Structural Biochemistry/Nucleic Acid/DNA/DNA structure - Wikibooks, open books for an open world
In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and While most complementarity is seen between two separate strings of DNA or RNA, Purines are larger than pyrimidines. Only later in evolutionary time did DNA take over as the genetic material and proteins become As we have seen in this and the preceding chapter, such complementary In each case, B indicates the positions of purine and pyrimidine bases. Some of these interactions can join distant parts of the same RNA molecule or. Two types of bases are found: purines and pyrimidines. (a) The purines The pyrimidines in DNA are cytosine (C) (sigh-toe-seen) and thymine (T) (thigh-mean ). But the relationship between the two is even more specific. Adenine and thymine are therefore said to be complementary bases, as are guanine and cytosine.
DNA replication occurs by the sequential unzipping of segments of the double helix. Each new nucleotide is brought into position by DNA polymerase and is added to the growing strand by the formation of a phosphate ester bond. Thus, two double helixes form from one, and each consists of one old strand and one new strand, an outcome called semiconservative replications.DNA - Wikipedia audio article
This representation is simplified; many more proteins are involved in replication. What is the sequence of nucleotides in the opposite, or complementary, DNA chain?
What do we mean when we say information is encoded in the DNA molecule? Letters of the alphabet are arranged into words, and these words direct the individual to perform certain operations with specific materials. If all the directions are followed correctly, a model airplane or sweater is produced.
In DNA, the particular sequences of nucleotides along the chains encode the directions for building an organism. Just as saw means one thing in English and was means another, the sequence of bases CGT means one thing, and TGC means something different. Although there are only four letters—the four nucleotides—in the genetic code of DNA, their sequencing along the DNA strands can vary so widely that information storage is essentially unlimited.
There are three key differences between replication and transcription: RNA is built from ribonucleotides rather than deoxyribonucleotides. The DNA sequence that is transcribed to make RNA is called the template strand, while the complementary sequence on the other DNA strand is called the coding or informational strand. Thymine in DNA calls for adenine in RNA, cytosine specifies guanine, guanine calls for cytosine, and adenine requires uracil.
Only a short segment of the RNA molecule is hydrogen-bonded to the template strand at any time during transcription. The nucleotide sequence of the RNA strand formed during transcription is identical to that of the corresponding coding strand of the DNA, except that U replaces T.
When heat is applied to a double-stranded DNAeach individual strand will eventually separate denature because hydrogen bonds are disrupted between base pairs. Upon separation, the separated strands spontaneously reassociate to form the double helix again. This process is known as annealing. In biological systems, both denaturing and annealing can occur. Helicases use chemical energy from ATP to disrupt the structure of double-stranded nucleic acid molecules.
The study of the ability of DNA to reanneal within the laboratory is important in discovering gene structure and expression. A stem-loop is formed when complementary sequences, within the same strand, pair to form a double helix. Hydrogen bonds between base pairs within the same strand occur. Often, these structures include mismatched bases, resulting in destabilization of the local structure. Such action can be important in higher-order folding, like in tertiary structures.
With the increase in light energy, its structure and therefore its function will still remain intact since there is low disturbance to its structure.
The decreased absorbance observed with the DNA double helix with respect to the native and denatured forms is explained by the fact that the stacking of the nitrogenous bases that takes place with the double helix does not leave them as exposed to radiation and thus they are able to absorb less. The aromaticity of the nitrogenous bases specifically in the purine and pyrimidine like ring structures accounts for the absorption peak being at nm.
Hydrogen bonds, linkage between bases, although weak energy-wise, is able to stabilize the helix because of the large number present in DNA molecule. Stacking interactions, or also known as Van der Waals interactions between bases are weak, but the large amounts of these interactions help to stabilize the overall structure of the helix.
Double helix is stabilized by hydrophobic effects by burying the bases in the interior of the helix increases its stability; having the hydrophobic bases clustered in the interior of the helix keeps it away from the surrounding water, whereas the more polar surfaces, hence hydrophilic heads are exposed and interaction with the exterior water Stacked base pairs also attract to one another through Van der Waals forces the energy associated with a single van der Waals interaction has small significant to the overall DNA structure however, the net effect summed over the numerous atom pairs, results in substantial stability.
Stacking also favors the conformations of rigid five-membered rings of the sugars of backbone. Nitrogenous Bases[ edit ] Nitrogenous Bases are the foundational structure of DNA polymers, the structure of DNA polymers vary with the different attached nitrogenous bases.
Nitrogenous Bases can tautomerize between keto and enol forms. The keto tautomer is called a lactam and the enol tautomer is called lactim. The lactam predominates at pH 7. Keto-enol tautomerization is the interconversion of a keto and enol involving the movement of a proton and the shifting of bonding electrons, hence the isomerism qualifies as tautomerism. Keto-enol tautomerism is important in DNA structure because high phosphate-transfer potential of phosphenolpyruvate results in the phosphorylated compound to be trapped in the less stable enol form, whereas dephosphorylation results in the keto form.
Structural Biochemistry/Nucleic Acid/DNA/DNA structure
Rare enol tautomers of bases guanine and thymine can lead to mutation because of the altered base-pairing properties. Base-stacking interactions[ edit ] The two strands of double-stranded DNA are held together by a number of weak interactions such as hydrogen bonds, stacking interactions, and hydrophobic effects.
Of these, the stacking interactions between base pairs are the most significant. The strength of base stacking interactions depends on the bases. It is strongest for stacks of G-C base pairs and weakest for stacks of A-T base pairs. The hydrophobic effect stacks the bases on top of one another. In addition, base stacking in DNA is favored by the conformations of the somewhat rigid five membered rings of the backbone phosphate-sugars.
The base-stacking interactions, which are largely nonspecific with respect to the identity of the stacked base, make the major contribution to the stability of the double helix. A phosphodiester bond is the linkage formed between the 3' carbon atom and the 5' carbon of the sugar deoxyribose in DNA.
The phosphate groups in a phosphodiester bond are negatively-charged. This charge-charge repulsion forces the phosphates groups to take opposite positions of the DNA strands and is neutralized by proteins histonesmetal ions such as magnesium, and polyamines.
The tri-phosphate or di-phosphate forms of the nucleotide building are blocks, first have to be broken apart to release the energy require to drive an enzyme-catalyzed reaction for a phosphodiester bond to form and for the nucleotide to join. Once a single phosphate or two phosphates pyrophosphates break apart and participate in a catalytic reaction, the phosphodiester bond is formed.
An important role in repairing DNA sequences is due to the hydrolysis of phosphodiester bonds being catalyzed by phoshodiesterases, an enzyme that facilitates the repairs. A nucleophile base can pull out the H when everything is in the correct trajectory and the phosphate part of the backbone will rearrange and eventually a P-O bond is broken to break the connection site between two sugars.
DNA Replication, the Double Helix, and Protein Synthesis - Chemistry LibreTexts
A single-stranded DNA may participate in intramolecular base pairing between complementary base pairs and therefore make up secondary structure as well. This means the is no "bulges" or "gaps the exist within the double helix.
Irregular placement of base pairs in a double helix will result in consequences that will render the macromolecule nonfunctional. Therefore if there is something wrong with the structure, signals will be alerted and DNA repair will work to fix damages.
Complementarity (molecular biology)
As a result of the double helical nature of DNAthe molecule has two asymmetric grooves. One groove is smaller than the other. This asymmetry is a result of the geometrical configuration of the bonds between the phosphate, sugar, and base groups that forces the base groups to attach at degree angles instead of degree.
The larger groove is called the major groove, occurs when the backbones are far apart; while the smaller one is called the minor groove, occurs when they are close together. Since the major and minor grooves expose the edges of the bases, the grooves can be used to tell the base sequence of a specific DNA molecule.
The possibility for such recognition is critical, since proteins must be able to recognize specific DNA sequences on which to bind in order for the proper functions of the body and cell to be carried out. As you might expect, the major groove is more information rich than the minor groove, allowing the DNA proteins to interact with the bases. This fact makes the minor groove less ideal for protein binding.
Shorter, wider helix than B. It is about 20 angstroms with a C-2' endo sugar pucker conformation. B-DNA has two principal grooves, a wide major groove and a narrow minor groove. Many proteins interact in the space of the major groove, where they make sequence-specific contacts with the bases. In addition, a few proteins are known to make contacts via the minor groove. Z form of DNA is a more radical departure from the B structure; the most obvious distinction is the left-handed helical rotation.
The Z form is about 18 angstroms and there are 12 base pairs per helical turn, and the structure appears more slender and elongated. The DNA backbone takes on a zigzag appearance.
Certain nucleotide sequences fold into left-handed Z helices much more readily than others. Prominent examples are sequences in which pyrimidines alternate with purinesespecially alternating C and G or 5-methyl-C and G residues. To form the left-handed helix in Z-DNA, the purine residues flip to the syn conformation alternating with pyrimidines in the anti conformation. The major groove is barely apparent in Z-DNA, and the minor groove is narrow and deep. For pyrimidines, the sugar pucker conformation is C-2' endo and for purines, it is a C-3' endo.
Z- DNA formation occurs during transcription of genes, at transcription start sites near promoters of actively transcribed genes. During transcription, the movement of RNA polymerase induces negative supercoiling upstream and positive supercoiling downstream the site of transcription.
At the end of transcription, topoisomerase relaxes DNA back to B conformation. Tertiary structure 3 dimensional [ edit ] The tertiary structure of DNA molecule is made up of the two strands of DNA wind around each other.
DNA double helix can be arranged in space, in a tertiary arrangement of strands.
Structure of DNA - An Introduction to Genetic Analysis - NCBI Bookshelf
Linking Number Lk in a covalently closed circular DNAwhere the two strands cannot be separated will result in a constant number of turns in a given molecule.
Lk of DNA is an integral composed of two components: However, DNA can also be supercoiled with two "underwindings" which is made up of negative supercoils.
This is muck like the two "turns- worth" of a single stranded DNA and no supercoils. This kinds of interconversion of helical and superhelical turns in important in gene transcription and regulation. Quaternary structure and other unusual structure[ edit ] DNA is connected with histones and non-histone proteins to form the chromatin. The negative charge due to the phosphate group in DNA makes it relatively acidic.
This negative charge binds to the basic histone groups. Histone Modification[ edit ] Recent studies provide that actively transcribed regions are characterized by specific modification pattern of histone.