Nucleic Acids and Information Flow

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					HL Chemistry - Option B :
 Human Biochemistry



   Nucleic Acids


                            1
      DNA, RNA, & Flow of Genetic Information
  DNA & RNA are long linear polymers, called nucleic acids.
Genetic information is stored in a sequence of 4 kinds of bases
along the chain, and is passed from one generation to the next
• A nucleic acid consists of 4 kinds of bases linked to a sugar-phosphate
backbone
• A pair of nucleic acid chains with complimentary sequences
can form a double-helical structure
• DNA is replicated by polymerases that take instructions from
templates
• Gene expression is the transformation of DNA information into functional
molecules
• Amino acids are encoded by groups of three bases starting from a fixed
point
• Most eucaryotic genes are mosaics of introns & exons


                                                                       2
           Polymeric structure of nucleic acids

Linear polymers of covalent structures, built from similar units




Sequence of bases uniquely characterizes nucleic acids
Represents a form of linear information

Backbone is constant: repeating units of sugar-phosphate

                                                             3
       Different pentose sugars in RNA & DNA


RNA



                                     Sugar carbons
                                     have prime
                                     numbers, to
                                     distinguish them
                                     from atoms in
 DNA
                                     bases




                                                 4
                Backbone of DNA & RNA
3’-to-5’ phosphodiester linkages




Sugar, red. Phosphate, blue             5
                     Purines & Pyrimidines




                                                   6
Note: ring atom #s                RNA        DNA
                       Sugar - base linkage




                                               Base above plane of
Nucleoside                                     sugar, linkage is 

RNA: adenosine, guanosine, cytidine, & uridine                    7
DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, & thymidine
      Nucleotides: monomeric units of nucleic acids
                                          Deoxyguanosine
     Adenosine 5’-triphosphate            3’ monophosphate




     5’ nucleotide - most common          3’ nucleotide
Nucleotide: nucleoside joined to one or more phosphate groups
by an ester linkage                                        8
                 Adenosine 5’-triphosphate




                                   Adenosine linked to sugar C1’
Triphosphate linked to sugar C5’                          9
Deoxyguanosine 3’-monophosphate




                                  10
                   Structure of DNA chain




5’ end, phosphate attached         3’ end, free hydroxyl group
                                                       11
X-ray diffraction of DNA hydrated fiber
                               Shows double-helix
                               structure

                             Meridian arcs -
                             stack of nucleotide
                             bases, 3.4 A apart


                             Central X - indicates
                             helical structure



                            R. Franklin &
                            M. Wilkins photograph
                                             12
             Watson-Crick model - DNA double helix
Axial view                              Features:
Bases separated
by 3.4 Å                               Two helical
                                       polynucleotide chains,
10 bases / turn                        coiled around common
                                       axis, run in opposite
Rotation: 36                           directions
degrees / base
                                       Sugar-phosphate
Helix pitch: 34 Å                      backbones outside,
                                       bases inside
Helix diameter:
20 Å                                   Bases nearly
                                       perpendicular to helix
                                       axis
                                                       13
              DNA double helix - radial view
Looking down the helix axis




                                               14
                  Watson and Crick base pairs




Essentially the
same shape




                                                15
Axial view of DNA
                Base pairs stacked
                on top of one-another,
                contributes stability to
                double helix in 2 ways:

                Base attraction:
                van der Walls forces

                Hydrophobic effect of
                base stacking,
                exposure of polar
                surfaces to surrounding
                water


                                  16
Semiconservative replication of DNA


                            Parental DNA, blue




                            Newly synthesized
                            DNA, red




                                        17
Hypochromism of DNA

                  Used to detect
                  separation of
                  single strands,
                  DNA melting




                               18
DNA melting
              At Tm ,50% of
              helix is
              separated

              Below Tm,
              DNA is
              renatured or
              annealed

              Separation by
              by helicases
              inside cells



                      19
           EM of circular DNA, mitochondria

Relaxed form




                                              20
           EM of circular DNA, mitochondria

Supercoiled form




                                              21
  Single stranded nucleic acids: elaborate structures
Stem & loop structures




                                                  22
RNA stem & loop




                  23
                  RNA complex structure

Base pairing &
loops




    Long-rang
    interaction


                                          24
Long-range interaction
     W & C base pairing, dashed black lines
     Other base pairing, dashed green lines




                                    25
                DNA polymerization reaction

By DNA polymerase

Step by step addition of deoxyribonucleotide units to a DNA chain
New DNA chain assembled directly on a preexisting DNA template




Primer & template required

Activated precursors required: dATP, dGTP, TTP, dCTP

 Also required: Mg2+ ion                                   26
          DNA replication, phosphodiester bridge
Nucleophilic attack by 3’ -hydroxyl group of primer on innermost
phosphorus atom of deoxynucleotide triphosphate (dNTP)
Elongation proceeds, 5’ -to- 3’




                                                           27
Hydrolysis of pyrophosphate (PPi) helps drive polymerization
         Retroviruses reverse flow of information

Reverse transcriptase brought into cell by the virus (eg. HIV-1)




ssRNA                                               Incorporated
genome                                              into host DNA
                                                            28
             Roles of RNA in gene expression




Messenger RNA: template for translation (protein synthesis)

Transfer RNA: carriers of activated AAs to ribosomes
(at least one kind for each of 20 AAs)

Ribosomal RNA: major component of ribosomes
(play structural and catalytic roles)                     29
              mRNA & DNA complementarity




mRNA sequence is the compliment of that of the DNA template
& is the same as that of the coding DNA strand, except for T in
place of U




                                                          30
Genetic code, nonoverlapping




                               31
               Genetic code, no punctuation

Sequence of bases is read in blocks of 3 bases from a fixed
starting point (64 combinations of 4 bases)




                                                              32
Genetic code, degenerate (64 codons, 20 aas)

                              Trp & Met, one codon
                              each,
                              other 18 aas, two or
                              more codons,
                              Leu, Arg, & Ser, six
                              codons each,
                              Synonyms, codons
                              for same aa,
                              Synonyms differ in
                              last base,
                              3 stop codons,
                              designate translation
                              termination
                                            33
         DNA Profiling (part 1)
• Every human has a unique genetic “fingerprint”
• The genetic fingerprint can be obtained by
  looking at how many pieces DNA can be broken
  into using one of two different methods
• Method #1: Restriction Enzymes
 Cleave DNA between known base sequences and
 compare fragment lengths from the sample to the person
 in question


                                                   34
        DNA Profiling (part 2)

• Method #2: VNTR
  - VNTR stands for “Variable Number of Tandem
 Repeats”
 - DNA contains repetitive base patterns (function
 unknown) that varies from person to person
 - use enzymes to reproduce these sections millions of
 times and compare lengths of fragments



                                                    35
DNA Profiling - Electrophoresis
• A gel (agar, agarose) is created between 2 plates
  of glass
• A solution of the aforementioned DNA fragments
  is loaded into the gel, and an electric current
  applied
• The negatively charged DNA (phosphates) attracts
  the fragments to the + end of the gel
• Smaller fragments move faster than the larger
  fragments
• A fluorescent dye is added (ethidium bromide)
  which causes the DNA to glow under UV light
• The gel is photographed and the number and
  position of DNA fragment bands is compared to a
  sample from the human donor (suspect?)            36
 DNA Profiling – What it Shows
• The techniques discussed in the previous
  slides are used to identify people and solve
  crimes
• DNA-containing material at the scene of a
  crime is compared to samples obtained from
  suspects (Forensics)
• VNTR can also be used to identify the
  father of a child in paternity cases

                                             37

				
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