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					         Types of Molecules
• DNA: code for genetic information
• RNA
  – mRNA intermediates in protein synthesis
  – rRNA carry out protein synthesis
  – tRNA translate info on mRNA into a.a.
• Gene
      Nucleotide Components
• Bases + sugar + phosphate
• Bases
  – purine
     • adenine
     • guanine
  – pyrimidines
     • thymine
     • cytosine
     • uracil
                        Bases
Purines                         Pyrimidines


            NH2                       O
    N                     H3C
                 N                        N
    N       N                         N       O

Adenine (A)               Thymine (T) (DNA only)



        O
                                  NH2
N
             N
                                      N
N       N         NH2
                                  N       O

    Guanine (G)
                                Cytosine (C)


                                   O

                                          N

                                      N       O

                                 Uracil (U) (RNA only)
        Nucleotide Components
• Sugars                     HOH2C       O    OH

  – ribose
                                   HO        OH
  – Deoxyribose
  – Rings numbered using           ribose (RNA)
    primes
     • C1 = 1’ etc
                           HOH2C     O       OH
• PO43-

                               HO        H


                                   2-deoxyribose (DNA)
           Nucleotide Structure
                                                                            NH2
                                                                   N
• Base-sugar-phosphate                                                          N

                                                                   N        N
• Base attached to C1           O         O       O            O
                           HO   P   O     P   O P       O               OH
  of sugar                      O         O     O                  OH

• Phosphate attached to             Adenosine Triphosphate (ATP) (a ribonucleotide)
  C5 of sugar                                                      O
                                                             H3C
• Usually nucleotides                                                   N

                                                                   N        O
  are triphosphates, but        O         O       O            O
  can be mono or di        HO   P   O     P    O P       O              H
                                O         O      O                 OH


                                        Thymidine Triphosphate (TTP) (a deoxyribonucleotide)
Nucleic Acid, a polymer of
       nucleotides
              Nucleic Acids
• Polymer of nucleotides
• Phosphodiester linkage
  – 3’ of one sugar to 5’ of other
  – vectorial
• Sequence read 5’ - 3’
• Previous slide is C-A-A
• Next slide (a cartoon drawing) is A-T-G-C
Phosphodiester Bond
                   Chain elongation
• 3’ hydroxyl on chain has unshared pair on oxygen
   – attacks phosphorus on first phosphate of new nucleotide
   – Nucleophilic attack
• Driven by hydrolysis of PPi
          O        O
                                            O
    HO    P    O   P     OH          2 O     P    OH
          O        O
                                            O
         pyrophosphate
                                           phosphate
         Chain elongation
                                                     O
     R             O
          O                              N
               P                                             N
           O         O                                                         chain
                                 O       N           N           N

                                                                         NH2
         3- OH         H O           H
                                                             N
                                             +                               N

                                                             N           N
     O             O                                                                 nucleotide
                                 O               O
HO   P     O       P       O P       O                               H
     O             O         O                               OH




                                                                 O
                 R               O
                       O                                 N
                                                                         N
                             P
                         O       O                       N
                                             O                   N           N
                                                                                                            O        O
                                                                                          NH2
                                                                                 N                +   HO    P    O   P     OH
                                                     H                                        N             O        O
     longer chain                        O           O                           N        N                pyrophosphate
                                                 P                       O
                                                             O
                                         O                                            H

                                                                                 OH
                 Base pairs
– Bases are planar
   • sp2 hybridization
   • Bases nonpolar
– In Nucleic acids, there is base pairing
– Complementarity
   • Purines always base-pair with pyrimidines
      – Cytosine hydrogen bonds with guanine
      – Thymine hydrogen bonds with adenine or uracil
   • Due to distancing and proximity of unshared pairs
     and hydrogens
        GC base pair
                               H
                             N
                O -- -- -- H
        N
                               N
                 NH -- -- --         N
    N
R           N                            R
                               O
                  N H -- -- --
                 H

        Guanine                  cytosine



                 3 H- bonds
        AT base Pair
                H
        N           N H -- -- -- O

    N               N   -- -- -- -- HN    N
R           N                                 R
                                     O
        adenine                 thymine

                     2 H-bonds
    A-U base Pair (RNA)
                H
        N           N H         O

    N               N               N       N
                                H                R
R
            N
                                        O

adenine                                 uracil

                    2 H bonds
Base Pairs (Cartoon drawing)
              DNA structure
• Double helix
• http://sbchem.sunys
  b.edu/msl/dna.gif
               DNA structure
• B-DNA is most common
• Antiparallel
• bases inside
  – Hydrophobic
  – Perpendicular to helix
• stands complementary
  – Very important for information transfer
  – Each strand a template for the other.
• right handed
• major and minor groove
        Other forms of DNA
• Z - DNA left handed; structure not fully
  understood
• A- DNA; tighter helix
                       DNA Types
                  B- DNA (most common)




•   http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&
    imgrefurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=
    32&tbnid=muC9F_v90eYO7M:&tbnh=100&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26nd
    sp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
                       A-DNA (supercoiled)




•   http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.
    bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tb
    nw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
                                                    Z-DNA




•   http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.
    bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tb
    nw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
               Look down Axis




• http://www.accelrys.com/reference/gallery/life/dna.gif
    Sequence dependent structures
•   palindromes
•   hairpins
•   inverted repeats
•   mirror repeats
                     RNA
•   codes for protein
•   no consistent secondary structure
•   single stranded
•   Ribose instead of deoxyribose
•   Thymine (T) replaced by Uracil
                           RNA                  NH2
        5' end
                                    N
                                                    N
    O
        O    CH2                                                   A
O   P                  O            N
                                                N
    O


                               OH           O
             O O
                                                                           U
         O   P                                  N
             O     CH2
                                O
                                            N        O


                                                                  O
                           O        OH
                   O                                     N
                                                                       N
                                                                                  G
             O P                                         N        N        NH 2
                       O            CH2
                                                O


                                                                  NH 2
                               O        O           OH
                                                                       N
                       O P                                                            C
                                     O      CH 2                  N        O
                                                         O




                                                    OH       OH
                                                                               3 ' end
                    Transfer RNA




• http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/12.07.jpg
          Instability of RNA
• RNA unstable due to reactivity of 2’
  hydroxyl on ribose
• Very labile
• DNA extremely stable
      Nucleic Acid Chemistry
• Denaturation
  – unzip by heating
  – reannealing
  – CoT curves: more GC=higher temp
• Uses of DNA to find sequences
  – probes
  – forensic
             DNA probes
• Take DNA from crime scene
• DNA from suspect, random other person etc
• See what matches
      Nucleic Acid Chemistry
• Mutations
  – changes in
    sequence/structure
  – nonenzymatic changes
     • thymine dimers
     • deamination
     • oxidative damage
      Nucleic Acid Chemistry
• http://www.dnalc.org/resources/BiologyAni
  mationLibrary.htm
• Sequencing
• PCR
• Southern Blotting
• Probes
  DNA sequencing, Sanger dideoxy
            method
• 4 samples
• Each gets template and nucleotides
    – One dideoxy nucleotide
    – Has no 3’ OH so chain can’t elongate
• Sample 1
    – ddTTP…stops at T
• Sample 2
    – ddATP…stops at A
• Sample 3
    – ddCTP…stops at C
• Sample 4
    – ddGTP…stops at G
• Run on Gel
    – Read from bottom up
Sample Sanger Gel
      Human Genome Project
• http://www.ornl.gov/sci/techresources/Hum
  an_Genome/home.shtml

				
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