Chapter 19 (part 2) - PowerPoint PPT Presentation

1 / 33
About This Presentation
Title:

Chapter 19 (part 2)

Description:

Cruciform structures. Supercoils. In duplex DNA, ten bp per turn of helix (relaxed form) ... base pairing (i.e.cruciform structures). Multiple functions. Type ... – PowerPoint PPT presentation

Number of Views:38
Avg rating:3.0/5.0
Slides: 34
Provided by: davidsh1
Learn more at: http://www.ag.unr.edu
Category:

less

Transcript and Presenter's Notes

Title: Chapter 19 (part 2)


1
Chapter 19 (part 2)
  • Nucleic Acids

2
DNA
  • 1o Structure - Linear array of nucleotides
  • 2o Structure double helix
  • 3o Structure - Super-coiling, stem-loop formation
  • 4o Structure Packaging into chromatin

3
Determination of the DNA 1o Structure (DNA
Sequencing)
  • Can determine the sequence of DNA base pairs in
    any DNA molecule
  • Chain-termination method developed by Sanger
  • Involves in vitro replication of target DNA
  • Technology led to the sequencing of the human
    genome

4
DNA Replication
  • DNA is a double-helical molecule
  • Each strand of the helix must be copied in
    complementary fashion by DNA polymerase
  • Each strand is a template for copying
  • DNA polymerase requires template and primer
  • Primer an oligonucleotide that pairs with the
    end of the template molecule to form dsDNA
  • DNA polymerases add nucleotides in 5'-3' direction

5
(No Transcript)
6
Chain Termination Method
  • Based on DNA polymerase reaction
  • 4 separate rxns
  • Each reaction mixture contains dATP, dGTP, dCTP
    and dTTP
  • Each reaction also contains a small amount of one
    dideoxynucleotide (ddATP, ddGTP, ddCTP and
    ddTTP).
  • Each of the 4 dideoxynucleotides are labeled with
    a different fluorescent dye.
  • Dideoxynucleotides missing 3-OH group. Once
    incorporated into the DNA chain, chain elongation
    stops)

7
Chain Termination Method
  • Most of the time, the polymerase uses normal
    nucleotides and DNA molecules grow normally
  • Occasionally, the polymerase uses a
    dideoxynucleotide, which adds to the chain and
    then prevents further growth in that molecule
  • Random insertion of dd-nucleotides leaves
    (optimally) at least a few chains terminated at
    every occurrence of a given nucleotide

8
(No Transcript)
9
(No Transcript)
10
Chain Termination Method
  • Run each reaction mixture on electrophoresis gel
  • Short fragments go to bottom, long fragments on
    top
  • Read the "sequence" from bottom of gel to top
  • Convert this "sequence" to the complementary
    sequence
  • Now read from the other end and you have the
    sequence you wanted - read 5' to 3'

11
(No Transcript)
12
(No Transcript)
13
DNA Secondary structure
  • DNA is double stranded with antiparallel strands
  • Right hand double helix
  • Three different helical forms (A, B and Z DNA.

14
Comparison of A, B, Z DNA
  • A right-handed, short and broad, 2.3 A, 11 bp
    per turn
  • B right-handed, longer, thinner, 3.32 A, 10 bp
    per turn
  • Z left-handed, longest, thinnest, 3.8 A, 12 bp
    per turn

15
A-DNA
B-DNA
Z-DNA
16
Z-DNA
  • Found in GC-rich regions of DNA
  • G goes to syn conformation
  • C stays anti but whole C nucleoside (base and
    sugar) flips 180 degrees

17
DNA sequence Determines Melting Point
  • Double Strand DNA can be denatured by heat (get
    strand separation)
  • Can determine degree of denturation by measuring
    absorbance at 260 nm.
  • Conjugated double bonds in bases absorb light at
    260 nm.
  • Base stacking causes less absorbance.
  • Increased single strandedness causes increase in
    absorbance

18
DNA sequence Determines Melting Point
  • Melting temperature related to GC and AT
    content.
  • 3 H-bonds of GC pair require higher temperatures
    to denture than 2 H-bonds of AT pair.

19
DNA 3o Structure
  • Super coiling
  • Cruciform structures

20
Supercoils
  • In duplex DNA, ten bp per turn of helix (relaxed
    form)
  • DNA helix can be over-wound.
  • Over winding of DNA helix can be compensated by
    supercoiling.
  • Supercoiling prevalent in circular DNA molecules
    and within local regions of long linear DNA
    strands
  • Enzymes called topoisomerases or gyrases can
    introduce or remove supercoils
  • In vivo most DNA is negatively supercoiled.
  • Therefore, it is easy to unwind short regions of
    the molecule to allow access for enzymes

21
Each super coil compensates for one or turn
of the double helix
22
  • Cruciforms occur in palindromic regions of DNA
  • Can form intrachain base pairing
  • Negative supercoiling may promote cruciforms

23
DNA and Nanotechnology
24
DNA and Nanotechnology
25
DNA 4o Structure
  • In chromosomes, DNA is tightly associated with
    proteins

26
Chromosome Structure
  • Human DNAs total length is 2 meters!
  • This must be packaged into a nucleus that is
    about 5 micrometers in diameter
  • This represents a compression of more than
    100,000!
  • It is made possible by wrapping the DNA around
    protein spools called nucleosomes and then
    packing these in helical filaments

27
Nucleosome Structure
  • Chromatin, the nucleoprotein complex, consists of
    histones and nonhistone chromosomal proteins
  • major histone proteins H1, H2A, H2B, H3 and H4
  • Histone octamers are major part of the protein
    spools
  • Nonhistone proteins are regulators of gene
    expression

28
  • 4 major histone (H2A, H2B, H3, H4) proteins for
    octomer
  • 200 base pair long DNA strand winds around the
    octomer
  • 146 base pair DNA spacer separates individual
    nucleosomes
  • H1 protein involved in higher-order chromatin
    structure.
  • W/O H1, Chromatin looks like beads on string

29
Solenoid Structure of Chromatin
30
(No Transcript)
31
RNA
  • Single stranded molecule
  • Chemically less stable than DNA
  • presence of 2-OH makes RNA more susceptible to
    hydrolytic attack (especially form bases)
  • Prone to degradation by Ribonucleases (Rnases)
  • Has secondary structure. Can form intrachain base
    pairing (i.e.cruciform structures).
  • Multiple functions

32
Type of RNA
  • Ribosomal RNA (rRNA) integral part of ribosomes
    (very abundant)
  • Transfer RNA (tRNA) carries activated amino
    acids to ribosomes.
  • Messenger RNA (mRNA) endcodes sequences of
    amino acids in proteins.
  • Catalytic RNA (Ribozymes) catalzye cleavage of
    specific RNA species.

33
RNA can have extensive 2o structure
Write a Comment
User Comments (0)
About PowerShow.com