

DNA replication

DNA replication or DNA synthesis is the process of copying the double-stranded DNA prior to cell division. The two resulting double strands are generally almost perfectly identical, but occasionally errors in replication can result in a less than perfect copy (see mutation), and each of them consists of one original and one newly synthesized strand. This is called semiconservative replication. The process of replication consists of three steps: initiation, replication and termination.

DNA undergoes transcription to make RNA.

Hereditary

polymorphisms


History of DNA

Frequently Asked DNA Questions

What is DNA?

Where is DNA?

What is a gene?


Related DNA Articles

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