DNA Structure and Function

DNA Structure and Function

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA). Mitochondria are structures within cells that convert the energy from food into a form that cells can use.

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The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.

DNA bases pair up with each other, A with T and C with G, to form units called base pairs. Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar, and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix. The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder’s rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder.

An important property of DNA is that it can replicate, or make copies of itself. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. This is critical when cells divide because each new cell needs to have an exact copy of the DNA present in the old cell.

DNA Structure

Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. The two DNA strands are antiparallel, such that the 3ʹ end of one strand faces the 5ʹ end of the other. The 3ʹ end of each strand has a free hydroxyl group, while the 5ʹ end of each strand has a free phosphate group. The sugar and phosphate of the polymerized nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. These nitrogenous bases on the interior of the molecule interact with each other, base pairing.

Analysis of the diffraction patterns of DNA has determined that there are approximately 10 bases per turn in DNA. The asymmetrical spacing of the sugar-phosphate backbones generates major grooves (where the backbone is far apart) and minor grooves (where the backbone is close together) (Figure 6). These grooves are locations where proteins can bind to DNA. The binding of these proteins can alter the structure of DNA, regulate replication, or regulate transcription of DNA into RNA.

DNA Structure and FunctionWatson and Crick proposed the double helix model for DNA. (a) The sugar-phosphate backbones are on the outside of the double helix and purines and pyrimidines form the “rungs” of the DNA helix ladder. (b) The two DNA strands are antiparallel to each other. (c) The direction of each strand is identified by numbering the carbons (1 through 5) in each sugar molecule. The 5ʹ end is the one where carbon #5 is not bound to another nucleotide; the 3ʹ end is the one where carbon #3 is not bound to another nucleotide.

Base pairing takes place between a purine and pyrimidine. In DNA, adenine (A) and thymine (T) are complementary base pairs, and cytosine (C) and guanine (G) are also complementary base pairs, explaining Chargaff’s rules. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds between them, whereas cytosine and guanine form three hydrogen bonds between them.

DNA Structure and Function

In the laboratory, exposing the two DNA strands of the double helix to high temperatures or to certain chemicals can break the hydrogen bonds between complementary bases, thus separating the strands into two separate single strands of DNA (single-stranded DNA [ssDNA]). This process is called DNA denaturation and is analogous to protein denaturation, as described in Proteins. The ssDNA strands can also be put back together as double-stranded DNA (dsDNA), through reannealing or renaturing by cooling or removing the chemical denaturants, allowing these hydrogen bonds to reform. The ability to artificially manipulate DNA in this way is the basis for several important techniques in biotechnology (Figure 8). Because of the additional hydrogen bonding between the C = G base pair, DNA with a high GC content is more difficult to denature than DNA with a lower GC content.

DNA Structure and Function

DNA Function

DNA stores the information needed to build and control the cell. The transmission of this information from mother to daughter cells is called vertical gene transfer and it occurs through the process of DNA replication. DNA is replicated when a cell makes a duplicate copy of its DNA, then the cell divides, resulting in the correct distribution of one DNA copy to each resulting cell. DNA can also be enzymatically degraded and used as a source of nucleosides and nucleotides for the cell. Unlike other macromolecules, DNA does not serve a structural role in cells.

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Types of DNA:

DNA duplex model proposed by Watson and Crick is right handed spiral and is called B-DNA (Balanced DNA). In the model the base pairs lie at nearly right angles to the axis of helix. Another right handed duplex model is A-DNA (Alternate DNA). Here, a single turn of helix has 11 base pairs.The base pairs lie 20° away from perpendicular to the axis. C-DNA has 9 base pairs per turn of spiral while in D-DNA the number is only 8 base pairs. Both are right handed. Z-DNA (Zigzag DNA) is left-handed double helix with zigzag back-bone, alternate purine and pyrimidine bases, single turn of 45 A length with 12 base pairs and a single groove.B-DNA is more hydrated and most frequently found DNA in living cells. It is physiologically and biologically active form. However, it can get changed into other forms. Right handed DNA is known to change temporarily into the left handed form at least for a short distance.

Such changes may cause changes in gene expression.DNA Structure and FunctionCircular and Linear DNA:In many prokaryotes the two ends of a DNA duplex are covalently linked to form circular DNA. Circular DNA is naked, that is, without association with histone proteins, though polyamines do occur. In linear DNA the two ends are free. It is found in eukaryotic nuclei where it is associated with histone proteins.Modes Of DNA RepicationDNA Structure and FunctionSemi-Conservative, Conservative, & Dispersive models of DNA replication
In the semi-conservative model, the two parental strands separate and each makes a copy of itself. After one round of replication, the two daughter molecules each comprises one old and one new strand. Note that after two rounds, two of the DNA molecules consist only of new material, while the other two contain one old and one new strand. 
In the conservative model, the parental molecule directs synthesis of an entirely new double-stranded molecule, such that after one round of replication, one molecule is conserved as two old strands. This is repeated in the second round.
In the dispersive model, material in the two parental strands is distributed more or less randomly between two daughter molecules. In the model shown here, old material is distributed symmetrically between the two daughters molecules. Other distributions are possible.
The semi-conservative model is the intuitively appealing model, because separation of the two strands provides two templates, each of which carries all the information of the original molecule. It also turns out to be the correct one (Meselson & Stahl 1958).

DNA repair mechanism

Direct reversal of DNA damage is a mechanism of repair that does not require a template and is applied to two main types of damage. UV light induces the formation of pyrimidine dimers which can distort the DNA chain structure, blocking transcription beyond the area of damage.Direct reversal through photoreactivation can inverse this dimerization reaction by utilizing light energy for the destruction of the abnormal covalent bond between adjacent pyrimidine bases. This type of photoreactivation does not occur in humans.The damage caused by alkylating agents reacting with DNA can also be repaired through direct reversal. Methylation of guanine bases produces a change in the structure of DNA by forming a product that is complimentary to thymine rather than cytosine. The protein methyl guanine methyl transferase (MGMT) can restore the original guanine by transferring the methylation product to its active site.

DNA repair by excision

Excision is the general mechanism by which repairs are made when one of the double helix strands is damaged. The non-defective strand is used as a template with the damaged DNA on the other strand removed and replaced by the synthesis of new nucleotides. There are three types of excision repair:

  1. Base-excision repair.
  2. Nucleotide excision repair.
  3. Mismatch repair.

Base-excision repair involves the recognition and removal of a single damaged base. The mechanism requires a family of enzymes called glycosylases. The enzymes remove the damaged base forming an AP site which is repaired by AP endonuclease before the nucleotide gap in the DNA strand is filled by DNA polymerase.Nucleotide excision repair is a widespread mechanism for repairing damage to DNA and recognizes multiple damaged bases.  This mechanism is used to repair the formation of pyrimidine dimers from UV light within humans. The process involves the recognition of damage which is then cleaved on both sides by endonucleases before resynthesis by DNA polymerase.The third excision mechanism is called mismatch repair and occurs when mismatched bases are incorporated into the DNA strand during replication and are not removed by proofreading DNA polymerase. In mismatch repair, the missed errors are later corrected by enzymes which recognize and excise the mismatched base to restore the original sequence.

DNA double strand break repair

The repair of damage to both DNA strands is particularly important in maintaining genomic integrity. There are two main mechanisms for repairing double strand breaks: homologous recombination and classical nonhomologous end joining.Homologous recombination involves the exchange of nucleotide sequences to repair damaged bases on both strands of DNA through the utilization of a sister chromatid. Classical nonhomologous end joining connects the break ends without a homologous template through the use of short DNA sequences called microhomologies. The mechanism is prone to error but protects genome integrity from possible chromosomal translocations that can occur through homologous recombination.Studies have also found that double strand breaks can be repaired through alternative mechanisms such as single-stranded annealing and alternative joining during certain conditions. These mechanisms are mutagenic and can lead to a loss in genetic information.Single-stranded annealing provides end joining between interspersed nucleotide repeats within the genome leading to one copy of the repeat and the intervening sequence being deleted in the process.  Alternative joining has an undefined mechanism for repairing double strand breaks but is known to risk genomic integrity by joining end breaks on different chromosomes.

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