Hyrogen bonding dna


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Hyrogen bonding dna

  1. 1. By Pritvir, Gurvinder and Aaron
  2. 2. What is DNA? <ul><li> DNA is the ‘everyday’ name given to the material, while it’s formal ‘IUPAC’ name is Deoxyribonucleic Acid. DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of most living organisms. </li></ul>
  3. 3. What is DNA Used for? <ul><li>DNA is the code that decides everything about what it makes up. It is the reason you have your hair, eye, and skin colour. The main role of DNA molecules is the long-term storage of information, it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. </li></ul><ul><li>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. 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. </li></ul>
  4. 4. Simple Molecular Structure Of DNA <ul><li>DNA has a basic formula: </li></ul><ul><li>It consists of two long polymers of simple units called nucleotides, the two strands are antiparallel and complimentary and known as deoxyribonucleic acid. </li></ul><ul><li>DNA has two hydrophilic polar external backbones made of sugars and phosphate groups joined by ester bonds. </li></ul><ul><li>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). The core bases are hydrophobic. </li></ul>
  5. 5. Full structure formula of DNA Figure 1 shows the structural formula of a DNA molecule, which is described in the previous slide. Figure 2 shows a closer look at a section of the structure. Figure 1 Figure 2
  6. 6. Chemical Formulas of DNA Monomers <ul><li>The chemical formula of the base pairs and sugars are shown below these are DNA’s monomers: </li></ul><ul><li>Adenine: C 5 H 5 N 5 </li></ul><ul><li>Guanine: C 5 H 5 N 5 O </li></ul><ul><li>Cytosine: C 4 H 5 N 3 O </li></ul><ul><li>Thymine: C 5 H 5 N 2 O 2 </li></ul><ul><li>Phosphate: PO 4 </li></ul><ul><li>2-deoxyribose: C 5 H 9 O 4 </li></ul>
  7. 7. Hydrogen Bonds found in DNA <ul><li>The base pairs described in the previous slides (two nucleotides on opposite complementary DNA or RNA strands) are connected via hydrogen bonds . A hydrogen bond is a type of attractive (dipole-dipole) interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom. In the case of DNA hydrogen bonding is the chemical interaction that underlies and connects the base-pairing. The DNA hydrogen bonds are responsible for holding together the double helix structure. </li></ul><ul><li>The two strands of DNA stay together by H bonds that occur between complementary nucleotide base pairs. Two hydrogen bonds occur between the adenosine and the thymine base pairs, and between the cytosine and the guanine there are three. </li></ul><ul><li>A key aspect to look out for is that a smaller base is always paired with a bigger one. The effect of this is to keep the two chains at a fixed distance from each other all the way along. Also the pairing has to be as follows: </li></ul><ul><li>adenine (A) pairs with thymine (T); </li></ul><ul><li>guanine (G) pairs with cytosine (C). </li></ul><ul><li>This is because these particular pairs fit exactly to form very effective hydrogen bonds with each other. It is these hydrogen bonds which hold the two chains together. The base pairs will not be paired in any other order i.e. adenine (A) paired with cytosine (C). </li></ul>Example of a Hydrogen Bond Example of hydrogen bond in DNA.
  8. 8. Hydrogen Bonds in DNA <ul><li>Here are the two diagrams outlining where the hydrogen bonds are within DNA (red lines). </li></ul><ul><li>Base A and T are held together by two hydrogen bonds ( an O-H and N-H bonds)and bases G and C are bonded together by three hydrogen bonds ( 2 O-H bonds and 1 N-H bond). </li></ul><ul><li>The different number of Hydrogen bonds ensure that the bases link together correctly </li></ul>
  9. 9. Bond Dissociation Enthalpies <ul><li>The table above shows the average bond enthalpy’s of hydrogen bonds and a few other common intermolecular bonds. </li></ul><ul><li>The enthalpy for hydrogen molecules is roughly 460 kg mol , the bond energy of the covalent O-H bonds in water is 458.9 kJ/mol, Hydrogen bond dissociation energy in water is therefore about 23 kJ/mol. This is useful for hydrogen bonding in DNA as it shows the amount of energy required to break the hydrogen bonds during DNA replication is roughly 464+ kg mol. </li></ul><ul><li>The enthalpy for nitrogen molecules is 946 kg mol. </li></ul>
  10. 10. Melting and Boiling Points of DNA <ul><li>Generally the melting and boiling point of DNA would remain quiet low, as you don't have to break any covalent bonds in order to melt or boil a molecular substance. It’s difficult to determine a n exact boiling or melting point of DNA as they exist in long chains and therefore each chain is of different size however smaller chains will have less hydrogen bonds and therefore will need less energy to break it down which means it will have a lower boiling point. Also the larger the molecule the more van der waals attractions are possible and those will also need more energy to break. The size of the melting or boiling point would also depend on the strength of the intermolecular forces. However overall the presence of hydrogen bonding will lift the melting and boiling points slightly. </li></ul><ul><li>The DNA double helix is stable because of the formation of hydrogen bonds between the two base pairs. As hydrogen bonds are not covalent bonds can break and form again relatively easily. For this reason, the two strands of the double helix can be separated like a zipper, either by mechanical force or high temperature. Therefore DNA must not have a very high temperature or else DNA replication cannot take place easily. </li></ul><ul><li>As mentioned previously, the two types of base pairs form different numbers of hydrogen bonds, (A = T form two hydrogen bonds and C ≡ G form three hydrogen bonds ). The GC base pair is therefore stronger than the AT base pair. As a result, both the percentage of GC base pairs as the total length of the double helix of DNA determine the strength of association between the two strands of DNA. Therefore the melting point will be different at different sections of the DNA as different amounts of energy is required. </li></ul><ul><li>The long double helix of DNA with high GC content have more strongly interacting strands that short double helices with high AT content. For this reason, areas of the double helix of DNA that need to be separated easily tend to have high in AT, such as the sequence TATAAT. The temperature required to break hydrogen bonds, i.e. the melting temperature (T m value) is therefore low. This is useful for DNA replication as it mean less energy is required to ‘unzip’ the base pairs as if the base pairs where covalently bonded a large amount of energy would be required to break the bond and therefore the process of DNA replication (a vital process to living organisms) would be affected. </li></ul>
  11. 11. Physical Properties of DNA <ul><li>DNA is a long chain polymer made up of chemical units called nucleotides. The molecule is arranged in a structure called a double helix. </li></ul><ul><li>DNA is soluble in water but not other substances such as ethanol even though both water and ethanol are polar (charged). Water is not more negatively charged as it’s not an ion so it therefore has zero charge. However ethanol is ‘less polar’ than water so much so that DNA is relatively insoluble in it. However the negatively charged phosphate backbone of DNA makes it polar and therefore soluble in water. As DNA is soluble in water, the polar molecules interact through hydrogen bonds. However the inside of DNA is hydrophobic (the base pairs) therefore the outside backbone of the DNA is able to protect the inside of DNA. </li></ul><ul><li>The atomic weight of each DNA strand can be determined, but it is not practical since the various combination to make a code for a protein is so numerous. Therefore you’d have to Separate the individual components and to determine their atomic weight </li></ul><ul><li>The molar concentration of a human DNA is 2.1. </li></ul><ul><li>DNA rigidity is an important physical property originating from the DNA three-dimensional structure. </li></ul>
  12. 12. Chemical Properties of DNA <ul><li>Some chemical properties of DNA are: </li></ul><ul><li>It’s an organic compound </li></ul><ul><li>It is a biopolymer (nucleotides chains) </li></ul><ul><li>Consist of macromolecules </li></ul><ul><li>It’s An essential compounds for all living cells </li></ul><ul><li>A chain-like molecules consisting of smaller subunit held together by bonds. It also has repeating units and is a long polymer. </li></ul><ul><li>DNA is usually double stranded, with 2 complementary strands facing each other base to base. </li></ul><ul><li>DNA is replicated every time a cell divides, and because it is double stranded, each strand will serve as the template to generate 2 new daughter molecules. Hydrogen bonds allow the replication process so be easy as a small amount of energy is required to break the bonds between the base pairs. </li></ul>
  13. 13. Chemical properties of DNA continued <ul><li>To form the a hydrogen bond in DNA the bases must submit a &quot;donor&quot; of hydrogen with a hydrogen atom with partial positive charge (-NH 2 or-NH) and the other a group basis must submit &quot;acceptor&quot; of hydrogen with a charged atom electronegativity (C = O or N). </li></ul><ul><li>As hydrogen bonds are not covalent bonds can break and form again relatively easily. For this reason, the two strands of the double helix can be separated like a zipper, either by mechanical force or high temperature. </li></ul><ul><li>The double helix is stabilized also by the effect hydrophobic and stacking, which are not influenced by the sequence DNA bases. Therefore the internal and external hydrogen bonding both stabilize the DNA molecule </li></ul><ul><li>Hydrogen bonds are bonds weaker than typical chemical bonds-covalent, however they are stronger them other bonds such as van der waals meaning DNA is stable yet is easily ‘unzipped’ when the DNA replicates. </li></ul><ul><li>DNA is made from amino acids which are made up from proteins Its formed by nucleonic acid which creates 4 bases known as A,C,G and T. </li></ul>