Biomolecules (PL1003) Notes on Nucleic Acids PDF

Biomolecules (PL1003) -- Notes on Nucleic acids +-------------+-------------+-------------+-------------+-------------+ | | |  | | | +=============+=============+======...

Biomolecules (PL1003) -- Notes on Nucleic acids +-------------+-------------+-------------+-------------+-------------+ | | |  | | | +=============+=============+=============+=============+=============+ | | | | | | +-------------+-------------+-------------+-------------+-------------+ | Polynucleic | Sugar/phosp | | | | | acids, | hate | | | | | primary | backbone | | | | | | | | | | | level | Base groups | | | | | structure | protruding | | | | | | from the | | | | | | chain at | | | | | | regular | | | | | | intervals. | | | | | | Primary | | | | | | level | | | | | | structure | | | | | | is formed | | | | | | by 3'‐5' | | | | | | phosphodies | | | | | | ter | | | | | | bonds | | | | | | between | | | | | | nucleotides | | | | | | and is the | | | | | | sequence of | | | | | | bases. | | | | | | | | | | | | In DNA the | | | | | | bases are: | | | | | | A, G, C, T | | | | | | | | | | | | In RNA the | | | | | | bases are: | | | | | | A, G, C, U | | | | | | | | | | | | By | | | | | | convention | | | | | | the | | | | | | sequence of | | | | | | bases is | | | | | | listed | | | | | | [from]{.und | | | | | | erline} | | | | | | the 5' end, | | | | | | (phosphate | | | | | | ester), | | | | | | [to]{.under | | | | | | line} | | | | | | the 3' end | | | | | | (free | | | | | | hydroxyl | | | | | | group) e.g. | | | | | | | | | | | | DNA: | | | | | | ‐dT‐A‐G‐C‐C | | | | | | ‐ | | | | | | "d" | | | | | | *denotes | | | | | | deoxy | | | | | | ribose* | | | | | | | | | | | | RNA: | | | | | | ‐U‐C‐G‐A‐U‐ | | | | +-------------+-------------+-------------+-------------+-------------+ | DNA, | C | | | | | level | hargaff | | | | | structure | showed the | | | | | | following | | | | | | pattern of | | | | | | base | | | | | | occurrence | | | | | | in DNA: | | | | | | | | | | | | \%A = %T | | | | | | | | | | | | \%G = %C | | | | | | | | | | | | And that | | | | | | the amounts | | | | | | of total | | | | | | purines and | | | | | | total | | | | | | pyrimidines | | | | | | were the | | | | | | same e.g. | | | | | | human DNA | | | | | | contains | | | | | | approximate | | | | | | ly | | | | | | 30% | | | | | | adenine; | | | | | | 30% | | | | | | thymine; | | | | | | 20% | | | | | | guanine; | | | | | | 20% | | | | | | cytosine. | | | | | | | | | | | | Based on | | | | | | published | | | | | | work Watson | | | | | | and Crick | | | | | | proposed | | | | | | the double | | | | | | helix model | | | | | | for DNA: | | | | | | The bases | | | | | | on one | | | | | | strand | | | | | | hydrogen | | | | | | bond to | | | | | | complementa | | | | | | ry | | | | | | bases on | | | | | | the other | | | | | | strand of | | | | | | DNA. The | | | | | | two strands | | | | | | run | | | | | | antiparalle | | | | | | l | | | | | | (in | | | | | | opposite | | | | | | directions | | | | | | to each | | | | | | other). | | | | | | | | | | | | The | | | | | | location of | | | | | | the | | | | | | sugar‐phosp | | | | | | hate | | | | | | backbones | | | | | | on the | | | | | | outside of | | | | | | the | | | | | | molecule, | | | | | | coupled | | | | | | with the | | | | | | twist, | | | | | | produces | | | | | | two grooves | | | | | | on the | | | | | | surface of | | | | | | the double | | | | | | helix. | | | | | | These | | | | | | grooves may | | | | | | provide | | | | | | binding | | | | | | sites for | | | | | | molecules | | | | | | which | | | | | | interact | | | | | | with DNA. | | | | | | | | | | | | The size of | | | | | | the | | | | | | interior of | | | | | | the DNA | | | | | | double | | | | | | helix | | | | | | limits the | | | | | | base pairs | | | | | | that can | | | | | | hydrogen | | | | | | bond to one | | | | | | another. | | | | | | Only pairs | | | | | | involving | | | | | | one small | | | | | | base (a | | | | | | pyrimidine) | | | | | | and one | | | | | | large base | | | | | | (a purine) | | | | | | correctly | | | | | | "fit" | | | | | | within the | | | | | | helix | | | | | | interior. | | | | | | | | | | | | Hydrogen | | | | | | bonding | | | | | | favours A‐T | | | | | | and G‐C | | | | | | pairings, | | | | | | | | | | | | Forces | | | | | | stabilising | | | | | | the double | | | | | | helix: | | | | | | | | | | | | Hydrogen | | | | | | bonding -- | | | | | | large | | | | | | number of | | | | | | relatively | | | | | | weak H | | | | | | bonds | | | | | | contribute | | | | | | greatly to | | | | | | preventing | | | | | | the strands | | | | | | from | | | | | | separating | | | | | | under | | | | | | normal | | | | | | physiologic | | | | | | al | | | | | | conditions | | | | | | | | | | | | Electrostat | | | | | | ic | | | | | | interaction | | | | | | s | | | | | | ‐ involves | | | | | | the | | | | | | phospho‐die | | | | | | ster | | | | | | group of | | | | | | the DNA | | | | | | backbone | | | | | | and a | | | | | | cation | | | | | | especially | | | | | | Mg^2+^ | | | | | | | | | | | | Hydrophobic | | | | | | affects ‐ | | | | | | produced by | | | | | | hydrophobic | | | | | | purines/ | | | | | | pyrimidine | | | | | | rings | | | | | | moving away | | | | | | from the | | | | | | aqueous | | | | | | solvent | | | | | | into the | | | | | | interior of | | | | | | the double | | | | | | helix. | | | | | | | | | | | | Stacking | | | | | | interaction | | | | | | ‐ stacked | | | | | | base pairs | | | | | | form weak | | | | | | Van der | | | | | | Waals | | | | | | attractions | | | | | |. | | | | | | These | | | | | | forces are | | | | | | additive. | | | | | | Therefore | | | | | | the greater | | | | | | the number | | | | | | of base | | | | | | pairs the | | | | | | more stable | | | | | | will be the | | | | | | helix. | | | | +-------------+-------------+-------------+-------------+-------------+ | RNA | RNA is | | | | | | single | | | | | | stranded | | | | | | and much | | | | | | smaller | | | | | | than DNA. | | | | | | Can loop | | | | | | back on | | | | | | itself and | | | | | | show some | | | | | | double | | | | | | helix | | | | | | structure. | | | | | | | | | | | | The sugar | | | | | | unit in the | | | | | | backbone is | | | | | | ribose. | | | | | | | | | | | | Uracil in | | | | | | RNA | | | | | | replaces | | | | | | thymine. | | | | | | Uracil | | | | | | pairs with | | | | | | adenine. | | | | +-------------+-------------+-------------+-------------+-------------+ | DNA |  | | | | | replication | The | | | | | | complementa | | | | | | ry | | | | | | strands | | | | | | unwind and | | | | | | separate. | | | | | | Each then | | | | | | acts as a | | | | | | template | | | | | | for a | | | | | | complementa | | | | | | ry | | | | | | strand to | | | | | | be built. | | | | | | Free | | | | | | nucleoside | | | | | | triphosphat | | | | | | es | | | | | | (high | | | | | | energy | | | | | | compounds) | | | | | | are added | | | | | | to the two | | | | | | growing | | | | | | chains. | | | | | | Base | | | | | | pairing | | | | | | always | | | | | | involves C | | | | | | pairing | | | | | | with G and | | | | | | A pairing | | | | | | with T. DNA | | | | | | polymerase | | | | | | builds the | | | | | | new double | | | | | | helices and | | | | | | repairs | | | | | | slightly | | | | | | damaged | | | | | | ones, by | | | | | | lining up | | | | | | nucleotides | | | | | | in the | | | | | | right | | | | | | order. | | | | +-------------+-------------+-------------+-------------+-------------+ | The | Mimics | | | | | | nature for | | | | | Polymerase | the rapid | | | | | | production | | | | | Chain | of multiple | | | | | | copies of a | | | | | Reaction | DNA | | | | | | nucleotide | | | | | (PCR) | sequence in | | | | | | the | | | | | | laboratory. | | | | | | | | | | | | The | | | | | | reaction | | | | | | mixture | | | | | | required | | | | | | is: | | | | | | | | | | | | 1. Target | | | | | | DNA | | | | | | | | | | | | 2. The two | | | | | | primers | | | | | | | | | | | | 3. All | | | | | | four | | | | | | deoxyri | | | | | | bonucleosid | | | | | | e | | | | | | triphos | | | | | | phates | | | | | | | | | | | | 4. A | | | | | | thermos | | | | | | table | | | | | | DNA | | | | | | polymer | | | | | | ase | | | | | | (*Therm | | | | | | us | | | | | | aquatic | | | | | | us* | | | | | | ‐TAQ) | | | | | | | | | | | | After 30 | | | | | | cycles | | | | | | (around 1 | | | | | | hour) the | | | | | | original | | | | | | sample of | | | | | | DNA is | | | | | | amplified a | | | | | | billion‐fol | | | | | | d | | | | +-------------+-------------+-------------+-------------+-------------+